diff --git a/.github/SECURITY.md b/.github/SECURITY.md new file mode 100644 index 0000000000..efe5624b9b --- /dev/null +++ b/.github/SECURITY.md @@ -0,0 +1,46 @@ +# PlasmaPy Security Policy + + + +## Supported versions + +Security updates will only be provided for the most recent release of PlasmaPy. + +| Version | Supported | +| ------- | --------- | +| latest | ✅ | +| older | ❌ | + +## Reporting security vulnerabilities + +Please use this link to [privately report a security vulnerability]. + +## Finding security vulnerabilities via continuous integration + +PlasmaPy has an extensive suite of continuous integration checks, +including several that identify and flag common security vulnerabilities. + +- [`zizmor`] finds security vulnerabilities in the GitHub workflows. +- [`ruff`] has several [rule sets] that find security vulnerabilities, + including the [`flake8-bandit` rule set]. + +The checks are usually either run as [`pre-commit`] hooks +(defined in [`.pre-commit-config.yaml`]) +or as [Nox] sessions (defined in [`noxfile.py`]) +invoked during GitHub workflows (located in [`.github/workflows/`]). +The configurations for most of these tools are located in [`pyproject.toml`], +but some have a dedicated configuration file +(for `zizmor`, this would be at [`.github/zizmor.yml`]) + +[nox]: https://nox.thea.codes +[privately report a security vulnerability]: https://github.com/plasmapy/plasmapy/security/advisories/new +[rule sets]: https://docs.astral.sh/ruff/rules +[`.github/workflows/`]: https://github.com/PlasmaPy/PlasmaPy/tree/main/.github/workflows +[`.github/zizmor.yml`]: https://github.com/PlasmaPy/PlasmaPy/blob/main/.github/zizmor.yml +[`.pre-commit-config.yaml`]: https://github.com/PlasmaPy/PlasmaPy/blob/main/.pre-commit-config.yaml +[`flake8-bandit` rule set]: https://docs.astral.sh/ruff/rules/#flake8-bandit-s +[`noxfile.py`]: https://github.com/PlasmaPy/PlasmaPy/blob/main/noxfile.py +[`pre-commit`]: https://pre-commit.com/ +[`pyproject.toml`]: https://github.com/PlasmaPy/PlasmaPy/blob/main/pyproject.toml +[`ruff`]: https://docs.astral.sh/ruff +[`zizmor`]: https://github.com/woodruffw/zizmor diff --git a/.github/labeler.yml b/.github/labeler.yml index 327552ff7b..c5a04d16ff 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -104,6 +104,14 @@ maintenance: 'licenses/**', ] +security: + - changed-files: + - any-glob-to-any-file: [ + '**/*security*', + '**/*SECURITY*', + '**/*zizmor*', + ] + notebooks: - changed-files: - any-glob-to-any-file: [ @@ -189,8 +197,6 @@ release: - changed-files: - any-glob-to-any-file: [ '.github/workflows/*weekly*.yml', - 'docs/conf.py', - 'noxfile.py', ] 'static type checking': diff --git a/.github/scripts/citation_updater.py b/.github/scripts/citation_updater.py index 9adea652eb..5b751eec40 100644 --- a/.github/scripts/citation_updater.py +++ b/.github/scripts/citation_updater.py @@ -1,3 +1,8 @@ +# /// script +# requires-python = ">=3.13" +# dependencies = [ "ruamel.yaml" ] +# /// + """Functionality to update citation information prior to making a release.""" import argparse diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 622db2fe80..57e51104b5 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -25,7 +25,7 @@ jobs: steps: - name: Add no changelog label - uses: actions/github-script@v7 + uses: actions/github-script@v8 with: github-token: ${{ secrets.GITHUB_TOKEN }} script: | diff --git a/.github/workflows/check-author-included.yml b/.github/workflows/check-author-included.yml index f9f9846415..c5908e8cf9 100644 --- a/.github/workflows/check-author-included.yml +++ b/.github/workflows/check-author-included.yml @@ -13,12 +13,12 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: enable-cache: true cache-suffix: author-cff diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6a5c595b9f..5257d3a0d5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,9 +49,9 @@ jobs: python: '3.11' nox_session: tests-3.11(lowest-direct-skipslow) - - name: Documentation, Python 3.12, Ubuntu + - name: Documentation, Python 3.13, Ubuntu os: ubuntu-latest - python: '3.12' + python: '3.13' nox_session: docs - name: Static type checking with mypy, Python 3.13, Ubuntu @@ -82,7 +82,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false @@ -98,14 +98,14 @@ jobs: sudo apt-get install -y pandoc - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: python-version: ${{ matrix.python }} - enable-cache: true + enable-cache: true # zizmor: ignore[cache-poisoning] cache-suffix: ${{ matrix.nox_session }}-${{ matrix.python }}-${{ runner.os }} - name: Run the check - run: uv run --with nox --frozen nox -s '${{ matrix.nox_session }}' + run: uvx nox -s '${{ matrix.nox_session }}' - name: Upload coverage reports to Codecov if: ${{ contains(matrix.nox_session, 'cov') }} diff --git a/.github/workflows/comment-on-pr.yml b/.github/workflows/comment-on-pr.yml index 9566345a60..3eecbcf351 100644 --- a/.github/workflows/comment-on-pr.yml +++ b/.github/workflows/comment-on-pr.yml @@ -13,7 +13,7 @@ jobs: steps: - - uses: actions/github-script@v7 + - uses: actions/github-script@v8 with: script: | github.rest.issues.createComment({ diff --git a/.github/workflows/create-release-issue.yml b/.github/workflows/create-release-issue.yml index e079695b17..f41de5874b 100644 --- a/.github/workflows/create-release-issue.yml +++ b/.github/workflows/create-release-issue.yml @@ -14,7 +14,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index f934e900e7..cdafddf72f 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -11,6 +11,6 @@ jobs: pull-requests: write runs-on: ubuntu-latest steps: - - uses: actions/labeler@v5 + - uses: actions/labeler@v6 with: configuration-path: .github/labeler.yml diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml index 5a92a19a2b..c7deed76ad 100644 --- a/.github/workflows/linkcheck.yml +++ b/.github/workflows/linkcheck.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false @@ -41,12 +41,12 @@ jobs: sudo apt-get install -y pandoc - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: - python: 3.12 + python-version: 3.12 - name: Install graphviz & pandoc run: sudo apt-get install graphviz pandoc - name: Check hyperlinks - run: uv run --with nox --frozen nox -s linkcheck + run: uvx nox -s linkcheck diff --git a/.github/workflows/mint-release.yml b/.github/workflows/mint-release.yml deleted file mode 100644 index 7ca682dbcb..0000000000 --- a/.github/workflows/mint-release.yml +++ /dev/null @@ -1,70 +0,0 @@ -name: Mint release 🍬 - -on: - workflow_dispatch: - inputs: - tag: - description: Release tag 🏷️ - required: true - default: 2024.5.0rc1 - DOI: - description: Reserved DOI from Zenodo - required: true - default: 10.5281/zenodo.1238132 - -jobs: - - tag: - runs-on: ubuntu-latest - - steps: - - - name: Checkout code - uses: actions/checkout@v4 - with: - persist-credentials: false - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.13' - - - name: Install dependencies - run: | - pip install towncrier pre-commit ruamel.yaml - - - name: Configure git - run: | - git config --global user.email "team@plasmapy.org" - git config --global user.name "PlasmaPy Release Bot" - - - name: Create or checkout branch - run: | - VERSION="v${{ github.event.inputs.tag }}" - BRANCH=$(echo $VERSION | awk 'BEGIN{FS=OFS="."} {$3="x"} 1' | cut -f1,2,3 -d'.' | awk -F'rc' '{print $1 ORS $2}') - git checkout $BRANCH 2>/dev/null || git checkout -b $BRANCH - - - name: Update CITATION.cff, docs/about/citation.rst with the DOI for the new version. - run: | - python .github/scripts/citation_updater.py CITATION.cff docs/about/citation.rst docs/changelog/index.rst --version=${{ github.event.inputs.tag}} --doi=${{ github.event.inputs.doi}} - git add . - git commit -m "Update citation and changelog index entry" - - - name: Create changelog - run: | - towncrier build --yes --version ${{ github.event.inputs.tag }} --draft | tee docs/changelog/${{ github.event.inputs.tag }}.rst - sed -i -e :a -e '/^\n*$/{$d;N;ba' -e '}' docs/changelog/${{ github.event.inputs.tag }}.rst # strip empty lines - git add . - towncrier build --yes --version ${{ github.event.inputs.tag }} - git commit --allow-empty -nm "Add changelog entries for v${{ github.event.inputs.tag }}" - - - name: Tag the release - run: | - git tag "v${{ github.event.inputs.tag }}" -m "Version v${{ github.event.inputs.tag }}" - git tag - - - name: Push tag, branch state - run: | - VERSION="v${{ github.event.inputs.tag }}" - BRANCH=$(echo $VERSION | awk 'BEGIN{FS=OFS="."} {$3="x"} 1' | cut -f1,2,3 -d'.' | awk -F'rc' '{print $1 ORS $2}') - git push -u origin $VERSION $BRANCH diff --git a/.github/workflows/prepare-release-pr.yml b/.github/workflows/prepare-release-pr.yml new file mode 100644 index 0000000000..b79ee527b7 --- /dev/null +++ b/.github/workflows/prepare-release-pr.yml @@ -0,0 +1,83 @@ +name: Prepare a release + +on: + workflow_dispatch: + inputs: + version: + description: Version + required: true + default: 2025.8.0 + doi: + description: Reserved DOI from Zenodo + required: true + default: 10.5281/zenodo.16747747 + +jobs: + create-pull-request: + name: Create pull request + runs-on: ubuntu-latest + + steps: + + - name: Validate version input + run: | + if [[ ! ${VERSION} =~ ^2[0-9]{3}\.[0-9]+\.[0-9]+$ ]]; then + echo "::error ::Provide a calendar version like `2025.8.0`" + exit 1 + fi + env: + VERSION: ${{ github.event.inputs.version }} + + - name: Validate DOI input + run: | + if [[ ! ${DOI} =~ ^10\.[0-9]{4,9}/.*$ ]]; then + echo "::error ::Provide a valid DOI reserved from Zenodo." + exit 1 + fi + env: + DOI: ${{ github.event.inputs.doi }} + + - name: Checkout code + uses: actions/checkout@v5 + with: + persist-credentials: false + + - name: Install uv + uses: astral-sh/setup-uv@v7 + + - name: Update version and DOI in CITATION.cff and docs/about/citation.rst + run: | + uv run .github/scripts/citation_updater.py CITATION.cff docs/about/citation.rst docs/changelog/index.rst --version=$VERSION --doi=$DOI + env: + VERSION: ${{ github.event.inputs.version }} + DOI: ${{ github.event.inputs.doi }} + + - name: Build the changelog with towncrier + run: | + uvx nox -s "changelog(final)" -- $VERSION + env: + VERSION: ${{ github.event.inputs.version }} + + # When a PR is created by a GitHub Action, normally the checks will + # not be run. While the simplest workaround would have been to open + # and close the PR, an alternative is to authenticate with GitHub + # App generated tokens (as done below). The instructions for how to + # do this are in the documentation for the create-pull-request + # action. + + - name: Generate token + uses: tibdex/github-app-token@3beb63f4bd073e61482598c45c71c1019b59b73a # v2.1.0 + id: generate_token + with: + app_id: ${{ secrets.APP_ID }} + private_key: ${{ secrets.APP_PRIVATE_KEY }} + + - name: Create pull request + uses: peter-evans/create-pull-request@271a8d0340265f705b14b6d32b9829c1cb33d45e # v7.0.8 + with: + title: Build changelog and update package metadata prior to a release + commit-message: Build changelog & update citation info + body: This automated pull request builds the changelog with towncrier and updates package metadata prior to a forthcoming release. Merge this pull request prior to drafting the release. + labels: skip changelog checks + delete-branch: true + token: ${{ steps.generate_token.outputs.token }} diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 39cff5876d..acd8317b44 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -15,12 +15,12 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: 3.13 @@ -33,7 +33,7 @@ jobs: run: python -m build - name: Upload package to PyPI - uses: pypa/gh-action-pypi-publish@v1.12.4 + uses: pypa/gh-action-pypi-publish@v1.13.0 with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index e37c3ae42a..ddbda67c2a 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -16,7 +16,7 @@ jobs: steps: - - uses: actions/stale@v9 + - uses: actions/stale@v10 with: repo-token: ${{ secrets.GITHUB_TOKEN }} stale-issue-message: This issue will be closed in 90 days due to five years of inactivity unless the stale label or comment is removed. diff --git a/.github/workflows/unlabel-pr-after-merge.yml b/.github/workflows/unlabel-pr-after-merge.yml index 03c0c5bdd5..be11f4457e 100644 --- a/.github/workflows/unlabel-pr-after-merge.yml +++ b/.github/workflows/unlabel-pr-after-merge.yml @@ -11,7 +11,7 @@ jobs: steps: - name: Remove specific labels - uses: actions/github-script@v7 + uses: actions/github-script@v8 with: github-token: ${{secrets.GITHUB_TOKEN}} script: | diff --git a/.github/workflows/update-pinned-reqs.yml b/.github/workflows/update-pinned-reqs.yml index 29702ae6be..29d1290108 100644 --- a/.github/workflows/update-pinned-reqs.yml +++ b/.github/workflows/update-pinned-reqs.yml @@ -2,7 +2,7 @@ name: Update pinned requirements on: schedule: - - cron: 0 12 * * 1 + - cron: 37 11 * * 4 workflow_dispatch: jobs: @@ -14,17 +14,17 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: python: 3.13 - name: Run Nox session to regenerate requirements - run: uv run --with nox --frozen nox -s requirements + run: uvx nox -s requirements # When a PR is created by a GitHub Action, normally the checks will # not be run. While the simplest workaround would have been to open diff --git a/.github/workflows/weekly.yml b/.github/workflows/weekly.yml index 9220d3b050..9fbf3c3681 100644 --- a/.github/workflows/weekly.yml +++ b/.github/workflows/weekly.yml @@ -75,24 +75,24 @@ jobs: python: '3.13' nox_session: run_tests_with_dev_version_of(lmfit) - - name: Documentation, Python 3.12, Ubuntu + - name: Documentation, Python 3.13, Ubuntu os: ubuntu-latest - python: '3.12' + python: '3.13' nox_session: docs - - name: Documentation, Python 3.12, sphinx-dev, Ubuntu + - name: Documentation, Python 3.13, sphinx-dev, Ubuntu os: ubuntu-latest - python: '3.12' + python: '3.13' nox_session: build_docs_with_dev_version_of(sphinx) - - name: Documentation, Python 3.12, sphinx_rtd_theme-dev, Ubuntu + - name: Documentation, Python 3.13, sphinx_rtd_theme-dev, Ubuntu os: ubuntu-latest - python: '3.12' + python: '3.13' nox_session: build_docs_with_dev_version_of(sphinx_rtd_theme) - - name: Documentation, Python 3.12, nbsphinx-dev, Ubuntu + - name: Documentation, Python 3.13, nbsphinx-dev, Ubuntu os: ubuntu-latest - python: '3.12' + python: '3.13' nox_session: build_docs_with_dev_version_of(nbsphinx) - name: Documentation, Python 3.12, plasmapy_sphinx-dev, Ubuntu @@ -148,7 +148,7 @@ jobs: steps: - name: Checkout code - uses: actions/checkout@v4 + uses: actions/checkout@v5 with: persist-credentials: false @@ -164,14 +164,14 @@ jobs: sudo apt-get install -y pandoc - name: Install uv - uses: astral-sh/setup-uv@v6 + uses: astral-sh/setup-uv@v7 with: python-version: ${{ matrix.python }} enable-cache: true cache-suffix: ${{ matrix.nox_session }}-${{ matrix.python }}-${{ runner.os }} - name: Run Nox session - run: uv run --with nox nox -s '${{ matrix.nox_session }}' + run: uvx nox -s '${{ matrix.nox_session }}' - name: Upload coverage reports to Codecov if: ${{ contains(matrix.nox_session, 'cov') }} diff --git a/.github/zizmor.yml b/.github/zizmor.yml index 18e8dd55b7..21e5ede1f8 100644 --- a/.github/zizmor.yml +++ b/.github/zizmor.yml @@ -24,17 +24,12 @@ rules: - changelog.yml:9:3 - changelog.yml:10:3 - comment-on-pr.yml:8:3 - - mint-release.yml:17:3 + - prepare-release-pr.yml:16:3 - unlabel-pr-after-merge.yml:8:3 - update-pinned-reqs.yml:9:3 template-injection: ignore: - create-release-issue.yml:21:7 - - mint-release.yml:41:7 - - mint-release.yml:47:7 - - mint-release.yml:53:7 - - mint-release.yml:61:7 - - mint-release.yml:66:7 use-trusted-publishing: ignore: - publish-to-pypi.yml:36:7 diff --git a/.mailmap b/.mailmap index 05b21ffe83..aa6e5e82e3 100644 --- a/.mailmap +++ b/.mailmap @@ -19,6 +19,7 @@ Elliot Johnson <77989826+etjohnson@users.noreply.github.com> Erik Everson Jasper Beckers Jayden Roberts <109694185+JaydenR2305@users.noreply.github.com> +Joseph Smith <11745431+josephrhsmith@users.noreply.github.com> Julien Hillairet Leah Nick Murphy @@ -27,5 +28,6 @@ Pawel Kozlowski Poh Zi How Rajagopalan Gangadharan Ritiek Malhotra +Tien Vo Tiger Du <56400881+Tiger-Du@users.noreply.github.com> Wu Tingfeng diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 26c98231f3..1f448a4d0e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,15 +1,11 @@ ci: autofix_prs: false - autoupdate_schedule: monthly - -# Specify the default version of Ruby in case it is not installed -default_language_version: - ruby: 2.7.2 + autoupdate_schedule: quarterly repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: check-ast name: validate Python code @@ -28,12 +24,12 @@ repos: - id: check-yaml - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.0 + rev: 0.34.0 hooks: - id: check-github-workflows - repo: https://github.com/sirosen/texthooks - rev: 0.6.8 + rev: 0.7.1 hooks: - id: fix-smartquotes - id: fix-spaces @@ -41,7 +37,7 @@ repos: - id: forbid-bidi-controls - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks - rev: v2.14.0 + rev: v2.15.0 hooks: - id: pretty-format-ini args: [--autofix] @@ -53,13 +49,6 @@ repos: # run this hook on `labeler.yml` (or certain other files). exclude: .github/labeler.yml|.pre-commit-search-and-replace.yaml -- repo: https://github.com/mattlqx/pre-commit-search-and-replace - # keep at v1.0.5 - rev: v1.0.5 - hooks: - - id: search-and-replace - exclude: changelog/README.rst|docs/changelog/.*|.sourcery.yaml|docs/_global_substitutions.py|CHANGELOG.rst|docs/contributing/doc_guide.rst - - repo: https://github.com/pre-commit/pygrep-hooks rev: v1.10.0 hooks: @@ -80,13 +69,14 @@ repos: - tomli - repo: https://github.com/crate-ci/typos - rev: v1.33.1 + rev: v1.36.0 hooks: - id: typos name: typos (add false positives to _typos.toml) + exclude: .pre-commit-search-and-replace.yaml - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.12 + rev: v0.13.2 hooks: - id: ruff name: ruff (see https://docs.astral.sh/ruff/rules) @@ -95,7 +85,7 @@ repos: name: autoformat source code with ruff-format - repo: https://github.com/asottile/blacken-docs - rev: 1.19.1 + rev: 1.20.0 hooks: - id: blacken-docs name: autoformat code blocks in docs diff --git a/.pre-commit-search-and-replace.yaml b/.pre-commit-search-and-replace.yaml deleted file mode 100644 index b4c68d5ddc..0000000000 --- a/.pre-commit-search-and-replace.yaml +++ /dev/null @@ -1,73 +0,0 @@ -# Include regular expressions between slashes. The "|" means "or". -# If there are special characters in one of the fields, put it in single -# quotes. - -- search: /Plasmapy|PlasmaPY/PlasmPy|Plasmpy|Palsmapy|PlasmaPY/ - replacement: PlasmaPy - description: Fix common misspellings and use consistent capitalization for PlasmaPy - -- search: /plasmpy|plaspmy|plasapy|palsmapy/ - replacement: plasmapy - description: Fix common misspellings of plasmapy - -- search: AstroPy - replacement: Astropy - -- search: from astropy import units as u - replacement: import astropy.units as u - -- search: from astropy import constants as const - replacement: import astropy.constants as const - -- search: '|array-like|' - replacement: '|array_like|' - description: NumPy uses an underscore in 'array_like' - -- search: ':term:`particle-like`' - replacement: '|particle-like|' - description: Apply reStructuredText substitution - -- search: ':term:`array_like`' - replacement: '|array_like|' - description: Apply reStructuredText substitution - -- search: 'optional, |keyword-only|' - replacement: '|keyword-only|, optional' - description: Keep a consistent order in type specifications - -- search: ', optional, default:' - replacement: ', default:' - description: No need to specify that a parameter is optional if there is a default value - -- search: 'the the ' - replacement: 'the ' - description: Fix common grammar error - -- search: 'MacOS' - replacement: 'macOS' - -- search: 'particle="e"' - replacement: 'particle="e-"' - description: Use canonical symbol for electron - -- search: 'particle="p"' - replacement: 'particle="p+"' - description: Use canonical symbol for proton - -- search: 'ion="p"' - replacement: 'ion="p+"' - description: Use canonical symbol for proton - -- search: '|nox|' - replacement: '|Nox|' - description: Nox is capitalized except when used as a command - -- search: 'nox -e' - replacement: 'nox -s' - description: The -s refers to Nox sessions, while the -e is from tox environments - -- search: '``~plasmapy' - description: Either enclose the namespace with single backticks to make it a link, or remove the tilde and keep it a literal - -- search: /astropy\.unit\./ - replacement: 'astropy.units.' diff --git a/.readthedocs.yml b/.readthedocs.yml index eabdc55869..38401fb62d 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -12,7 +12,7 @@ formats: build: os: ubuntu-24.04 tools: - python: '3.12' + python: '3.13' apt_packages: - graphviz @@ -23,7 +23,7 @@ build: - asdf plugin add uv - asdf install uv latest - asdf global uv latest - - uv venv --python=3.12 + - uv venv --python=3.13 install: - uv sync --extra docs --frozen --exact diff --git a/CHANGELOG.rst b/CHANGELOG.rst index dabd3c7674..4498c4938d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,272 +1,234 @@ -PlasmaPy v2024.10.0 (2024-10-30) -================================ +PlasmaPy v2025.8.0 (2025-08-07) +=============================== New Features ------------ -- Added the option to pass |inf| to the - `~plasmapy.particles.particle_class.Particle.ionize` method of |Particle| to - return the nucleus of the particle. (:pr:`2800`) -- Implemented - `~plasmapy.simulation.resolution_constraints.CFL_limit_electromagnetic_yee` - to calculate the CFL condition for electromagnetic simulations. (:pr:`2832`) -- - `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.synthetic_radiograph` - now accepts a file path to an - HDF5 file saved by +- Enabled |particle_input| to convert |particle-list-like| arguments passed + to parameters decorated with |ParticleListLike| into |ParticleList| + instances. (:pr:`2790`) +- The new method `~plasmapy.plasma.grids.CartesianGrid.soften_edges` applies an + error function mask + to the edges of all quantities on a grid. This is useful for any application + where the grid must + go to zero smoothly at the edges (e.g., for particle tracking with + |ParticleTracker|). (:pr:`2911`) +- Added the ``source_vdir`` keyword to the + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker.create_particles` + method of `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` - as input to create - a synthetic radiograph. (:pr:`2868`) -- Save routines in `~plasmapy.simulation.particle_tracker.save_routines` now - take an optional keyword argument ``output_basename`` - that sets the basename of the saved file(s). + to explicitly define the + orientation of the mean velocity of the source particles. (:pr:`2968`) +- Added the ``detector_vdir`` keyword to `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` - now - also accepts an ``output_basename`` keyword, which is passed to the save - routine. (:pr:`2868`) + to explicitly define the detector's vertical surface vector. (:pr:`2968`) +- Added a new module, `plasmapy.formulary.laser`, to make calculations related + to laser pulses. Added the first function, + `~plasmapy.formulary.laser.electric_field_amplitude`, which calculates the + electric field strength from intensity. (:pr:`3021`) +- Added `plasmapy.formulary.laser.intensity` to calculate intensity from the + electric field amplitude for a laser. (:pr:`3032`) +- Added helper function + `~plasmapy.analysis.swept_langmuir.helpers.sort_sweep_arrays` to + `plasmapy.analysis.swept_langmuir`. (:pr:`3034`) +- Added `~plasmapy.formulary.laser.em_wavelength`, + `~plasmapy.formulary.laser.em_angular_frequency`, + `~plasmapy.formulary.laser.Gaussian_beam_waist_radius`, + `~plasmapy.formulary.laser.Gaussian_spot_size_FWHM`, + `~plasmapy.formulary.laser.Gaussian_power`, + `~plasmapy.formulary.laser.Gaussian_Rayleigh_length`, and + `~plasmapy.formulary.laser.normalized_vector_potential` to + `plasmapy.formulary.laser`. (:pr:`3036`) +- Added helper function + `~plasmapy.analysis.swept_langmuir.helpers.merge_voltage_clusters` to + `plasmapy.analysis.swept_langmuir`. (:pr:`3037`) Documentation Improvements -------------------------- -- Updated the docstring of `~plasmapy.formulary.dimensionless.beta` to - explicitly - use definitions of :math:`p_{th}` and :math:`p_{mag}`, and added links - to `~plasmapy.formulary.misc.thermal_pressure` - and `~plasmapy.formulary.misc.magnetic_pressure`. (:pr:`2822`) -- Restructured sections in the `~plasmapy.formulary.mathematics.rot_a_to_b` - docstring to be consistent with other docstrings, and added 'Raises' and - 'Examples' sections. (:pr:`2824`) -- Added the :term:`force-free` definition to the |glossary|. (:pr:`2830`) -- Updated docstrings in `plasmapy.formulary` to follow the numpydoc standard. - (:pr:`2831`) -- Added examples to the |ParticleTracker| docstring. (:pr:`2833`) -- Added a section in the installation instructions for installing PlasmaPy with - |uv|. (:pr:`2861`) +- Incorporated the ``plasmapy_theme`` via the `plasmapy_sphinx.theme` + extension. (:pr:`1643`) +- Removed :file:`docs/plasmapy_sphinx` and put `plasmapy_sphinx` into its own + repository at https://github.com/PlasmaPy/plasmapy_sphinx\ . (:pr:`1643`) +- Added `plasmapy_sphinx` as a ``docs`` dependency. (:pr:`1643`) +- Removed upper dependency limit on `sphinx`, and added lower limit of + ``>=8.2.3``. (:pr:`1643`) +- Created a GitHub workflow (in :file:`weekly.yml` and :file:`noxfile.py`) + to build documentation using the latest development version of + `plasmapy_sphinx` on a weekly basis. (:pr:`1643`) +- Incorporated `sphinx` extensions `plasmapy_sphinx.ext.autodoc` and + `plasmapy_sphinx.ext.directives`. (:pr:`1643`) +- Updated author metadata in :file:`CITATION.cff`. (:pr:`2890`) +- Removed duplicate section headers for example notebooks in the documentation + for `plasmapy.formulary`. (:pr:`2892`) +- Added acknowledgements to several organizations that have supported PlasmaPy + or are aligned with its mission. (:pr:`2895`) +- Fixed formatting problems and improved verb tense consistency in prior + changelog entries. (:pr:`2901`) +- Fixed references to the ``astropy.units.equivalencies`` module in the docs. + Astropy now considers + this file to be private API (which broke PlasmaPy's intersphinx links), and + recommends that its contents be imported through the `astropy.units` + namespace. + This pull request changes those links to a direct URL to |Astropy + Equivalencies|. (:pr:`2915`) +- Added a sentence to the documentation for `plasmapy.dispersion` to describe + dispersion relations and their usefulness. (:pr:`2932`) +- Updated the instructions for accessing test results and documentation + previews in the |contributor guide| after recent changes to GitHub's user + interface. (:pr:`2935`) +- Expanded the docstring of `~plasmapy.formulary.dimensionless.Hall_parameter`. + (:pr:`2938`) +- Bumped the Python version for documentation builds from 3.12 to 3.13. + (:pr:`2943`) +- Updated the instructions on how to install PlasmaPy. (:pr:`2999`) +- Put office hours an an indefinite hiatus due to the conclusion of the NSF + collaborative awards supporting the development and growth of PlasmaPy. + (:pr:`3013`) +- Removed the `sphinx-hoverxref + `_ |Sphinx| extension, since + it has been deprecated in favor of the |Read the Docs| add-on for `Link + Previews `_\ + . (:pr:`3024`) +- Fixed broken hyperlinks and permanent redirects. (:pr:`3056`) +- Summarized the dependency support policy from |SPEC 0| at the end of the + installation instructions. (:pr:`3059`) +- Updated the |contributor guide| pages on the |code contribution workflow| + and :ref:`using pre-commit `. (:pr:`3068`) +- Upgraded :ref:`PlasmaPy's Code of Conduct ` to + version 3.0 of the Contributor Covenant. (:pr:`3069`) +- Updated the :ref:`Feedback and Communication ` page. + (:pr:`3070`) +- Limited the allowed version of |Sphinx| to ``sphinx>=8.2.3,<8.3`` + because planned breaking changes to Sphinx are causing documentation + build errors due to incompatibilities with some extensions. (:pr:`3073`) Backwards Incompatible Changes ------------------------------ -- Removed the ``optical_density`` keyword argument in - `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography`. - (:pr:`2843`) -- The property `~plasmapy.plasma.grids.AbstractGrid.recognized_quantities` of - `~plasmapy.plasma.grids.AbstractGrid` is now a class method - instead of a class property, as using `classmethod` and `property` decorators - together is no longer - allowed in Python 3.13. The syntax for accessing this dictionary has - therefore changed - from :py:`AbstractGrid.recognized_quantities` to - :py:`AbstractGrid.recognized_quantities()`. (:pr:`2871`) - - -Bug Fixes ---------- - -- Patched a bug in - `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography` in - which particles stopped - before the detector were still included in synthetic radiographs. - (:pr:`2843`) - - -Internal Changes and Refactorings +- Variables in |ParticleTracker| + and + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` + have been updated + such that ``n*`` is now ``num_*`` (e.g., ``nparticles`` is now + ``num_particles``). Similarly, ``v_init`` is + now ``v0`` to be consistent with ``x0``. (:pr:`2911`) +- The method + `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker.add_stopping` + requires that the argument ``I`` must now be a list of |Quantity| objects + rather than a single + |Quantity| array. This change is needed because `None` entries are now also + accepted to that + keyword as placeholders for grids on which stopping will not be applied. + (:pr:`2911`) +- |ParticleTracker| no longer accepts the parameter ``req_quantities``, but + instead automatically requires + quantities required by the tracker for the given setup. Users wishing to + require quantities + may use the method `~plasmapy.plasma.grids.AbstractGrid.require_quantities`. + (:pr:`2911`) +- Removed the prototype plasma calculator from PlasmaPy so that it can be + included in the |plasmapy-calculator| standalone package. (:pr:`3060`) + + +Deprecations and Planned Removals --------------------------------- -- Updated the release checklist. (:pr:`2784`) -- Added a |Nox| session to verify that the pinned requirements files used in - continuous integration tests are consistent with the requirements in - :file:`pyproject.toml`. (:pr:`2794`) -- Fixed a bug in the |Nox| session for running tests that prevented - doctests from being run, and fixed doctest errors that were introduced - while doctests were not enabled. (:pr:`2834`) -- Removed Numba as a project dependency. Consequently, - `~plasmapy.formulary.frequencies.plasma_frequency_lite` and - `~plasmapy.formulary.speeds.thermal_speed_lite` are no longer just-in-time - compiled by Numba. (:pr:`2841`) -- Adjusted the Sphinx configuration to account for recent deprecations in Read - the Docs. (:pr:`2857`) -- Added testing support for Python 3.13. (:pr:`2869`) -- Updated the versions of Python used in continuous integration workflows. - (:pr:`2879`) - - -Additional Changes ------------------- - -- Tentatively reverted :pr:`2715` because it introduced doctest errors during a - time when doctests were not enabled. (:pr:`2834`) - - -PlasmaPy v2024.7.0 (2024-07-21) -=============================== - -New Features ------------- - -- Implemented `~plasmapy.particles.atomic.stopping_power` to calculate stopping - powers using the NIST's ASTAR and PSTAR data. (:pr:`2555`) -- Added ionization energy data from NIST to the |Particle| class. - This can now be accessed using the - `~plasmapy.particles.particle_class.Particle.ionization_energy` attribute - from the |Particle| class. (:pr:`2657`) -- Renamed the `~plasmapy.particles.particle_class.Particle.binding_energy` - attribute of |Particle| to - `~plasmapy.particles.particle_class.Particle.nuclear_binding_energy` to avoid - confusion with - `~plasmapy.particles.particle_class.Particle.electron_binding_energy`. - (:pr:`2693`) -- Added electron binding energy data, relying on ionization energy data from - NIST, to the |Particle| class. - This can now be accessed using the - `~plasmapy.particles.particle_class.Particle.electron_binding_energy` - attribute - from the |Particle| class. (:pr:`2693`) -- Added a ``return_interpolator`` keyword to - `~plasmapy.particles.atomic.stopping_power` to allow the user to specify the - return of an interpolator function (`~scipy.interpolate.CubicSpline` under - the hood). (:pr:`2712`) -- Added the `~plasmapy.formulary.collisions.misc.Bethe_stopping` function to - the `~plasmapy.formulary.collisions` subpackage. (:pr:`2712`) -- Added the ability to enable particle stopping in the |ParticleTracker|. - (:pr:`2712`) - - -Documentation Improvements --------------------------- - -- Updated the |coding guide| with information on |static type checking| - with |mypy|. (:pr:`2454`) -- Updated the section in the |coding guide| about requirements and - dependencies. (:pr:`2720`) -- Updated docstrings in `plasmapy.dispersion`. (:pr:`2735`) -- Updated docstrings in `plasmapy.formulary.collisions`. (:pr:`2736`) -- Updated docstrings in `plasmapy.formulary`. (:pr:`2737`) -- Updated docstrings for `plasmapy.diagnostics` and `plasmapy.plasma.grids`. - (:pr:`2738`) -- Added :file:`README.md` files in the :file:`src/plasmapy`, :file:`tests`, - :file:`docs`, :file:`type_stubs`, :file:`.github/content`, - :file:`.github/scripts`, and :file:`.github/workflows` directories. The - contents of these files now appear as local documentation for each of these - directories in |PlasmaPy's GitHub repository|. (:pr:`2742`) -- Automated creation of the index file for the release changelogs. The page for - unreleased changes is included in the table of contents only if there are - unreleased changes. (:pr:`2754`) -- Re-wrote the "Test independence and parametrization" section of the |testing - guide| to use extremely simple math. (:pr:`2763`) -- Added functionality to generate a table of global substitutions in the - |documentation guide|. (:pr:`2766`) -- Renamed :file:`docs/_cff_to_rst.py` to :file:`docs/_author_list_from_cff.py`. - (:pr:`2766`) -- Based the version of PlasmaPy that gets included in development documentation - builds on the current date and most recent git hash. (:pr:`2775`) -- Merged the release guide into the |coding guide|. (:pr:`2777`) -- Added a new page to the |contributor guide| on |many ways to contribute| to - an open source project. (:pr:`2777`) -- Updated the |coding guide|, |testing guide|, and |documentation guide| - within the |contributor guide|. (:pr:`2777`) -- Moved the |contributor guide| section on example Jupyter notebooks from the - |coding guide| to the |documentation guide|. (:pr:`2777`) -- Added ``sphinxemoji`` as a |Sphinx| extension. (:pr:`2781`) - -Backwards Incompatible Changes ------------------------------- - -- Added a ``__str__`` method to the |CustomParticle| - class that returns the symbol of the particle if provided, and - otherwise falls back to using ``__repr__``. (:pr:`2702`) -- Changed default keyword argument for the ``fraction_exited_threshold`` in - `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` - and - `~plasmapy.simulation.particle_tracker.termination_conditions.AllParticlesOffGridTerminationCondition` - to correspond with the fraction of particles that have entered and - subsequently exited the grids. Previously this keyword was a misnomer, - causing the simulation to instead terminate when the specified fraction of - particles remaining on the grids was less than or equal to the provided - ``fraction_exited_threshold``. (:pr:`2712`) -- Convert ``particle`` to a required argument of the - `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker.load_particles` - method of |ParticleTracker|. (:pr:`2746`) +- Removed :file:`src/plasmapy/dispersion/dispersionfunction.py`, which was + deprecated in ``v2023.10.0``. The functionality for the plasma dispersion + function is in `plasmapy.dispersion.dispersion_functions`. (:pr:`2897`) Bug Fixes --------- -- - Enabled |validate_quantities| to be compatible with postponed evaluation of - annotations (see :pep:`563`). (:pr:`2479`) (:pr:`2506`) -- Changed the |charge number| (:math:`Z`) dependence of the ion contribution to - the optical Thomson scattering - spectral density function in - `~plasmapy.diagnostics.thomson.spectral_density_lite` from :math:`Z` - to :math:`z^2 / \bar{z}` to match Eq. 5.1.2 and following equations in - :cite:t:`sheffield:2011`. - The result is a small change in the ion acoustic wave spectrum for plasmas - with multiple ion species. (:pr:`2699`) -- Add axes removed by `numpy.squeeze` to arrays in - `~plasmapy.dispersion.analytical.mhd_waves_` (:pr:`2715`) +- Enabled |Particle| to accept a `numpy.integer` object as the first argument + to indicate the atomic number. (:pr:`3045`) +- Fixed a possible bug when using + `plasmapy.plasma.grids.AbstractGrid.add_quantities` + alongside newer versions of |xarray|. (:pr:`3065`) Internal Changes and Refactorings --------------------------------- -- Converted the tox environment for regenerating the requirements files - used in continuous integration checks to |Nox|. (:pr:`2664`) -- Created a parametrized |Nox| session to run tests. (:pr:`2681`) -- Added |Nox| sessions to test importing PlasmaPy, validating - :file:`CITATION.cff`, - and building a source distribution and wheel. (:pr:`2682`) -- Switched the GitHub workflows for running tests from using tox environments - to using |Nox| sessions. (:pr:`2685`) -- Added ``pytest-filter-subpackage`` to the ``tests`` dependency set. This - dependency enables - us to run, for example, ``pytest -P particles`` to invoke tests for - `plasmapy.particles`. (:pr:`2688`) -- Added |Nox| sessions to run tests and build documentation against unreleased - versions - of major dependencies. (:pr:`2694`) -- Deleted :file:`tox.ini`, since all tox environments defined therein - have been converted to |Nox| sessions. (:pr:`2694`) -- Removed :file:`requirements.txt`, along with the requirements files - in :file:`ci_requirements/` that were used in tox environments - that have since been replaced with |Nox| sessions. (:pr:`2694`) -- Switched over weekly tests to use |Nox| sessions rather than tox - environments. (:pr:`2694`) -- Added the ``lint`` and ``manifest`` sessions for |Nox| to run |pre-commit| on - all files - and verify :file:`MANIFEST.in` with ``check-manifest``, respectively. - (:pr:`2695`) -- Added a |Nox| session that invokes ``autotyping`` to automatically - add |type hint annotations|, using either the ``--safe`` or - ``--aggressive`` options. (:pr:`2696`) -- Added ``typos`` as a |pre-commit| hook to perform spellchecking. (:pr:`2700`) -- Added a condition to check if the GitHub API can be reached to be used by the - `~plasmapy.utils.data.downloader.Downloader` object. (:pr:`2710`) -- Applied |type hint annotations| using ``autotyping``, and made other updates - to type - hint annotations and docstrings. (:pr:`2728`) -- Added |type hint annotations| to `plasmapy.utils.roman`. (:pr:`2733`) -- Added |type hint annotations| to ``plasmapy.utils._units_helpers``. - (:pr:`2734`) -- Added a |Nox| session for building the changelog. (:pr:`2744`) -- Added an experimental |Nox| session for adding |type hint annotations| using - `MonkeyType `__. - This session creates a database of variable types from running pytest, and - then applies the observed types to a particular module. (:pr:`2747`) -- Updated |Nox| sessions, including docstrings and troubleshooting messages. - (:pr:`2750`) -- Enabled tests to pass with ``numpy == 2.0.0``. (:pr:`2772`) +- Dropped support for Python 3.10 and bumped the minimum required + versions of several dependencies following |SPEC 0|. (:pr:`2880`) +- Updated the release checklist following the ``v2024.10.0`` release. + (:pr:`2886`) +- Used `typing.Self` for type hint annotations for |Particle| and + |CustomParticle|. (:pr:`2887`) +- Modified tests for `~plasmapy.diagnostics.thomson.spectral_density` to cover + the case of multiple electron species. (:pr:`2906`) +- The internal structure of + `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker` was + optimized by caching some variables (e.g., ``tracked_particle_mask``) which + are then reset after every + push cycle by a ``_reset_cache`` method. Instead of adding zero arrays for + missing quantities, only + quantities provided on the grid are interpolated, and other required + quantities are filled in with an + array of zeros automatically. Particle stopping can now be enabled on a + subset of the provided grids. + Adaptive time steps do not include magnetic field candidates if a magnetic + field does not exist on the grid. + The adaptive timestep is now set to that of the highest resolution grid for + particles that are not + currently on any grid. (:pr:`2911`) +- Added ``User-Agent`` to the header of + `~plasmapy.utils.data.downloader.Downloader` to + resolve an issue with GitHub blocking API access. (:pr:`2915`) +- Updated :file:`validators.py`. (:pr:`2919`) +- Began using :file:`uv.lock` to pin the versions of dependencies used + in tests and documentation builds. Previously, pinned requirements had + been stored in :file:`requirements.txt` style files in + :file:`ci_requirements/` that were generated with ``uv pip compile`` + for each operating system, Python version, and dependency set. Using + :file:`uv.lock` lets us store requirements information for + different operating systems, Python versions, and dependency sets in + a single file. (:pr:`2937`) +- Switched from using ``actions/setup-python`` to ``astral-sh/setup-uv`` in + GitHub workflows. (:pr:`2959`) +- Enabled :file:`noxfile.py` to be run as a script. + The commands ``python noxfile.py -s 'tests-3.13(all)'`` and ``nox -s + 'tests-3.13(all)'`` can now both be used to run all tests for Python 3.13. + (:pr:`2961`) +- Updated the ``requirements`` session for Nox so that the GitHub workflow + now includes a table of the old and new versions of dependencies in the + body of the pull request. (:pr:`2964`) +- Enabled ``pyproject-fmt`` as an autoformatter and ``validate-pyproject`` as a + validator for :file:`pyproject.toml` via |pre-commit|. (:pr:`2974`) +- Added a |Nox| session to perform security audits of GitHub workflows with + ``zizmor`` in CI. (:pr:`2975`) +- Enabled a |pre-commit| hook for ``mdformat`` to automatically format + GitHub-flavored Markdown files. (:pr:`2981`) +- Added a security policy at :file:`.github/SECURITY.md` and enabled private + security reporting through GitHub. (:pr:`2985`) +- Reorganized :file:`.gitignore` to put content that is custom or + PlasmaPy-specific + at the top of the file, followed by content adapted from :file:`.gitignore` + templates at the bottom. (:pr:`2997`) +- Set |uv| as the sole backend to Nox, and changed the ``docs`` and ``tests`` + dependency sets to include ``nox[uv]`` instead of ``nox``. (:pr:`2998`) +- Refactored tests for the `~plasmapy.diagnostics.charged_particle_radiography` + module to reduce test runtime. (:pr:`3039`) +- Removed upper limits on the allowed versions of Astropy and xarray. + (:pr:`3065`) +- Parametrized tests within :file:`tests/utils/decorators.test_checks.py`. + (:pr:`3065`) +- Updated :file:`tests/utils/decorators/test_checks.py` for compatibility with + updates to how `astropy.units.Equivalency` handles equality comparisons. + (:pr:`3065`) Additional Changes ------------------ -- Refactored - `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` - to use |ParticleTracker|. (:pr:`2704`) -- Included :file:`src/plasmapy/_version.py` in :file:`MANIFEST.in`. This file - is automatically generated using ``setuptools_scm``, but is necessary for the - version to be correct in the titles of pages in development documentation - builds. (:pr:`2756`) -- Updated the comment that gets posted to new pull requests via a GitHub - workflow. (:pr:`2765`) +- The ``ax#``, ``dx#`` and ``*_si`` properties of + `~plasmapy.plasma.grids.AbstractGrid` are now + cached properties for faster access, since these attributes do not change + after the grid has been initialized. (:pr:`2911`) +- Updated the configuration to automatically label pull requests on GitHub. + (:pr:`2984`) diff --git a/CITATION.cff b/CITATION.cff index 577381b2fa..9e6ac99dc8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,10 +1,10 @@ title: PlasmaPy type: software -version: 2024.10.0 +version: 2025.8.0 identifiers: - type: doi - value: 10.5281/zenodo.14010450 -date-released: '2024-10-30' + value: 10.5281/zenodo.16747747 +date-released: '2025-08-07' message: >- Please cite the specific version of PlasmaPy used during a research project. @@ -256,6 +256,11 @@ authors: orcid: https://orcid.org/0000-0003-0223-7004 alias: samaiyahfarid +- given-names: Emmanuel + family-names: Ferdman + orcid: https://orcid.org/0009-0004-8953-0151 + alias: emmanuel-ferdman + - given-names: Michael family-names: Fischer @@ -282,6 +287,11 @@ authors: orcid: https://orcid.org/0009-0008-3588-0497 alias: s-gerow +- given-names: Mahlet + family-names: Getahun + affiliation: Marietta College + alias: Getahun-yw-Mahl + - given-names: Jessica family-names: Gonzalez affiliation: California Institute of Technology @@ -479,6 +489,12 @@ authors: affiliation: College of William & Mary alias: LeoMurphy037 +- given-names: Bao + family-names: Nguyen + affiliation: Imperial College London + orcid: https://orcid.org/0000-0002-1753-4223 + alias: wnguyen1312 + - given-names: Suzanne family-names: Nie alias: sznie @@ -519,6 +535,8 @@ authors: family-names: Pérez alias: RoberTnf +- alias: Physics-is-awesome + - given-names: Preston family-names: Pitzer affiliation: Virginia Tech @@ -731,18 +749,7 @@ authors: family-names: Zhang alias: carolyz -- given-names: Bao - family-names: Nguyen - affiliation: Imperial College London - orcid: https://orcid.org/0000-0002-1753-4223 - alias: wnguyen1312 - -- given-names: Emmanuel - family-names: Ferdman - orcid: https://orcid.org/0009-0004-8953-0151 - alias: emmanuel-ferdman - -- given-names: Mahlet - family-names: Getahun - affiliation: Marietta College - alias: Getahun-yw-Mahl +- given-names: Clément + family-names: Robert + orcid: https://orcid.org/0000-0001-8629-7068 + alias: neutrinoceros diff --git a/README.md b/README.md index 36e479394d..7548ce918d 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,7 @@ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1436011.svg)](https://doi.org/10.5281/zenodo.1436011) [![astropy](http://img.shields.io/badge/powered%20by-Astropy-orange.svg?style=flat&logo=astropy)](http://www.astropy.org/) [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) +[![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) [PlasmaPy] is an open source, community-developed [Python] package for plasma research and education. PlasmaPy intends to be for plasma science @@ -55,7 +56,7 @@ On some systems, it might be necessary to specify the Python version number, for example by using `python3` or `python3.13` instead of `python`. -To install PlasmaPy on Windows, open a terminal and run +To install PlasmaPy in Windows via PowerShell, run: ```Shell py -3.13 -m pip install plasmapy @@ -101,11 +102,12 @@ about these meetings is on the [meetings] page of PlasmaPy's website. ### Community meetings -PlasmaPy's weekly [community meetings] are a place to talk about code -development, event planning, and other community happenings. If you have -an idea for a new feature or would like to become involved in the +PlasmaPy's [community meetings] are a place to talk about code +development, event planning, and other community happenings. If you +have an idea for a new feature or would like to become involved in the PlasmaPy project, community meetings are a great place to start. As of -May 2025, our community meetings are on most Thursdays at 2 pm ET. +September 2025, our community meetings are usually held every other +Monday at 1 pm ET. ## Community @@ -131,8 +133,8 @@ channel; Gitter uses a bridge to link the two. ### Mailing list -You can subscribe to PlasmaPy's low-volume [mailing list] to receive -PlasmaPy newsletters and other announcements. +Subscribe to PlasmaPy's low-volume [mailing list] to receive occasional +newsletters and announcements. ## License @@ -142,7 +144,7 @@ added [protections against software patents]. ## Acknowledgments Development of PlasmaPy has been supported in part by the -[National Science Foundation], [Department of Energy], [NASA], and the +[National Science Foundation], [NASA], [Department of Energy], and the [Smithsonian Institution]. For more details, please see PlasmaPy's documentation page on [authors and credits]. diff --git a/_typos.toml b/_typos.toml index e9f704263a..22c2e5515f 100644 --- a/_typos.toml +++ b/_typos.toml @@ -10,3 +10,6 @@ hax = "hax" iy = "iy" nd = "nd" rety = "rety" +newshape = "newshape" +texttt = "texttt" +nbins = "nbins" diff --git a/changelog/1643.doc.1.rst b/changelog/1643.doc.1.rst deleted file mode 100644 index 9e8882233c..0000000000 --- a/changelog/1643.doc.1.rst +++ /dev/null @@ -1,2 +0,0 @@ -Removed :file:`docs/plasmapy_sphinx` and put `plasmapy_sphinx` into its own -repository, https://github.com/PlasmaPy/plasmapy_sphinx\ . diff --git a/changelog/1643.doc.2.rst b/changelog/1643.doc.2.rst deleted file mode 100644 index e747f50a9e..0000000000 --- a/changelog/1643.doc.2.rst +++ /dev/null @@ -1 +0,0 @@ -Added `plasmapy_sphinx` as a ``docs`` dependency. diff --git a/changelog/1643.doc.3.rst b/changelog/1643.doc.3.rst deleted file mode 100644 index 30faabde0b..0000000000 --- a/changelog/1643.doc.3.rst +++ /dev/null @@ -1,2 +0,0 @@ -Removed upper dependency limit on `sphinx`, and added lower limit of -``>=8.2.3``. diff --git a/changelog/1643.doc.4.rst b/changelog/1643.doc.4.rst deleted file mode 100644 index 2da2208275..0000000000 --- a/changelog/1643.doc.4.rst +++ /dev/null @@ -1,2 +0,0 @@ -Incorporated the ``plasmapy_theme`` via the `plasmapy_sphinx.theme` -extension. diff --git a/changelog/1643.doc.5.rst b/changelog/1643.doc.5.rst deleted file mode 100644 index b9e1f29de8..0000000000 --- a/changelog/1643.doc.5.rst +++ /dev/null @@ -1,2 +0,0 @@ -Incorporated `sphinx` extensions `plasmapy_sphinx.ext.autodoc` and -`plasmapy_sphinx.ext.directives`. diff --git a/changelog/1643.doc.6.rst b/changelog/1643.doc.6.rst deleted file mode 100644 index 670af13f15..0000000000 --- a/changelog/1643.doc.6.rst +++ /dev/null @@ -1,3 +0,0 @@ -Created a GitHub Action (in :file:`weekly.yml` and :file:`noxfile.py`) -to build documentation using the latest development version of -`plasmapy_sphinx` on a weekly basis. diff --git a/changelog/2790.feature.rst b/changelog/2790.feature.rst deleted file mode 100644 index 467dc308e2..0000000000 --- a/changelog/2790.feature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Enabled |particle_input| to convert |particle-list-like| arguments passed -to parameters decorated with |ParticleListLike| into |ParticleList| instances. diff --git a/changelog/2880.internal.rst b/changelog/2880.internal.rst deleted file mode 100644 index 025073363d..0000000000 --- a/changelog/2880.internal.rst +++ /dev/null @@ -1,2 +0,0 @@ -Dropped support for Python 3.10 and bumped the minimum required -versions of several dependencies following |SPEC 0|. diff --git a/changelog/2886.internal.rst b/changelog/2886.internal.rst deleted file mode 100644 index 4b48c9b1c7..0000000000 --- a/changelog/2886.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Updated the release checklist following the ``v2024.10.0`` release. diff --git a/changelog/2890.doc.rst b/changelog/2890.doc.rst deleted file mode 100644 index 0581b02b9c..0000000000 --- a/changelog/2890.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Updated author metadata in :file:`CITATION.cff`. diff --git a/changelog/2892.doc.rst b/changelog/2892.doc.rst deleted file mode 100644 index 48db46fe25..0000000000 --- a/changelog/2892.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Removed duplicate section headers for example notebooks in documentation for `plasmapy.formulary`. diff --git a/changelog/2895.doc.rst b/changelog/2895.doc.rst deleted file mode 100644 index c67705c12b..0000000000 --- a/changelog/2895.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Added acknowledgements to several organizations that have supported PlasmaPy or are aligned with its mission. diff --git a/changelog/2897.removal.rst b/changelog/2897.removal.rst deleted file mode 100644 index ccf3072b59..0000000000 --- a/changelog/2897.removal.rst +++ /dev/null @@ -1 +0,0 @@ -Removed :file:`src/plasmapy/dispersion/dispersionfunction.py`, which was deprecated in ``v2023.10.0``. The functionality for the plasma dispersion function is in `plasmapy.dispersion.dispersion_functions`. diff --git a/changelog/2901.doc.rst b/changelog/2901.doc.rst deleted file mode 100644 index 1a1e8374d6..0000000000 --- a/changelog/2901.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed formatting problems and improved verb tense consistency in prior changelog entries. diff --git a/changelog/2906.internal.rst b/changelog/2906.internal.rst deleted file mode 100644 index fabe66c508..0000000000 --- a/changelog/2906.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Modified tests for `~plasmapy.diagnostics.thomson.spectral_density` to cover the case of multiple electron species. diff --git a/changelog/2911.breaking.1.rst b/changelog/2911.breaking.1.rst deleted file mode 100644 index 54fb8e0bbd..0000000000 --- a/changelog/2911.breaking.1.rst +++ /dev/null @@ -1,3 +0,0 @@ -|ParticleTracker| no longer takes the keyword ``req_quantities``, but instead automatically requires -quantitities required by the tracker for the given setup. Users wishing to require quantitities -may use the method `~plasmapy.plasma.grids.AbstractGrid.require_quantities`. diff --git a/changelog/2911.breaking.2.rst b/changelog/2911.breaking.2.rst deleted file mode 100644 index d99d629e1d..0000000000 --- a/changelog/2911.breaking.2.rst +++ /dev/null @@ -1,4 +0,0 @@ -The method `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker.add_stopping` -argument ``I`` must now be a list of `~astropy.units.Quantity` objects rather than a single -`~astropy.units.Quantity` array. This is because ``None`` entries are now also accepted to that -keyword as placeholders for grids on which stopping will not be applied. diff --git a/changelog/2911.breaking.3.rst b/changelog/2911.breaking.3.rst deleted file mode 100644 index cba592317a..0000000000 --- a/changelog/2911.breaking.3.rst +++ /dev/null @@ -1,4 +0,0 @@ -Variables in |ParticleTracker| -and `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` have been updated -such that ``n*`` is now ``num_*``, e.g. ``nparticles`` is now ``num_particles``. Similarly, ``v_init`` is -now ``v0`` to be consistent with ``x0``. diff --git a/changelog/2911.feature.rst b/changelog/2911.feature.rst deleted file mode 100644 index 9c9fdf407d..0000000000 --- a/changelog/2911.feature.rst +++ /dev/null @@ -1,3 +0,0 @@ -The new method `~plasmapy.plasma.grids.CartesianGrid.soften_edges` applies an error function mask -to the edges of all quantities on a grid. This is useful for any application where the grid must -go to zero smoothly at the edges, e.g. for particle tracking with |ParticleTracker|. diff --git a/changelog/2911.internal.1.rst b/changelog/2911.internal.1.rst deleted file mode 100644 index f414a34e26..0000000000 --- a/changelog/2911.internal.1.rst +++ /dev/null @@ -1,8 +0,0 @@ -The internal structure of `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker` was -optimized by caching some variables (e.g., ``tracked_particle_mask``) which are then reset after every -push cycle by a ``_reset_cache`` method. Instead of adding zero arrays for missing quantities, only -quantities provided on the grid are interpolated, and other required quantities are filled in with an -array of zeros automatically. Particle stopping can now be enabled on a subset of the provided grids. -Adaptive time steps do not include magnetic field candidates if a magnetic field does not exist on the grid. -The adaptive timestep is now set to that of the highest resolution grid for particles that are not -currently on any grid. diff --git a/changelog/2911.trivial.1.rst b/changelog/2911.trivial.1.rst deleted file mode 100644 index 283ca48685..0000000000 --- a/changelog/2911.trivial.1.rst +++ /dev/null @@ -1,2 +0,0 @@ -``ax#``, ``dx#`` and ``*_si`` properties of `~plasmapy.plasma.grids.AbstractGrid` are now -cached properties for faster access, since these attributes do not change after the grid has been initialized. diff --git a/changelog/2915.doc.rst b/changelog/2915.doc.rst deleted file mode 100644 index e1eb2afc41..0000000000 --- a/changelog/2915.doc.rst +++ /dev/null @@ -1,4 +0,0 @@ -Fixed references to the ``astropy.units.equivalencies`` module in the docs. Astropy now considers -this file to be private API, and wants its contents imported through the ``units`` module namespace, -which broke PlasmaPy's intersphinx links. This PR changes those links to a direct URL to the page in the -astropy docs: |Astropy Equivalencies|. diff --git a/changelog/2915.internal.rst b/changelog/2915.internal.rst deleted file mode 100644 index 6192cfbdbf..0000000000 --- a/changelog/2915.internal.rst +++ /dev/null @@ -1,2 +0,0 @@ -Added ``User-Agent`` to the header of `~plasmapy.utils.data.downloader.Downloader` to -resolve an issue with GitHub blocking API access. diff --git a/changelog/2932.doc.rst b/changelog/2932.doc.rst deleted file mode 100644 index aba2223f69..0000000000 --- a/changelog/2932.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Added a sentence to introduce what a dispersion relation is and why it's useful. diff --git a/changelog/2935.doc.rst b/changelog/2935.doc.rst deleted file mode 100644 index c7e0b7287a..0000000000 --- a/changelog/2935.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Updated how to access test results and documentation previews in the |contributor guide| after recent changes to GitHub's user interface. diff --git a/changelog/2937.internal.rst b/changelog/2937.internal.rst deleted file mode 100644 index 9c97b63952..0000000000 --- a/changelog/2937.internal.rst +++ /dev/null @@ -1,8 +0,0 @@ -Began using :file:`uv.lock` to pin the versions of dependencies used -in tests and documentation builds. Previously, pinned requirements had -been stored in :file:`requirements.txt` style files in -:file:`ci_requirements/` that were generated with ``uv pip compile`` -for each operating system, Python version, and dependency set. Using -:file:`uv.lock` lets us store requirements information for -different operating systems, Python versions, and dependency sets in -a single file. diff --git a/changelog/2959.internal.rst b/changelog/2959.internal.rst deleted file mode 100644 index 25d77f62a1..0000000000 --- a/changelog/2959.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Switched from using ``actions/setup-python`` to ``astral-sh/setup-uv`` in GitHub workflows. diff --git a/changelog/2961.internal.rst b/changelog/2961.internal.rst deleted file mode 100644 index 26dd965ef5..0000000000 --- a/changelog/2961.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Enabled :file:`noxfile.py` to be run as a script, in alignment with :pep:`723`. diff --git a/changelog/2964.internal.rst b/changelog/2964.internal.rst deleted file mode 100644 index 52002f8f94..0000000000 --- a/changelog/2964.internal.rst +++ /dev/null @@ -1,3 +0,0 @@ -Updated the ``requirements`` session for Nox so that the GitHub workflow -now includes a table of the old and new versions of dependencies in the -body of the pull request. diff --git a/changelog/2968.feature.rst b/changelog/2968.feature.rst deleted file mode 100644 index fb91b2ab73..0000000000 --- a/changelog/2968.feature.rst +++ /dev/null @@ -1,4 +0,0 @@ -Added the ``detector_vdir`` keyword to `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` -to explicitly define the detector's vertical surface vector. Added the ``source_vdir`` keyword to the ``create_particles`` -method of `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` to explicitly define the -orientation of the mean velocity of the source particles. diff --git a/changelog/2974.internal.rst b/changelog/2974.internal.rst deleted file mode 100644 index f2419577af..0000000000 --- a/changelog/2974.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Enabled ``pyproject-fmt`` as an autoformatter and ``validate-pyproject`` as a validator for :file:`pyproject.toml`. diff --git a/changelog/2975.internal.rst b/changelog/2975.internal.rst deleted file mode 100644 index 813a11881b..0000000000 --- a/changelog/2975.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Added a |Nox| session to perform security audits of GitHub workflows with ``zizmor`` in CI. diff --git a/changelog/2981.internal.rst b/changelog/2981.internal.rst deleted file mode 100644 index 3039d42e76..0000000000 --- a/changelog/2981.internal.rst +++ /dev/null @@ -1 +0,0 @@ -Enabled a ``pre-commit`` hook for ``mdformat`` to automatically format GitHub-flavored Markdown files. diff --git a/changelog/2984.trivial.rst b/changelog/2984.trivial.rst deleted file mode 100644 index 412642b25a..0000000000 --- a/changelog/2984.trivial.rst +++ /dev/null @@ -1 +0,0 @@ -Updated the configuration to automatically label pull requests on GitHub. diff --git a/changelog/2997.internal.rst b/changelog/2997.internal.rst deleted file mode 100644 index 8114301178..0000000000 --- a/changelog/2997.internal.rst +++ /dev/null @@ -1,3 +0,0 @@ -Updated :file:`.gitignore` to put content that is custom or PlasmaPy-specific -at the top of the file, followed by content adapted from :file:`.gitignore` -templates at the bottom. diff --git a/changelog/3013.doc.rst b/changelog/3013.doc.rst deleted file mode 100644 index 414fb1ad30..0000000000 --- a/changelog/3013.doc.rst +++ /dev/null @@ -1 +0,0 @@ -Put office hours an an indefinite hiatus due to the conclusion of the NSF award supporting the development of PlasmaPy. diff --git a/changelog/3021.feature.rst b/changelog/3021.feature.rst deleted file mode 100644 index 419c0ee6fb..0000000000 --- a/changelog/3021.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Added a new module, `plasmapy.formulary.laser`, to make calculations related to laser pulses. Added the first function, `~plasmapy.formulary.laser.electric_field_amplitude`, which calculates the electric field strength from intensity. diff --git a/changelog/3032.feature.rst b/changelog/3032.feature.rst deleted file mode 100644 index b920e16ce3..0000000000 --- a/changelog/3032.feature.rst +++ /dev/null @@ -1 +0,0 @@ -Added the second function to `plasmapy.formulary.laser`, `~plasmapy.formulary.laser.intensity`, which calculates intensity from the electric field amplitude. diff --git a/changelog/3094.internal.rst b/changelog/3094.internal.rst new file mode 100644 index 0000000000..9f23a3dbe5 --- /dev/null +++ b/changelog/3094.internal.rst @@ -0,0 +1 @@ +Removed obsolete configuration settings from :file:`mypy.ini`. diff --git a/changelog/3113.internal.rst b/changelog/3113.internal.rst new file mode 100644 index 0000000000..a4a4b7d0a9 --- /dev/null +++ b/changelog/3113.internal.rst @@ -0,0 +1 @@ +Removed ``pre-commit-search-and-replace`` as a |pre-commit| hook. diff --git a/docs/CODE_OF_CONDUCT.rst b/docs/CODE_OF_CONDUCT.rst index 404ebf4def..756a8ae06d 100644 --- a/docs/CODE_OF_CONDUCT.rst +++ b/docs/CODE_OF_CONDUCT.rst @@ -1,150 +1,203 @@ .. _plasmapy-code-of-conduct: -Contributor Covenant Code of Conduct -==================================== - -We adopt the `Contributor Covenant`_, version 2.1, which is reproduced -below. - -Our Pledge 🤞 -------------- - -We as members, contributors, and leaders pledge to make participation in -our community a harassment-free experience for everyone, regardless of -age, body size, visible or invisible disability, ethnicity, sex -characteristics, gender identity and expression, level of experience, -education, socioeconomic status, nationality, personal appearance, -race, caste, color, religion, or sexual identity and orientation. - -We pledge to act and interact in ways that contribute to an open, -welcoming, diverse, inclusive, and healthy community. ✨ - -Our Standards -------------- - -Examples of behavior that contributes to a positive environment for our -community include: - -- Demonstrating empathy and kindness toward other people -- Being respectful of differing opinions, viewpoints, and experiences -- Giving and gracefully accepting constructive feedback -- Accepting responsibility and apologizing to those affected by our - mistakes, and learning from the experience -- Focusing on what is best not just for us as individuals, but for the - overall community - -Examples of unacceptable behavior include: - -- The use of sexualized language or imagery, and sexual attention or - advances of any kind -- Trolling, insulting or derogatory comments, and personal or political - attacks -- Public or private harassment -- Publishing others' private information, such as a physical or email - address, without their explicit permission -- Other conduct which could reasonably be considered inappropriate in a - professional setting - -Enforcement Responsibilities ----------------------------- - -Community leaders are responsible for clarifying and enforcing our -standards of acceptable behavior and will take appropriate and fair -corrective action in response to any behavior that they deem -inappropriate, threatening, offensive, or harmful. - -Community leaders have the right and responsibility to remove, edit, or -reject comments, commits, code, wiki edits, issues, and other -contributions that are not aligned to this Code of Conduct, and will -communicate reasons for moderation decisions when appropriate. +Contributor Covenant 3.0 +======================== + +To respect the inherent worth and dignity of every person, the +PlasmaPy community abides by the Contributor Covenant Code of Conduct, +version 3.0. + +.. important:: + + To report a possible violation of the code of conduct, please email + conduct@plasmapy.org. + +Our Pledge +---------- + +We pledge to make our community welcoming, safe, and equitable for all. + +We are committed to fostering an environment that respects and promotes +the dignity, rights, and contributions of all individuals, regardless of +characteristics including race, ethnicity, caste, color, age, physical +characteristics, neurodiversity, disability, sex or gender, gender +identity or expression, sexual orientation, language, philosophy or +religion, national or social origin, socio-economic position, level of +education, or other status. The same privileges of participation are +extended to everyone who participates in good faith and in accordance +with this Covenant. + +Encouraged Behaviors +-------------------- + +While acknowledging differences in social norms, we all strive to meet +our community's expectations for positive behavior. We also understand +that our words and actions may be interpreted differently than we intend +based on culture, background, or native language. + +With these considerations in mind, we agree to behave mindfully toward +each other and act in ways that center our shared values, including: + +1. Respecting the **purpose of our community**, our activities, and our + ways of gathering. +2. Engaging **kindly and honestly** with others. +3. Respecting **different viewpoints** and experiences. +4. **Taking responsibility** for our actions and contributions. +5. Gracefully giving and accepting **constructive feedback**. +6. Committing to **repairing harm** when it occurs. +7. Behaving in other ways that promote and sustain the **well-being of + our community**. + +Restricted Behaviors +-------------------- + +We agree to restrict the following behaviors in our community. +Instances, threats, and promotion of these behaviors are violations of +this Code of Conduct. + +1. **Harassment.** Violating explicitly expressed boundaries or engaging + in unnecessary personal attention after any clear request to stop. +2. **Character attacks.** Making insulting, demeaning, or pejorative + comments directed at a community member or group of people. +3. **Stereotyping or discrimination.** Characterizing anyone's + personality or behavior on the basis of immutable identities or + traits. +4. **Sexualization.** Behaving in a way that would generally be + considered inappropriately intimate in the context or purpose of the + community. +5. **Violating confidentiality**. Sharing or acting on someone's + personal or private information without their permission. +6. **Endangerment.** Causing, encouraging, or threatening violence or + other harm toward any person or group. +7. Behaving in other ways that **threaten the well-being** of our + community. + +Other Restrictions +~~~~~~~~~~~~~~~~~~ + +1. **Misleading identity.** Impersonating someone else for any reason, + or pretending to be someone else to evade enforcement actions. +2. **Failing to credit sources.** Not properly crediting the sources of + content you contribute. +3. **Promotional materials**. Sharing marketing or other commercial + content in a way that is outside the norms of the community. +4. **Irresponsible communication.** Failing to responsibly present + content which includes, links or describes any other restricted + behaviors. + +Reporting an Issue +------------------ + +Tensions can occur between community members even when they are trying +their best to collaborate. Not every conflict represents a code of +conduct violation, and this Code of Conduct reinforces encouraged +behaviors and norms that can help avoid conflicts and minimize harm. + +When an incident does occur, it is important to report it promptly. +To report a possible violation of the code of conduct, please email +conduct@plasmapy.org. + +Community Moderators take reports of violations seriously and will make +every effort to respond in a timely manner. They will investigate all +reports of code of conduct violations, reviewing messages, logs, and +recordings, or interviewing witnesses and other participants. Community +Moderators will keep investigation and enforcement actions as +transparent as possible while prioritizing safety and confidentiality. +In order to honor these values, enforcement actions are carried out in +private with the involved parties, but communicating to the whole +community may be part of a mutually agreed upon resolution. + +Addressing and Repairing Harm +----------------------------- + +If an investigation by the Community Moderators finds that this Code of +Conduct has been violated, the following enforcement ladder may be used +to determine how best to repair harm, based on the incident's impact on +the individuals involved and the community as a whole. Depending on the +severity of a violation, lower rungs on the ladder may be skipped. + +1) Warning + + 1) Event: A violation involving a single incident or series of + incidents. + 2) Consequence: A private, written warning from the Community + Moderators. + 3) Repair: Examples of repair include a private written apology, + acknowledgement of responsibility, and seeking clarification on + expectations. + +2) Temporarily Limited Activities + + 1) Event: A repeated incidence of a violation that previously + resulted in a warning, or the first incidence of a more serious + violation. + 2) Consequence: A private, written warning with a time-limited + cooldown period designed to underscore the seriousness of the + situation and give the community members involved time to process + the incident. The cooldown period may be limited to particular + communication channels or interactions with particular community + members. + 3) Repair: Examples of repair may include making an apology, using + the cooldown period to reflect on actions and impact, and being + thoughtful about re-entering community spaces after the period is + over. + +3) Temporary Suspension + + 1) Event: A pattern of repeated violation which the Community + Moderators have tried to address with warnings, or a single + serious violation. + 2) Consequence: A private written warning with conditions for return + from suspension. In general, temporary suspensions give the person + being suspended time to reflect upon their behavior and possible + corrective actions. + 3) Repair: Examples of repair include respecting the spirit of the + suspension, meeting the specified conditions for return, and being + thoughtful about how to reintegrate with the community when the + suspension is lifted. + +4) Permanent Ban + + 1) Event: A pattern of repeated code of conduct violations that other + steps on the ladder have failed to resolve, or a violation so + serious that the Community Moderators determine there is no way to + keep the community safe with this person as a member. + 2) Consequence: Access to all community spaces, tools, and + communication channels is removed. In general, permanent bans + should be rarely used, should have strong reasoning behind them, + and should only be resorted to if working through other remedies + has failed to change the behavior. + 3) Repair: There is no possible repair in cases of this severity. + +This enforcement ladder is intended as a guideline. It does not limit +the ability of Community Managers to use their discretion and judgment, +in keeping with the best interests of our community. Scope ----- This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in -public spaces. Examples of representing our community include using an -official e-mail address, posting via an official social media account, -or acting as an appointed representative at an online or offline event. - -Enforcement ------------ - -Instances of abusive, harassing, or otherwise unacceptable behavior may -be reported to the community leaders responsible for enforcement at -conduct@plasmapy.org. All complaints will be reviewed and investigated -promptly and fairly. - -All community leaders are obligated to respect the privacy and security -of the reporter of any incident. - -Enforcement Guidelines ----------------------- - -Community leaders will follow these Community Impact Guidelines in -determining the consequences for any action they deem in violation of -this Code of Conduct: - -1. Correction -~~~~~~~~~~~~~ - -**Community Impact**: Use of inappropriate language or other behavior -deemed unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, -providing clarity around the nature of the violation and an explanation -of why the behavior was inappropriate. A public apology may be -requested. - -2. Warning -~~~~~~~~~~ - -**Community Impact**: A violation through a single incident or series of -actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, for a specified period of -time. This includes avoiding interactions in community spaces as well as -external channels like social media. Violating these terms may lead to a -temporary or permanent ban. - -3. Temporary Ban -~~~~~~~~~~~~~~~~ - -**Community Impact**: A serious violation of community standards, -including sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No -public or private interaction with the people involved, including -unsolicited interaction with those enforcing the Code of Conduct, is -allowed during this period. Violating these terms may lead to a -permanent ban. - -4. Permanent Ban -~~~~~~~~~~~~~~~~ - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of -individuals. - -**Consequence**: A permanent ban from any sort of public interaction -within the community. +public or other spaces. Examples of representing our community include +using an official email address, posting via an official social media +account, or acting as an appointed representative at an online or +offline event. Attribution ----------- -This Code of Conduct is adapted from the `Contributor Covenant`_, -version 2.1, available at -https://www.contributor-covenant.org/version/2/1/code_of_conduct\ . - -Community Impact Guidelines were inspired by `Mozilla's code of conduct -enforcement ladder `__. - -For answers to common questions about this code of conduct, see the FAQ -at https://www.contributor-covenant.org/faq. Translations are available -at https://www.contributor-covenant.org/translations. - -.. _Contributor Covenant: https://www.contributor-covenant.org +This Code of Conduct is adapted from the Contributor Covenant, version +3.0, permanently available at +https://www.contributor-covenant.org/version/3/0/. + +Contributor Covenant is stewarded by the Organization for Ethical Source +and licensed under CC BY-SA 4.0. To view a copy of this license, visit +https://creativecommons.org/licenses/by-sa/4.0/ + +For answers to common questions about Contributor Covenant, see the FAQ +at https://www.contributor-covenant.org/faq. Translations are provided +at https://www.contributor-covenant.org/translations. Additional +enforcement and community guideline resources can be found at +https://www.contributor-covenant.org/resources. The enforcement ladder +was inspired by the work of `Mozilla's code of conduct +team `__. diff --git a/docs/COMMUNICATION.rst b/docs/COMMUNICATION.rst index 327a4ccd4c..706647c203 100644 --- a/docs/COMMUNICATION.rst +++ b/docs/COMMUNICATION.rst @@ -3,44 +3,66 @@ Feedback and Communication ========================== -Matrix chat room ----------------- +Requesting features +------------------- -The primary communication channel for PlasmaPy is our `Matrix chat -room`_ 💬. There is also a `Gitter bridge`_ to this chat room. +Please `submit a feature request`_ on |PlasmaPy's GitHub repository| if +you have an idea for new or improved functionality. PlasmaPy is +community-driven, and feature requests really help guide the future of +the project! + +Submitting bug reports +---------------------- + +Please `submit a bug report`_ on PlasmaPy's GitHub repository if you +notice any problems. We greatly appreciate it! + +Meetings and events +------------------- + +To meet with members of the PlasmaPy team, we encourage you to stop by +our regularly scheduled `community meetings`_. + +Please check `PlasmaPy meetings`_ for other regularly scheduled meetings +and special events. GitHub Discussions page ----------------------- PlasmaPy's `GitHub Discussions page`_ is a great place to suggest ideas, -bring up discussion topics, and ask questions in threaded public -discussions. +bring up discussion topics, and ask questions. -Mailing list ------------- +Matrix chat room +---------------- -We also have a low traffic `mailing list`_ for occasional announcements -and infrequent discussions. +PlasmaPy team members are occasionally available via the `Matrix chat +room`_, which has a `Gitter bridge`_. -Suggestion box --------------- +Email +----- -We have a `suggestion box`_ if you would like to (optionally -anonymously) suggest a feature/topic for consideration. These will be -reposted as GitHub issues, as appropriate, for further discussion. +Members of the PlasmaPy team can be reached at team@plasmapy.org. -Meetings and events -------------------- +Please use these links to `submit a feature request`_ or +`submit a bug report`_ on |PlasmaPy's GitHub repository|. + +Mailing list +------------ + +Subscribe to PlasmaPy's low-volume `mailing list`_ to receive occasional +newsletters and announcements. + +Reporting security vulnerabilities +---------------------------------- -Please check `PlasmaPy meetings`_ for regularly scheduled meetings and -special events. The regularly scheduled meetings include a community -meeting to discuss code development, a project meeting to discuss -broader aspects of the PlasmaPy project like education and outreach to -the broader plasma community, and meetings of PlasmaPy working groups. -The special events include |Plasma Hack Week|. +Please use this link to `privately report a security vulnerability`_ +.. _community meetings: https://www.plasmapy.org/meetings/weekly/ .. _GitHub Discussions page: https://github.com/PlasmaPy/PlasmaPy/discussions .. _Gitter bridge: https://app.gitter.im/#/room/#PlasmaPy_Lobby:gitter.im .. _mailing list: https://groups.google.com/forum/#!forum/plasmapy +.. _matrix chat room: https://app.element.io/#/room/#plasmapy:openastronomy.org .. _PlasmaPy meetings: https://www.plasmapy.org/meetings -.. _suggestion box: https://docs.google.com/forms/d/e/1FAIpQLSdT3O5iHZrLJRuavFyzoR23PGy0Prfzx2SQOcwJGWtvHyT2lw/viewform?usp=sf_link +.. _privately report a security vulnerability: https://github.com/plasmapy/plasmapy/security/advisories/new +.. _submit a bug report: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=Bug&template=bug_report.yml +.. _submit a feature request: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=Feature+request&template=feature_request.yml diff --git a/docs/_global_substitutions.py b/docs/_global_substitutions.py index 3e46625021..aa29ca85b1 100644 --- a/docs/_global_substitutions.py +++ b/docs/_global_substitutions.py @@ -98,7 +98,6 @@ "parameters": r":term:`parameters `\ ", "particle-like": r":term:`particle-like`\ ", "particle-list-like": r":term:`particle-list-like`\ ", - "plasma-calculator": r":ref:`plasmapy-calculator`\ ", "src/plasmapy": r":file:`src/plasmapy`\ ", "testing guide": r":ref:`testing guide`\ ", "tests": r":file:`tests`\ ", @@ -144,6 +143,7 @@ "pandas": "https://pandas.pydata.org", "pip": "https://pip.pypa.io", "Plasma Hack Week": "https://hack.plasmapy.org", + "plasmapy-calculator": "https://github.com/PlasmaPy/plasmapy-calculator", "PlasmaPy": "https://www.plasmapy.org", "PlasmaPy's data repository": "https://github.com/PlasmaPy/PlasmaPy-data", "PlasmaPy's documentation": "https://docs.plasmapy.org/en/stable", @@ -156,13 +156,13 @@ "pytest": "https://docs.pytest.org", "Python": "https://www.python.org", "Python's documentation": "https://docs.python.org/3", - "Read the Docs": "https://about.readthedocs.com/", + "Read the Docs": "https://about.readthedocs.com", "reStructuredText": "https://docutils.sourceforge.io/rst.html", "ruff": "https://docs.astral.sh/ruff", "SciPy": "https://scipy.org", "SPEC 0": "https://scientific-python.org/specs/spec-0000", "Sphinx": "https://www.sphinx-doc.org", - "static type checking": "https://realpython.com/lessons/python-type-checking-overview", + "static type checking": "https://realpython.com/videos/python-type-checking-overview", "towncrier": "https://github.com/twisted/towncrier", "type hint annotations": "https://peps.python.org/pep-0484", "xarray": "https://docs.xarray.dev", diff --git a/docs/about/citation.rst b/docs/about/citation.rst index cb80be453e..cdb43730a6 100644 --- a/docs/about/citation.rst +++ b/docs/about/citation.rst @@ -1,11 +1,11 @@ .. _citation: -Acknowledging and citing PlasmaPy +Acknowledging and Citing PlasmaPy ================================= -.. |version_to_cite| replace:: 2024.10.0 -.. |doi_hyperlink| replace:: https://doi.org/10.5281/zenodo.14010450 -.. |citation_year| replace:: 2024 +.. |version_to_cite| replace:: 2025.8.0 +.. |doi_hyperlink| replace:: https://doi.org/10.5281/zenodo.16747747 +.. |citation_year| replace:: 2025 .. These substitutions are automatically updated by the GitHub Action to mint a release. diff --git a/docs/about/policies.rst b/docs/about/policies.rst new file mode 100644 index 0000000000..28a42e6975 --- /dev/null +++ b/docs/about/policies.rst @@ -0,0 +1,48 @@ +.. _policies: + +********************** +Policies and Practices +********************** + +.. contents:: Contents + :local: + +.. _version-support: + +Version support policy for dependencies +======================================= + +.. image:: https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038 + :target: https://scientific-python.org/specs/spec-0000/ + +PlasmaPy generally follows the time-based policy for dropping +dependencies as recommended in |SPEC 0|. SPEC 0 recommends a common +dependency support window across the scientific Python ecosystem, while +limiting the maintenance burden associated with supporting older +versions of dependencies. The specific recommendations are that: + +1. Support for Python versions be dropped **3 years** after their + initial release. +2. Support for core package dependencies be dropped **2 years** after + their initial release. + +Support for dependencies may be dropped sooner than what SPEC 0 +recommends if a more recent release of a dependency contains critical +bug fixes or includes important new features. + +.. note:: + + Dependency groups used primarily for code development activities such + as running tests and building documentation are excluded from this + policy because they are not intended for use by end users. + +.. _security-policy: + +Security policy +=============== + +PlasmaPy's `security policy`_ is maintained within its GitHub repository. +Please use this link to `privately report a security vulnerability`_. + +.. _privately report a security vulnerability: https://github.com/plasmapy/plasmapy/security/advisories/new +.. _security policy: https://github.com/PlasmaPy/PlasmaPy?tab=security-ov-file diff --git a/docs/api_static/plasmapy.analysis.swept_langmuir.plasma_potential.rst b/docs/api_static/plasmapy.analysis.swept_langmuir.plasma_potential.rst new file mode 100644 index 0000000000..4d04f058db --- /dev/null +++ b/docs/api_static/plasmapy.analysis.swept_langmuir.plasma_potential.rst @@ -0,0 +1,8 @@ +:orphan: + +`plasmapy.analysis.swept_langmuir.plasma_potential` +=================================================== + +.. currentmodule:: plasmapy.analysis.swept_langmuir.plasma_potential + +.. automodapi:: plasmapy.analysis.swept_langmuir.plasma_potential diff --git a/docs/bibliography.bib b/docs/bibliography.bib index 5b4e6dff12..39f3cc4ec6 100644 --- a/docs/bibliography.bib +++ b/docs/bibliography.bib @@ -195,6 +195,15 @@ @article{gericke:2002 pages = 036418, doi = {10.1103/PhysRevE.65.036418} } +@inproceedings{gibbon:2016, + title = {{Introduction to Plasma Physics}}, + author = {P. Gibbons}, + year = 2016, + booktitle = {Proceedings of the 2014 CAS-CERN Accelerator School: Plasma Wake Acceleration}, + publisher = {CERN}, + pages = {51 - 65}, + doi = {10.5170/CERN-2016-001.51}, +} @article{hasegawa:1982, title = {{Alfven wave. DOE Critical Review Series}}, author = {A. Hasegawa and C. Uberoi}, diff --git a/docs/changelog/0.8.1.rst b/docs/changelog/0.8.1.rst index 524d0e85e0..4c00b276c8 100644 --- a/docs/changelog/0.8.1.rst +++ b/docs/changelog/0.8.1.rst @@ -95,7 +95,7 @@ Deprecations and Removals policy laid out in `NumPy Enhancement Proposal 29 `__. (`#1465 `__) -- The ``[all]`` option when using |pip| to install `plasmapy` is now +- The ``[all]`` option when using |pip| to install PlasmaPy is now deprecated and may be removed in a future release. Packages that were previously optional (|h5py|, |lmfit|, |mpmath|, and Numba) are now installed by default when running ``pip install @@ -371,8 +371,7 @@ Improved Documentation :file:`README.md`. (`#1327 `__) - Enabled the `sphinx-hoverxref - `_ extension to - |Sphinx|. (`#1353 + `__ extension to |Sphinx|. (`#1353 `__) - Added bullet points on module level docstrings and ``__all__`` to the documentation guide. (`#1359 @@ -400,7 +399,7 @@ Improved Documentation - Added an example notebook that introduces how to use `plasmapy.particles`. (`#1382 `__) -- Described the |plasma-calculator| in the narrative +- Described the prototype plasma-calculator in the narrative documentation. (`#1390 `__) - Updated the cold magnetized plasma dielectric permittivity tensor @@ -424,9 +423,9 @@ Improved Documentation - Added a discussion of doctests to the |documentation guide|. (`#1478 `__) - Removed the section on package requirements from the instructions on - how to install `plasmapy`. (`#1482 + how to install PlasmaPy. (`#1482 `__) -- Updated the instructions on how to install `plasmapy`. (`#1482 +- Updated the instructions on how to install PlasmaPy`. (`#1482 `__) - Defined ``autodoc_typehints_format="short"`` so signature type hints are displayed in short form, i.e. without the leading module diff --git a/docs/changelog/2024.5.0.rst b/docs/changelog/2024.5.0.rst index 5737158998..cefca2b1d8 100644 --- a/docs/changelog/2024.5.0.rst +++ b/docs/changelog/2024.5.0.rst @@ -124,14 +124,14 @@ Internal Changes and Refactorings to follow the updated recommendation from the Python Packaging Authority's `packaging guide `__. The motivation for this change is described in :issue:`2581`. Source - code previously in :file:`plasmapy` is now located in - :file:`src/plasmapy` and tests are now in a separate :file:`tests` - directory. Tests previously in :file:`plasmapy/**/tests` are now in + code previously in :file:`plasmapy/` is now located in + :file:`src/plasmapy/` and tests are now in a separate :file:`tests` + directory. Tests previously in :file:`plasmapy/**/tests/` are now in :file:`tests/**/`, where :file:`**` refers to an arbitrary number of subdirectories. For example, the source code of `plasmapy.formulary` - is now located in :file:`src/plasmapy/formulary` and the tests for + is now located in :file:`src/plasmapy/formulary/` and the tests for `plasmapy.formulary` are now in - :file:`tests/formulary`. (:pr:`2598`) + :file:`tests/formulary/`. (:pr:`2598`) - Reconfigured the auto-generated requirements files used during continuous integration and for documentation builds, while adding corresponding documentation. (:pr:`2650`) diff --git a/docs/changelog/2025.8.0.rst b/docs/changelog/2025.8.0.rst new file mode 100644 index 0000000000..eb1f81f35b --- /dev/null +++ b/docs/changelog/2025.8.0.rst @@ -0,0 +1,232 @@ +PlasmaPy v2025.8.0 (2025-08-07) +=============================== + +New Features +------------ + +- Enabled |particle_input| to convert |particle-list-like| arguments passed + to parameters decorated with |ParticleListLike| into |ParticleList| + instances. (:pr:`2790`) +- The new method `plasmapy.plasma.grids.CartesianGrid.soften_edges` applies an + error function mask + to the edges of all quantities on a grid. This is useful for any application + where the grid must + go to zero smoothly at the edges (e.g., for particle tracking with + |ParticleTracker|). (:pr:`2911`) +- Added the ``source_vdir`` keyword to the + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker.create_particles` + method of + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` + to explicitly define the + orientation of the mean velocity of the source particles. (:pr:`2968`) +- Added the ``detector_vdir`` keyword to + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` + to explicitly define the detector's vertical surface vector. (:pr:`2968`) +- Added a new module, `plasmapy.formulary.laser`, to make calculations related + to laser pulses. Added the first function, + `~plasmapy.formulary.laser.electric_field_amplitude`, which calculates the + electric field strength from intensity. (:pr:`3021`) +- Added `plasmapy.formulary.laser.intensity` to calculate intensity from the + electric field amplitude for a laser. (:pr:`3032`) +- Added helper function + `~plasmapy.analysis.swept_langmuir.helpers.sort_sweep_arrays` to + `plasmapy.analysis.swept_langmuir`. (:pr:`3034`) +- Added `~plasmapy.formulary.laser.em_wavelength`, + `~plasmapy.formulary.laser.em_angular_frequency`, + `~plasmapy.formulary.laser.Gaussian_beam_waist_radius`, + `~plasmapy.formulary.laser.Gaussian_spot_size_FWHM`, + `~plasmapy.formulary.laser.Gaussian_power`, + `~plasmapy.formulary.laser.Gaussian_Rayleigh_length`, and + `~plasmapy.formulary.laser.normalized_vector_potential` to + `plasmapy.formulary.laser`. (:pr:`3036`) +- Added helper function + `~plasmapy.analysis.swept_langmuir.helpers.merge_voltage_clusters` to + `plasmapy.analysis.swept_langmuir`. (:pr:`3037`) + + +Documentation Improvements +-------------------------- + +- Incorporated the ``plasmapy_theme`` via the `plasmapy_sphinx.theme` + extension. (:pr:`1643`) +- Removed :file:`docs/plasmapy_sphinx` and put `plasmapy_sphinx` into its own + repository at https://github.com/PlasmaPy/plasmapy_sphinx\ . (:pr:`1643`) +- Added `plasmapy_sphinx` as a ``docs`` dependency. (:pr:`1643`) +- Removed upper dependency limit on `sphinx`, and added lower limit of + ``>=8.2.3``. (:pr:`1643`) +- Created a GitHub workflow (in :file:`weekly.yml` and :file:`noxfile.py`) + to build documentation using the latest development version of + `plasmapy_sphinx` on a weekly basis. (:pr:`1643`) +- Incorporated `sphinx` extensions `plasmapy_sphinx.ext.autodoc` and + `plasmapy_sphinx.ext.directives`. (:pr:`1643`) +- Updated author metadata in :file:`CITATION.cff`. (:pr:`2890`) +- Removed duplicate section headers for example notebooks in the documentation + for `plasmapy.formulary`. (:pr:`2892`) +- Added acknowledgements to several organizations that have supported PlasmaPy + or are aligned with its mission. (:pr:`2895`) +- Fixed formatting problems and improved verb tense consistency in prior + changelog entries. (:pr:`2901`) +- Fixed references to the ``astropy.units.equivalencies`` module in the docs. + Astropy now considers + this file to be private API (which broke PlasmaPy's intersphinx links), and + recommends that its contents be imported through the `astropy.units` + namespace. + This pull request changes those links to a direct URL to + |Astropy Equivalencies|. (:pr:`2915`) +- Added a sentence to the documentation for `plasmapy.dispersion` to describe + dispersion relations and their usefulness. (:pr:`2932`) +- Updated the instructions for accessing test results and documentation + previews in the |contributor guide| after recent changes to GitHub's user + interface. (:pr:`2935`) +- Expanded the docstring of `~plasmapy.formulary.dimensionless.Hall_parameter`. + (:pr:`2938`) +- Bumped the Python version for documentation builds from 3.12 to 3.13. + (:pr:`2943`) +- Updated the instructions on how to install PlasmaPy. (:pr:`2999`) +- Put office hours on an indefinite hiatus. (:pr:`3013`) +- Removed the `sphinx-hoverxref + `_ |Sphinx| extension, since + it has been deprecated in favor of the |Read the Docs| add-on for `Link + Previews `_\ + . (:pr:`3024`) +- Fixed broken hyperlinks and permanent redirects. (:pr:`3056`) +- Summarized the dependency support policy from |SPEC 0| at the end of the + installation instructions. (:pr:`3059`) +- Updated the |contributor guide| pages on the |code contribution workflow| + and :ref:`using pre-commit `. (:pr:`3068`) +- Upgraded :ref:`PlasmaPy's Code of Conduct ` to + version 3.0 of the Contributor Covenant. (:pr:`3069`) +- Updated the :ref:`Feedback and Communication ` page. + (:pr:`3070`) +- Limited the allowed version of |Sphinx| to ``sphinx>=8.2.3,<8.3`` + because planned breaking changes to Sphinx are causing documentation + build errors due to incompatibilities with some extensions. (:pr:`3073`) + + +Backwards Incompatible Changes +------------------------------ + +- Variables in |ParticleTracker| + and + `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiography.Tracker` + have been updated + such that ``n*`` is now ``num_*`` (e.g., ``nparticles`` is now + ``num_particles``). Similarly, ``v_init`` is + now ``v0`` to be consistent with ``x0``. (:pr:`2911`) +- The method + `plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker.add_stopping` + requires that the argument ``I`` must now be a list of |Quantity| objects + rather than a single + |Quantity| array. This change is needed because `None` entries are now also + accepted to that + keyword as placeholders for grids on which stopping will not be applied. + (:pr:`2911`) +- |ParticleTracker| no longer accepts the parameter ``req_quantities``, but + instead automatically requires + quantities required by the tracker for the given setup. Users wishing to + require quantities + may use the method `~plasmapy.plasma.grids.AbstractGrid.require_quantities`. + (:pr:`2911`) +- Removed the prototype plasma calculator from PlasmaPy so that it can be + included in the |plasmapy-calculator| standalone package. (:pr:`3060`) + + +Deprecations and Planned Removals +--------------------------------- + +- Removed :file:`src/plasmapy/dispersion/dispersionfunction.py`, which was + deprecated in ``v2023.10.0``. The functionality for the plasma dispersion + function is in `plasmapy.dispersion.dispersion_functions`. (:pr:`2897`) + + +Bug Fixes +--------- + +- Enabled |Particle| to accept a `numpy.integer` object as the first argument + to indicate the atomic number. (:pr:`3045`) +- Fixed a possible bug when using + `plasmapy.plasma.grids.AbstractGrid.add_quantities` + alongside newer versions of |xarray|. (:pr:`3065`) + + +Internal Changes and Refactorings +--------------------------------- + +- Dropped support for Python 3.10 and bumped the minimum required + versions of several dependencies following |SPEC 0|. (:pr:`2880`) +- Updated the release checklist following the ``v2024.10.0`` release. + (:pr:`2886`) +- Used `typing.Self` for type hint annotations for |Particle| and + |CustomParticle|. (:pr:`2887`) +- Modified tests for `~plasmapy.diagnostics.thomson.spectral_density` to cover + the case of multiple electron species. (:pr:`2906`) +- The internal structure of + `~plasmapy.simulation.particle_tracker.particle_tracker.ParticleTracker` was + optimized by caching some variables (e.g., ``tracked_particle_mask``) which + are then reset after every + push cycle by a ``_reset_cache`` method. Instead of adding zero arrays for + missing quantities, only + quantities provided on the grid are interpolated, and other required + quantities are filled in with an + array of zeros automatically. Particle stopping can now be enabled on a + subset of the provided grids. + Adaptive time steps do not include magnetic field candidates if a magnetic + field does not exist on the grid. + The adaptive timestep is now set to that of the highest resolution grid for + particles that are not + currently on any grid. (:pr:`2911`) +- Added ``User-Agent`` to the header of + `~plasmapy.utils.data.downloader.Downloader` to + resolve an issue with GitHub blocking API access. (:pr:`2915`) +- Updated :file:`validators.py`. (:pr:`2919`) +- Began using :file:`uv.lock` to pin the versions of dependencies used + in tests and documentation builds. Previously, pinned requirements had + been stored in :file:`requirements.txt` style files in + :file:`ci_requirements/` that were generated with ``uv pip compile`` + for each operating system, Python version, and dependency set. Using + :file:`uv.lock` lets us store requirements information for + different operating systems, Python versions, and dependency sets in + a single file. (:pr:`2937`) +- Switched from using ``actions/setup-python`` to ``astral-sh/setup-uv`` in + GitHub workflows. (:pr:`2959`) +- Enabled :file:`noxfile.py` to be run as a script. + The commands ``python noxfile.py -s 'tests-3.13(all)'`` and ``nox -s + 'tests-3.13(all)'`` can now both be used to run all tests for Python 3.13. + (:pr:`2961`) +- Updated the ``requirements`` session for Nox so that the GitHub workflow + now includes a table of the old and new versions of dependencies in the + body of the pull request. (:pr:`2964`) +- Enabled ``pyproject-fmt`` as an autoformatter and ``validate-pyproject`` as a + validator for :file:`pyproject.toml` via |pre-commit|. (:pr:`2974`) +- Added a |Nox| session to perform security audits of GitHub workflows with + ``zizmor`` in CI. (:pr:`2975`) +- Enabled a |pre-commit| hook for ``mdformat`` to automatically format + GitHub-flavored Markdown files. (:pr:`2981`) +- Added a security policy at :file:`.github/SECURITY.md` and enabled private + security reporting through GitHub. (:pr:`2985`) +- Reorganized :file:`.gitignore` to put content that is custom or + PlasmaPy-specific + at the top of the file, followed by content adapted from :file:`.gitignore` + templates at the bottom. (:pr:`2997`) +- Set |uv| as the sole backend to Nox, and changed the ``docs`` and ``tests`` + dependency sets to include ``nox[uv]`` instead of ``nox``. (:pr:`2998`) +- Refactored tests for the `~plasmapy.diagnostics.charged_particle_radiography` + module to reduce test runtime. (:pr:`3039`) +- Removed upper limits on the allowed versions of Astropy and xarray. + (:pr:`3065`) +- Parametrized tests within :file:`tests/utils/decorators.test_checks.py`. + (:pr:`3065`) +- Updated :file:`tests/utils/decorators/test_checks.py` for compatibility with + updates to how `astropy.units.Equivalency` handles equality comparisons. + (:pr:`3065`) + + +Additional Changes +------------------ + +- The ``ax#``, ``dx#`` and ``*_si`` properties of + `~plasmapy.plasma.grids.AbstractGrid` are now + cached properties for faster access, since these attributes do not change + after the grid has been initialized. (:pr:`2911`) +- Updated the configuration to automatically label pull requests on GitHub. + (:pr:`2984`) diff --git a/docs/conf.py b/docs/conf.py index e43a570a92..eaf0660c75 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -85,7 +85,6 @@ "plasmapy_sphinx.ext.autodoc", "plasmapy_sphinx.ext.directives", # other 3rd party extensions - "hoverxref.extension", "IPython.sphinxext.ipython_console_highlighting", "nbsphinx", "notfound.extension", @@ -132,6 +131,10 @@ maximum_signature_line_length = 90 sphinxemoji_style = "twemoji" +suppress_warnings = [ + "autosummary.import_cycle", +] + # Specify patterns to ignore when doing a nitpicky documentation build. # These may include common expressions like "real number" as well as # workarounds for nested inline literals as defined in docs/common_links.py @@ -270,45 +273,6 @@ ), } -# hoverxref - -hoverxref_intersphinx = list(intersphinx_mapping.keys()) - -hoverxref_auto_ref = True -hoverxref_domains = ["py", "cite"] -hoverxref_mathjax = True -hoverxref_roles = ["confval", "term"] -hoverxref_sphinxtabs = True -hoverxref_tooltip_maxwidth = 600 # RTD main window is 696px - -hoverxref_role_types = { - # roles with cite domain - "p": "tooltip", - "t": "tooltip", - # roles with py domain - "attr": "tooltip", - "class": "tooltip", - "const": "tooltip", - "data": "tooltip", - "exc": "tooltip", - "func": "tooltip", - "meth": "tooltip", - "mod": "tooltip", - "obj": "tooltip", - # roles with std domain - "confval": "tooltip", - "hoverxref": "tooltip", - "ref": "tooltip", - "term": "tooltip", -} - -if building_on_readthedocs := os.environ.get("READTHEDOCS"): - # Using the proxied API endpoint is a Read the Docs strategy to - # avoid a cross-site request forgery block for docs using a custom - # domain. See conf.py for sphinx-hoverxref. - use_proxied_api_endpoint = os.environ.get("PROXIED_API_ENDPOINT") - hoverxref_api_host = "/_" if use_proxied_api_endpoint else "https://readthedocs.org" - # sphinx-issues issues_github_path = "PlasmaPy/PlasmaPy" @@ -436,6 +400,7 @@ r"https://doi\.org/10\.1371/journal\.pcbi\.1005510", r"https://doi\.org/10\.2172/5259641", r"https://doi\.org/10\.3847/1538-4357/accc32", + r"https://doi\.org/10\.5170/CERN-2016-001\.51", r"https://doi\.org/10\.5281/zenodo\.1436011", r"https://doi\.org/10\.5281/zenodo\.1460977", r"https://doi\.org/10\.5281/zenodo\.3406803", @@ -445,6 +410,8 @@ r"https://doi\.org/10\.5281/zenodo\.8015753", r"https://doi\.org/10\.18434/T4NC7P", r"https://github\.com/PlasmaPy/PlasmaPy/settings/secrets/actions", + r"https://www\.gnu\.org/software/make", + r"https://hdl\.handle\.net/10037/29416", r"https://orcid\.org/0000-0001-5050-6606", r"https://orcid\.org/0000-0001-5270-7487", r"https://orcid\.org/0000-0001-5308-6870", @@ -507,8 +474,8 @@ r"https://orcid\.org/0009-0008-3588-0497", r"https://orcid\.org/0009-0008-5134-6171", r"https://orcid\.org/0009-0009-9490-5284", - r"https://hdl\.handle\.net/10037/29416", - r"https://www\.iter\.org/", + r"https://www\.iter\.org", + r"https://www\.pppl\.gov", r"https://www\.sciencedirect\.com/book/9780123748775/.*", ] diff --git a/docs/contributing/coding_guide.rst b/docs/contributing/coding_guide.rst index efad7ce738..7d8d12d967 100644 --- a/docs/contributing/coding_guide.rst +++ b/docs/contributing/coding_guide.rst @@ -777,7 +777,7 @@ not noticeably impact performance during typical interactive use, but the performance penalty can become significant for numerically intensive applications. -A :term:`lite-function` is an optimized version of another `plasmapy` +A :term:`lite-function` is an optimized version of another PlasmaPy function that accepts numbers and |NumPy| arrays in assumed SI units. :term:`Lite-functions` skip all validations and instead prioritize performance. Most :term:`lite-functions` are defined in @@ -1059,6 +1059,13 @@ an angular frequency to get a length scale: .. _performing releases: +Security policy +=============== + +PlasmaPy's `security policy`_ is located at :file:`.github/SECURITY.md`. +The GitHub repository has a link to +`privately report security vulnerabilities`_. + Performing releases =================== @@ -1089,7 +1096,7 @@ The overall process of performing a release is: .. _ASCII: https://en.wikipedia.org/wiki/ASCII .. _autotyping: https://github.com/JelleZijlstra/autotyping -.. _cognitive complexity: https://docs.codeclimate.com/docs/cognitive-complexity +.. _cognitive complexity: https://getdx.com/blog/cognitive-complexity/ .. _create a release issue: https://github.com/PlasmaPy/PlasmaPy/actions/workflows/create-release-issue.yml .. _Cython: https://cython.org .. _equivalencies: https://docs.astropy.org/en/stable/units/equivalencies.html @@ -1103,10 +1110,12 @@ The overall process of performing a release is: .. _NEP 29: https://numpy.org/neps/nep-0029-deprecation_policy.html .. _not a number: https://en.wikipedia.org/wiki/NaN .. _NumPy Enhancement Proposal 29: https://numpy.org/neps/nep-0029-deprecation_policy.html +.. _privately report security vulnerabilities: https://github.com/PlasmaPy/PlasmaPy/security/advisories/new .. _Python Packaging User Guide: https://packaging.python.org .. _pyupgrade: https://github.com/asottile/pyupgrade .. _release checklist: https://github.com/PlasmaPy/PlasmaPy/blob/main/.github/content/release-checklist.md .. _rename refactoring in PyCharm: https://www.jetbrains.com/help/pycharm/rename-refactorings.html +.. _security policy: https://github.com/PlasmaPy/PlasmaPy/blob/main/.github/SECURITY.md .. _TOML: https://toml.io/en/v1.0.0 .. _type hints cheat sheet: https://mypy.readthedocs.io/en/stable/cheat_sheet_py3.html .. _update pinned requirements: https://github.com/PlasmaPy/PlasmaPy/actions/workflows/update-pinned-reqs.yml diff --git a/docs/contributing/doc_guide.rst b/docs/contributing/doc_guide.rst index a134016dd3..39e341172d 100644 --- a/docs/contributing/doc_guide.rst +++ b/docs/contributing/doc_guide.rst @@ -1066,8 +1066,6 @@ extensions: * |IPython.sphinxext.ipython_console_highlighting|_. * |sphinx_changelog|_ for rendering |towncrier| changelogs. * |sphinx-tabs|_ for creating tabbed content. -* |sphinx-hoverxref|_ for showing floating windows on cross references - of the documentation. * |sphinx-notfound-page|_ to add a :wikipedia:`404 ` page for the documentation. * |sphinx-issues|_ to add roles for linking to GitHub (:rst:role:`commit`, @@ -1596,7 +1594,7 @@ example Jupyter notebooks, the tables of contents are in .. _BibTeX: https://www.bibtex.org .. _BibTeX format: https://www.bibtex.com/g/bibtex-format .. _configuration options: https://www.sphinx-doc.org/en/master/usage/configuration.html -.. _CSS: https://www.w3schools.com:443/css +.. _CSS: http://www.w3schools.com/css/ .. _define substitutions: https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#substitution-definitions .. _doctests: https://docs.pytest.org/en/6.2.x/doctest.html .. _full list of emoji codes: https://sphinxemojicodes.readthedocs.io/en/stable/#supported-codes @@ -1625,7 +1623,7 @@ example Jupyter notebooks, the tables of contents are in .. _sphinx-codeautolink: https://sphinx-codeautolink.readthedocs.io .. _Sphinx's glossary: https://www.sphinx-doc.org/en/master/glossary.html .. _Sphinx's templating page: https://www.sphinx-doc.org/en/master/development/templating.html -.. _style overrides: https://docs.readthedocs.io/en/stable/guides/adding-custom-css.html +.. _style overrides: https://docs.readthedocs.com/platform/stable/guides/adding-custom-css.html .. _toctree: https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#table-of-contents .. _warns: https://numpydoc.readthedocs.io/en/latest/format.html#warns .. _weekly tests: https://github.com/PlasmaPy/PlasmaPy/actions/workflows/weekly.yml @@ -1698,9 +1696,6 @@ example Jupyter notebooks, the tables of contents are in .. _`sphinx-reredirects`: https://documatt.gitlab.io/sphinx-reredirects .. |sphinx-reredirects| replace:: `sphinx-reredirects` -.. _`sphinx-hoverxref`: https://sphinx-hoverxref.readthedocs.io -.. |sphinx-hoverxref| replace:: `sphinx-hoverxref` - .. _`sphinx-issues`: https://github.com/sloria/sphinx-issues .. |sphinx-issues| replace:: `sphinx-issues` diff --git a/docs/contributing/getting_ready.rst b/docs/contributing/getting_ready.rst index eed96db178..ce207c6758 100644 --- a/docs/contributing/getting_ready.rst +++ b/docs/contributing/getting_ready.rst @@ -264,7 +264,7 @@ when you :py:`import plasmapy`. .. group-tab:: Windows - .. code-block:: bash + .. code-block:: PowerShell py -m pip install -e .[docs,tests] @@ -313,19 +313,19 @@ when you :py:`import plasmapy`. >>> reload(plasmapy) .. _Add a new SSH key to your GitHub account: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account -.. _Anaconda Navigator: https://docs.anaconda.com/navigator -.. _Anaconda: https://docs.anaconda.com +.. _Anaconda Navigator: https://www.anaconda.com/docs/tools/anaconda-navigator/main +.. _Anaconda: https://www.anaconda.com/docs/main .. _clone: https://github.com/git-guides/git-clone .. _Conda: https://docs.conda.io -.. _creating an environment: https://docs.anaconda.com/navigator/tutorials/manage-environments/#creating-a-new-environment +.. _creating an environment: https://www.anaconda.com/docs/tools/anaconda-navigator/tutorials/manage-environments#creating-a-new-environment .. _download Python: https://www.python.org/downloads .. _fork: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/about-forks -.. _frequently used Unix commands: https://faculty.tru.ca/nmora/Frequently%20used%20UNIX%20commands.pdf +.. _frequently used Unix commands: https://www.geeksforgeeks.org/linux-unix/essential-linuxunix-commands/ .. _git commands for setup and config: https://git-scm.com/book/en/v2/Appendix-C%3A-Git-Commands-Setup-and-Config .. _install git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git .. _install Graphviz: https://graphviz.org/download .. _install pandoc: https://pandoc.org/installing.html -.. _installing Anaconda Navigator: https://docs.anaconda.com/navigator/install +.. _installing Anaconda Navigator: https://www.anaconda.com/docs/tools/anaconda-navigator/install .. _installing Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html .. _installing Python: https://realpython.com/installing-python .. _installing WSL: https://learn.microsoft.com/en-us/windows/wsl/install @@ -338,7 +338,7 @@ when you :py:`import plasmapy`. .. _terminal user guide: https://support.apple.com/guide/terminal/welcome/mac .. _this xkcd comic: https://xkcd.com/1987 .. _unix tutorial: https://www.hpc.iastate.edu/guides/unix-introduction/unix-tutorial-1 -.. _using an environment: https://docs.anaconda.com/navigator/tutorials/manage-environments/#using-an-environment +.. _using an environment: https://www.anaconda.com/docs/tools/anaconda-navigator/tutorials/manage-environments#using-an-environment .. _venv: https://docs.python.org/3/library/venv.html .. _virtual environment: https://realpython.com/python-virtual-environments-a-primer .. _Windows Subsystem for Linux: https://learn.microsoft.com/en-us/windows/wsl diff --git a/docs/contributing/pre-commit.rst b/docs/contributing/pre-commit.rst index 16cde20534..170e7c76a1 100644 --- a/docs/contributing/pre-commit.rst +++ b/docs/contributing/pre-commit.rst @@ -1,4 +1,4 @@ -.. _pre-commit: +.. _using-pre-commit: **************** Using pre-commit @@ -13,24 +13,37 @@ Introduction ============ PlasmaPy uses |pre-commit| to automate code quality checks and perform -auto-fixes. +auto-fixes. |pre-commit| checks are performed on GitHub for every pull +request. -.. _pre-commit-troubleshooting: +.. important:: -Troubleshooting pre-commit failures -=================================== + Automatically fix most |pre-commit| failures on pull requests by + commenting: -.. tip:: + pre-commit.ci autofix - Many common |pre-commit| test failures related to formatting can be - automatically fixed by adding a comment on a pull request that says: + Adding this comment to the :guilabel:`Conversation` tab of a pull + request triggers a new commit that applies automatic fixes made by + PlasmaPy's pre-commit hooks. Use :bash:`git pull` to bring changes on + GitHub back to your computer. - pre-commit.ci autofix +Running pre-commit locally +========================== - This comment will produce a new commit to applies auto-fixes from - pre-commit. After doing this, don't forget to do a :bash:`git pull` - in your clone of the repository to pull back the changes to your - computer. +After `installing pre-commit`_, |pre-commit| can be run locally for all +files in your clone of the repository by running: + +.. code-block:: bash + + pre-commit run -a + +The ``-a`` is short for ``--all-files``. + +.. _pre-commit-troubleshooting: + +Troubleshooting pre-commit failures +=================================== The following sections contain suggestions for how to fix pre-commit failures that were not corrected by commenting ``pre-commit.ci autofix`` @@ -39,52 +52,48 @@ on the issue. ruff ---- -PlasmaPy uses |ruff| as its primary linter and code quality tool. |ruff| -can quickly find code quality issues and is able to do many code quality -fixes. - -Every issue detected by ruff corresponds to a specific lint rule. For -example, lint rule F401_ removes unused :py:`import` statements. If you -encounter a confusing ruff rule, search `ruff's documentation page on -rules`_ for the rule code and click on its name for more information. +PlasmaPy uses |ruff| as its primary linter and code formatter. |ruff| +quickly finds and often fixes many code quality issues. -Problems flagged by C901_ occur when a function is too complex (i.e., -when it contains heavily nested control flow), which makes code much -more difficult to maintain. +Every issue detected by |ruff| corresponds to a specific linter rule. For +example, lint rule F401_ removes unused :py:`import` statements. .. tip:: - Reduce complexity by breaking up complicated functions into short - functions that do exactly one thing with no side effects. + Find more information about issues flagged by |ruff| by searching + `ruff's documentation page on rules`_ for the rule code and clicking + on its name. Disabling a ruff rule ~~~~~~~~~~~~~~~~~~~~~ -While |ruff| usually suggests improvements, there will occasionally be -times where a departure from a |ruff| rule is (at least temporarily) -justified. In these cases, we can append a :samp:`# noqa {}` -comment to the end of a line (where :samp:`{}` is replaced -with the corresponding |ruff| rule codes, and ``noqa`` stands for "no -quality assurance") to tell |ruff| to ignore that error on that line. +While |ruff| usually suggests improvements, there are occasionally +times when a departure from a |ruff| rule is preferable. -For example, we can tell |ruff| to ignore a function with excessive -code complexity (C901_), too many branches (PLR0912_), and too many -statements (PLR0915_) by adding the following ``noqa`` comment: +To ignore a |ruff| rule on a specific line, append a comment of the form +:samp:`# noqa {}`, where :samp:`` is replaced by +the |ruff| rule code(s) to ignore. + +For example, we can tell |ruff| to ignore a function with excessive code +complexity (C901_), too many branches (PLR0912_), and too many +statements (PLR0915_) by adding a ``noqa`` comment like in the following +example: .. code-block:: python def overly_complicated_function(): # noqa: C901, PLR0912, PLR0915 - """A function with 100+ lines of code and lots of if/else branches.""" + """A function with 97 lines and multiple nested if/else blocks.""" + +When writing new code, it is almost always preferable to refactor the +code to remove the error than to add a ``# noqa`` comment to ignore the +rule. Complex functions flagged by C901_ could be simplified by +extracting sections of code into separate functions that do exactly one +thing with no side effects. .. important:: - When writing new code, it is almost always better to refactor the - code to remove the error rather than add a ``noqa`` comment. In the - above example, it would be better to refactor an overly complicated - function into multiple short functions that do exactly one thing with - no side effects so that the code is easier to understand, modify, and - maintain. We should only add ``noqa`` statements when we have a good - reason to. + Use ``# noqa`` comments sparingly, and only when you have a strong + reason to do so. Spellchecks ----------- @@ -93,97 +102,18 @@ PlasmaPy uses codespell_ and typos_ to spellcheck source code. While these tools generally work well, occasionally there will be false positives. -* If you encounter a false positive with codespell, add it to - ``ignore-words-list`` under ``[codespell]`` in :file:`pyproject.toml`. - -* False positives from typos_ should be added to :file:`_typos.toml`. - - -Using pre-commit locally -======================== - -|pre-commit| checks are performed on GitHub for every pull request, but -it is also possible to set up pre-commit locally. - -.. tip:: - - We recommend enabling pre-commit for the clone of - |PlasmaPy's GitHub repository| only *after* you have become - comfortable with the |code contribution workflow|. - -Enabling pre-commit -------------------- - -To enable pre-commit on your computer: - -#. |Open a terminal|. - -#. If you use a Conda or virtual environment for developing PlasmaPy, - activate it (i.e., with ``conda activate plasmapy-dev``). - -#. Make sure that pre-commit is installed to your Python environment by - running: - - .. tabs:: - - .. group-tab:: Windows - - .. code-block:: bash - - py -m pip install pre-commit - - .. group-tab:: macOS - - .. code-block:: bash - - python -m pip install pre-commit - - .. group-tab:: Linux/WSL - - .. code-block:: bash - - python -m pip install pre-commit - -#. Navigate to the :file:`PlasmaPy` directory that contains your clone - of PlasmaPy's repository. For example, if you cloned PlasmaPy into - the :file:`~/repos` directory, then run: - - .. code-block:: bash - - cd ~/repos/PlasmaPy - -#. Enable pre-commit with: - - .. code-block:: bash - - pre-commit install - -Changes to the workflow ------------------------ - -Once |pre-commit| has been installed for a repository, pre-commit will -run every time you try to commit a change. - -If any pre-commit checks fail, or if pre-commit changes any files, it -will be necessary to redo :bash:`git add` on the changed files and -:bash:`git commit` once again. - -.. tip:: - - To commit a change without running pre-commit, use the :bash:`-n` - flag (short for :bash:`--no-verify`) with |git|. - .. tip:: - To run pre-commit on all files, use - - .. code-block:: bash + Add false positives found by codespell_ to ``ignore-words-list`` in + the ``[tool.codespell]`` section of :file:`pyproject.toml`. - pre-commit run --all-files + Add false positives found by typos_ to the ``[default.extend-words]`` + section of :file:`_typos.toml`. .. _C901: https://docs.astral.sh/ruff/rules/complex-structure .. _codespell: https://github.com/codespell-project/codespell .. _F401: https://docs.astral.sh/ruff/rules/unused-import +.. _installing pre-commit: https://pre-commit.com/#installation .. _PLR0912: https://docs.astral.sh/ruff/rules/too-many-branches .. _PLR0915: https://docs.astral.sh/ruff/rules/too-many-statements .. _ruff's documentation page on rules: https://docs.astral.sh/ruff/rules diff --git a/docs/contributing/testing_guide.rst b/docs/contributing/testing_guide.rst index 56acfa855a..4b94bb7676 100644 --- a/docs/contributing/testing_guide.rst +++ b/docs/contributing/testing_guide.rst @@ -31,7 +31,7 @@ install |Nox| and |uv|: .. group-tab:: Windows - .. code-block:: bash + .. code-block:: PowerShell py -m pip install nox uv diff --git a/docs/contributing/workflow.rst b/docs/contributing/workflow.rst index d2145d2c89..2345fc3213 100644 --- a/docs/contributing/workflow.rst +++ b/docs/contributing/workflow.rst @@ -132,16 +132,6 @@ each step, try running :bash:`git status`. Committing a change is like preserving a snapshot of what each file looks like at this point in history. - .. hint:: - - If it has been installed, |pre-commit| will perform automated - checks and possibly auto-fixes. If pre-commit fails, then - it'll be necessary to fix any remaining problems and do the - :bash:`git add` and :bash:`git commit` steps once more. Try using - :bash:`git diff` and :bash:`git diff --cached` to view the - changes, and :guilabel:`↑` and :guilabel:`↓` to scroll through - previous commands in a terminal. - #. To push the changes to GitHub, run: .. code-block:: bash @@ -219,30 +209,19 @@ Creating a pull request At this stage, a reviewer will perform a code review, unless it has been marked as a draft pull request. Thank you for contributing! -Pulling changes from GitHub ---------------------------- - -If your branch changes on GitHub, run - -.. code-block:: bash - - git pull - -to pull the changes from GitHub to your computer. If you'd like to pull -the changes from the ``main`` branch, instead run - -.. code-block:: bash +.. tip:: - git pull upstream main + If a continuous integration check at the bottom of a pull request + fails, click on the name of the test for more details. -If any of the changes conflict with each other, it will be necessary to -`resolve the merge conflict`_. +.. hint:: -.. note:: + Most ``pre-commit.ci`` failures can be fixed by adding a comment that + says ``pre-commit.ci autofix`` in the conversation tab of a pull + request. - After the pull request has been created, it can be updated by - using :bash:`git push` to update the corresponding branch on - GitHub. + To learn more about fixing common |pre-commit| failures, see + :ref:`pre-commit-troubleshooting`. .. important:: @@ -264,6 +243,31 @@ If any of the changes conflict with each other, it will be necessary to unique, persistent identifier used by researchers, authors, and open source contributors. +Pulling changes from GitHub +--------------------------- + +If your branch changes on GitHub, run + +.. code-block:: bash + + git pull + +to pull the changes from GitHub to your computer. If you'd like to pull +the changes from the ``main`` branch, instead run + +.. code-block:: bash + + git pull upstream main + +If any of the changes conflict with each other, it will be necessary to +`resolve the merge conflict`_. + +.. note:: + + After the pull request has been created, it can be updated by + using :bash:`git push` to update the corresponding branch on + GitHub. + .. _Add a new SSH key to your GitHub account: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account .. _branch: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches .. _fork: https://docs.github.com/en/get-started/quickstart/fork-a-repo diff --git a/docs/examples.rst b/docs/examples.rst index a7a17786a0..b2d3428762 100644 --- a/docs/examples.rst +++ b/docs/examples.rst @@ -1,6 +1,6 @@ .. _examples: -Example notebooks +Example Notebooks ================= Here we catalog all the example Jupyter notebooks that have been created diff --git a/docs/glossary.rst b/docs/glossary.rst index 94bd9e584d..31f5d8eae1 100644 --- a/docs/glossary.rst +++ b/docs/glossary.rst @@ -95,7 +95,7 @@ Glossary lite-function lite-functions - An optimized version of an existing `plasmapy` function intended + An optimized version of an existing PlasmaPy function intended for applications where computational efficiency is most important. While most `~plasmapy.formulary` functions accept |Quantity| objects created using `astropy.units`, lite-functions accept diff --git a/docs/index.rst b/docs/index.rst index 9ad570e09b..eff5bf46a2 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -22,13 +22,13 @@ If you are new to PlasmaPy, please check out our PlasmaPy is developed openly `on GitHub`_, where you can `request a new feature`_ or `report a bug`_. We invite you to share -ideas and ask questions in our |Matrix chat room| or during our -virtual |community meetings|. +ideas and ask questions as `GitHub discussions`_ or during our +|community meetings|. .. important:: If you use PlasmaPy for work presented in a publication or talk, - please help the project by following these instructions to + please support the project by following these instructions to :ref:`cite or acknowledge ` PlasmaPy. .. toctree:: @@ -77,8 +77,9 @@ Example notebooks bibliography glossary performance_tips + about/policies PlasmaPy Enhancement Proposals - PlasmaPy website + PlasmaPy Project GitHub Repository .. toctree:: @@ -91,10 +92,11 @@ Example notebooks contributing/workflow Coding Guide contributing/testing_guide + contributing/pre-commit contributing/doc_guide contributing/changelog_guide - contributing/pre-commit +.. _GitHub discussions: https://github.com/PlasmaPy/PlasmaPy/discussions .. _new discussion on GitHub: https://github.com/PlasmaPy/PlasmaPy/discussions/new/choose .. _on GitHub: https://github.com/PlasmaPy/PlasmaPy .. _report a bug: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=Bug&template=bug_report.yml diff --git a/docs/install.rst b/docs/install.rst index 1b8671f0bc..9340ad6d14 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -1,13 +1,13 @@ .. _plasmapy-install: -********************** -Installing PlasmaPy ☀️ -********************** +******************* +Installing PlasmaPy +******************* .. note:: If you would like to contribute to PlasmaPy, please check out the - |contributor guide|. + |contributor guide|. :sunny: .. contents:: Contents :local: @@ -20,7 +20,7 @@ Installing Python PlasmaPy requires a version of |Python| between |minpython| and |maxpython|. If you do not have |Python| installed already, here are the -instructions to `download Python`_ and install it. 🐍 +instructions to `download Python`_ and install it. :snake: .. tip:: @@ -248,7 +248,7 @@ package should also be installed. and create branches so that you may make contributions via pull requests. -.. _Anaconda Navigator: https://docs.anaconda.com/navigator +.. _Anaconda Navigator: https://www.anaconda.com/docs/tools/anaconda-navigator/main .. _clone a repository using SSH: https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories#cloning-with-ssh-urls .. _Conda: https://docs.conda.io .. _conda-forge: https://conda-forge.org @@ -257,11 +257,11 @@ package should also be installed. .. _from PyPI: https://pypi.org/project/plasmapy .. _from Zenodo: https://doi.org/10.5281/zenodo.6774349 .. _improving Conda performance: https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/conda-performance.html#improving-conda-performance -.. _installing Anaconda Navigator: https://docs.anaconda.com/navigator/install +.. _installing Anaconda Navigator: https://www.anaconda.com/docs/tools/anaconda-navigator/install .. _installing Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html .. _installing packages: https://packaging.python.org/en/latest/tutorials/installing-packages/#installing-from-vcs .. _installing uv: https://docs.astral.sh/uv/getting-started/installation/#installing-uv -.. _getting started with Anaconda Navigator: https://docs.anaconda.com/navigator/getting-started +.. _getting started with Anaconda Navigator: https://www.anaconda.com/docs/tools/anaconda-navigator/getting-started .. _miniconda: https://docs.conda.io/en/latest/miniconda.html .. _pip drop-in interface: https://docs.astral.sh/uv/pip/#the-pip-interface .. _publish a package: https://docs.astral.sh/uv/guides/publish/#publishing-a-package diff --git a/docs/notebooks/analysis/swept_langmuir/find_didv_peak_location.ipynb b/docs/notebooks/analysis/swept_langmuir/find_didv_peak_location.ipynb new file mode 100644 index 0000000000..7ba188e1bf --- /dev/null +++ b/docs/notebooks/analysis/swept_langmuir/find_didv_peak_location.ipynb @@ -0,0 +1,277 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "881e5b44-992f-45fb-b7b0-0ec3db38512d", + "metadata": {}, + "source": [ + "# Swept Langmuir Analysis: Finding Peak Slope\n", + "\n", + "This notebook covers the use of the [**find_didv_peak_location()**](../../../api/plasmapy.analysis.swept_langmuir.plasma_potential.find_didv_peak_location.rst#find-didv-peak-location) function which finds the bias location associated with the peak slope of the swept Langmuir traces.\n", + "\n", + "The bias voltage at the peaks slope is often used as a rough estimate for the plasma potential, but will always be slightly lower than the actual plasma potential." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d60a04df-c4cc-4b16-956c-e1967d07d4c5", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "%matplotlib inline\n", + "\n", + "from pathlib import Path\n", + "\n", + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "from scipy import signal\n", + "\n", + "from plasmapy.analysis import swept_langmuir as sla\n", + "\n", + "plt.rcParams[\"figure.figsize\"] = [10.5, 0.56 * 10.5]" + ] + }, + { + "cell_type": "markdown", + "id": "50e81f77-5218-43b4-aa4f-a5aece966c65", + "metadata": { + "editable": true, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "source": [ + "## Contents:\n", + "\n", + "1. [How find_didv_peak_location() works](#How-find_didv_peak_location()-works)\n", + " 1. [Notes about usage](#Notes-about-usage)\n", + " 1. [Knobs to turn](#Knobs-to-turn)\n", + "1. [Calculate the Floating Potential](#Calculate-the-Floating-Potential)\n", + " 1. [Interpreting results](#Interpreting-results)\n", + " 1. [Plotting results](#Plotting-results)" + ] + }, + { + "cell_type": "markdown", + "id": "d00a4864-f2c6-4606-ba19-a35ab420ac5b", + "metadata": {}, + "source": [ + "## How `find_didv_peak_location()` works" + ] + }, + { + "cell_type": "markdown", + "id": "c8f84fdd-6ec3-4633-bb0c-d827635f66cc", + "metadata": {}, + "source": [ + "## Calculate the Peak Slope" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ab816d3e-caf5-4654-a1e1-b4c7f15c1cb0", + "metadata": {}, + "outputs": [], + "source": [ + "# load data\n", + "filename = \"Beckers2017_noisy.npy\"\n", + "# filename = \"Pace2015.npy\"\n", + "filepath = (Path.cwd() / \"..\" / \"..\" / \"langmuir_samples\" / filename).resolve()\n", + "voltage, current = np.load(filepath)\n", + "\n", + "# voltage array needs to be monotonically increasing/decreasing\n", + "voltage, current = sla.sort_sweep_arrays(voltage, current)\n", + "\n", + "# grabbing floating potential for future use\n", + "vf, _ = sla.find_floating_potential(voltage, current)\n", + "print(f\"floating potential = {vf:.2f} V\")" + ] + }, + { + "cell_type": "markdown", + "id": "8963f972-1159-4058-b313-400023f0ad14", + "metadata": {}, + "source": [ + "### Interpreting results" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e46204b7-a825-4c3a-b00a-46af218a7a05", + "metadata": {}, + "outputs": [], + "source": [ + "results = sla.find_didv_peak_location(voltage, current, voltage_window=[vf, None])\n", + "\n", + "# bias at peak slope\n", + "results[0]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5a544261-3fef-4519-bcaa-489df4ab209a", + "metadata": {}, + "outputs": [], + "source": [ + "results[1].data_slice" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3f20ecd4-5a8f-46e7-8094-c5f0a859277c", + "metadata": {}, + "outputs": [], + "source": [ + "np.where(voltage >= -30)[0][0]" + ] + }, + { + "cell_type": "markdown", + "id": "759e0477-6fb2-4bd4-88d2-29bcd833265f", + "metadata": {}, + "source": [ + "### Plotting results" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7ad1273f-69f8-49f2-bf5e-d9b63311e6fd", + "metadata": { + "editable": true, + "nbsphinx-thumbnail": { + "tooltip": "Peak dI/dV" + }, + "slideshow": { + "slide_type": "" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "figwidth, figheight = plt.rcParams[\"figure.figsize\"]\n", + "figheight = 1.5 * figheight\n", + "fig, axs = plt.subplots(2, 1, figsize=[figwidth, figheight])\n", + "_font_size = 12\n", + "\n", + "bias = results[0]\n", + "extras = results[1]\n", + "\n", + "# first (I vs. V) plot\n", + "axs[0].set_xlabel(\"Bias Voltage (V)\", fontsize=_font_size)\n", + "axs[0].set_ylabel(\"Current (A)\", fontsize=_font_size)\n", + "\n", + "axs[0].plot(voltage, current, label=\"Sweep Data\")\n", + "\n", + "ylim = axs[0].get_ylim()\n", + "xlim = axs[0].get_xlim()\n", + "axs[0].set_ylim(ylim)\n", + "axs[0].axvline(bias, color=\"grey\")\n", + "axs[0].fill_between(\n", + " [bias - extras.std, bias + extras.std],\n", + " 2 * [ylim[0]],\n", + " 2 * [ylim[1]],\n", + " color=\"grey\",\n", + " alpha=0.2,\n", + ")\n", + "\n", + "txt = f\"${bias:.2f} \\\\pm {extras.std:.2f}$ V\\n\"\n", + "txt_loc = [bias, ylim[1]]\n", + "txt_loc = axs[0].transData.transform(txt_loc)\n", + "txt_loc = axs[0].transAxes.inverted().transform(txt_loc)\n", + "txt_loc[0] -= 0.02\n", + "txt_loc[1] -= 0.15\n", + "axs[0].text(\n", + " txt_loc[0],\n", + " txt_loc[1],\n", + " txt,\n", + " fontsize=\"large\",\n", + " transform=axs[0].transAxes,\n", + " ha=\"right\",\n", + ")\n", + "\n", + "# second (dI/dV vs V) plot\n", + "axs[1].set_xlabel(\"Bias Voltage (V)\", fontsize=_font_size)\n", + "axs[1].set_ylabel(\"$dI/dV$ (A / V)\", fontsize=_font_size)\n", + "\n", + "axs[1].set_xlim(xlim)\n", + "\n", + "voltage_merge, current_merge = sla.merge_voltage_clusters(\n", + " voltage, current, voltage_step_size=0\n", + ")\n", + "voltage_slice = voltage_merge[extras.data_slice]\n", + "current_slice = current_merge[extras.data_slice]\n", + "\n", + "_colors = plt.get_cmap(\"OrRd\")(np.linspace(0.2, 0.8, len(extras.savgol_windows)))\n", + "for ii, _window in enumerate(extras.savgol_windows):\n", + " v_smooth = signal.savgol_filter(voltage_slice, _window, 1)\n", + " c_smooth = signal.savgol_filter(current_slice, _window, 1)\n", + "\n", + " didv = np.gradient(c_smooth, v_smooth)\n", + "\n", + " axs[1].plot(\n", + " v_smooth[_window:-_window],\n", + " didv[_window:-_window],\n", + " color=_colors[ii],\n", + " label=f\"Savgol window {_window}\",\n", + " )\n", + "\n", + "ylim = axs[1].get_ylim()\n", + "axs[1].set_ylim(ylim)\n", + "\n", + "axs[1].axvline(bias, color=\"grey\", zorder=100)\n", + "axs[1].fill_between(\n", + " [bias - extras.std, bias + extras.std],\n", + " 2 * [ylim[0]],\n", + " 2 * [ylim[1]],\n", + " color=\"grey\",\n", + " alpha=0.2,\n", + " zorder=0,\n", + ")\n", + "\n", + "axs[1].legend();" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "50eefb5e-788c-4796-a76f-c27f702eca3b", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.7" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb b/docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb index f6b12c9f07..57019031a5 100644 --- a/docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb +++ b/docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb @@ -17,7 +17,7 @@ "\n", "[Bragg peak]:\n", "https://en.wikipedia.org/wiki/Bragg_peak\n", - " \n", + "\n", "Charged particle radiographs are often recorded on detector stacks with multiple layers (often either radiochromic film or CR39 plastic). Since charged particles deposit most of their energy at a depth related to their energy (the [Bragg peak]), each detector layer records a different energy band of particles. The energy bands recorded on each layer are further discriminated by including layers of filter material (eg. thin strips of aluminum) between the active layers. In order to analyze this data, it is necessary to calculate what range of particle energies are stopped in each detector layer.\n", "\n", "The [charged_particle_radiography] module includes a tool for calculating the energy bands for a given stack of detectors. This calculation is a simple approximation (more accurate calculations can be made using Monte Carlo codes), but is sufficient in many cases." @@ -57,7 +57,7 @@ "../../api/plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack.rst#plasmapy.diagnostics.charged_particle_radiography.detector_stacks.Stack\n", "\n", "[astropy Quantity]:\n", - "https://docs.astropy.org/en/stable/api/astropy.units.quantity.Quantity.html\n", + "https://docs.astropy.org/en/stable/units/quantity.html\n", "\n", "[PSTAR]:\n", "https://physics.nist.gov/PhysRefData/Star/Text/PSTAR.html\n", @@ -71,9 +71,9 @@ "- `thickness`: an [astropy Quantity] defining the thickness of the layer.\n", "- `active`: a boolean flag which indicates whether the layer is active (detector) or inactive (eg. a filter).\n", "- `energy_axis`: An [astropy Quantity] array of energies.\n", - "- `stopping_power`: An [astropy Quantity] array containing the product of stopping power and material density at each energy in `energy_axis`. \n", + "- `stopping_power`: An [astropy Quantity] array containing the product of stopping power and material density at each energy in `energy_axis`.\n", "\n", - "The stopping power in various materials for protons and electrons is tabulated by NIST in the [PSTAR] and [ESTAR] databases. The stopping powers are tabulated in units of MeV cm$^2$ / g, so the product of stopping power and density has units of MeV/cm. \n", + "The stopping power in various materials for protons and electrons is tabulated by NIST in the [PSTAR] and [ESTAR] databases. The stopping powers are tabulated in units of MeV cm$^2$ / g, so the product of stopping power and density has units of MeV/cm.\n", "\n", "For this demonstration, we will load two stopping power tables, downloaded from [PSTAR], for aluminum and a human tissue equivalent that is a good approximation for many radiochromic films." ] @@ -144,9 +144,7 @@ "cell_type": "markdown", "id": "59d7daf8", "metadata": {}, - "source": [ - "If we plot the stopping powers as a function of energy on a log-log scale, we see that they are non-linear, with much higher values at lower energies. This is why particles deposit most of their energy at a characteristic depth. As particles propagate into material, they lose energy slowly at first. But, as they loose energy, the effective stopping power increases expontentially. " - ] + "source": "If we plot the stopping powers as a function of energy on a log-log scale, we see that they are non-linear, with much higher values at lower energies. This is why particles deposit most of their energy at a characteristic depth. As particles propagate into material, they lose energy slowly at first. But, as they loose energy, the effective stopping power increases expontentially." }, { "cell_type": "code", diff --git a/docs/notebooks/getting_started/particles.ipynb b/docs/notebooks/getting_started/particles.ipynb index f1049dcb85..f154e9a6fb 100644 --- a/docs/notebooks/getting_started/particles.ipynb +++ b/docs/notebooks/getting_started/particles.ipynb @@ -321,7 +321,7 @@ "metadata": {}, "outputs": [], "source": [ - "iron56_nuclide.binding_energy" + "iron56_nuclide.nuclear_binding_energy" ] }, { diff --git a/docs/notebooks/getting_started/units.ipynb b/docs/notebooks/getting_started/units.ipynb index 1d757ea98d..e3263ad794 100644 --- a/docs/notebooks/getting_started/units.ipynb +++ b/docs/notebooks/getting_started/units.ipynb @@ -73,7 +73,7 @@ "## Contents\n", "\n", "1. [Unit basics](#Unit-basics)\n", - "2. [Unit operations](#Unit-operations) \n", + "2. [Unit operations](#Unit-operations)\n", "3. [Unit conversations](#Unit-conversions)\n", "4. [Detaching units and values](#Detaching-units-and-values)\n", "5. [Equivalencies](#Equivalencies)\n", @@ -341,7 +341,7 @@ "[Quantity]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity\n", "[Quantity objects lose their units with some operations]: https://docs.astropy.org/en/stable/known_issues.html#quantities-lose-their-units-with-some-operations\n", "\n", - "Most frequently encountered [NumPy] and [SciPy] functions can be used with [Quantity] objects. However, [Quantity objects lose their units with some operations]. " + "Most frequently encountered [NumPy] and [SciPy] functions can be used with [Quantity] objects. However, [Quantity objects lose their units with some operations]." ] }, { @@ -386,7 +386,7 @@ "[si]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity.si\n", "[cgs]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity.cgs\n", "\n", - "The [si] and [cgs] attributes convert the [Quantity] to SI or CGS units, respectively. " + "The [si] and [cgs] attributes convert the [Quantity] to SI or CGS units, respectively." ] }, { @@ -416,7 +416,7 @@ "source": [ "## Detaching units and values\n", "\n", - "[value]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity.value \n", + "[value]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity.value\n", "[Quantity]: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html#astropy.units.Quantity\n", "\n", "The [value] attribute of a [Quantity] provides the number (as a NumPy scalar) or NumPy array without the unit." @@ -513,7 +513,7 @@ "id": "b4c492cc", "metadata": {}, "source": [ - "[dimensionless_angles()]: https://docs.astropy.org/en/stable/api/astropy.units.equivalencies.dimensionless_angles.html#dimensionless-angles\n", + "[dimensionless_angles()]: https://docs.astropy.org/en/stable/api/astropy.units.dimensionless_angles.html\n", "\n", "[frequency]: https://en.wikipedia.org/wiki/Frequency\n", "[angular frequency]: https://en.wikipedia.org/wiki/Angular_frequency\n", diff --git a/docs/plasma_calculator/index.rst b/docs/plasma_calculator/index.rst index 21c22010d1..b2a2893f3a 100644 --- a/docs/plasma_calculator/index.rst +++ b/docs/plasma_calculator/index.rst @@ -6,29 +6,8 @@ Plasma Calculator .. currentmodule:: plasmapy.utils.calculator -.. attention:: +.. important:: - |expect-api-changes| - -Overview --------- - -The Plasma Calculator is an interactive Jupyter notebook that is -packaged with `plasmapy`, and allows users to input a set of plasma -properties and immediately calculate multiple plasma parameters. - -.. note:: - - This functionality is still under development and the API may change - in future releases. - -Using Plasma Calculator ------------------------ - -To invoke the app use ``plasma-calculator`` in the command line. By -default this opens the app in a browser, bootstrapping the notebook in a -light theme and using port 8866 by default. - -``plasma-calculator`` takes optional arguments such as ``--dark``, -``--port``, and ``--no-browser``. Pass flag ``-h`` or ``--help`` to get -full list of supported arguments. + The prototype plasma calculator has been removed from PlasmaPy and + extracted into its own package. See |plasmapy-calculator| for + up-to-date usage information. diff --git a/mypy.ini b/mypy.ini index a6b8fd8ae4..48a4a17e96 100644 --- a/mypy.ini +++ b/mypy.ini @@ -5,6 +5,11 @@ exclude = (?x)( docs| \.run| \.tox| + \.nox| + env| + .env| + venv| + \.venv| ^conftest.py| build| _version.py| @@ -41,18 +46,12 @@ ignore_missing_imports = true [mypy-hypothesis.*] ignore_missing_imports = true -[mypy-ipywidgets.*] -ignore_missing_imports = true - [mypy-lmfit.*] ignore_missing_imports = true [mypy-mpmath.*] ignore_missing_imports = true -[mypy-numba.*] -ignore_missing_imports = true - [mypy-pkg_resources.*] ignore_missing_imports = true @@ -62,9 +61,6 @@ ignore_missing_imports = true [mypy-scipy.*] ignore_missing_imports = true -[mypy-setuptools.*] -ignore_missing_imports = true - [mypy-plasmapy._dev.scm_version] ignore_errors = true @@ -331,6 +327,9 @@ disable_error_code = arg-type,no-untyped-def,union-attr [mypy-tests.analysis.swept_langmuir.test_swept_langmuir_helpers] disable_error_code = no-untyped-def +[mypy-tests.analysis.swept_langmuir.test_helpers__merge_voltage_clusters] +disable_error_code = no-untyped-def + [mypy-tests.analysis.test_fit_functions] disable_error_code = assignment,index,no-any-return,no-untyped-call,no-untyped-def,override,type-arg diff --git a/noxfile.py b/noxfile.py index db4ac85a60..617bf010d6 100644 --- a/noxfile.py +++ b/noxfile.py @@ -59,15 +59,13 @@ current_python = f"{sys.version_info.major}.{sys.version_info.minor}" nox.options.sessions = [f"tests-{current_python}(skipslow)"] -nox.options.default_venv_backend = "uv|virtualenv" +nox.options.default_venv_backend = "uv" uv_sync = ("uv", "sync", "--no-progress", "--frozen") running_on_ci = os.getenv("CI") running_on_rtd = os.environ.get("READTHEDOCS") == "True" -uv_requirement = "uv >= 0.6.5" - def _create_requirements_pr_message(uv_output: str, session: nox.Session) -> None: """ @@ -160,8 +158,6 @@ def requirements(session: nox.Session) -> None: pull request message for the GitHub workflow that updates the pinned requirements (:file:`.github/workflows/update-pinned-reqs.yml`). """ - session.install(uv_requirement) - uv_lock_upgrade = ["uv", "lock", "--upgrade", "--no-progress"] # When silent is `True`, `session.run()` returns a multi-line string @@ -184,7 +180,6 @@ def validate_requirements(session: nox.Session) -> None: Verify that the requirements in :file:`uv.lock` are compatible with the requirements in `pyproject.toml`. """ - session.install(uv_requirement) session.log( "🛡 If this check fails, regenerate the pinned requirements in " "`uv.lock` with `nox -s requirements`." @@ -238,8 +233,6 @@ def validate_requirements(session: nox.Session) -> None: def tests(session: nox.Session, test_specifier: nox._parametrize.Param) -> None: """Run tests with pytest.""" - session.install(uv_requirement) - options: list[str] = [] if test_specifier in {"skip slow tests", "lowest-direct-skipslow"}: @@ -259,12 +252,20 @@ def tests(session: nox.Session, test_specifier: nox._parametrize.Param) -> None: match test_specifier: case "lowest-direct" | "lowest-direct-skipslow": - session.install(".[tests]", "--resolution=lowest-direct") + session.install( + ".[tests]", + "--resolution=lowest-direct", + "--no-all-extras", + f"--python={session.virtualenv.location}", + env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location}, + ) case _: # From https://nox.thea.codes/en/stable/cookbook.html#using-a-lockfile session.run_install( *uv_sync, "--extra=tests", + "--no-default-groups", + f"--python={session.virtualenv.location}", env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location}, ) @@ -290,8 +291,6 @@ def run_tests_with_dev_version_of(session: nox.Session, repository: str) -> None changes in an upstream dependency before its official release. """ - session.install(uv_requirement) - if repository == "numpy": # From: https://numpy.org/doc/1.26/dev/depending_on_numpy.html session.run_install( @@ -361,11 +360,11 @@ def docs(session: nox.Session) -> None: if running_on_ci: session.log(doc_troubleshooting_message) - session.install(uv_requirement) - session.run_install( *uv_sync, "--extra=docs", + "--no-default-groups", + f"--python={session.virtualenv.location}", env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location}, ) session.run(*sphinx_base_command, *build_html, *session.posargs) @@ -481,14 +480,18 @@ def build_docs_with_dev_version_of( @nox.session(python=docpython) def linkcheck(session: nox.Session) -> None: """Check hyperlinks in documentation.""" + if running_on_ci: session.log(LINKCHECK_TROUBLESHOOTING) - session.install(uv_requirement) + session.run_install( *uv_sync, "--extra=docs", + "--no-default-groups", + f"--python={session.virtualenv.location}", env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location}, ) + session.run(*sphinx_base_command, *check_hyperlinks, *session.posargs) @@ -516,10 +519,14 @@ def mypy(session: nox.Session) -> None: Configuration file: mypy.ini """ - session.install(uv_requirement) + session.install("pip") # mypy uses pip if --install-types is used + session.run_install( *uv_sync, + "--quiet", "--extra=tests", + "--no-default-groups", + f"--python={session.virtualenv.location}", env={"UV_PROJECT_ENVIRONMENT": session.virtualenv.location}, ) @@ -573,13 +580,15 @@ def build(session: nox.Session) -> None: @nox.session -@nox.parametrize("draft", [nox.param(False, id="draft"), nox.param(True, id="final")]) +@nox.parametrize("final", [nox.param(False, id="draft"), nox.param(True, id="final")]) def changelog(session: nox.Session, final: str) -> None: """ Build the changelog with towncrier. - - 'final': build the combined changelog for the release, and delete - the individual changelog entries in `changelog`. + - 'final': build the combined changelog for the release, delete + the individual changelog entries in `changelog`, and replace + `CHANGELOG.rst`. Be sure to commit changes before running this + session. - 'draft': print the draft changelog to standard output, without writing to files @@ -592,54 +601,36 @@ def changelog(session: nox.Session, final: str) -> None: if len(session.posargs) != 1: raise TypeError( "Please provide the version of PlasmaPy to be released " - "(i.e., `nox -s changelog -- 2024.9.0`" - ) - - source_directory = pathlib.Path("./changelog") - - extraneous_files = source_directory.glob("changelog/*[0-9]*.*.rst?*") - if final and extraneous_files: - session.error( - "Please delete the following extraneous files before " - "proceeding, as the presence of these files may cause " - f"towncrier errors: {extraneous_files}" + "(i.e., `nox -s changelog -- 2025.10.0`)" ) version = session.posargs[0] - year_pattern = r"(202[4-9]|20[3-9][0-9]|2[1-9][0-9]{2}|[3-9][0-9]{3,})" month_pattern = r"(1[0-2]|[1-9])" patch_pattern = r"(0?[0-9]|[1-9][0-9])" version_pattern = rf"^{year_pattern}\.{month_pattern}\.{patch_pattern}$" - if not re.match(version_pattern, version): raise ValueError( "Please provide a version of the form YYYY.M.PATCH, where " - "YYYY is the year past 2024, M is the one or two digit month, " + "YYYY is he year, M is the one or two digit month, " "and PATCH is a non-negative integer." ) session.install(".", "towncrier") - options = ("--yes",) if final else ("--draft", "--keep") + towncrier = ["towncrier", "build", "--version", version] - session.run( - "towncrier", - "build", - "--config", - "pyproject.toml", - "--dir", - ".", - "--version", - version, - *options, - *session.posargs, - ) + if not final: + session.run(*towncrier, "--draft", "--keep") + return + + original_file = pathlib.Path("./CHANGELOG.rst") + original_file.unlink() + + session.run(*towncrier, "--yes") - if final: - original_file = pathlib.Path("./CHANGELOG.rst") - destination = pathlib.Path(f"./docs/changelog/{version}.rst") - original_file.rename(destination) + destination = pathlib.Path(f"./docs/changelog/{version}.rst") + shutil.copy(original_file, destination) @nox.session diff --git a/pyproject.toml b/pyproject.toml index 77843ccda4..793ef31b2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,47 +56,40 @@ dynamic = [ "version" ] # pinned environments in `uv.lock`. dependencies = [ - # astropy upper limit described in https://github.com/PlasmaPy/PlasmaPy/issues/2883 - "astropy>=5.2,<7", + "astropy>=6", "h5py>=3.8", - # Minimum version of ipykernel should not exceed what's used by Google Colab - "ipykernel>=5.5.6", - "ipywidgets>=6", "lmfit>=1.1", "matplotlib>=3.7", "mpmath>=1.3", - "numpy>=1.24", + "numpy>=1.25", "packaging>=22", "pandas>=2", "requests>=2.28", "scipy>=1.10", - "setuptools>=66", "tqdm>=4.65", - # Use loose requirements for voila because it impacts ipykernel version - "voila>=0.2.7", "wrapt>=1.15", - # xarray upper limit described in: https://github.com/PlasmaPy/PlasmaPy/issues/2922 - "xarray>=2022.12,<=2024.10", + "xarray>=2023.7", ] # The documentation build occurs in an isolated environment that is not # user-facing, so we can have stricter requirements. optional-dependencies.docs = [ "docutils>=0.20.1", + "ipykernel>=6.30", + "ipywidgets>=8.1.7", "jinja2>=3.1.4", "nbsphinx>=0.9.4", - "nox>=2024.10.9", + "nox[uv]>=2025.5.1", "numpydoc>=1.7", "pillow>=10.4", - "plasmapy-sphinx>=0.2.0b1", + "plasmapy-sphinx>=2025.5.1", "pygments==2.18", - "sphinx>=8.2.3", + "sphinx>=8.2.3,<8.3", "sphinx-changelog>=1.5", "sphinx-codeautolink==0.15.2", "sphinx-collapse>=0.1.3", "sphinx-copybutton>=0.5.2", "sphinx-gallery>=0.16", - "sphinx-hoverxref>=1.4", "sphinx-issues>=4.1", "sphinx-notfound-page>=1.0.2", "sphinx-reredirects>=0.1.5", @@ -112,8 +105,8 @@ optional-dependencies.docs = [ # requirements to ensure that tests are run in consistent environments. optional-dependencies.tests = [ "hypothesis>=6.108.2", - "mypy>=1.11", - "nox>=2024.10.9", + "mypy>=1.18.2", + "nox[uv]>=2025.5.1", "pytest>=8.3.1", "pytest-cov>=5", "pytest-filter-subpackage>=0.2", @@ -128,6 +121,8 @@ urls.Documentation = "https://docs.plasmapy.org/" urls.Issues = "https://github.com/PlasmaPy/plasmapy/issues/" urls.Source = "https://github.com/PlasmaPy/plasmapy" urls.website = "https://www.plasmapy.org" + +# Remove references to plasma calculator after mid-2026 scripts.plasma-calculator = "plasmapy.utils.calculator:main" [tool.setuptools] @@ -136,7 +131,6 @@ include-package-data = true [tool.setuptools.package-data] "plasmapy.particles.data" = [ "*" ] "plasmapy.tests" = [ "coveragerc" ] -"plasmapy.utils.calculator" = [ "*" ] [tool.setuptools.packages.find] where = [ "src" ] @@ -155,7 +149,6 @@ extend-exclude = [ ".jupyter", "__pycache__", "_dev", - "docs/plasmapy_sphinx", ] show-fixes = true @@ -183,6 +176,7 @@ lint.extend-select = [ "FBT003", # flake8-boolean-trap "FIX", # flake8-fixme "FLY", # flynt + "FURB", # refurb "G", # flake8-logging-format "I", # isort "ICN", # flake8-import-conventions @@ -202,6 +196,7 @@ lint.extend-select = [ "PT", # flake8-pytest-style "PTH", # flake8-use-pathlib "PYI", # flake8-pyi + "Q", # flake8-quotes "RET", # flake8-return "RSE", # flake8-raise "RUF001", # ambiguous-unicode-character-string @@ -225,6 +220,7 @@ lint.extend-select = [ "RUF023", # unsorted-dunder-slots "RUF024", # mutable-fromkeys-value "RUF026", # default-factory-kwarg + "RUF028", # invalid-formatter-suppression-comment "RUF030", # assert-with-print-message "RUF032", # decimal-from-float-literal "RUF033", # post-init-default @@ -233,7 +229,11 @@ lint.extend-select = [ "RUF041", # unnecessary-nested-literal "RUF046", # unnecessary-cast-to-int "RUF048", # map-int-version-parsing + "RUF049", # dataclass-enum "RUF051", # if-key-in-dict-del + "RUF053", # class-with-mixed-type-vars + "RUF057", # unnecessary-round + "RUF058", # starmap-zip "RUF100", # unused-noqa "RUF101", # redirected-noqa "RUF200", # invalid-pyproject-toml @@ -300,7 +300,7 @@ lint.per-file-ignores.".github/scripts/*.py" = [ "D103", "INP001" ] lint.per-file-ignores."__init__.py" = [ "D104", "E402", "F401", "F402", "F403" ] # ignore import errors lint.per-file-ignores."docs/conf.py" = [ "D100", "D103", "E402", "EXE001", "EXE005", "F401" ] -# Most ruff rule violations in the following notebooks should eventually be fixed +# Most ruff rule violations in the following files should eventually be fixed lint.per-file-ignores."docs/notebooks/analysis/fit_functions.ipynb" = [ "NPY002" ] lint.per-file-ignores."docs/notebooks/analysis/nullpoint.ipynb" = [ "D103" ] lint.per-file-ignores."docs/notebooks/analysis/swept_langmuir/find_floating_potential.ipynb" = [ "FBT003" ] @@ -326,11 +326,12 @@ lint.per-file-ignores."docs/notebooks/plasma/grids_nonuniform.ipynb" = [ "NPY002 lint.per-file-ignores."setup.py" = [ "D100" ] lint.per-file-ignores."src/plasmapy/analysis/fit_functions.py" = [ "D301" ] +lint.per-file-ignores."src/plasmapy/analysis/swept_langmuir/**" = [ "E402" ] lint.per-file-ignores."src/plasmapy/formulary/braginskii.py" = [ "C901", "RET503", "RET504" ] lint.per-file-ignores."src/plasmapy/plasma/sources/*.py" = [ "D102" ] lint.per-file-ignores."src/plasmapy/utils/_pytest_helpers/pytest_helpers.py" = [ "BLE001", "PLR", "SLF001" ] -lint.per-file-ignores."src/plasmapy/utils/calculator/plasma_calculator.ipynb" = [ "SLF001" ] lint.per-file-ignores."tests/**/__init__.py" = [ "D104" ] +lint.per-file-ignores."tests/**/conftest.py" = [ "D103" ] lint.per-file-ignores."tests/**/test_*.py" = [ "D100", "D101", @@ -349,7 +350,9 @@ lint.per-file-ignores."tests/**/test_*.py" = [ "RUF012", "SLF001", ] +lint.per-file-ignores."tests/formulary/collisions/test_coulomb.py" = [ "PT031" ] lint.per-file-ignores."tests/formulary/test_distribution.py" = [ "ARG005" ] +lint.per-file-ignores."tests/formulary/test_transport.py" = [ "PT031" ] lint.per-file-ignores."tests/particles/test_decorators.py" = [ "ARG001", "ARG002" ] lint.per-file-ignores."tests/utils/_pytest_helpers/test_pytest_helpers.py" = [ "BLE001", "TRY002" ] lint.per-file-ignores."tests/utils/decorators/test_converters.py" = [ "ARG001", "ARG005" ] @@ -532,7 +535,6 @@ exclude_lines = [ branch = true source = [ "src" ] omit = [ - "*/plasmapy/utils/calculator/*", "*/plasmapy/tests/*", "*/plasmapy/*version.py", "*/plasmapy/_dev/*", diff --git a/src/plasmapy/__init__.py b/src/plasmapy/__init__.py index fa2d301366..839fca4c76 100644 --- a/src/plasmapy/__init__.py +++ b/src/plasmapy/__init__.py @@ -80,8 +80,8 @@ def online_help(query: str) -> None: # coverage: ignore query : str The search query. """ - import webbrowser - from urllib.parse import urlencode + import webbrowser # noqa: PLC0415 + from urllib.parse import urlencode # noqa: PLC0415 url = ( "http://docs.plasmapy.org/en/stable/search.html?" diff --git a/src/plasmapy/analysis/nullpoint.py b/src/plasmapy/analysis/nullpoint.py index 567b0862bb..8ea5cfb520 100644 --- a/src/plasmapy/analysis/nullpoint.py +++ b/src/plasmapy/analysis/nullpoint.py @@ -105,7 +105,7 @@ def get_loc(self): loc = property(get_loc) -class NullPoint(Point): +class NullPoint(Point): # noqa: PLW1641 """ A class for defining a null point in 3D space. diff --git a/src/plasmapy/analysis/swept_langmuir/__init__.py b/src/plasmapy/analysis/swept_langmuir/__init__.py index 2c65d8359e..be428289e1 100644 --- a/src/plasmapy/analysis/swept_langmuir/__init__.py +++ b/src/plasmapy/analysis/swept_langmuir/__init__.py @@ -7,21 +7,32 @@ "check_sweep", "find_floating_potential", "find_ion_saturation_current", + "find_didv_peak_location", + "merge_voltage_clusters", + "sort_sweep_arrays", + "dIdVExtras", "ISatExtras", "VFExtras", ] __aliases__ = ["find_isat_", "find_vf_"] +__all__ += __aliases__ from plasmapy.analysis.swept_langmuir.floating_potential import ( VFExtras, find_floating_potential, find_vf_, ) -from plasmapy.analysis.swept_langmuir.helpers import check_sweep +from plasmapy.analysis.swept_langmuir.helpers import ( + check_sweep, + merge_voltage_clusters, + sort_sweep_arrays, +) from plasmapy.analysis.swept_langmuir.ion_saturation_current import ( ISatExtras, find_ion_saturation_current, find_isat_, ) - -__all__ += __aliases__ +from plasmapy.analysis.swept_langmuir.plasma_potential import ( + dIdVExtras, + find_didv_peak_location, +) diff --git a/src/plasmapy/analysis/swept_langmuir/helpers.py b/src/plasmapy/analysis/swept_langmuir/helpers.py index 54f5edf46d..073358af36 100644 --- a/src/plasmapy/analysis/swept_langmuir/helpers.py +++ b/src/plasmapy/analysis/swept_langmuir/helpers.py @@ -1,53 +1,67 @@ """Helper functions for analyzing swept Langmuir traces.""" -__all__ = ["check_sweep"] +__all__ = ["check_sweep", "merge_voltage_clusters", "sort_sweep_arrays"] + +import numbers +import warnings +from collections.abc import Sequence +from typing import Literal import astropy.units as u import numpy as np +from plasmapy.utils.exceptions import PlasmaPyWarning + def check_sweep( # noqa: C901, PLR0912 voltage: np.ndarray, current: np.ndarray, strip_units: bool = True, + allow_unsorted: bool = False, ) -> tuple[np.ndarray, np.ndarray]: """ - Function for checking that the voltage and current arrays are properly - formatted for analysis by `plasmapy.analysis.swept_langmuir`. + Check that the voltage and current arrays are properly formatted + for analysis by `plasmapy.analysis.swept_langmuir`. Parameters ---------- voltage: `numpy.ndarray` - 1D `numpy.ndarray` representing the voltage of the swept Langmuir trace. - Voltage should be monotonically increasing. *No units are assumed or - checked, but values should be in volts.* + 1D `numpy.ndarray` representing the voltage of the swept + Langmuir trace. Voltage should be monotonically increasing. + *No units are assumed or checked, but values should be in + volts.* current: `numpy.ndarray` - 1D `numpy.ndarray` representing the current of the swept Langmuir trace. - Values should start from a negative ion-saturation current and increase - to a positive electron-saturation current. *No units are assumed or - checked, but values should be in amperes.* - - strip_units: `bool` - (Default: `True`) If `True`, then the units on ``voltage`` and/or - ``current`` will be stripped if either are passed in as an Astropy + 1D `numpy.ndarray` representing the current of the swept + Langmuir trace. Values should start from a negative + ion-saturation current and increase to a positive + electron-saturation current. *No units are assumed or checked, + but values should be in amperes.* + + strip_units: `bool`, default: `True` + If `True`, then the units on ``voltage`` and/or ``current`` + will be stripped if either are passed in as an Astropy `~astropy.units.Quantity`. + allow_unsorted: `bool`, default: `False` + If `True`, then the supplied ``voltage`` array must be + monotonically increasing. + Returns ------- voltage : `numpy.ndarray` - Input argument ``voltage`` after it goes through all of its checks - and conditioning. + Input argument ``voltage`` after it goes through all of its + checks and conditioning. current : `numpy.ndarray` - Input argument ``current`` after it goes through all of its checks - and conditioning. + Input argument ``current`` after it goes through all of its + checks and conditioning. Raises ------ `TypeError` - If either the ``voltage`` or ``current`` arrays are not instances of a - `numpy.ndarray`. + If either the ``voltage`` or ``current`` arrays are not + instances of a `numpy.ndarray`. `ValueError`: If either the ``voltage`` or ``current`` arrays are not 1D. @@ -56,12 +70,13 @@ def check_sweep( # noqa: C901, PLR0912 If the ``voltage`` array is not monotonically increasing. `ValueError` - If the ``current`` array never crosses zero (i.e. has no floating - potential). + If the ``current`` array never crosses zero (i.e. has no + floating potential). `ValueError` - If the ``current`` array does not start form a negative ion-saturation - current and increases to a positive electron-saturation current. + If the ``current`` array does not start form a negative + ion-saturation current and increases to a positive + electron-saturation current. `ValueError` If either the ``voltage`` or ``current`` array does not have a @@ -93,7 +108,7 @@ def check_sweep( # noqa: C901, PLR0912 f"Expected 1D numpy array for voltage, but got array with " f"{voltage.ndim} dimensions.", ) - elif not np.all(np.diff(voltage) >= 0): + elif not np.all(np.diff(voltage) >= 0) and not allow_unsorted: raise ValueError("The voltage array is not monotonically increasing.") if isinstance(voltage, u.Quantity) and strip_units: @@ -131,8 +146,8 @@ def check_sweep( # noqa: C901, PLR0912 ) elif current[0] > 0.0 or current[-1] < 0.0: raise ValueError( - "The current array needs to start from a negative ion-saturation current" - " to a positive electron-saturation current." + "The current array needs to start from a negative ion-saturation " + "current to a positive electron-saturation current." ) if voltage.size != current.size: @@ -145,3 +160,501 @@ def check_sweep( # noqa: C901, PLR0912 current = current.value return voltage, current + + +def sort_sweep_arrays( + voltage: np.ndarray, + current: np.ndarray, + voltage_order: Literal["ascending", "descending"] = "ascending", +) -> tuple[np.ndarray, np.ndarray]: + """ + Sort the swept langmuir ``voltage`` and ``current`` traces to + ensure the ``voltage`` array is either monotonically increasing or + decreasing. + + Parameters + ---------- + voltage: `numpy.ndarray` + 1D `numpy.ndarray` representing the voltage of the swept + Langmuir trace. *No units are assumed or checked, but values + should be in volts.* + + current: `numpy.ndarray` + 1D `numpy.ndarray` representing the current of the swept + Langmuir trace. Values should start from a negative + ion-saturation current and increase to a positive + electron-saturation current. *No units are assumed or checked, + but values should be in amperes.* + + voltage_order: `str` + Either ``'ascending'`` or ``'descending'`` to indicate how the + ``voltage`` array should be sorted. (DEFAULT: ``'ascending'``) + + Returns + ------- + voltage : `numpy.ndarray` + Sorted ``voltage`` array. + + current : `numpy.ndarray` + Matched ``current`` array to the sorted ``voltage`` array. + """ + if not isinstance(voltage_order, str): + raise TypeError( + "Expected 'voltage_order' to be a string equal to 'ascending' " + f"or 'descending', but got type {type(voltage_order)}." + ) + elif voltage_order not in ["ascending", "descending"]: + raise ValueError( + "Expected 'voltage_order' to be a string equal to 'ascending' " + f"or 'descending', but got '{voltage_order}'." + ) + + voltage, current = check_sweep( + voltage, current, strip_units=True, allow_unsorted=True + ) + + # determine order + voltage_diff = np.diff(voltage) + if np.all(voltage_diff >= 0): + _order = "ascending" + elif np.all(voltage_diff <= 0): + _order = "descending" + else: + _order = None + + if _order == voltage_order: + # already ordered + return voltage, current + + # perform sorting + if _order is None: + index_sort = np.argsort(voltage) + if voltage_order == "descending": + index_sort = index_sort[::-1] + + voltage = voltage[index_sort] + current = current[index_sort] + else: + voltage = voltage[::-1] + current = current[::-1] + + return voltage, current + + +def _is_voltage_regularly_spaced( + voltage_diff: np.ndarray, + mask_zero_diff: np.ndarray, +) -> bool: + """ + Determine if the voltage difference array ``voltage_diff`` is + regularly spaced; that is the differences are all equal or some + integer multiple of the smallest difference. + """ + is_regular_grid = False + if np.count_nonzero(mask_zero_diff) > 0: + # is_regular_grid = False + return False + elif np.allclose(voltage_diff, voltage_diff[0]): + # grid is already regularly spaced + is_regular_grid = True + elif np.allclose( + np.rint(voltage_diff / np.min(voltage_diff)) + - voltage_diff / np.min(voltage_diff), + 0, + ): + # grid has a common dV, but at times jumps N * dV times + min_dV = np.min(voltage_diff) + ndV = np.rint(voltage_diff / min_dV) + + is_regular_grid = not np.any(ndV > 10) + + return is_regular_grid + + +def _merge_voltage_clusters__zero_diff_neighbors( + voltage: np.ndarray, current: np.ndarray +) -> tuple[np.ndarray, np.ndarray]: + """ + Take the ``voltage`` and ``current`` arrays associated with a swept + langmuir trace and average together clusters of identical voltage + values. + """ + # generate boolean mask for zero diff locations + voltage_diff = np.diff(voltage) + mask_zero_diff = np.isclose(voltage_diff, 0.0) + mask_zero_diff = np.append(mask_zero_diff, [mask_zero_diff[-1]]) + + # initialize new voltage and current arrays + new_voltage = np.full(voltage.shape, np.nan, dtype=voltage.dtype) + new_current = np.full(current.shape, np.nan, dtype=current.dtype) + + mask = np.logical_not(mask_zero_diff) + new_voltage[mask] = voltage[mask] + new_current[mask] = current[mask] + + # merge zero diff clusters + while np.any(mask_zero_diff): + leading_cluster_volt = voltage[mask_zero_diff][0] + index = np.where(new_voltage == leading_cluster_volt)[0] + if len(index) == 0: + index = np.where(mask_zero_diff)[0] + + index = index[0] + volt_mask = np.isclose(voltage, leading_cluster_volt) + + new_voltage[index] = leading_cluster_volt + new_current[index] = np.average(current[volt_mask]) + + mask_zero_diff[volt_mask] = False + + # remove nan entries + mask = np.logical_not(np.isnan(new_voltage)) + new_voltage = new_voltage[mask] + new_current = new_current[mask] + + return new_voltage, new_current + + +def _merge_voltage_clusters__within_dv( # noqa: C901 + voltage: np.ndarray, + current: np.ndarray, + voltage_step_size: float, +) -> tuple[np.ndarray, np.ndarray]: + """ + Take the ``voltage`` and ``current`` arrays associated with a swept + langmuir trace and average together clusters of voltage values + within step size ``voltage_step_size``. + """ + # initialize new voltage and current arrays + new_voltage = voltage.copy() + new_current = current.copy() + + voltage_diff = np.diff(voltage) + + # generate global cluster mask + mask1 = voltage_diff < voltage_step_size + mask2 = np.isclose(voltage_diff, voltage_step_size) + cluster_mask = np.logical_or(mask1, mask2) + + # determine cluster locations + indices = np.where(np.diff(cluster_mask))[0] + if cluster_mask[0]: + # 1st element in voltage is in a cluster + indices = np.append([0], indices) + indices[1] = indices[1] + 1 + else: + indices[0:2] = indices[0:2] + 1 + if indices.size > 1: + indices[2:] = indices[2:] + 1 + if cluster_mask[-1] and indices[-1] != voltage.size - 1: + # last element in voltage is in a cluster + indices = np.append(indices, [voltage.size - 1]) + indices = np.reshape(indices, newshape=(int(indices.size / 2), 2)) + # ^ using newshape kwarg for backwards compatibility, newshape kwarg + # has been deprecated since numpy v2.1 + + # merge clusters and update new_voltage and new_current + for ii in range(indices.shape[0]): + start_index = indices[ii][0] + stop_index = indices[ii][1] + 1 + + new_voltage[start_index:stop_index] = np.nan + new_current[start_index:stop_index] = np.nan + + sub_voltage = voltage[start_index:stop_index] + sub_current = current[start_index:stop_index] + + v_range = sub_voltage[-1] - sub_voltage[0] + nbins = int(np.rint(v_range / voltage_step_size)) + if not np.isclose(nbins - (v_range / voltage_step_size), 0): + nbins = int( + np.floor((sub_voltage[-1] - sub_voltage[0]) / voltage_step_size) + ) + + if nbins == 0: + nbins = 1 + + if nbins == 1: + new_voltage[start_index] = np.average(sub_voltage) + new_current[start_index] = np.average(sub_current) + continue + + range_array = np.linspace(sub_voltage[0], sub_voltage[-1], nbins + 1) + for jj in range(nbins): + start_voltage = range_array[jj] + stop_voltage = range_array[jj + 1] + + mask1 = sub_voltage >= start_voltage + if jj == nbins - 1: + mask2 = sub_voltage <= stop_voltage + else: + mask2 = sub_voltage < stop_voltage + mask = np.logical_and(mask1, mask2) + + if np.count_nonzero(mask) > 0: + new_voltage[start_index + jj] = np.average(sub_voltage[mask]) + new_current[start_index + jj] = np.average(sub_current[mask]) + + # filter out NaN values + nan_mask = np.logical_not(np.isnan(new_voltage)) + new_voltage = new_voltage[nan_mask] + new_current = new_current[nan_mask] + + return new_voltage, new_current + + +def merge_voltage_clusters( # noqa: C901, PLR0912 + voltage: np.ndarray, + current: np.ndarray, + voltage_step_size: float | None = None, + filter_nan: bool = False, +) -> tuple[np.ndarray, np.ndarray]: + r""" + Search the ``voltage`` array for closely spaced voltage clusters + based on the ``voltage_step_size`` parameter and merge those + clusters, and associated ``current`` values, into a single point. + + This function is intended to merge together identical, or close, + voltage points to remove small step sizes in the swept langmuir + trace before differentiation. + + Parameters + ---------- + voltage: `numpy.ndarray` + 1D `numpy.ndarray` representing the voltage of the swept + Langmuir trace. Voltage needs to be monotonically ascending. + *No units are assumed or checked, but values should be in + volts.* + + current: `numpy.ndarray` + 1D `numpy.ndarray` representing the current of the swept + Langmuir trace. Values should start from a negative + ion-saturation current and increase to a positive + electron-saturation current. *No units are assumed or checked, + but values should be in amperes.* + + voltage_step_size: `float` | `None`, default: `None` + A non-zero, positive step size for the ``voltage`` array + cluster identification. A value of ``0`` will merge only + duplicate voltage values. A value of `None` will default to + 95% of the average step size of the ``voltage`` array (only + counting duplicate voltages once). + + filter_nan: `bool`, default: `False` + Set `True` to automatically filter `~numpy.nan` values from the + ``voltage`` and ``current`` arrays. + + Returns + ------- + voltage : `numpy.ndarray` + The new ``voltage`` array. + + current : `numpy.ndarray` + The new ``current`` array. + + Notes + ----- + An identified voltage cluster can span a voltage range larger than + ``voltage_step_size`` and still have every voltage step being + smaller than ``voltage_step_size``. In this scenario, the voltage + cluster will be divided up into :math:`N`-sections for averaging, + where :math:`N` is given by + + .. math:: + + N = \texttt{floor}\left( + \frac{V_{cluster,max} - V_{cluster,min}}{\texttt{voltage_step_size}} + \right) + """ + # condition voltage_step_size + if voltage_step_size is not None and not isinstance( + voltage_step_size, numbers.Real + ): + raise TypeError( + "Expected 'voltage_step_size' to be a float or None, got type " + f"{type(voltage_step_size)}." + ) + elif isinstance(voltage_step_size, numbers.Integral): + voltage_step_size = float(voltage_step_size) + + try: + voltage, current = check_sweep(voltage, current) + except ValueError as err: + # check if the ValueError was a result of voltage containing nan + # values + if not np.any(np.isnan(voltage)): + # voltage array has no nan values + raise ValueError(*err.args) from err + + if not filter_nan: + raise ValueError( + "The voltage array contains NaN values. If you want NaN " + "values to be automatically filtered, then set argument " + "filter_nan=True." + ) from err + + # filter (voltage) NaN values and check sweep again + nan_mask = np.logical_not(np.isnan(voltage)) + voltage = voltage[nan_mask] + current = current[nan_mask] + + voltage, current = check_sweep(voltage, current) + + # filter (current) NaN values + if not np.any(np.isnan(current)): + # voltage array has no nan values + pass + elif filter_nan: + # mask out current NaN values + nan_mask = np.logical_not(np.isnan(current)) + voltage = voltage[nan_mask] + current = current[nan_mask] + else: + raise ValueError( + "The current array contains NaN values. If you want NaN " + "values to be automatically filtered, then set argument " + "filter_nan=True." + ) + + # check if grid is regularly spaced + voltage_diff = np.diff(voltage) + mask_zero_diff = np.isclose(voltage_diff, 0.0) + is_regular_grid = _is_voltage_regularly_spaced(voltage_diff, mask_zero_diff) + + # return if voltage is already regularly spaced and no voltage merging is + # requested + if is_regular_grid and voltage_step_size is None: + warnings.warn( + "The supplied ``voltage`` array is already regularly spaced. If " + "you want to re-bin the arrays to a different voltage_step_size, " + "then use something like numpy.interp. No merging performed.", + PlasmaPyWarning, + ) + + return voltage.copy(), current.copy() + + # condition voltage_step_size ... Round 2 + if voltage_step_size is None: + voltage_step_size = 0.95 * np.abs( + np.average(voltage_diff[np.logical_not(mask_zero_diff)]) + ) + elif voltage_step_size == 0: + voltage_step_size = 0.0 + elif voltage_step_size < 0: + voltage_step_size = -voltage_step_size + + if np.all(voltage_step_size <= np.abs(voltage_diff)) and voltage_step_size != 0: + warnings.warn( + f"The supplied voltage_step_size ({voltage_step_size}) is smaller than " + f"any of the voltage steps in the voltage array. Supply a step size " + f"greater than the smallest voltage step ({np.min(voltage_diff)}). " + f"No merging performed.", + PlasmaPyWarning, + ) + + return voltage.copy(), current.copy() + + # now merge clusters + if voltage_step_size == 0: + new_voltage, new_current = _merge_voltage_clusters__zero_diff_neighbors( + voltage, current + ) + + else: + new_voltage, new_current = _merge_voltage_clusters__within_dv( + voltage, current, voltage_step_size + ) + + return new_voltage, new_current + + +def _condition_voltage_window( # noqa: C901, PLR0912 + voltage, voltage_window +) -> slice: + """ + Condition ``voltage_window`` and return resulting `slice` object to + index ``voltage``. + + Parameters + ---------- + voltage : `numpy.ndarray` + 1-D numpy array of monotonically increasing probe biases + (should be in volts). + + voltage_window : `list[float | None]` | `None`, default: `None` + A two-element list ``[v_min, v_max]`` that specifies the voltage + range in which the peak slope will be looked for. Specifying + `None` for either the first or second element will result in a + window using the lower or upper bound of ``voltage`` + respectively. If set to `None` (default), then the whole + ``voltage`` window will be used. + + Returns + ------- + voltage_window : `slice` + A `slice` object representing the window originally defined + by the input ``voltage_window``. + + """ + if isinstance(voltage_window, np.ndarray): + voltage_window = voltage_window.tolist() + + if voltage_window is None: + voltage_window = [None, None] + elif not isinstance(voltage_window, Sequence) or isinstance(voltage_window, str): + raise TypeError( + f"Expected a 2-element list of floats or None for 'voltage_window', " + f"but got type {type(voltage_window)}." + ) + elif len(voltage_window) != 2: + raise ValueError( + f"Expected a 2-element list of floats or None for 'voltage_window', " + f"but got type {len(voltage_window)} elements." + ) + elif not all( + isinstance(element, numbers.Real) or element is None + for element in voltage_window + ): + raise TypeError("Not all elements of 'voltage_window' are floats or None.") + elif None not in voltage_window: + voltage_window = np.sort(voltage_window).tolist() + + # determine data window + if voltage_window[0] is not None and voltage_window[0] >= voltage[-1]: + raise ValueError( + f"The min value for the voltage window ({voltage_window[0]}) " + f"is larger than the max value of the langmuir trace " + f"({voltage[-1]})." + ) + + if voltage_window[1] is not None and voltage_window[1] <= voltage[0]: + raise ValueError( + f"The max value for the voltage window ({voltage_window[1]}) " + f"is smaller than the min value of the langmuir trace " + f"({voltage[0]})." + ) + + if all(isinstance(element, numbers.Real) for element in voltage_window): + voltage_window = np.sort(voltage_window).tolist() + + first_index = ( + None + if voltage_window[0] is None + else int(np.where(voltage >= voltage_window[0])[0][0]) + ) + if first_index == 0: + first_index = None + + last_index = ( + None + if voltage_window[1] is None + else int(np.where(voltage <= voltage_window[1])[0][-1]) + ) + if last_index is None: + pass + elif last_index == voltage.size - 1: + last_index = None + else: + last_index += 1 + + return slice(first_index, last_index, 1) diff --git a/src/plasmapy/analysis/swept_langmuir/plasma_potential.py b/src/plasmapy/analysis/swept_langmuir/plasma_potential.py new file mode 100644 index 0000000000..9a9e3f80c5 --- /dev/null +++ b/src/plasmapy/analysis/swept_langmuir/plasma_potential.py @@ -0,0 +1,251 @@ +""" +Functionality for determining the plasma potential of a Langmuir sweep. +""" + +__all__ = ["find_didv_peak_location", "dIdVExtras"] +__aliases__ = [] +__all__ += __aliases__ + +from collections.abc import Sequence +from typing import NamedTuple + +import numpy as np +from scipy import signal + +from plasmapy.analysis.swept_langmuir.helpers import ( + _condition_voltage_window, + check_sweep, + merge_voltage_clusters, +) + + +class dIdVExtras(NamedTuple): # noqa: N801 + """ + `~typing.NamedTuple` structured to contain the extra parameters + calculated by + `~plasmapy.analysis.swept_langmuir.plasma_potential.find_didv_peak_location`. + """ + + std: float | None + """ + Alias for field number 0, standard deviation of all the computed + peak slope bias locations for each Savitzky-Golay filtered Langmuir + trace. Standard deviation of :attr:`savgol_peaks`. + """ + + data_slice: slice | None + """ + Alias for field number 1, `slice` objected corresponding to the + sub-arrays of the Langmuir trace used for the calculation. + """ + + savgol_windows: list[int] | None + """ + Alias for field number 2, list of windows sizes used for each + Savitzky-Golay filtered Langmuir trace. + """ + + savgol_peaks: list[float] | None + """ + Alias for field number 3, list of computed peak slope bias locations + for each Savitzky-Golay filtered Langmuir trace. + """ + + +def _condition_smooth_fractions( # noqa: C901 + smooth_fractions, data_size: int +): + """ + Condition ``smooth_fractions`` and return the resulting + Savitzky-Golay filter windows sizes, based on the ``data_size``. + """ + # condition smooth_fractions + if smooth_fractions is None: + # Note: If this default value is changed, then the docstring entry + # for smooth_fractions in the find_didv_peak() docstring + # needs to be updated accordingly. + smooth_fractions = np.linspace(0.01, 0.25, num=30) + elif isinstance(smooth_fractions, np.ndarray): + pass + elif not isinstance(smooth_fractions, Sequence) or isinstance( + smooth_fractions, str + ): + raise TypeError( + f"Expected a list-like object for 'smooth_fractions', " + f"but got type {type(smooth_fractions)}." + ) + else: + smooth_fractions = np.array(smooth_fractions) + + if smooth_fractions.ndim != 1: + raise ValueError( + "Expected a 1-D list of floats in the interval [0, 1] for argument " + f"'smooth_fractions', but got a {smooth_fractions.ndim}-D list." + ) + elif not np.issubdtype(smooth_fractions.dtype, np.floating): + raise ValueError( + "Expected a 1-D list of floats in the interval [0, 1] for argument " + "'smooth_fractions', not all elements are floats." + ) + + smooth_fractions = np.unique(np.sort(smooth_fractions)) + mask1 = smooth_fractions < 0 + mask2 = smooth_fractions > 1 + mask = np.logical_or(mask1, mask2) + if np.count_nonzero(mask) > 0: + raise ValueError( + "Expected a 1-D list of floats in the interval [0, 1] for argument " + f"'smooth_fractions', no elements are within this interval " + f"{smooth_fractions.tolist()}." + ) + + # condition data_size + if not isinstance(data_size, int): + raise TypeError( + "Expected a positive, non-zero integer for argument 'data_size', " + f"but got type {type(data_size)}." + ) + elif data_size < 1: + raise ValueError( + "Expected a positive, non-zero integer for argument 'data_size', " + f"but got {data_size}." + ) + + # create bin sizes (savgol_windows) for the savgol_filter + savgol_windows = np.unique(np.rint(smooth_fractions * data_size).astype(int)) + + # windows need to have at least 2 points + mask = savgol_windows > 2 + savgol_windows = savgol_windows[mask] + + if 0.0 in smooth_fractions: + savgol_windows = np.sort(np.append(savgol_windows, 0)) + + # do not let windows sizes exceed data_size + mask = savgol_windows <= data_size + savgol_windows = savgol_windows[mask] + + # check savgol_windows is not null + if savgol_windows.size == 0: + raise ValueError( + f"The given smooth_fractions ({smooth_fractions}) and " + f"window size ({data_size}) resulted in no valid Savitzky-Golay " + f"filter windows. Computed windows must be odd, greater than 3, " + f"and less than or equal to the windows size." + ) + + return savgol_windows + + +def find_didv_peak_location( + voltage: np.ndarray, + current: np.ndarray, + *, + voltage_window: list[float | None] | None = None, + smooth_fractions: list[float] | None = None, +) -> tuple[float, dIdVExtras]: + """ + Find the bias voltage at which the peak slope (:math:`dI/dV_{max}`) + of the swept Langmuir trace occurs. + + The peak slope bias voltage is often used as a rough estimate of + the plasma potential. However, the value will always be slightly + less than the actual plasma potential. + + Parameters + ---------- + voltage : `numpy.ndarray` + 1-D numpy array of monotonically increasing probe biases + (should be in volts). + + current : `numpy.ndarray` + 1-D numpy array of probe current (should be in amperes) + corresponding to the ``voltage`` array. + + voltage_window : `list[float | None]` | `None`, default: `None` + A two-element list ``[v_min, v_max]`` that specifies the voltage + range in which the peak slope will be looked for. Specifying + `None` for either the first or second element will result in a + window using the lower or upper bound of ``voltage`` + respectively. If set to `None` (default), then the whole + ``voltage`` window will be used. + + smooth_fractions : `list[float]` | `None`, default: `None` + An order list of fractions in the interval :math:`[0, 1]` used + to compute the Savitzky-Golay filter window sizes. For example, + if the ``voltage_windows`` had a size of 50, then a + ``smooth_fraction`` value of 0.5 would result in a + Savitzky-Golay window size of 25. For ``smooth_fraction`` + value of ``0.0`` no smoother will be performed. If `None` + (default), then ``smooth_fractions`` will default to + ``numpy.linspace(0.01, 0.25, num=30)``. + + Notes + ----- + Add details about algorithm. + """ + rtn_extras = dIdVExtras( + std=None, + data_slice=None, + savgol_windows=None, + savgol_peaks=None, + )._asdict() + + # check voltage and current arrays + voltage, current = check_sweep(voltage, current, strip_units=True) + voltage, current = merge_voltage_clusters(voltage, current, voltage_step_size=0) + + # condition voltage_window + _slice = _condition_voltage_window(voltage, voltage_window) + rtn_extras["data_slice"] = _slice + data_size = voltage[_slice].size + if data_size < 3: + raise ValueError( + f"The specified voltage_window ({voltage_window}) would result " + f"in a null window or a window with fewer than 3 elements." + ) + + # define starting savgol windows + savgol_windows = _condition_smooth_fractions(smooth_fractions, data_size) + + voltage_slice = voltage[_slice] + current_slice = current[_slice] + plasma_potentials = [] + rtn_extras["savgol_windows"] = [] + for _window in savgol_windows: + if _window == 0: + v_smooth = voltage_slice + c_smooth = current_slice + else: + v_smooth = signal.savgol_filter(voltage_slice, _window, 1) + c_smooth = signal.savgol_filter(current_slice, _window, 1) + + didv = np.gradient(c_smooth, v_smooth) + didv_max = np.max(didv) + imax = np.where(np.isclose(didv, didv_max, atol=0.0))[0] + if imax.size > 1: + if np.all(np.diff(imax) == 1): + # neighboring indices have the same peak value, take + # voltage average + vp = np.average(voltage_slice[imax]) + else: + # peaks occur at separated indices (i.e. NOT neighboring + # indices) ... unable to determine vp just go to the next + # savgol window + continue + elif np.isscalar(imax): + vp = voltage_slice[imax] + else: + vp = voltage_slice[imax[0]] + + plasma_potentials.append(float(vp)) + rtn_extras["savgol_windows"].append(int(_window)) + + if len(plasma_potentials) == 0: + raise RuntimeError("Unable to identify any dI/dV peaks in the Langmuir trace.") + + rtn_extras["savgol_peaks"] = plasma_potentials + rtn_extras["std"] = float(np.std(plasma_potentials)) + + vp = float(np.average(plasma_potentials)) + return vp, dIdVExtras(**rtn_extras) diff --git a/src/plasmapy/diagnostics/langmuir.py b/src/plasmapy/diagnostics/langmuir.py index e1ee537aad..5892177a73 100644 --- a/src/plasmapy/diagnostics/langmuir.py +++ b/src/plasmapy/diagnostics/langmuir.py @@ -23,6 +23,7 @@ import warnings import astropy.units as u +import matplotlib.pyplot as plt import numpy as np from astropy.constants import si as const from astropy.visualization import quantity_support @@ -200,8 +201,6 @@ def get_padded_limit(self, padding, log: bool = False): def plot(self) -> None: r"""Plot the characteristic in matplotlib.""" - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() plt.scatter(self.bias.to(u.V), self.current.to(u.mA), marker=".", color="k") @@ -365,8 +364,6 @@ def swept_probe_analysis( # noqa: PLR0915 ) if visualize: - import matplotlib.pyplot as plt - with quantity_support(): fig, (ax1, ax2) = plt.subplots(2, 1) ax1.plot( @@ -975,8 +972,6 @@ def get_electron_temperature( T_e = np.array([T0, T0 + Delta_T]) * u.eV if visualize: - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() @@ -1083,8 +1078,6 @@ def extrapolate_electron_current( ) if visualize: - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() plt.scatter( @@ -1236,8 +1229,6 @@ def get_ion_density_OML( ) if visualize: - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() plt.scatter( @@ -1303,8 +1294,6 @@ def extrapolate_ion_current_OML(probe_characteristic, fit, visualize: bool = Fal ion_characteristic = Characteristic(probe_characteristic.bias, ion_current) if visualize: - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() plt.scatter( @@ -1398,8 +1387,6 @@ def get_EEDF(probe_characteristic, visualize: bool = False): probability = probability / integral if visualize: - import matplotlib.pyplot as plt - with quantity_support(): plt.figure() plt.semilogy(energy, probability, c="k") diff --git a/src/plasmapy/formulary/dimensionless.py b/src/plasmapy/formulary/dimensionless.py index d67d203bb5..5cae4d23dc 100644 --- a/src/plasmapy/formulary/dimensionless.py +++ b/src/plasmapy/formulary/dimensionless.py @@ -138,6 +138,10 @@ def Hall_parameter( collision frequency between plasma species :math:`s` (``particle``) and species :math:`s^{\prime}` (``ion``). + If the Hall parameter is low, the trajectory of electrons between + two encounters of heavy particles is approximately linear. If the Hall + parameter is high, the motion of the electrons is highly curved. + **Aliases:** `betaH_` Parameters @@ -209,7 +213,7 @@ def Hall_parameter( >>> Hall_parameter(1e10 * u.m**-3, 2.8e2 * u.eV, 2.3 * u.T, "He-4 +1", "e-") """ - from plasmapy.formulary.collisions import ( + from plasmapy.formulary.collisions import ( # noqa: PLC0415 fundamental_electron_collision_freq, fundamental_ion_collision_freq, ) diff --git a/src/plasmapy/formulary/frequencies.py b/src/plasmapy/formulary/frequencies.py index 18aef9744e..c68849361b 100644 --- a/src/plasmapy/formulary/frequencies.py +++ b/src/plasmapy/formulary/frequencies.py @@ -91,7 +91,7 @@ def gyrofrequency( Warns ----- - : `~astropy.units.UnitsWarning` + `~astropy.units.UnitsWarning` If units are not provided, and SI units are assumed. Notes @@ -284,7 +284,7 @@ def plasma_frequency( Warns ----- - : `~astropy.units.UnitsWarning` + `~astropy.units.UnitsWarning` If units are not provided, SI units are assumed. Notes @@ -392,7 +392,7 @@ def lower_hybrid_frequency( Warns ----- - : `~astropy.units.UnitsWarning` + `~astropy.units.UnitsWarning` If units are not provided, SI units are assumed. Notes @@ -484,7 +484,7 @@ def upper_hybrid_frequency( Warns ----- - : `~astropy.units.UnitsWarning` + `~astropy.units.UnitsWarning` If units are not provided, SI units are assumed. Notes @@ -590,7 +590,7 @@ def Buchsbaum_frequency( Warns ----- - : `~astropy.units.UnitsWarning` + `~astropy.units.UnitsWarning` If units are not provided, SI units are assumed. Notes @@ -601,11 +601,12 @@ def Buchsbaum_frequency( to as the Buchsbaum frequency :cite:p:`buchsbaum:1960`, also called the bi-ion hybrid resonance frequency :cite:p:`thompson:1995`, or ion-ion hybrid frequency :cite:p:`vincena:2013`. This frequency - can be defined as: + can be defined as .. math:: + ω_{BB} ≡ \sqrt{\frac{ω_{p1}^2 ω_{c2}^2 - + ω_{p2}^2 ω_{c1}^2}{ω_{p2}^2 + ω_{p2}^2}} + + ω_{p2}^2 ω_{c1}^2}{ω_{p2}^2 + ω_{p2}^2}} Examples -------- diff --git a/src/plasmapy/formulary/laser.py b/src/plasmapy/formulary/laser.py index 40fe7c14be..162a87422e 100644 --- a/src/plasmapy/formulary/laser.py +++ b/src/plasmapy/formulary/laser.py @@ -7,14 +7,27 @@ """ __all__ = [ + "em_angular_frequency", "electric_field_amplitude", "intensity", + "normalized_vector_potential", + "Gaussian_beam_waist_radius", + "Gaussian_power", + "Gaussian_Rayleigh_length", + "Gaussian_spot_size_FWHM", + "em_wavelength", +] +__aliases__ = [ + "a0_", + "omega_", + "E0_", + "I_", + "w0_", ] -__aliases__ = ["E0_", "I_"] import astropy.units as u import numpy as np -from astropy.constants.si import c, eps0 +from astropy.constants.si import c, e, eps0, m_e from plasmapy.utils.decorators import validate_quantities @@ -119,3 +132,353 @@ def intensity( I_ = intensity """Alias to `~plasmapy.formulary.laser.intensity`.""" + + +@validate_quantities( + angular_frequency={"can_be_negative": False}, +) +def em_wavelength(angular_frequency: u.Quantity[u.rad / u.s]) -> u.Quantity[u.m]: + r""" + Calculate the wavelength of a laser :math:`\lambda` given the + the angular frequency :math:`\omega`. + + The wavelength of an electromagnetic wave :math:`\lambda` + is calculated using: + + .. math:: + \lambda = \frac{2\pi c}{\omega}, + + where :math:`\omega` is the angular frequency of the beam. + + Parameters + ---------- + angular_frequency : `~astropy.units.Quantity` + angular frequency of the laser beam (convertible to rad / s). + + Returns + ------- + wavelength : `~astropy.units.Quantity` + The wavelength of a laser with a given angular frequency. + + Notes + ----- + For details, see :cite:t:`ling:2016`\ . + + Examples + -------- + >>> import astropy.units as u + >>> em_wavelength(2.354307546e15 * u.rad / u.s) + + """ + return (2 * np.pi * c / angular_frequency).to( + u.m, equivalencies=u.dimensionless_angles() + ) + + +@validate_quantities( + wavelength={"can_be_negative": False}, +) +def em_angular_frequency(wavelength: u.Quantity[u.m]) -> u.Quantity[u.rad / u.s]: + r""" + Calculate the angular frequency :math:`\omega` of a laser given the + the wavelength of the beam :math:`\lambda`. + + The angular frequency of a wave :math:`\omega` + can be calculated using: + + .. math:: + \omega = \frac{2\pi c}{\lambda}, + + where :math:`\lambda` is the wavelength of the beam and :math:`c` is the speed of light. + + **Aliases:** `omega_` + + Parameters + ---------- + wavelength : `~astropy.units.Quantity` + Wavelength of the laser beam (convertible to m). + + Returns + ------- + omega_0 : `~astropy.units.Quantity` + The angular frequency of a laser with a given wavelength. + + Notes + ----- + For details, see :cite:t:`ling:2016`\ . + + Examples + -------- + >>> import astropy.units as u + >>> em_angular_frequency(800 * u.nm) + + """ + return ((c / wavelength) * 2 * np.pi).to( + u.rad / u.s, equivalencies=u.dimensionless_angles() + ) + + +omega_ = em_angular_frequency +"""Alias to `~plasmapy.formulary.laser.em_angular_frequency`.""" + + +@validate_quantities( + intensity={"can_be_negative": False}, + wavelength={"can_be_negative": False}, +) +def normalized_vector_potential( + intensity: u.Quantity[u.watt / u.m**2], + wavelength: u.Quantity[u.m], +) -> float | np.ndarray: + r""" + Calculate the normalized vector potential :math:`a_0` from the intensity :math:`I` + and the wavelength :math:`\lambda`. + + The normalized vector potential is also known as a dimensionless oscillation amplitude, + quiver velocity, or normalized quiver momentum of an electron. + + The normalized vector potential of a laser + is calculated using: + + .. math:: + a_0= \frac{e E_0}{m_e \omega c}=\frac{e \lambda}{m_e \pi} \sqrt{\frac{I} {2 \epsilon_0 c^5}}, + + where :math:`e` is the fudamental charge, + :math:`E_0` is the electric field amplitude, + :math:`m_e` is the mass of an electron, + :math:`\omega` is the angular frequency of the electromagnetic wave, + :math:`c` is the speed of light, + :math:`\lambda` is the wavelength, + :math:`I` is the intensity of the elecromagnetic wave, and + :math:`\epsilon_0` is the permitivity of free space. + + **Aliases:** `a0_` + + Parameters + ---------- + intensity : `~astropy.units.Quantity` + Intensity of the laser pulse (convertible to W / m\ :sup:`2`). + + wavelength : `~astropy.units.Quantity` + Wavelength of the laser (convertible to m). + + Returns + ------- + a_0 : float | numpy.ndarray + The normalized vector potential of a plasma given the intensity and wavelength of + a laser. + + Notes + ----- + For details, see :cite:t:`gibbon:2016`\ . + + Examples + -------- + >>> import astropy.units as u + >>> normalized_vector_potential(1e18 * u.watt / u.cm**2, 1 * u.um) + np.float64(0.8549297...) + """ + + a0 = (e * wavelength * np.sqrt(intensity / (2 * eps0 * c**5))) / (m_e * np.pi) + return a0.to(u.dimensionless_unscaled).value # type: ignore[no-any-return] + + +a0_ = normalized_vector_potential +"""Alias to `~plasmapy.formulary.laser.normalized_vector_potential`.""" + + +@validate_quantities( + intensity={"can_be_negative": False}, + beam_waist_radius={"can_be_negative": False}, +) +def Gaussian_power( + intensity: u.Quantity[u.watt / u.m**2], + beam_waist_radius: u.Quantity[u.m], +) -> u.Quantity[u.Watt]: + r""" + Calculate the total power of a Gaussian beam :math:`P_0` from the intensity :math:`I` + and the beam waist radius :math:`w_0`. + + The total power of a Gaussian beam + is calculated using: + + .. math:: + P_0=\frac{1}{2}I_0 \pi w_0^2, + + where :math:`w_0` is the beam waist radius and + :math:`I_0` is the intensity of the beam. + + Parameters + ---------- + intensity : `~astropy.units.Quantity` + Intensity of the laser pulse (convertible to W / m\ :sup:`2`). + beam_waist_radius : `~astropy.units.Quantity` + Beam waist of the laser pulse (convertible to m). + + Returns + ------- + P_0 : `~astropy.units.Quantity` + The total power of the Gaussian beam for the given intensity + and spot size. + + Notes + ----- + For details, see :wikipedia:`Gaussian beam`\ . + + Examples + -------- + >>> import astropy.units as u + >>> Gaussian_power(1e18 * u.watt / u.cm**2, 1 * u.um) # Total beam power + + """ + + return (1 / 2) * intensity * np.pi * beam_waist_radius**2 + + +@validate_quantities( + spot_size_FWHM={"can_be_negative": False}, +) +def Gaussian_beam_waist_radius(spot_size_FWHM: u.Quantity[u.m]) -> u.Quantity[u.m]: + r""" + Calculate the beam waist radius :math:`w_0` for the intensity profile + of a Gaussian beam given the Full Width at Half Maximum spot size :math:`FWHM`. + + At focus, :math:`w_0` is the transverse distance from the center of the beam + to where the intensity drops by a factor of :math:`1/e^2`. + + The beam waist radius of a Gaussian beam + is calculated using: + + .. math:: + w_0=\frac{FWHM}{\sqrt{2 \ln {2}}}, + + where :math:`FWHM` is the full width at half maximum spot size of the beam. + + **Aliases:** `w0_` + + Parameters + ---------- + spot_size_FWHM : `~astropy.units.Quantity` + Full Width at Half Maximum spot size of the Gaussian beam (convertible to m). + + Returns + ------- + w_0 : `~astropy.units.Quantity` + The beam waist radius of the Gaussian beam for the given FWHM spot size. + + See Also + -------- + Gaussian_spot_size_FWHM + + Notes + ----- + For details, see :wikipedia:`Gaussian beam`\ . + + Examples + -------- + >>> import astropy.units as u + >>> Gaussian_beam_waist_radius(8.242 * u.um) + + """ + return spot_size_FWHM / np.sqrt(2 * np.log(2)) + + +w0_ = Gaussian_beam_waist_radius +"""Alias to `~plasmapy.formulary.laser.Gaussian_beam_waist_radius`.""" + + +@validate_quantities( + beam_waist_radius={"can_be_negative": False}, +) +def Gaussian_spot_size_FWHM(beam_waist_radius: u.Quantity[u.m]) -> u.Quantity[u.m]: + r""" + Calculate the Full Width at Half Maximum spot size :math:`FWHM` at focus given the + beam waist radius of a Gaussian beam :math:`w_0`. + + The FWHM spot size of a Gaussian beam + is calculated using: + + .. math:: + FWHM = w_0 \sqrt{2 \ln {2}}, + + where :math:`w_0` is the beam waist radius of the beam. + + Parameters + ---------- + beam_waist_radius : `~astropy.units.Quantity` + beam waist radius of the Gaussian beam (convertible to nm). + + Returns + ------- + FWHM : `~astropy.units.Quantity` + The FWHM spot size of the Gaussian beam for the given beam waist. + + See Also + -------- + Gaussian_beam_waist_radius + + Notes + ----- + For details, see :wikipedia:`Gaussian beam`\ . + + Examples + -------- + >>> import astropy.units as u + >>> Gaussian_spot_size_FWHM(7 * u.um) + + """ + return beam_waist_radius * np.sqrt(2 * np.log(2)) + + +# use kwargs +@validate_quantities( + wavelength={"can_be_negative": False}, + beam_waist_radius={"can_be_negative": False}, +) +def Gaussian_Rayleigh_length( + wavelength: u.Quantity[u.m], + beam_waist_radius: u.Quantity[u.m], +) -> u.Quantity[u.m]: + r""" + Calculate the Rayleigh length :math:`z_R` from the beam waist radius :math:`w_0` + and the wavelength :math:`\lambda`. + + The Rayleigh length of a Gaussian beam + is calculated using: + + .. math:: + z_R=\frac{\pi w_0 ^2}{\lambda}, + + where :math:`w_0` is the beam waist and + :math:`\lambda` is the wavelength of the beam. + + Parameters + ---------- + wavelength : `~astropy.units.Quantity` + Wavelength of the laser pulse (convertible to m). + beam_waist_radius : `~astropy.units.Quantity` + Beam waist of the laser pulse (convertible to m). + + Returns + ------- + z_R : `~astropy.units.Quantity` + The Rayleigh length of the Gaussian beam for the given wavelength + and beam waist. + + See Also + -------- + Gaussian_beam_waist_radius + Gaussian_spot_size_FWHM + + Notes + ----- + For details, see :wikipedia:`Rayleigh length`. + + Examples + -------- + >>> import astropy.units as u + >>> Gaussian_Rayleigh_length(800 * u.nm, 1 * u.um) + + """ + + return (np.pi * beam_waist_radius**2) / wavelength diff --git a/src/plasmapy/formulary/relativity.py b/src/plasmapy/formulary/relativity.py index ca82656871..f47eaae7d6 100644 --- a/src/plasmapy/formulary/relativity.py +++ b/src/plasmapy/formulary/relativity.py @@ -533,3 +533,6 @@ def __eq__(self, other) -> bool: if self_value != other_value: return False return True + + def __hash__(self) -> int: + return hash(repr(self)) diff --git a/src/plasmapy/particles/_factory.py b/src/plasmapy/particles/_factory.py index d09609db40..14ab01fb44 100644 --- a/src/plasmapy/particles/_factory.py +++ b/src/plasmapy/particles/_factory.py @@ -205,6 +205,9 @@ def _physical_particle_factory( return constructor(*args, **kwargs) # type: ignore[return-value] if args and not isinstance(args[0], str | Integral | u.Quantity): - raise TypeError("Invalid type for particle.") + raise TypeError( + f"{args[0]!r} is of type {type(args[0]).__name__}, which is not a " + f"valid particle type." + ) raise InvalidParticleError(_generate_particle_factory_error_message(args, kwargs)) diff --git a/src/plasmapy/particles/_parsing.py b/src/plasmapy/particles/_parsing.py index 896a92c3f0..a479eee669 100644 --- a/src/plasmapy/particles/_parsing.py +++ b/src/plasmapy/particles/_parsing.py @@ -380,6 +380,9 @@ def reconstruct_ion_symbol( return ion + if isinstance(argument, np.integer): # see issue 3044 + argument = int(argument) + if not isinstance(argument, str | int): raise TypeError(f"The argument {argument} is not an integer or string.") diff --git a/src/plasmapy/particles/ionization_state.py b/src/plasmapy/particles/ionization_state.py index ff58214245..b31f9e92e3 100644 --- a/src/plasmapy/particles/ionization_state.py +++ b/src/plasmapy/particles/ionization_state.py @@ -101,6 +101,9 @@ def __repr__(self) -> str: f"IonicLevel({self.ionic_symbol!r}, ionic_fraction={self.ionic_fraction})" ) + def __hash__(self) -> int: + return hash(repr(self)) + @property def ionic_symbol(self) -> str: """The symbol of the ion.""" @@ -698,7 +701,7 @@ def charge_numbers(self) -> np.ndarray: @property def Z_mean(self) -> np.float64: """Return the mean charge number.""" - if np.nan in self.ionic_fractions: + if np.nan in self.ionic_fractions: # noqa: PLW0177 raise ChargeError( "Z_mean cannot be found because no ionic fraction " f"information is available for {self.base_particle}." @@ -914,3 +917,6 @@ def summarize( for line in output: print(line) # noqa: T201 + + def __hash__(self) -> int: + return hash(repr(self)) diff --git a/src/plasmapy/particles/ionization_state_collection.py b/src/plasmapy/particles/ionization_state_collection.py index 531b071b2e..16e6e20efe 100644 --- a/src/plasmapy/particles/ionization_state_collection.py +++ b/src/plasmapy/particles/ionization_state_collection.py @@ -29,7 +29,7 @@ def _atomic_number_and_mass_number(p: ParticleLike): return p.atomic_number, p.mass_number if p.isotope else 0 -class IonizationStateCollection: +class IonizationStateCollection: # noqa: PLW1641 """ Describe the ionization state distributions of multiple elements or isotopes. diff --git a/src/plasmapy/particles/particle_class.py b/src/plasmapy/particles/particle_class.py index ed2b9c977f..cffaf8ac25 100644 --- a/src/plasmapy/particles/particle_class.py +++ b/src/plasmapy/particles/particle_class.py @@ -2,7 +2,7 @@ from __future__ import annotations -from typing import Any, Literal +from typing import Any, Literal, Self __all__ = [ "AbstractParticle", @@ -223,7 +223,9 @@ class AbstractPhysicalParticle(AbstractParticle): @property def _as_particle_list(self) -> ParticleList: # Avoid circular imports by importing here - from plasmapy.particles.particle_collections import ParticleList + from plasmapy.particles.particle_collections import ( # noqa: PLC0415 + ParticleList, + ) return ParticleList([self]) @@ -379,7 +381,7 @@ def become_set(arg: str | set | Sequence) -> set[str]: return require <= self.categories - def __add__(self, other: str | Particle | ParticleList) -> ParticleList: + def __add__(self, other: str | Self | ParticleList) -> ParticleList: return self._as_particle_list + other def __radd__(self, other: str) -> ParticleList: @@ -966,7 +968,7 @@ def __hash__(self) -> int: """ return hash(self.__repr__()) - def __invert__(self) -> Particle: + def __invert__(self) -> Self: """ Return the corresponding antiparticle, or raise an `~plasmapy.particles.exceptions.ParticleError` if the particle @@ -1023,7 +1025,7 @@ def symbol(self) -> str: return self._attributes["symbol"] @property - def antiparticle(self) -> Particle: + def antiparticle(self) -> Self: """ The antiparticle corresponding to the particle. @@ -1083,7 +1085,7 @@ def isotope(self) -> str | None: return self._attributes["isotope"] @property - def nucleus(self) -> Particle: + def nucleus(self) -> Self: """ Return the nucleus of an atom. @@ -1592,7 +1594,7 @@ def isotopic_abundance(self) -> float: >>> D.isotopic_abundance 0.000115 """ - from plasmapy.particles.atomic import common_isotopes + from plasmapy.particles.atomic import common_isotopes # noqa: PLC0415 if not self.isotope or self.is_ion: raise InvalidIsotopeError(_category_errmsg(self.symbol, "isotope")) @@ -1795,7 +1797,7 @@ def is_ion(self) -> bool: def ionize( self, n: int | Literal[np.inf] = 1, inplace: bool = False - ) -> Particle | None: + ) -> Self | None: """ Create a new |Particle| instance corresponding to the current |Particle| after being ionized ``n`` times. @@ -1886,7 +1888,7 @@ def ionize( else: return Particle(base_particle, Z=new_charge_number) - def recombine(self, n: int = 1, inplace: bool = False) -> Particle | None: + def recombine(self, n: int = 1, inplace: bool = False) -> Self | None: """ Create a new |Particle| instance corresponding to the current |Particle| after undergoing recombination ``n`` times. @@ -2130,7 +2132,7 @@ def _validate_parameter(obj: Any, can_be_negative: bool = True) -> np.float64: # TODO: Replace with validator? Use an equivalency between # coulombs and reals - if obj is None or obj is np.nan: + if obj is None or np.isnan(obj): return np.nan elif np.isinf(obj): return obj @@ -2337,7 +2339,7 @@ def _from_quantities( *quantities, symbol: str | None = None, Z: float | None = None, - ) -> CustomParticle: + ) -> Self: """ An alternate constructor for |CustomParticle| objects where the positional arguments correspond to the mass and/or charge in diff --git a/src/plasmapy/particles/particle_collections.py b/src/plasmapy/particles/particle_collections.py index a3b03662a9..2aada0f1f4 100644 --- a/src/plasmapy/particles/particle_collections.py +++ b/src/plasmapy/particles/particle_collections.py @@ -223,7 +223,7 @@ def __repr__(self) -> str: return f"ParticleList({self.symbols!r})" def __gt__(self, other): - from plasmapy.particles.nuclear import nuclear_reaction_energy + from plasmapy.particles.nuclear import nuclear_reaction_energy # noqa: PLC0415 other_as_particle_list = self._cast_other_as_particle_list(other) return nuclear_reaction_energy( diff --git a/src/plasmapy/plasma/grids.py b/src/plasmapy/plasma/grids.py index b6009f0742..29ba301ac3 100644 --- a/src/plasmapy/plasma/grids.py +++ b/src/plasmapy/plasma/grids.py @@ -667,9 +667,15 @@ def add_quantities(self, **kwargs: u.Quantity) -> None: f"does not match the grid shape {self.shape}." ) + # xarray gained better Quantity support around v2024.11.0, but + # this file was originally written with the assumption that + # xarray lacks Quantity support. As a workaround, use + # `quantity.value` instead of `quantity` in the creation of + # this DataArray. data = xr.DataArray( - quantity, dims=dims, coords=coords, attrs={"unit": quantity.unit} + quantity.value, dims=dims, coords=coords, attrs={"unit": quantity.unit} ) + self.ds[key] = data @property @@ -891,7 +897,7 @@ def vector_intersects(self, p1, p2): # This property holds the list of quantity keys currently being interpolated # It's used in the following cached properties - _interp_args: ClassVar = [] + _interp_args: ClassVar[list[str]] = [] @cached_property def _interp_quantities(self): diff --git a/src/plasmapy/simulation/particle_tracker/particle_tracker.py b/src/plasmapy/simulation/particle_tracker/particle_tracker.py index f9036c0a90..e3a6d5c976 100644 --- a/src/plasmapy/simulation/particle_tracker/particle_tracker.py +++ b/src/plasmapy/simulation/particle_tracker/particle_tracker.py @@ -855,7 +855,7 @@ def _adaptive_dt(self) -> NDArray[np.float64] | float: return dt - def _interpolate_grid(self): + def _interpolate_grid(self) -> None: # Get a list of positions (input for interpolator) pos_tracked = self.x[self._tracked_particle_mask] @@ -1075,7 +1075,7 @@ def _push(self) -> None: np.bool_ ) - def _reset_cache(self): + def _reset_cache(self) -> None: """ Reset the cached properties. diff --git a/src/plasmapy/utils/calculator/__init__.py b/src/plasmapy/utils/calculator/__init__.py index db2cdf6cce..c9ef57b1d9 100644 --- a/src/plasmapy/utils/calculator/__init__.py +++ b/src/plasmapy/utils/calculator/__init__.py @@ -1,59 +1,20 @@ """ -Script and utilities to launch the plasma calculator. -""" - -__all__ = ["main"] - -import argparse -import pathlib -import shlex -import subprocess +Subpackage formerly containing a prototype plasma calculator. -_description = """ -Plasma calculator is a tool that opens a page in a web browser for -interactive calculation of plasma parameters. +.. important:: -This tool is currently in the prototype stage and is expected to change in -the future. Please raise an issue at the following link to provide suggestions -and feedback: https://github.com/PlasmaPy/PlasmaPy/issues/new + The plasma calculator has been removed from PlasmaPy + so that it can be included in the |plasmapy-calculator| standalone + package. """ +from typing import NoReturn # coverage: ignore -def main() -> None: - """ - Stub function for command line tool that launches the plasma calculator notebook. - """ - parser = argparse.ArgumentParser(description=_description) - parser.add_argument( - "--port", type=int, default=8866, help="Port to run the notebook" - ) - parser.add_argument( - "--dark", action="store_true", help="Turn on dark mode, reduces eye strain" - ) - parser.add_argument( - "--no-browser", action="store_true", help="Do not open the browser" - ) - - module_path = pathlib.Path(__file__).parent.absolute() - notebook_path = module_path / "plasma_calculator.ipynb" - favicon_path = module_path / "favicon.ico" - - args = parser.parse_args() - theme = "dark" if args.dark else "light" - no_browser = "--no-browser" if args.no_browser else "" - command = [ - "voila", - notebook_path, - f"--port={args.port}", - f"--theme={theme}", - f"--VoilaConfiguration.file_whitelist={favicon_path}", - ] - if no_browser: - command.append(no_browser) - - try: - subprocess.call(command) # noqa: S603 - except KeyboardInterrupt: - # We'll need to switch from print() to using logging library - print("Stopping calculator! Bye") # noqa: T201 +def main() -> NoReturn: # coverage: ignore + """Plasma calculator.""" + raise RuntimeError( + "The plasma calculator has been extracted from PlasmaPy into a " + "standalone package. For more details, see: " + "https://github.com/PlasmaPy/plasmapy-calculator" + ) diff --git a/src/plasmapy/utils/calculator/favicon.ico b/src/plasmapy/utils/calculator/favicon.ico deleted file mode 100644 index 5714d36a33..0000000000 Binary files a/src/plasmapy/utils/calculator/favicon.ico and /dev/null differ diff --git a/src/plasmapy/utils/calculator/main_interface.py b/src/plasmapy/utils/calculator/main_interface.py deleted file mode 100644 index 1af97871c7..0000000000 --- a/src/plasmapy/utils/calculator/main_interface.py +++ /dev/null @@ -1,180 +0,0 @@ -""" -Collection of private functions to load properties and construct widgets. -""" - -__all__: list[str] = [] - -import json -import warnings -from pathlib import Path - -import astropy.units as u -from ipywidgets import widgets - -from plasmapy.utils.calculator.widget_helpers import ( - _calculate_button, - _CheckBox, - _clear_button, - _create_label, - _create_widget, - _FloatBox, - _FunctionInfo, - _IonBox, - _ParticleBox, - _process_queue, -) - -warnings.filterwarnings( - action="ignore", - message="Passing unrecognized arguments", - category=DeprecationWarning, -) # see issue 2370 for a deprecation warning from traitlets - -LIGHT_BLUE = "#00BFD8" -""" -LIGHT_BLUE: Constant for light blue color 00BFD8 -""" -LIGHT_GRAY = "#A9A9A9" -""" -LIGHT_GRAY: Constant for light gray color A9A9A9 -""" - -grid_data = [ - [ - _create_label("Parameter", color=LIGHT_BLUE), - _create_label("Value", color=LIGHT_BLUE), - _create_label("Unit", color=LIGHT_BLUE), - ], - [ - _create_label("B - Magnetic Field Magnitude:"), - *_create_widget( - _FloatBox, - property_name="B", - unit=u.T, - opts=[u.T, u.G, u.uG], - ), - ], - [ - _create_label("Particle:"), - _create_widget( - _ParticleBox, - property_name="particle", - property_alias="particle_type", - placeholder="Enter particle e.g. neutron,He", - ), - ], - [ - _create_label("Ion:"), - _create_widget( - _IonBox, - property_name="ion", - property_alias="ion_type", - placeholder="Enter ion e.g. He 2+", - ), - ], - [ - _create_label("Convert to Hertz:"), - _create_widget(_CheckBox, property_name="to_hz"), - ], - [ - _create_label("_" * 20, color=LIGHT_BLUE), - _create_label("Density Number"), - _create_label("_" * 20, color=LIGHT_BLUE), - ], - [ - _create_label("n - Standard Density Number:"), - *_create_widget( - _FloatBox, - property_name="n", - unit=u.m**-3, - opts=[u.m**-3, u.cm**-3, u.mm**-3], - ), - ], - [ - _create_label("ne - Electron Density Number:"), - *_create_widget( - _FloatBox, - property_name="n_e", - unit=u.m**-3, - opts=[u.m**-3, u.cm**-3, u.mm**-3], - ), - ], - [ - _create_label("ni - Ion Number Density:"), - *_create_widget( - _FloatBox, - property_name="n_i", - unit=u.m**-3, - opts=[u.m**-3, u.cm**-3, u.mm**-3], - ), - ], - [ - _create_label("_" * 20, color=LIGHT_BLUE), - _create_label("Temperature"), - _create_label("_" * 20, color=LIGHT_BLUE), - ], - [ - _create_label("T - Standard Temperature:"), - _create_widget(_FloatBox, property_name="T", min=0, unit=u.K), - _create_label("K", color=LIGHT_GRAY), - ], - [ - _create_label("Te - Electron Temperature:"), - _create_widget(_FloatBox, property_name="T_e", min=0, unit=u.K), - _create_label("K", color=LIGHT_GRAY), - ], - [ - _create_label("Ti - Ion Temperature:"), - _create_widget(_FloatBox, property_name="T_i", min=0, unit=u.K), - _create_label("K", color=LIGHT_GRAY), - ], -] -""" -grid_data: Contains widgets layout for input parameters -""" - - -def _create_interactive_layout(): - """ - Interactive grid layout for input parameters populated in grid_data. - """ - grid = widgets.GridspecLayout(18, 3) - grid.layout.margin = "10px" - - for i, row in enumerate(grid_data): - for j, cell in enumerate(row): - grid[i, j] = cell - - grid[-1, 0] = _calculate_button - grid[-1, 1] = _clear_button - return grid - - -def _create_output_layout(): - """ - Tab layout for output parameters, populated from - ``properties_metadata.json``. - """ - app = widgets.Tab() - children = [] - - properties_metadata = Path("properties_metadata.json") - - with properties_metadata.open() as f: - data = json.load(f) - - for i, title in enumerate(data): - grid_layout = widgets.GridspecLayout(10, 2, width="100%") - for j, prop in enumerate(data[title]): - fn = _FunctionInfo(prop["module_name"], prop["function_name"]) - if "spec_combo" in prop: - for spec_combo in prop["spec_combo"]: - fn.add_combo(spec_combo) - grid_layout[j, 0] = _create_label(prop["function_name"] + ":") - grid_layout[j, 1] = fn.get_output_widget() - _process_queue.append(fn) - children.append(grid_layout) - app.set_title(i, title) - app.children = children - - return app diff --git a/src/plasmapy/utils/calculator/plasma_calculator.ipynb b/src/plasmapy/utils/calculator/plasma_calculator.ipynb deleted file mode 100644 index 19f0d947e3..0000000000 --- a/src/plasmapy/utils/calculator/plasma_calculator.ipynb +++ /dev/null @@ -1,70 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Calculate plasma parameters" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "%matplotlib inline" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import plasmapy.utils.calculator.main_interface as pc" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pc._create_interactive_layout()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "pc._create_output_layout()" - ] - } - ], - "metadata": { - "interpreter": { - "hash": "a1fafe92487e6823dbe852514612f53ec74aa37737c5bc2c8ee36ad7d3fbdcd4" - }, - "kernelspec": { - "display_name": "Python 3.9.7 64-bit (windows store)", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.9.7" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/src/plasmapy/utils/calculator/properties_metadata.json b/src/plasmapy/utils/calculator/properties_metadata.json deleted file mode 100644 index 2c9c82a94e..0000000000 --- a/src/plasmapy/utils/calculator/properties_metadata.json +++ /dev/null @@ -1,77 +0,0 @@ -{ - "Speed":[ - { - "function_name":"Alfven_speed", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"thermal_speed", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"ion_sound_speed", - "module_name":"plasmapy.formulary" - } - ], - "Length":[ - { - "function_name":"inertial_length", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"gyroradius", - "module_name":"plasmapy.formulary", - "spec_combo":[ - ["B","particle","Vperp"], - ["B","particle","T"] - ] - }, - { - "function_name":"Debye_length", - "module_name":"plasmapy.formulary" - } - ], - "Frequency":[ - { - "function_name":"gyrofrequency", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"plasma_frequency", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"lower_hybrid_frequency", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"upper_hybrid_frequency", - "module_name":"plasmapy.formulary" - } - ], - "Dimensionless numbers":[ - { - "function_name":"Hall_parameter", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"Debye_number", - "module_name":"plasmapy.formulary" - } - ], - "Magnetics":[ - { - "function_name":"magnetic_pressure", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"magnetic_energy_density", - "module_name":"plasmapy.formulary" - }, - { - "function_name":"Bohm_diffusion", - "module_name":"plasmapy.formulary" - } - ] - -} diff --git a/src/plasmapy/utils/calculator/widget_helpers.py b/src/plasmapy/utils/calculator/widget_helpers.py deleted file mode 100644 index 6ee61de81c..0000000000 --- a/src/plasmapy/utils/calculator/widget_helpers.py +++ /dev/null @@ -1,684 +0,0 @@ -""" -Contains functions that create widgets and process properties for the calculator. -""" - -__all__: list[str] = [] - -import abc -import importlib -from inspect import signature - -import ipywidgets as widgets - -from plasmapy.particles import Particle - -BLACK = (0, 0, 0) -"""RGB constant for black.""" - -DARK_RED = (255, 0, 0) -"""RGB Constant for dark red.""" - -LIGHT_GREEN = (0, 128, 0) -"""RGB Constant for light green.""" - -ERROR_STYLE = "2px solid red" -"""Constant for error style.""" - -EQUAL_SPACING_CONFIG = "10px 10px 10px 10px" -"""Constant for equal spacing config among widgets.""" - -values_container = {} -"""stores the values of widget with corresponding ``property_name``.""" - -_process_queue = [] -""" -Stores the functions to be processed. This data is gathered from -``properties_metadata.json``. -""" - - -class _GenericWidget(abc.ABC): - """ - Generic widget class. - - Parameters - ---------- - property_name: `str` - Name of the property the widget is associated with. - This value is key for the values_container. - - property_alias: `str` - Alias of the property. Useful to display in validation error messages. - - values_cont: `dict` - Reference to global dictionary to store the values of the widgets. - - Raises - ------ - `NotImplementedError` - If the method `create_widget` is not implemented. - """ - - def __init__( - self, property_name: str, property_alias: str = "", values_cont=values_container - ) -> None: - self.property_name = property_name - self.property_alias = property_alias or property_name - self.widget = None - self.values_cont = values_cont - self.unit = None - self.units_dropdown = None - - def set_unit(self, unit) -> None: - """ - Set unit for the value of widget, defaults to `None`. - - Parameters - ---------- - unit: `astropy.units.Unit` - Unit to be set for the value of widget - """ - self.unit = unit - - def get_widget(self): - """ - Get current widget object reference. - - Returns - ------- - `ipywidgets.Widget` - Current widget object reference - """ - return self.widget - - def get_dropdown_widget(self): - """ - Get dropdown widget associated with current widget, defaults to `None`. - - Returns - ------- - `ipywidgets.Dropdown` - Dropdown widget associated with current widget - """ - return self.units_dropdown - - def set_place_holder(self, text: str) -> None: - """ - Set place holder text of the widget, defaults to empty string. - - Parameters - ---------- - text: `str` - Place holder text to be set - """ - self.widget.placeholder = text - - @abc.abstractmethod - def create_widget(self): - """ - Virtual method to create widget. - """ - - def post_creation(self) -> None: - """ - Default method that is called after widget creation. - Attaches change listener to the widget. - """ - self.set_place_holder("") - self.widget.observe(self.handle_change, names="value") - - def edge_case(self, value) -> None: # noqa: B027 - """ - Edge case handling for the widget. This is called within handle_change. - - Parameters - ---------- - value: `any` - Value of the widget - """ - - def edge_case_condition(self, value) -> bool: # noqa: ARG002 - """ - Edge case condition for the widget. - - Parameters - ---------- - value: `any` - Value of the widget - - Returns - ------- - `bool` - `True` if the value is an edge case, `False` otherwise - """ - return False - - def try_change_value(self, value) -> None: - """ - Set property_name in values_container to value. - - Parameters - ---------- - value: `any` - Value to be set - """ - self.values_cont[self.property_name] = value - - def display_error(self, value) -> None: # noqa: ARG002 - """ - Handle invalid input provide realtime validation. - - Parameters - ---------- - value: `any` - Value of the widget - """ - if self.widget: - self.widget.layout.border = ERROR_STYLE - self.widget.description = f"Invalid {self.property_alias}" - self.values_cont[self.property_name] = None - - def convert_to_unit(self, change): - """ - Convert the value of the widget to the unit specified by the dropdown. - - Parameters - ---------- - change: `any` - New value of the widget - - Returns - ------- - `any` - Value of the widget in the unit specified by the dropdown - """ - return change.new * self.unit if self.unit else change.new - - def attach_units_dropdown(self, options) -> None: - """ - Special method that attaches dropdown widget to the input widget, - and handles the change event of the dropdown widget. - - Parameters - ---------- - options: `list` - List of units to be displayed in the dropdown widget - """ - self.units_dropdown = widgets.Dropdown( - options=options, value=options[0], layout=widgets.Layout(width="100px") - ) - self.units_dropdown.observe(self.handle_dropdown_change, names="value") - - def handle_dropdown_change(self, change) -> None: # noqa: ARG002 - """ - Handle change event of the dropdown widget. - - Parameters - ---------- - change: `any` - New value of the dropdown widget - """ - self.set_unit(self.units_dropdown.value) - if self.property_name in self.values_cont: - self.values_cont[self.property_name] = ( - self.values_cont[self.property_name].value * self.unit - ) - - def handle_change(self, change) -> None: - """ - Handle change event of the widget, follows same process - for all widgets. - - Gets the new value with units, checks for invalid input, - edge case and updates values_container accordingly. - - Parameters - ---------- - change: `any` - New value of the widget - """ - value = self.convert_to_unit(change) - if self.edge_case_condition(value): - self.edge_case(value) - else: - try: - self.try_change_value(value) - except ValueError: - self.display_error(value) - - -class _FloatBox(_GenericWidget): - """ - Derived from _GenericWidget, a FloatBox input widget - with incremental options. - - Parameters - ---------- - property_name: `str` - Name of the property the widget is associated with. - - min: `float` - Minimum value the widget can take - - max: `float` - Maximum value the widget can take - """ - - def __init__( - self, - property_name: str, - min: float = -1e50, # noqa: A002 - max: float = 1e50, # noqa: A002 - ) -> None: - super().__init__(property_name) - self.min = min - self.max = max - - def create_widget(self, style=None) -> None: - """ - Implements create_widget. description_width is set to initial - to make the widget as wide as possible. - """ - if style is None: - style = {"description_width": "initial"} - self.widget = widgets.BoundedFloatText( - name=self.property_name, - min=self.min, - max=self.max, - value=0, - step=0.1, - style=style, - ) - self.post_creation() - - -class _CheckBox(_GenericWidget): - """ - Derived from _GenericWidget, a CheckBox input widget. - - Parameters - ---------- - property_name: `str` - Name of the property the widget is associated with. - """ - - def __init__(self, property_name: str) -> None: - super().__init__(property_name) - - def create_widget(self) -> None: - """ - Implements create_widget. - """ - self.widget = widgets.Checkbox(value=False) - self.post_creation() - - -class _ParticleBox(_GenericWidget): - """ - Derived from _GenericWidget, input widget specific for particle - name. - - Parameters - ---------- - property_name: `str` - Name of the property the widget is associated with. - - property_alias: `str` - Alias of the property the widget is associated with. - (particle_type in this case) - """ - - def __init__(self, property_name: str, property_alias=None) -> None: - super().__init__(property_name, property_alias=property_alias) - - def edge_case_condition(self, value): - """ - Edge case for particle box, checks if value is empty. - - Parameters - ---------- - value: `str` - Value of the widget - - Returns - ------- - `bool` - `True` if the value is empty, `False` otherwise - """ - return value is None or value == "" - - def edge_case(self, value) -> None: # noqa: ARG002 - """ - Edge case to handle empty value of particle box - resets the container value to `None`, and resets the error status. - """ - self.values_cont[self.property_name] = None - self.widget.description = "" - self.widget.layout.border = "" - - def try_change_value(self, value) -> None: - """ - Set property_name in values_container to value, - and resets the error status. - - Parameters - ---------- - value: `str` - Value to be set - - Raises - ------ - `~plasmapy.particles.exceptions.InvalidParticleError` - Raised when the particle input does not correspond to a valid - particle or is contradictory. - """ - particle = Particle(value) - self.values_cont[self.property_name] = particle - self.widget.layout.border = "" - self.widget.description = "" - - def create_widget(self, style=None) -> None: - """ - Implements create_widget. description_width is set to initial - to make the widget as wide as possible. - """ - if style is None: - style = {"description_width": "initial"} - self.widget = widgets.Text(style=style) - self.post_creation() - - -class _IonBox(_ParticleBox): - """ - Derived from _ParticleBox, input widget specific for ion. - - Parameters - ---------- - property_name: `str` - Name of the property the widget is associated with. - - property_alias: `str` - Alias of the property the widget is associated with. - """ - - def __init__(self, property_name: str, property_alias=None) -> None: - super().__init__(property_name, property_alias=property_alias) - - def try_change_value(self, value): - """ - Set property_name in values_container to value on validating input. - - Parameters - ---------- - value: `str` - Value to be set - - Raises - ------ - `~plasmapy.particles.exceptions.InvalidParticleError` - Raised when the particle input does not correspond to a valid - particle or is contradictory. - `ValueError` - Raised when the input is not a valid ion - """ - ion = Particle(value) - if not ion.is_ion: - raise ValueError(f"{ion} is not an ion") - - self.values_cont[self.property_name] = ion - self.widget.layout.border = "" - self.widget.description = "" - - -class _FunctionInfo: - """ - Class to store information about a function. Gets the function's parameters, - and uses to process input based on function signature. - - Parameters - ---------- - module_name: `str` - Name of the module the function is in - - function_name: `str` - Name of the function - - values_container: `dict` - Reference to global dictionary of values to be passed to the function - """ - - def __init__( - self, module_name: str, function_name: str, values_cont=values_container - ) -> None: - self.module = module_name - self.fname = function_name - self.fattr = getattr(importlib.import_module(module_name), function_name) - self.values_cont = values_cont - self.spec_combo = None - self.sig = list(signature(self.fattr).parameters.keys()) - self.output_widget = widgets.Output() - self.output_widget.layout.margin = EQUAL_SPACING_CONFIG - self.output_widget.layout.padding = EQUAL_SPACING_CONFIG - - def add_combo(self, spec_combo) -> None: - """ - Specify selective combination of parameters to be used in the function, - This is the case for few functions where having all parameters doesn't yield - output. - - Parameters - ---------- - spec_combo: `list` - List of parameters to be used in the function - - Examples - -------- - For `plasmapy.formulary.gyroradius` the specific combos are as follows: - :py:`["B","particle","Vperp"]` and :py:`["B","particle","T"]` - """ - if not self.spec_combo: - self.spec_combo = [] - self.spec_combo.append(spec_combo) - - def get_output_widget(self): - """ - Returns the output widget of the function. - - Returns - ------- - `~ipywidgets.widgets.Output` - Output widget of the function - """ - return self.output_widget - - def produce_arg(self, spec): - """ - Prepares a dictionary of arguments that is present in both values_container, - and in spec. - - Parameters - ---------- - spec: `list` - List of parameters to be used in the function - - Returns - ------- - `dict` - Dictionary of arguments that is available - """ - return { - arg: self.values_cont[arg] - for arg in spec - if arg in self.values_cont and self.values_cont[arg] is not None - } - - def error_message(self, spec) -> None: - """ - Generates an error message for the function when parameters are missing. - - Parameters - ---------- - spec: `list` - List of parameters to be used in the function - """ - # We'll need to switch from print() to using logging library - - print(_colored_text(BLACK, "["), end="") # noqa: T201 - - for arg in spec: - if arg in self.values_cont and self.values_cont[arg] is not None: - print( # noqa: T201 - _colored_text(LIGHT_GREEN, f"{arg}:present,"), - end="", - ) - else: - print( # noqa: T201 - _colored_text(DARK_RED, f"{arg}:missing,"), - end="", - ) - - print(_colored_text(BLACK, "]")) # noqa: T201 - - def process(self) -> None: - """ - Processes the function based on signatures and spec_combo provided. - Spec_combo is prioritized over the function signature. - """ - self.output_widget.clear_output() - args_dict = {} - if self.spec_combo: - for spec in self.spec_combo: - args_dict = self.produce_arg(spec) - - if len(args_dict) == len(spec): - break - else: - args_dict = self.produce_arg(self.sig) - with self.output_widget: - try: - self.output_widget.layout.border = "0px" - - # We'll need to switch from print() to using logging library - - print(f" : {self.fattr(**args_dict)}") # noqa: T201 - - except Exception as e: # noqa: BLE001 - self.output_widget.layout.border = ERROR_STYLE - print(e) # noqa: T201 - print( # noqa: T201 - " : could not be computed one or more parameter is missing - check below for missing parameters" - ) - if self.spec_combo: - for spec in self.spec_combo: - self.error_message(spec) - else: - self.error_message(self.sig) - - -def _create_label(label: str, color: str = "black"): - """ - Creates a label widget with the given text and color. - - Parameters - ---------- - label: `str` - Text of the label - - color: `str` - Color of the label, defaults to black - """ - # This is done so voila switches colors according to theme - color_param = f"color:{color}" if color != "black" else "" - return widgets.HTML(f"

{label}

") - - -def _handle_button_click(event) -> None: - """ - Handles the click event of the calculate properties button. - """ - for fn in _process_queue: - fn.process() - - -def _handle_clear_click(event) -> None: - """ - Handles the click event of the clear properties button. - Clears output of all functions. - """ - for fn in _process_queue: - fn.output_widget.clear_output() - - -def _colored_text(color, text: str) -> str: - """ - Prepares an inline string with the given color. - - Parameters - ---------- - color: `list` - RGB color of the text - - text: `str` - Text to be colored - - Returns - ------- - `str` - Colored text - """ - return f"\033[38;2;{color[0]};{color[1]};{color[2]}m{text} \033[38;2;255;255;255m" - - -_calculate_button = widgets.Button( - description="Calculate Properties", button_style="info" -) -_calculate_button.on_click(_handle_button_click) - -_clear_button = widgets.Button(description="Clear Output", button_style="danger") -_clear_button.on_click(_handle_clear_click) - - -def _create_widget(widget_type, **kwargs): - """ - Creates a widget of the given type with the given parameters. - Widget can be with/without units dropdown. - - Parameters - ---------- - widget_type: `any` - Type of the widget to be created. - - **kwargs: `dict` - Parameters specific to the widget. - - Returns - ------- - |Widget| or [|Widget|, |Widget|] - widget or [widget, units_dropdown] - - .. |Widget| replace:: `~ipywidgets.widgets.Widget` - """ - unit = None - placeholder = None - opts = None - if "unit" in kwargs: - unit = kwargs["unit"] - kwargs.pop("unit") - if "placeholder" in kwargs: - placeholder = kwargs["placeholder"] - kwargs.pop("placeholder") - if "opts" in kwargs: - opts = kwargs["opts"] - kwargs.pop("opts") - widget_element = widget_type(**kwargs) - widget_element.create_widget() - if unit: - widget_element.set_unit(unit) - if placeholder: - widget_element.set_place_holder(placeholder) - - if opts: - widget_element.attach_units_dropdown(opts) - return [widget_element.get_widget(), widget_element.get_dropdown_widget()] - - return widget_element.get_widget() diff --git a/src/plasmapy/utils/decorators/validators.py b/src/plasmapy/utils/decorators/validators.py index d263abc704..341d6ba395 100644 --- a/src/plasmapy/utils/decorators/validators.py +++ b/src/plasmapy/utils/decorators/validators.py @@ -500,7 +500,8 @@ def foo(x: u.Quantity[u.m], time: u.Quantity[u.s]) -> u.Quantity[u.m / u.s]: Allow `None` values to pass:: @validate_quantities( - arg2={"none_shall_pass": True}, validations_on_return=[u.cm, None] + arg2={"none_shall_pass": True}, + validations_on_return=[u.cm, None], ) def foo(arg1: u.cm, arg2: u.cm = None): return None diff --git a/tests/analysis/swept_langmuir/conftest.py b/tests/analysis/swept_langmuir/conftest.py new file mode 100644 index 0000000000..4857bd0ff0 --- /dev/null +++ b/tests/analysis/swept_langmuir/conftest.py @@ -0,0 +1,95 @@ +""" +pytest fixtures for all swept_langmuir tests. +""" + +from pathlib import Path + +import numpy as np +import pytest + +from plasmapy.analysis.swept_langmuir import sort_sweep_arrays + +PACE_DATA_FILE = (Path(__file__).parent / "Pace2015.npy").resolve() +PACE_DATA = sort_sweep_arrays(*np.load(PACE_DATA_FILE)) + + +@pytest.fixture(scope="module") +def simple_voltage(): + return np.linspace(-20.0, 20.0, 200) + + +@pytest.fixture(scope="module") +def simple_current(simple_voltage): + return simple_voltage.copy() + + +def arch_current(voltage, *, radius, centroid, positive_arch=True): + # radius: float + # radius of the arch/circle to be generated + # + # centroid: 2 element array + # center (x, y) location of the circle + # + # positive_arch: bool + # if True draw the positive (upper) arch + # if False draw the negative (lower) arch + # + + sign = 1.0 if positive_arch else -1.0 + return sign * np.sqrt(radius**2 - (voltage - centroid[0]) ** 2) + centroid[1] + + +@pytest.fixture(scope="module") +def simple_current_two_arches(simple_voltage): + voltage = simple_voltage + current = np.full_like(voltage, np.nan) + + # inflection_point = location where the two arches transition from + # one to the other + # slope_angle = angle of the slope line at the two arch inflection + # point + # bisect_line_angle = the angle of the line that bisects the + # centroids of the two arch circles + # + inflection_point = np.array([0.0, 0.0]) + slope_angle = np.deg2rad(65.0) + bisect_line_angle = slope_angle - np.deg2rad(90) + + centroid_1 = np.array([1.1 * np.min(voltage), np.nan]) + centroid_2 = np.array([1.1 * np.max(voltage), np.nan]) + + radius_1 = np.abs(centroid_1[0]) / np.cos(bisect_line_angle) + radius_2 = np.abs(centroid_2[0]) / np.cos(bisect_line_angle) + + centroid_1[1] = -radius_1 * np.sin(bisect_line_angle) + inflection_point[1] + centroid_2[1] = radius_2 * np.sin(bisect_line_angle) + inflection_point[1] + + # generate first (left) arch + mask = voltage <= 0 + current[mask] = arch_current( + voltage[mask], + centroid=centroid_1, + radius=radius_1, + positive_arch=False, + ) + + # generate second (right) arch + mask = voltage > 0 + current[mask] = arch_current( + voltage[mask], + centroid=centroid_2, + radius=radius_2, + positive_arch=True, + ) + + return current + + +@pytest.fixture(scope="module") +def pace_voltage(): + return PACE_DATA[0] + + +@pytest.fixture(scope="module") +def pace_current(): + return PACE_DATA[1] diff --git a/tests/analysis/swept_langmuir/test_floating_potential.py b/tests/analysis/swept_langmuir/test_floating_potential.py index b330ebb8f3..e07ce67658 100644 --- a/tests/analysis/swept_langmuir/test_floating_potential.py +++ b/tests/analysis/swept_langmuir/test_floating_potential.py @@ -212,7 +212,8 @@ def test_warnings(self, kwargs, expected, _warning) -> None: """Test scenarios that issue warnings.""" with pytest.warns(_warning): vf, extras = find_floating_potential(**kwargs) - assert isinstance(extras, VFExtras) + + assert isinstance(extras, VFExtras) for key, val in expected.items(): rtn_val = vf if key == "vf" else getattr(extras, key) diff --git a/tests/analysis/swept_langmuir/test_helpers__condition_voltage_window.py b/tests/analysis/swept_langmuir/test_helpers__condition_voltage_window.py new file mode 100644 index 0000000000..d99cd8f5e0 --- /dev/null +++ b/tests/analysis/swept_langmuir/test_helpers__condition_voltage_window.py @@ -0,0 +1,59 @@ +""" +Tests for +`plasmapy.analysis.swept_langmuir.helpers._condition_voltage_window`. +""" + +import numpy as np +import pytest + +from plasmapy.analysis.swept_langmuir.helpers import _condition_voltage_window + + +class TestConditionVoltageWindow: + @pytest.mark.parametrize( + ("_raises", "voltage", "voltage_window"), + [ + # voltage_window is not a list-like or None + (pytest.raises(TypeError), np.arange(10.0), {"one": 1, "two": 2}), + (pytest.raises(TypeError), np.arange(10.0), "invalid window"), + (pytest.raises(TypeError), np.arange(10.0), 5.0), + # voltage_window is wrong size + (pytest.raises(ValueError), np.arange(10.0), []), + (pytest.raises(ValueError), np.arange(10.0), [5.0]), + (pytest.raises(ValueError), np.arange(10.0), (-1.0, 2.0, 5.0)), + # voltage_window does not have Real numbers or None + (pytest.raises(TypeError), np.arange(10.0), ["one", 2]), + (pytest.raises(TypeError), np.arange(10.0), ["one", "two"]), + (pytest.raises(TypeError), np.arange(10.0), [(1.0, 2.0), 2.0]), + # voltage_window is out of range + (pytest.raises(ValueError), np.arange(10.0), [-5, -2]), + (pytest.raises(ValueError), np.arange(10.0), [11, 18]), + ], + ) + def test_raises(self, _raises, voltage, voltage_window): + with _raises: + _condition_voltage_window(voltage, voltage_window) + + @pytest.mark.parametrize( + ("voltage", "voltage_window", "expected"), + [ + # voltage_window as list and numpy array + (np.arange(10), [3.3, 4.5], slice(4, 5, 1)), + (np.arange(10), np.array([3.3, 4.5]), slice(4, 5, 1)), + (np.arange(10), [3.3, 7.2], slice(4, 8, 1)), + (np.arange(10), np.array([3.3, 7.2]), slice(4, 8, 1)), + # voltage_window has None values + (np.arange(10), None, slice(None, None, 1)), + (np.arange(10), [None, None], slice(None, None, 1)), + (np.arange(10), [3.3, None], slice(4, None, 1)), + (np.arange(10), [None, 7.2], slice(None, 8, 1)), + # voltage_window is unsorted + (np.arange(10), [7.2, 3.3], slice(4, 8, 1)), + # voltage_window has one index out of bounds + (np.arange(10), [-5, 7.2], slice(None, 8, 1)), + (np.arange(10), [3.3, 20], slice(4, None, 1)), + ], + ) + def test_expected(self, voltage, voltage_window, expected): + result = _condition_voltage_window(voltage, voltage_window) + assert result == expected diff --git a/tests/analysis/swept_langmuir/test_helpers__merge_voltage_clusters.py b/tests/analysis/swept_langmuir/test_helpers__merge_voltage_clusters.py new file mode 100644 index 0000000000..2df5df136f --- /dev/null +++ b/tests/analysis/swept_langmuir/test_helpers__merge_voltage_clusters.py @@ -0,0 +1,197 @@ +""" +Tests for helper function `merge_voltage_clusters` contained in +`plasmapy.analysis.swept_langmuir.helpers`. +""" + +from contextlib import nullcontext as does_not_raise +from unittest import mock + +import numpy as np +import pytest + +from plasmapy.analysis.swept_langmuir.helpers import check_sweep, merge_voltage_clusters +from plasmapy.utils.exceptions import PlasmaPyWarning + + +@pytest.mark.parametrize( + ("voltage", "current", "kwargs", "with_context", "expected"), + [ + # raises + ( + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_step_size": "wrong type"}, + pytest.raises(TypeError), + None, + ), + ( # voltage array has np.nan values (hence not monotonic) + np.array([1.0, 1.2, np.nan, 2.5]), + np.array([-1, 0, np.nan, 4.3]), + {"filter_nan": False}, + pytest.raises(ValueError), + None, + ), + ( # current array has np.nan values (hence not monotonic) + np.array([1.0, 1.2, 1.8, 2.5]), + np.array([-1, 0, np.nan, 4.3]), + {"filter_nan": False}, + pytest.raises(ValueError), + None, + ), + # warnings (and values) + ( # voltage spacing is regular and not step size given + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_step_size": None}, + pytest.warns(PlasmaPyWarning), + None, # same as inputs + ), + ( # non-zero voltage_step_size < any step size + np.array([1.1, 1.5, 2, 3.8, 6.0, 6.2], dtype=float), + np.array([-5, -5.2, -2, 0, 4.2, 5], dtype=float), + {"voltage_step_size": 0.1}, + pytest.warns(PlasmaPyWarning), + None, + ), + ( + np.array([1, 1.5, 2.1, 4, 5.5, 6], dtype=float), + np.array([-5, -2, -2, 0, 5, 5], dtype=float), + {"voltage_step_size": 0.2}, + pytest.warns(PlasmaPyWarning), + None, + ), + # values + ( # no merging needed + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_step_size": 0.0}, + does_not_raise(), + None, # same as inputs + ), + ( # merge identical voltages + np.array([1, 2, 2, 4, 6, 6], dtype=float), + np.array([-5, -2, -2.1, 0, 5, 4.9], dtype=float), + {"voltage_step_size": 0.0}, + does_not_raise(), + ( + np.array([1, 2, 4, 6], dtype=float), + np.array([-5, -2.05, 0, 4.95], dtype=float), + ), + ), + ( # step size given as an integer + np.array([1, 2, 2, 4, 6, 6], dtype=float), + np.array([-5, -2, -2.1, 0, 5, 4.9], dtype=float), + {"voltage_step_size": 0}, # integer value + does_not_raise(), + ( + np.array([1, 2, 4, 6], dtype=float), + np.array([-5, -2.05, 0, 4.95], dtype=float), + ), + ), + ( # voltage_step_size is negative + np.array([1, 1.5, 1.56, 2.1, 4, 5.5, 5.52], dtype=float), + np.array([-5, -2, -2.1, 0, 5, 7, 7.1], dtype=float), + {"voltage_step_size": -0.1}, + does_not_raise(), + ( + np.array([1, 1.53, 2.1, 4, 5.51], dtype=float), + np.array([-5, -2.05, 0, 5, 7.05], dtype=float), + ), + ), + ( # voltage array starts with a cluster + np.array([1, 1.1, 1.2, 1.5, 2, 4, 5.5], dtype=float), + np.array([-5, -5.1, -4.9, -4, 0, 5, 7], dtype=float), + {"voltage_step_size": 0.1}, + does_not_raise(), + ( + np.array([1.0, 1.15, 1.5, 2, 4, 5.5], dtype=float), + np.array([-5.0, -5, -4, 0, 5, 7], dtype=float), + ), + ), + ( # voltage array starts with a cluster, spans < 2 * voltage_step_size + np.array([1, 1.1, 1.2, 1.5, 2, 4, 5.5], dtype=float), + np.array([-5, -5.1, -4.9, -4, 0, 5, 7], dtype=float), + {"voltage_step_size": 0.12}, + does_not_raise(), + ( + np.array([1.1, 1.5, 2, 4, 5.5], dtype=float), + np.array([-5.0, -4, 0, 5, 7], dtype=float), + ), + ), + ( # multiple voltage clusters, including at beginning and end + np.array( + [1, 1.01, 1.05, 1.5, 2, 3.88, 3.9, 3.92, 4.8, 5.5, 5.55], + dtype=float, + ), + np.array( + [-5, -5.1, -4.9, -4, -3, 0, 0.1, -0.1, 5, 7, 6.9], + dtype=float, + ), + {"voltage_step_size": 0.1}, + does_not_raise(), + ( + np.array([1.02, 1.5, 2, 3.9, 4.8, 5.525], dtype=float), + np.array([-5.0, -4, -3, 0, 5, 6.95], dtype=float), + ), + ), + ( # self determine voltage_step_size + np.array( + [1, 1.01, 1.05, 1.5, 2, 3.88, 3.9, 3.92, 4.8, 5.5, 5.55], + dtype=float, + ), + np.array( + [-5, -5.1, -4.9, -4, -3, 0, 0.1, -0.1, 5, 7, 6.9], + dtype=float, + ), + {"voltage_step_size": None}, + does_not_raise(), + ( + np.array([1.02, 1.5, 2, 3.9, 4.8, 5.525], dtype=float), + np.array([-5.0, -4, -3, 0, 5, 6.95], dtype=float), + ), + ), + ( # test case for auto filtering NaN values + np.array( + [1, 1.01, np.nan, 1.5, 2, 3.88, 3.9, np.nan, 4.8, 5.5, 5.55], + dtype=float, + ), + np.array( + [-5, -5.1, np.nan, -4, -3, 0, 0.1, np.nan, np.nan, 7, 6.9], + dtype=float, + ), + {"filter_nan": True, "voltage_step_size": 0.12}, + does_not_raise(), + ( + np.array([1.005, 1.5, 2, 3.89, 5.525], dtype=float), + np.array([-5.05, -4, -3, 0.05, 6.95], dtype=float), + ), + ), + ], +) +def test_merge_voltage_clusters( + voltage, current, kwargs, with_context, expected +) -> None: + with ( + with_context, + mock.patch( + "plasmapy.analysis.swept_langmuir.helpers.check_sweep", + wraps=check_sweep, + ) as mock_sweep, + ): + rtn_voltage, rtn_current = merge_voltage_clusters( + voltage=voltage, + current=current, + **kwargs, + ) + + if expected is not None: + assert np.allclose(rtn_voltage, expected[0]) + assert np.allclose(rtn_current, expected[1]) + else: + assert np.allclose(rtn_voltage, voltage) + assert np.allclose(rtn_current, current) + + # ensure check_sweep() is called...then we do not have to + # explicitly add test cases covered by check_sweep() + assert 0 < mock_sweep.call_count <= 2 + mock_sweep.reset_mock() diff --git a/tests/analysis/swept_langmuir/test_plasma_potential__condition_smooth_fractions.py b/tests/analysis/swept_langmuir/test_plasma_potential__condition_smooth_fractions.py new file mode 100644 index 0000000000..e1ddd3ecd4 --- /dev/null +++ b/tests/analysis/swept_langmuir/test_plasma_potential__condition_smooth_fractions.py @@ -0,0 +1,63 @@ +""" +Tests for +`plasmapy.analysis.swept_langmuir.plasma_potential._condition_smooth_fractions`. +""" + +import numpy as np +import pytest + +from plasmapy.analysis.swept_langmuir.plasma_potential import ( + _condition_smooth_fractions, +) + + +class TestConditionSmoothFractions: + @pytest.mark.parametrize( + ("_raises", "smooth_fractions", "data_size"), + [ + # smooth_fractions is not a list-like or None + (pytest.raises(TypeError), {"one": 1, "two": 2}, 10), + (pytest.raises(TypeError), "invalid fraction", 10), + (pytest.raises(TypeError), 5.0, 10), + # smooth_fractions is not 1D + (pytest.raises(ValueError), [[1, 2], [1, 2]], 10), + (pytest.raises(ValueError), np.zeros((2, 5)), 10), + # smooth_fractions elements are NOT floats + (pytest.raises(ValueError), [1, 2, 3], 10), + (pytest.raises(ValueError), ["one", 2.0, "three"], 10), + # smooth_fractions is out of range.. [0, 1] + (pytest.raises(ValueError), [-5.0], 10), + (pytest.raises(ValueError), [5.0], 10), + (pytest.raises(ValueError), [-0.5, 0.1, 0.9, 1.0], 10), + (pytest.raises(ValueError), [-0.5, 0, 0.9, 1.0], 10), + (pytest.raises(ValueError), [0.1, 0.9, 1.1], 10), + (pytest.raises(ValueError), [0.1, 0.9, 20.0], 10), + (pytest.raises(ValueError), [0, 0.1, 0.9, 1.1], 10), + (pytest.raises(ValueError), [-20.0, 0, 0.1, 0.9, 1.1], 10), + # data_size not integer + (pytest.raises(TypeError), [0.2, 0.5, 0.8], "hello"), + (pytest.raises(TypeError), [0.2, 0.5, 0.8], 90.5), + # data_size not positive, non-zero integer + (pytest.raises(ValueError), [0.2, 0.5, 0.8], 0), + (pytest.raises(ValueError), [0.2, 0.5, 0.8], -20), + # # computed savgol_windows is null + (pytest.raises(ValueError), [0.2, 0.5, 0.8], 1), + (pytest.raises(ValueError), [0.02], 20), + ], + ) + def test_raises(self, _raises, smooth_fractions, data_size): + with _raises: + _condition_smooth_fractions(smooth_fractions, data_size) + + @pytest.mark.parametrize( + ("smooth_fractions", "data_size", "expected"), + [ + ([0.2, 0.5, 0.8], 20, np.array([4, 10, 16], dtype=int)), + ([0.02, 0.2, 0.5, 0.8], 20, np.array([4, 10, 16], dtype=int)), + ([0.0, 0.02, 0.2, 0.5, 0.8], 20, np.array([0, 4, 10, 16], dtype=int)), + (None, 50, np.array([3, 4, 5, 6, 7, 8, 9, 10, 11, 12], dtype=int)), + ], + ) + def test_expected(self, smooth_fractions, data_size, expected): + result = _condition_smooth_fractions(smooth_fractions, data_size) + assert np.array_equal(result, expected) diff --git a/tests/analysis/swept_langmuir/test_plasma_potential__find_didv_peak_location.py b/tests/analysis/swept_langmuir/test_plasma_potential__find_didv_peak_location.py new file mode 100644 index 0000000000..4792788043 --- /dev/null +++ b/tests/analysis/swept_langmuir/test_plasma_potential__find_didv_peak_location.py @@ -0,0 +1,310 @@ +""" +Tests for functionality contained in +`plasmapy.analysis.swept_langmuir.plasma_potential` that calculates the +peak slope of the langmuir drives (i.e. peak dI/dV). +""" + +import operator +from unittest import mock + +import numpy as np +import pytest + +from plasmapy.analysis import swept_langmuir as sla +from plasmapy.analysis.swept_langmuir.plasma_potential import ( + dIdVExtras, + find_didv_peak_location, +) + + +@pytest.mark.parametrize( + ("assert_op", "arg1", "expected"), + [ + (issubclass, dIdVExtras, tuple), + (hasattr, dIdVExtras, "_fields"), + (hasattr, dIdVExtras, "_field_defaults"), + ( + operator.eq, + set(dIdVExtras._fields), + {"std", "data_slice", "savgol_windows", "savgol_peaks"}, + ), + (operator.eq, dIdVExtras._field_defaults, {}), + ], +) +def test_didv_namedtuple(assert_op, arg1, expected): + assert assert_op(arg1, expected) + + +@pytest.mark.parametrize( + ("index", "field_name"), + [(0, "std"), (1, "data_slice"), (2, "savgol_windows"), (3, "savgol_peaks")], +) +def test_didv_namedtuple_index_field_mapping(index, field_name): + extras = dIdVExtras( + std=0.1, + data_slice=slice(4, 20, 2), + savgol_windows=[4, 6, 8], + savgol_peaks=[1.1, 1.2, 1.3], + ) + + assert extras[index] == getattr(extras, field_name) + + +class TestFinddIdVPeakLocation: + @pytest.mark.parametrize( + ("helper", "used_callable"), + [ + ( + sla.helpers._condition_voltage_window, + sla.plasma_potential._condition_voltage_window, + ), + (sla.helpers.check_sweep, sla.plasma_potential.check_sweep), + ( + sla.helpers.merge_voltage_clusters, + sla.plasma_potential.merge_voltage_clusters, + ), + ], + ) + def test_helper_callable_consistency(self, helper, used_callable): + assert helper is used_callable + + def test_call_of_check_sweep(self, simple_voltage, simple_current) -> None: + with mock.patch(f"{sla.plasma_potential.__name__}.check_sweep") as mock_cs: + mock_cs.return_value = simple_voltage, simple_current + find_didv_peak_location(voltage=simple_voltage, current=simple_current) + + assert mock_cs.call_count == 1 + + # passed args + assert len(mock_cs.call_args[0]) == 2 + assert np.array_equal(mock_cs.call_args[0][0], simple_voltage) + assert np.array_equal(mock_cs.call_args[0][1], simple_current) + + # passed kwargs + assert mock_cs.call_args[1] == {"strip_units": True} + + def test_call_of_merge_voltage_clusters( + self, simple_voltage, simple_current + ) -> None: + with mock.patch( + f"{sla.plasma_potential.__name__}.merge_voltage_clusters" + ) as mock_mvc: + mock_mvc.return_value = simple_voltage, simple_current + find_didv_peak_location(voltage=simple_voltage, current=simple_current) + + assert mock_mvc.call_count == 1 + + # passed args + assert len(mock_mvc.call_args[0]) == 2 + assert np.array_equal(mock_mvc.call_args[0][0], simple_voltage) + assert np.array_equal(mock_mvc.call_args[0][1], simple_current) + + # passed kwargs + assert mock_mvc.call_args[1] == {"voltage_step_size": 0} + + def test_call_of_condition_voltage_window( + self, simple_voltage, simple_current + ) -> None: + with mock.patch( + f"{sla.plasma_potential.__name__}._condition_voltage_window", + side_effect=sla.plasma_potential._condition_voltage_window, + ) as mock_cvw: + # mock_cvw.return_value = varr, carr + find_didv_peak_location(voltage=simple_voltage, current=simple_current) + + assert mock_cvw.call_count == 1 + + # passed args + assert len(mock_cvw.call_args[0]) == 2 + assert np.array_equal(mock_cvw.call_args[0][0], simple_voltage) + assert mock_cvw.call_args[0][1] is None # voltage_window arg + + # passed kwargs + assert mock_cvw.call_args[1] == {} + + def test_call_of_condition_smooth_fractions( + self, simple_voltage, simple_current + ) -> None: + with mock.patch( + f"{sla.plasma_potential.__name__}._condition_smooth_fractions", + side_effect=sla.plasma_potential._condition_smooth_fractions, + ) as mock_csf: + find_didv_peak_location(voltage=simple_voltage, current=simple_current) + + assert mock_csf.call_count == 1 + + # passed args + assert len(mock_csf.call_args[0]) == 2 + assert mock_csf.call_args[0][0] is None # smooth_fractions arg + assert mock_csf.call_args[0][1] == simple_voltage.size # data_size arg + + # passed kwargs + assert mock_csf.call_args[1] == {} + + @pytest.mark.usefixtures("request") + @pytest.mark.parametrize( + ("_raises", "voltage", "current", "voltage_window", "smooth_fractions"), + [ + # voltage_window is too small (<3 points) + ( + pytest.raises(ValueError), + "simple_voltage", + "simple_current", + [4, 4.5], + None, + ), + # no valid computer plasma potentials + ( + pytest.raises(RuntimeError), + "simple_voltage", + np.append( + np.append(np.linspace(0, 10.0, 50), np.linspace(0, 10.0, 100)), + np.linspace(0, 10, 50), + ), + None, + [0.0], + ), + ], + ) + def test_raises( + self, _raises, voltage, current, voltage_window, smooth_fractions, request + ): + if isinstance(voltage, str): + # assume fixture name + voltage = request.getfixturevalue(voltage) + + if isinstance(current, str): + # assume fixture name + current = request.getfixturevalue(current) + + with ( + mock.patch( + f"{sla.plasma_potential.__name__}.check_sweep", + return_value=(voltage, current), + ), + mock.patch( + f"{sla.plasma_potential.__name__}.merge_voltage_clusters", + return_value=(voltage, current), + ), + _raises, + ): + find_didv_peak_location( + voltage=voltage, + current=current, + voltage_window=voltage_window, + smooth_fractions=smooth_fractions, + ) + + @pytest.mark.usefixtures("request") + @pytest.mark.parametrize( + ("voltage", "current", "kwargs", "expected"), + [ + ( + "simple_voltage", + "simple_current_two_arches", + {"smooth_fractions": [0.0]}, # no smoothing + {"vp": 0.0}, + ), + ], + ) + def test_designed_didv(self, voltage, current, kwargs, expected, request): + if isinstance(voltage, str): + # assume fixture name + voltage = request.getfixturevalue(voltage) + + if isinstance(current, str): + # assume fixture name + current = request.getfixturevalue(current) + + vp, extras = find_didv_peak_location(voltage, current, **kwargs) + + assert isinstance(vp, float) + assert isinstance(extras, dIdVExtras) + + dv = float(np.average(np.diff(voltage))) + vp_expected = expected["vp"] + + assert -0.5 * dv < (vp - vp_expected) < 0.5 * dv + + def test_on_pace_data(self, pace_voltage, pace_current): + vp, extras = find_didv_peak_location( + pace_voltage, + pace_current, + voltage_window=[-33.814, None], + ) + + # assertions on computed plasma potential + assert isinstance(vp, float) + assert np.isclose(vp, -16.6526) + + # assertions on extras from computation + assert isinstance(extras, dIdVExtras) + assert np.isclose(extras.std, 0.348483) + assert extras.data_slice == slice(78, None, 1) + assert extras.savgol_windows == [ + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + ] + assert extras.savgol_peaks == [ + -16.4, + -17.2, + -16.8, + -17.2, + -17.2, + -16.4, + -16.4, + -16.4, + -16.0, + -16.8, + -16.8, + -16.8, + -16.8, + -16.8, + -16.8, + -16.8, + -16.4, + -16.4, + -16.0, + ] + + @pytest.mark.parametrize( + ("argmax_return", "expected"), + [ + (np.array([10, 11, 12], dtype=np.int64), -17.78894472), + (np.array([45], dtype=np.int64), -10.95477386), + (np.int64(45), -10.95477386), + ], + ) + def test_peak_index_identification( + self, argmax_return, expected, simple_voltage, simple_current + ): + with mock.patch("numpy.where") as mock_argmax: + mock_argmax.return_value = (argmax_return,) + + vp, extras = find_didv_peak_location( + simple_voltage, + simple_current, + voltage_window=None, + smooth_fractions=[0.1], + ) + + assert np.isclose(vp, expected) + + mock_argmax.reset_mock() diff --git a/tests/analysis/swept_langmuir/test_swept_langmuir_helpers.py b/tests/analysis/swept_langmuir/test_swept_langmuir_helpers.py index fb34917fff..daab228c7b 100644 --- a/tests/analysis/swept_langmuir/test_swept_langmuir_helpers.py +++ b/tests/analysis/swept_langmuir/test_swept_langmuir_helpers.py @@ -1,12 +1,13 @@ """Tests for `plasmapy.analysis.swept_langmuir.helpers`.""" from contextlib import nullcontext as does_not_raise +from unittest import mock import astropy.units as u import numpy as np import pytest -from plasmapy.analysis.swept_langmuir.helpers import check_sweep +from plasmapy.analysis.swept_langmuir.helpers import check_sweep, sort_sweep_arrays @pytest.mark.parametrize( @@ -163,6 +164,14 @@ does_not_raise(), (np.linspace(-40.0, 40, 100), np.linspace(-10.0, 30, 100)), ), + # -- allow_unsorted == True -- + ( + 30.0 * np.random.default_rng().random(100) - 20.0, + np.linspace(-10.0, 30, 100), + {"allow_unsorted": True}, + does_not_raise(), + "expected same as inputs", + ), ], ) def test_check_sweep(voltage, current, kwargs, with_context, expected) -> None: @@ -180,3 +189,91 @@ def test_check_sweep(voltage, current, kwargs, with_context, expected) -> None: else: assert np.allclose(rtn_voltage, expected[0]) assert np.allclose(rtn_current, expected[1]) + + +@pytest.mark.parametrize( + ("voltage", "current", "kwargs", "with_context", "expected"), + [ + # raises + ( + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": 5.0}, # not a string + pytest.raises(TypeError), + None, + ), + ( + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": "wrong string"}, + pytest.raises(ValueError), + None, + ), + # values + ( + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": "ascending"}, + does_not_raise(), + None, + ), + ( + np.linspace(-40.0, 40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": "descending"}, + does_not_raise(), + (np.linspace(40.0, -40, 100), np.linspace(30.0, -10, 100)), + ), + ( + np.linspace(40.0, -40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": "descending"}, + does_not_raise(), + None, + ), + ( + np.linspace(40.0, -40, 100), + np.linspace(-10.0, 30, 100), + {"voltage_order": "ascending"}, + does_not_raise(), + (np.linspace(-40.0, 40, 100), np.linspace(30.0, -10, 100)), + ), + ( + np.array([-40.0, 20.0, -22.0, 40.0]), + np.array([-10.0, 10.0, -5.0, 30.0]), + {"voltage_order": "ascending"}, + does_not_raise(), + (np.array([-40.0, -22.0, 20.0, 40.0]), np.array([-10.0, -5.0, 10.0, 30.0])), + ), + ( + np.array([-40.0, 20.0, -22.0, 40.0]), + np.array([-10.0, 10.0, -5.0, 30.0]), + {"voltage_order": "descending"}, + does_not_raise(), + (np.array([40.0, 20.0, -22.0, -40.0]), np.array([30.0, 10.0, -5.0, -10.0])), + ), + ], +) +def test_sort_sweep_arrays(voltage, current, kwargs, with_context, expected) -> None: + with ( + with_context, + mock.patch( + "plasmapy.analysis.swept_langmuir.helpers.check_sweep", + wraps=check_sweep, + ) as mock_check_sweep, + ): + rtn_voltage, rtn_current = sort_sweep_arrays( + voltage=voltage, + current=current, + **kwargs, + ) + + if expected is not None: + assert np.allclose(rtn_voltage, expected[0]) + assert np.allclose(rtn_current, expected[1]) + else: + assert np.allclose(rtn_voltage, voltage) + assert np.allclose(rtn_current, current) + + mock_check_sweep.assert_called_once() + mock_check_sweep.reset_mock() diff --git a/tests/analysis/test_fit_functions.py b/tests/analysis/test_fit_functions.py index 23e3d0bd82..09a47ef8f1 100644 --- a/tests/analysis/test_fit_functions.py +++ b/tests/analysis/test_fit_functions.py @@ -529,8 +529,8 @@ def test_root_solve(self) -> None: ff_obj.params = (3.0, 0.5, 5.0) with pytest.warns(RuntimeWarning, match="invalid value encountered in log"): root, err = ff_obj.root_solve() - assert np.isnan(root) - assert np.isnan(err) + assert np.isnan(root) + assert np.isnan(err) class TestFFLinear(BaseFFTests): diff --git a/tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py b/tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py index ec9810fe57..b573608a7d 100644 --- a/tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py +++ b/tests/diagnostics/charged_particle_radiography/test_synthetic_radiography.py @@ -148,8 +148,8 @@ def test_multiple_grids() -> None: solution?? """ - grid1 = _test_grid("constant_bz", L=3 * u.cm, num=50, B0=0.7 * u.T) - grid2 = _test_grid("electrostatic_gaussian_sphere", L=1 * u.mm, num=50) + grid1 = _test_grid("constant_bz", L=3 * u.cm, num=20, B0=0.7 * u.T) + grid2 = _test_grid("electrostatic_gaussian_sphere", L=1 * u.mm, num=20) grids = [grid1, grid2] source = (0 * u.mm, -10 * u.mm, 0 * u.mm) @@ -159,7 +159,7 @@ def test_multiple_grids() -> None: grids, source, detector, field_weighting="nearest neighbor", verbose=True ) - sim.create_particles(1e5, 15 * u.MeV, max_theta=8 * u.deg, random_seed=42) + sim.create_particles(1e2, 15 * u.MeV, max_theta=8 * u.deg, random_seed=42) sim.run() @@ -167,13 +167,6 @@ def test_multiple_grids() -> None: bins = [100, 100] hax, vax, values = cpr.synthetic_radiograph(sim, size=size, bins=bins) - """ - import matplotlib.pyplot as plt - fig, ax = plt.subplots() - ax.set_aspect('equal') - ax.pcolormesh(hax.to(u.cm).value, vax.to(u.cm).value, values.T) - """ - def run_1D_example(name: str): """ @@ -215,7 +208,7 @@ def run_mesh_example( wire_diameter=20 * u.um, mesh_hdir=None, mesh_vdir=None, - nparticles: int = 10000, + nparticles: int = 1000, problem: str = "electrostatic_gaussian_sphere", ) -> cpr.Tracker: """ @@ -374,10 +367,11 @@ def test_input_validation() -> None: # Choose a very small synthetic radiograph size that misses most of the # particles + size = np.array([[-1, 1], [-1, 1]]) * 1 * u.mm + with pytest.warns( RuntimeWarning, match="of the particles are shown on this synthetic radiograph." ): - size = np.array([[-1, 1], [-1, 1]]) * 1 * u.mm hax, vax, values = cpr.synthetic_radiograph(sim, size=size) @@ -617,7 +611,7 @@ def test_warns(self) -> None: with pytest.warns(RuntimeWarning): cpr.synthetic_radiograph(sim_results) - def test_ignore_grid(self): + def test_ignore_grid(self) -> None: """ Verifies that the no grid option runs - no good tests for whether it is correct currently """ @@ -812,51 +806,60 @@ def test_gaussian_sphere_analytical_comparison() -> None: assert np.isclose(max_deflection, sim.max_deflection.to(u.rad).value, atol=1e-3) +@pytest.mark.parametrize( + "kwargs", + [ + # Test a circular mesh + ({"extent": 1 * u.mm}), + # Test providing hdir + ({"mesh_hdir": np.array([0.5, 0, 0.5])}), + # Test providing hdir and vdir + ({"mesh_hdir": np.array([0.5, 0, 0.5]), "mesh_vdir": np.array([0, 0.1, 1])}), + ], +) @pytest.mark.slow -def test_add_wire_mesh() -> None: - # ************************************************************ - # Test various input configurations - # ************************************************************ +def test_add_wire_mesh_inputs(kwargs) -> None: + run_mesh_example(**kwargs) - # Test a circular mesh - run_mesh_example(extent=1 * u.mm) - # Test providing hdir - run_mesh_example(mesh_hdir=np.array([0.5, 0, 0.5])) - - # Test providing hdir and vdir - run_mesh_example(mesh_hdir=np.array([0.5, 0, 0.5]), mesh_vdir=np.array([0, 0.1, 1])) - - # ************************************************************ - # Test invalid inputs - # ************************************************************ +@pytest.mark.parametrize( + ("kwargs", "exception"), + [ + # Test invalid extent (too many elements) + ({"extent": (1 * u.mm, 2 * u.mm, 3 * u.mm)}, ValueError), + # Test wire mesh completely blocks all particles (in this case because + # the wire diameter is absurdly large) + ({"wire_diameter": 5 * u.mm}, ValueError), + # Test if wire mesh is not between the source and object + ({"location": np.array([0, 3, 0]) * u.mm}, ValueError), + ], +) +@pytest.mark.slow +def test_add_wire_mesh_invalid_inputs(kwargs, exception) -> None: + with pytest.raises(exception): + run_mesh_example(**kwargs) - # Test invalid extent (too many elements) - with pytest.raises(ValueError): - run_mesh_example(extent=(1 * u.mm, 2 * u.mm, 3 * u.mm)) - # Test wire mesh completely blocks all particles (in this case because - # the wire diameter is absurdly large) - with pytest.raises(ValueError): - run_mesh_example(wire_diameter=5 * u.mm) +@pytest.mark.slow +def test_add_wire_mesh_accuracy() -> None: + """ + Test that a mesh is imaged correctly in the detector plane. - # Test if wire mesh is not between the source and object - with pytest.raises(ValueError): - run_mesh_example(location=np.array([0, 3, 0]) * u.mm) - - # ************************************************************ - # Test that mesh is the right size in the detector plane, and that - # the wire spacing images correctly. - # This is actually a good overall test of the whole proton radiography - # particle tracing algorithm. - # ************************************************************ + Test that mesh is the right size in the detector plane, and that + the wire spacing images correctly. + This is actually a good overall test of the whole proton radiography + particle tracing algorithm. + """ loc = np.array([0, -2, 0]) * u.mm extent = (1 * u.mm, 1 * u.mm) wire_diameter = 30 * u.um nwires = 9 + + # A large number of particles is needed to get a good image + # of the mesh, so this is a slow test sim = run_mesh_example( problem="empty", - nparticles=100000, + nparticles=10000, location=loc, extent=extent, wire_diameter=wire_diameter, @@ -924,42 +927,6 @@ def test_add_wire_mesh() -> None: assert np.isclose(measured_spacing, true_spacing, 0.5) -@pytest.mark.slow -@pytest.mark.filterwarnings("ignore::RuntimeWarning") -def test_multiple_grids2() -> None: - """ - Test that a case with two grids runs. - TODO: automate test by including two fields with some obvious analytical - solution?? - """ - - grid1 = _test_grid("constant_bz", L=3 * u.cm, num=50, B0=0.7 * u.T) - grid2 = _test_grid("electrostatic_gaussian_sphere", L=1 * u.mm, num=50) - grids = [grid1, grid2] - - source = (0 * u.mm, -10 * u.mm, 0 * u.mm) - detector = (0 * u.mm, 200 * u.mm, 0 * u.mm) - - sim = cpr.Tracker( - grids, source, detector, field_weighting="nearest neighbor", verbose=True - ) - - sim.create_particles(1e5, 15 * u.MeV, max_theta=8 * u.deg, random_seed=42) - - sim.run() - - size = np.array([[-1, 1], [-1, 1]]) * 5 * u.cm - bins = [100, 100] - hax, vax, values = cpr.synthetic_radiograph(sim, size=size, bins=bins) - - """ - import matplotlib.pyplot as plt - fig, ax = plt.subplots() - ax.set_aspect('equal') - ax.pcolormesh(hax.to(u.cm).value, vax.to(u.cm).value, values.T) - """ - - def test_radiography_disk_save_routine(tmp_path) -> None: grid = _test_grid("electrostatic_gaussian_sphere", L=1 * u.mm, num=50) diff --git a/tests/formulary/collisions/test_collisions_dimensionless.py b/tests/formulary/collisions/test_collisions_dimensionless.py index e9b9511ad3..42d6f1049a 100644 --- a/tests/formulary/collisions/test_collisions_dimensionless.py +++ b/tests/formulary/collisions/test_collisions_dimensionless.py @@ -132,6 +132,8 @@ def setup_class(cls) -> None: def test_symmetry(self) -> None: with pytest.warns(CouplingWarning): result = Knudsen_number(self.length, self.T, self.n_e, self.particles) + + with pytest.warns(CouplingWarning): resultRev = Knudsen_number( self.length, self.T, self.n_e, self.particles[::-1] ) diff --git a/tests/formulary/collisions/test_collisions_frequencies.py b/tests/formulary/collisions/test_collisions_frequencies.py index 338fc32e08..9d9489aa12 100644 --- a/tests/formulary/collisions/test_collisions_frequencies.py +++ b/tests/formulary/collisions/test_collisions_frequencies.py @@ -726,6 +726,7 @@ def setup_class(cls) -> None: def test_symmetry(self) -> None: with pytest.warns(CouplingWarning): result = collision_frequency(self.T, self.n, self.particles) + with pytest.warns(CouplingWarning): resultRev = collision_frequency(self.T, self.n, self.particles[::-1]) assert result == resultRev diff --git a/tests/formulary/collisions/test_collisions_lengths.py b/tests/formulary/collisions/test_collisions_lengths.py index 21c0a88e24..6b2494d06d 100644 --- a/tests/formulary/collisions/test_collisions_lengths.py +++ b/tests/formulary/collisions/test_collisions_lengths.py @@ -204,7 +204,7 @@ def setup_class(cls) -> None: cls.True1 = 4.4047571877932046e-07 def test_symmetry(self) -> None: - with pytest.warns(CouplingWarning): + with pytest.warns(CouplingWarning): # noqa: PT031 result = lengths.mean_free_path(self.T, self.n_e, self.particles) resultRev = lengths.mean_free_path(self.T, self.n_e, self.particles[::-1]) assert result == resultRev diff --git a/tests/formulary/collisions/test_collisions_misc.py b/tests/formulary/collisions/test_collisions_misc.py index 4d9ebc76f9..2240273ca0 100644 --- a/tests/formulary/collisions/test_collisions_misc.py +++ b/tests/formulary/collisions/test_collisions_misc.py @@ -149,7 +149,7 @@ def setup_class(cls) -> None: cls.True_zmean = 0.32665227217687254 def test_symmetry(self) -> None: - with pytest.warns(CouplingWarning): + with pytest.warns(CouplingWarning): # noqa: PT031 result = mobility(self.T, self.n_e, self.particles) resultRev = mobility(self.T, self.n_e, self.particles[::-1]) assert result == resultRev diff --git a/tests/formulary/test_laser.py b/tests/formulary/test_laser.py index 9abf970a19..05fc7af3b5 100644 --- a/tests/formulary/test_laser.py +++ b/tests/formulary/test_laser.py @@ -5,7 +5,22 @@ import pytest from astropy.tests.helper import assert_quantity_allclose -from plasmapy.formulary.laser import E0_, I_, electric_field_amplitude, intensity +from plasmapy.formulary.laser import ( + E0_, + I_, + Gaussian_beam_waist_radius, + Gaussian_power, + Gaussian_Rayleigh_length, + Gaussian_spot_size_FWHM, + a0_, + electric_field_amplitude, + em_angular_frequency, + em_wavelength, + intensity, + normalized_vector_potential, + omega_, + w0_, +) @pytest.mark.parametrize( @@ -51,6 +66,9 @@ def test_electric_field_amplitude_warnings(intensity, expected_warning) -> None: [ (E0_, electric_field_amplitude), (I_, intensity), + (w0_, Gaussian_beam_waist_radius), + (omega_, em_angular_frequency), + (a0_, normalized_vector_potential), ], ) def test_aliases(alias, parent) -> None: @@ -94,3 +112,350 @@ def test_intensity_errors(electric_field_amplitude, expected) -> None: def test_intensity_warnings(electric_field_amplitude, expected_warning) -> None: with pytest.warns(expected_warning): intensity(electric_field_amplitude=electric_field_amplitude) + + +@pytest.mark.parametrize( + ("intensity", "beam_waist_radius", "expected"), + [ + (1e-3 * u.watt / u.m**2, 1e-6 * u.m, 1.5707963267948967e-15 * u.Watt), + ( + [1, 1e21] * u.milliWatt / u.m**2, + [1, 1] * u.um, + [1.5707963267948967e-15, 1570796.3267948967] * u.Watt, + ), + ( + [1, 1] * u.milliWatt / u.m**2, + [1, 10] * u.um, + [1.5707963267948967e-15, 1.5707963267948967e-13] * u.Watt, + ), + ( + 1 * u.milliWatt / u.m**2, + [1, 10] * u.um, + [1.5707963267948967e-15, 1.5707963267948967e-13] * u.Watt, + ), + ( + [1, 1e21] * u.milliWatt / u.m**2, + 1 * u.um, + [1.5707963267948967e-15, 1570796.3267948967] * u.Watt, + ), + (0 * u.watt / u.m**2, 1e-6 * u.m, 0 * u.Watt), + (1e-3 * u.watt / u.m**2, 0 * u.m, 0 * u.Watt), + (np.nan * u.watt / u.m**2, np.nan * u.m, np.nan * u.Watt), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_Gaussian_power(intensity, beam_waist_radius, expected) -> None: + result = Gaussian_power(intensity=intensity, beam_waist_radius=beam_waist_radius) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.Watt + + +@pytest.mark.parametrize( + ("intensity", "beam_waist_radius", "expected"), + [ + (-5e4 * u.Watt / u.m**2, 2 * u.m, ValueError), + (5e4 * u.Watt / u.m**2, -2 * u.m, ValueError), + (1 * u.kg, 3 * u.s, u.UnitTypeError), + ], +) +def test_Gaussian_power_errors(intensity, beam_waist_radius, expected) -> None: + with pytest.raises(expected): + Gaussian_power(intensity=intensity, beam_waist_radius=beam_waist_radius) + + +@pytest.mark.parametrize( + ("intensity", "beam_waist_radius", "expected_warning"), + [(5, 2 * u.um, u.UnitsWarning), (5 * u.Watt / u.m**2, 2, u.UnitsWarning)], +) +def test_Gaussian_power_errors_warnings( + intensity, beam_waist_radius, expected_warning +) -> None: + with pytest.warns(expected_warning): + Gaussian_power(intensity=intensity, beam_waist_radius=beam_waist_radius) + + +@pytest.mark.parametrize( + ("spot_size_FWHM", "expected"), + [ + (8.242e-6 * u.m, 7.00011e-6 * u.m), + ([8.242, 0] * u.um, [7.00011e-6, 0] * u.m), + (np.nan * u.m, np.nan * u.m), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_Gaussian_beam_waist_radius(spot_size_FWHM, expected) -> None: + result = Gaussian_beam_waist_radius(spot_size_FWHM=spot_size_FWHM) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.m + + +@pytest.mark.parametrize( + ("spot_size_FWHM", "expected"), + [ + (-5e4 * u.m, ValueError), + (1 * u.kg, u.UnitTypeError), + ], +) +def test_Gaussian_beam_waist_radius_errors(spot_size_FWHM, expected) -> None: + with pytest.raises(expected): + Gaussian_beam_waist_radius(spot_size_FWHM=spot_size_FWHM) + + +@pytest.mark.parametrize( + ("spot_size_FWHM", "expected_warning"), + [ + (5, u.UnitsWarning), + ], +) +def test_Gaussian_beam_waist_radius_warnings(spot_size_FWHM, expected_warning) -> None: + with pytest.warns(expected_warning): + Gaussian_beam_waist_radius(spot_size_FWHM=spot_size_FWHM) + + +@pytest.mark.parametrize( + ("beam_waist_radius", "expected"), + [ + (7e-6 * u.m, 8.24187e-6 * u.m), + ([7, 0] * u.um, [8.24187e-6, 0] * u.m), + (np.nan * u.m, np.nan * u.m), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_Gaussian_spot_size_FWHM(beam_waist_radius, expected) -> None: + result = Gaussian_spot_size_FWHM(beam_waist_radius=beam_waist_radius) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.m + + +@pytest.mark.parametrize( + ("beam_waist_radius", "expected"), + [ + (-5e4 * u.m, ValueError), + (1 * u.kg, u.UnitTypeError), + ], +) +def test_Gaussian_spot_size_FWHM_errors(beam_waist_radius, expected) -> None: + with pytest.raises(expected): + Gaussian_spot_size_FWHM(beam_waist_radius=beam_waist_radius) + + +@pytest.mark.parametrize( + ("beam_waist_radius", "expected_warning"), + [ + (5, u.UnitsWarning), + ], +) +def test_Gaussian_spot_size_FWHM_warnings(beam_waist_radius, expected_warning) -> None: + with pytest.warns(expected_warning): + Gaussian_spot_size_FWHM(beam_waist_radius=beam_waist_radius) + + +@pytest.mark.parametrize( + ("angular_frequency", "expected"), + [ + (2.354307546e15 * u.rad / u.s, 800.0873e-9 * u.m), + ([2.354307546, 0] * u.Prad / u.s, [800.0873e-9, np.inf] * u.m), + (np.nan * u.rad / u.s, np.nan * u.m), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_em_wavelength(angular_frequency, expected) -> None: + result = em_wavelength(angular_frequency=angular_frequency) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.m + + +@pytest.mark.parametrize( + ("angular_frequency", "expected"), + [ + (-5e4 * u.rad / u.s, ValueError), + (1 * u.kg, u.UnitTypeError), + ], +) +def test_em_wavelength_errors(angular_frequency, expected) -> None: + with pytest.raises(expected): + em_wavelength(angular_frequency=angular_frequency) + + +@pytest.mark.parametrize( + ("angular_frequency", "expected_warning"), + [ + (5, u.UnitsWarning), + ], +) +def test_em_wavelength_warnings(angular_frequency, expected_warning) -> None: + with pytest.warns(expected_warning): + em_wavelength(angular_frequency=angular_frequency) + + +@pytest.mark.parametrize( + ("wavelength", "expected"), + [ + (800e-9 * u.m, 2.354564e15 * u.rad / u.s), + ([800, 0] * u.nm, [2.354564e15, np.inf] * u.rad / u.s), + (np.nan * u.m, np.nan * u.rad / u.s), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_em_angular_frequency(wavelength, expected) -> None: + result = em_angular_frequency(wavelength=wavelength) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.rad / u.s + + +@pytest.mark.parametrize( + ("wavelength", "expected"), + [ + (-5e4 * u.m, ValueError), + (1 * u.kg, u.UnitTypeError), + ], +) +def test_em_angular_frequency_errors(wavelength, expected) -> None: + with pytest.raises(expected): + em_angular_frequency(wavelength=wavelength) + + +@pytest.mark.parametrize( + ("wavelength", "expected_warning"), + [ + (5, u.UnitsWarning), + ], +) +def test_em_angular_frequency_warning(wavelength, expected_warning) -> None: + with pytest.warns(expected_warning): + em_angular_frequency(wavelength=wavelength) + + +@pytest.mark.parametrize( + ("intensity", "wavelength", "expected"), + [ + (1e-3 * u.watt / u.m**2, 800e-9 * u.m, 2.162820076644342e-13), + ( + [1, 1e-3] * u.milliWatt / u.m**2, + [800, 800] * u.nm, + [2.162820076644342e-13, 6.839437611336064e-15], + ), + ( + [1, 1] * u.milliWatt / u.m**2, + [800, 650] * u.nm, + [2.162820076644342e-13, 1.7572913122735275e-13], + ), + ( + [1, 1e-3] * u.milliWatt / u.m**2, + 800 * u.nm, + [2.162820076644342e-13, 6.839437611336064e-15], + ), + ( + 1 * u.milliWatt / u.m**2, + [800, 650] * u.nm, + [2.162820076644342e-13, 1.7572913122735275e-13], + ), + (0 * u.watt / u.m**2, 800e-9 * u.m, 0), + (1e-3 * u.watt / u.m**2, 0 * u.m, 0), + (np.nan * u.Watt / u.m**2, np.nan * u.m, np.nan), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_normalized_vector_potential(intensity, wavelength, expected) -> None: + result = normalized_vector_potential(intensity=intensity, wavelength=wavelength) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + + +# assert result.unit == u.dimensionless_unscaled + + +@pytest.mark.parametrize( + ("intensity", "wavelength", "expected"), + [ + (-5e-3 * u.Watt / u.m**2, 5e4 * u.m, ValueError), + (5e-3 * u.Watt / u.m**2, -5e4 * u.m, ValueError), + (7 * u.s, 1 * u.kg, u.UnitTypeError), + ], +) +def test_normalized_vector_potential_errors(intensity, wavelength, expected) -> None: + with pytest.raises(expected): + normalized_vector_potential(intensity=intensity, wavelength=wavelength) + + +@pytest.mark.parametrize( + ("intensity", "wavelength", "expected_warning"), + [ + (3, 5, u.UnitsWarning), + ], +) +def test_normalized_vector_potential_warning( + intensity, wavelength, expected_warning +) -> None: + with pytest.warns(expected_warning): + normalized_vector_potential(intensity=intensity, wavelength=wavelength) + + +@pytest.mark.parametrize( + ("wavelength", "beam_waist_radius", "expected"), + [ + (800e-9 * u.m, 1e-6 * u.m, 3.926990816987241e-06 * u.m), + ( + [800, 650] * u.nm, + [1, 1] * u.um, + [3.926990816987241e-06, 4.8332194670612195e-06] * u.m, + ), + ( + [800, 800] * u.nm, + [1, 20] * u.um, + [3.926990816987241e-06, 0.0015707963267948962] * u.m, + ), + ( + [800, 650] * u.nm, + 1 * u.um, + [3.926990816987241e-06, 4.8332194670612195e-06] * u.m, + ), + ( + 800 * u.nm, + [1, 20] * u.um, + [3.926990816987241e-06, 0.0015707963267948962] * u.m, + ), + (800e-9 * u.m, 0 * u.m, 0 * u.m), + (0 * u.m, 1e-6 * u.m, np.inf * u.m), + (np.nan * u.m, np.nan * u.m, np.nan * u.m), + ], +) +@pytest.mark.filterwarnings("ignore::astropy.units.UnitsWarning") +def test_Gaussian_Rayleigh_length(wavelength, beam_waist_radius, expected) -> None: + result = Gaussian_Rayleigh_length( + wavelength=wavelength, beam_waist_radius=beam_waist_radius + ) + assert_quantity_allclose(result, expected, rtol=1e-6, equal_nan=True, verbose=True) + assert result.unit == u.m + + +@pytest.mark.parametrize( + ("wavelength", "beam_waist_radius", "expected"), + [ + (-5e4 * u.m, 2 * u.m, ValueError), + (5e4 * u.m, -2 * u.m, ValueError), + (1 * u.kg, 3 * u.s, u.UnitTypeError), + ], +) +def test_Gaussian_Rayleigh_length_errors( + wavelength, beam_waist_radius, expected +) -> None: + with pytest.raises(expected): + Gaussian_Rayleigh_length( + wavelength=wavelength, beam_waist_radius=beam_waist_radius + ) + + +@pytest.mark.parametrize( + ("wavelength", "beam_waist_radius", "expected_warning"), + [ + (5 * u.m, 2, u.UnitsWarning), + (5, 2 * u.m, u.UnitsWarning), + ], +) +def test_Rayleigh_length_warnings_warnings( + wavelength, beam_waist_radius, expected_warning +) -> None: + with pytest.warns(expected_warning): + Gaussian_Rayleigh_length( + wavelength=wavelength, beam_waist_radius=beam_waist_radius + ) diff --git a/tests/formulary/test_lengths.py b/tests/formulary/test_lengths.py index 15a0a3f94d..16fbecaf26 100644 --- a/tests/formulary/test_lengths.py +++ b/tests/formulary/test_lengths.py @@ -332,8 +332,8 @@ def test_values(self, args, kwargs, expected, atol) -> None: def test_warns(self, args, kwargs, expected, _warns) -> None: with pytest.warns(_warns): rc = gyroradius(*args, **kwargs) - if expected is not None: - assert np.allclose(rc, expected) + if expected is not None: + assert np.allclose(rc, expected) def test_keeps_arguments_unchanged(self) -> None: Vperp1 = u.Quantity([np.nan, 1], unit=u.m / u.s) @@ -390,9 +390,7 @@ def test_inertial_length() -> None: with pytest.warns(u.UnitsWarning): inertial_length_no_units = inertial_length(1e19, particle="p+") - assert inertial_length_no_units == inertial_length( - 1e19 * u.m**-3, particle="p+" - ) + assert inertial_length_no_units == inertial_length(1e19 * u.m**-3, particle="p+") assert inertial_length(n_e, "e-").unit.is_equivalent(u.m) diff --git a/tests/formulary/test_plasma_frequency.py b/tests/formulary/test_plasma_frequency.py index f6d4a714c6..e852aeb81a 100644 --- a/tests/formulary/test_plasma_frequency.py +++ b/tests/formulary/test_plasma_frequency.py @@ -96,8 +96,8 @@ def test_warns(self, args, kwargs, _warning, expected) -> None: """ with pytest.warns(_warning): wp = plasma_frequency(*args, **kwargs) - assert isinstance(wp, u.Quantity) - assert wp.unit == u.rad / u.s + assert isinstance(wp, u.Quantity) + assert wp.unit == u.rad / u.s if expected is not None: assert np.allclose(wp, expected) diff --git a/tests/formulary/test_speeds.py b/tests/formulary/test_speeds.py index 13896435b8..164a6f0c20 100644 --- a/tests/formulary/test_speeds.py +++ b/tests/formulary/test_speeds.py @@ -108,7 +108,7 @@ def test_raises(self, args, kwargs, _error) -> None: ) def test_warns(self, args, kwargs, expected, isclose_kw, _warning) -> None: """Test scenarios that issue warnings""" - with pytest.warns(_warning): + with pytest.warns(_warning): # noqa: PT031 val = Alfven_speed(*args, **kwargs) assert isinstance(val, u.Quantity) assert val.unit == u.m / u.s @@ -331,7 +331,7 @@ def test_values(self, args, kwargs, expected, isclose_kw) -> None: ], ) def test_warns(self, kwargs1, kwargs2, _warning) -> None: - with pytest.warns(_warning): + with pytest.warns(_warning): # noqa: PT031 val = ion_sound_speed(**kwargs1) if kwargs2 != {}: val == ion_sound_speed(**kwargs2) # noqa: B015 diff --git a/tests/formulary/test_thermal_speed.py b/tests/formulary/test_thermal_speed.py index e45877fd13..3da0dbf9da 100644 --- a/tests/formulary/test_thermal_speed.py +++ b/tests/formulary/test_thermal_speed.py @@ -273,10 +273,10 @@ def test_warns(self, args, kwargs, _warning, expected) -> None: """Test scenarios where `thermal_speed` issues warnings.""" with pytest.warns(_warning): vth = thermal_speed(*args, **kwargs) - assert vth.unit == u.m / u.s + assert vth.unit == u.m / u.s - if expected is not None: - assert vth == expected + if expected is not None: + assert vth == expected def test_electron_vs_proton(self) -> None: """ @@ -397,8 +397,7 @@ def test_mean1(self) -> None: ) assert np.isclose(known1.value, self.mean1True, rtol=1e-8, atol=0.0), errstr - def test_handle_nparrays(self, kwargs=None) -> None: + def test_handle_nparrays(self) -> None: """Test for ability to handle numpy array quantities""" - if kwargs is None: - kwargs = {"kappa": 2} + kwargs = {"kappa": 2} assert_can_handle_nparray(kappa_thermal_speed, kwargs=kwargs) diff --git a/tests/particles/conftest.py b/tests/particles/conftest.py index e68c848228..2ddd50620f 100644 --- a/tests/particles/conftest.py +++ b/tests/particles/conftest.py @@ -8,12 +8,12 @@ @pytest.fixture(params=sorted(particle_zoo.everything)) -def particle(request): # noqa: D103 +def particle(request): return Particle(request.param) @pytest.fixture -def opposite(particle): # noqa: D103 +def opposite(particle): try: opposite_particle = ~particle except Exception as exc: @@ -38,5 +38,5 @@ def opposite(particle): # noqa: D103 ] ) ) -def particle_antiparticle_pair(request): # noqa: D103 +def particle_antiparticle_pair(request): return [Particle(p) for p in request.param] diff --git a/tests/particles/test_atomic.py b/tests/particles/test_atomic.py index c890d0600c..660cf97127 100644 --- a/tests/particles/test_atomic.py +++ b/tests/particles/test_atomic.py @@ -706,3 +706,11 @@ def test_stopping_power_no_interpolation() -> None: result = stopping_power(Particle("H+"), "COPPER") assert type(result) is tuple + + +def test_element_name_used_on_numpy_integer() -> None: + """ + Test that `element_name` works when provided with a numpy.integer + object acquired from an ndarray (see #3044). + """ + assert element_name(np.int32(18)) == "argon" diff --git a/tests/particles/test_parsing.py b/tests/particles/test_parsing.py index 632713931b..3d0ddc8a20 100644 --- a/tests/particles/test_parsing.py +++ b/tests/particles/test_parsing.py @@ -356,11 +356,11 @@ def test_parse_InvalidElementErrors(particle) -> None: @pytest.mark.parametrize(("arg", "kwargs", "num_warnings"), atomic_warnings_table) -def test_parse_AtomicWarnings(arg, kwargs, num_warnings: int) -> None: - r"""Tests that _parse_and_check_atomic_input issues an AtomicWarning +def test_parse_ParticleWarnings(arg, kwargs, num_warnings: int) -> None: + r"""Tests that _parse_and_check_atomic_input issues a ParticleWarning under the required conditions.""" - with pytest.warns(ParticleWarning) as record: + with pytest.warns(ParticleWarning) as record: # noqa: PT031 parse_and_check_atomic_input(arg, **kwargs) if not record: pytest.fail( @@ -375,8 +375,3 @@ def test_parse_AtomicWarnings(arg, kwargs, num_warnings: int) -> None: f"was {len(record)}, which differs from the expected number " f"of {num_warnings} warnings." ) - - -def test_Queen() -> None: - Queen = "Freddie Mercury (lead vocals, piano), Brian May (guitar, vocals), Roger Taylor (drums, vocals) and John Deacon (bass)" - assert Particle("Freddie").element_name.capitalize() in Queen diff --git a/tests/particles/test_particle_class.py b/tests/particles/test_particle_class.py index fa3661dc53..f4b2aac46f 100644 --- a/tests/particles/test_particle_class.py +++ b/tests/particles/test_particle_class.py @@ -510,6 +510,14 @@ "ionic_symbol": "C-14 3+", }, ), + ( + np.int32(26), # test that Particle accepts np.integer objects (see #3044) + {}, + { + "symbol": "Fe", + "atomic_number": 26, + }, + ), ] @@ -664,7 +672,7 @@ def test_Particle_warnings(arg, kwargs, attribute, warning) -> None: Test that the appropriate warnings are issued during the creation and use of a `~plasmapy.particles.Particle` object. """ - with pytest.warns(warning) as record: + with pytest.warns(warning) as record: # noqa: PT031 exec(f"Particle(arg, **kwargs){attribute}") # noqa: S102 if not record: pytest.fail( @@ -1666,7 +1674,7 @@ def test_undefined_electron_binding_energy() -> None: def test_warning_on_use_of_binding_energy() -> None: - with pytest.warns(FutureWarning): + with pytest.warns(FutureWarning): # noqa: PT031 particle = Particle("n") assert particle.binding_energy == particle.nuclear_binding_energy diff --git a/tests/plasma/sources/test_plasmablob.py b/tests/plasma/sources/test_plasmablob.py index 08159b9d34..914cdcc0e8 100644 --- a/tests/plasma/sources/test_plasmablob.py +++ b/tests/plasma/sources/test_plasmablob.py @@ -195,7 +195,7 @@ def test_weakly_coupled(self) -> None: n_e = 1e15 * u.cm**-3 Z = 2.5 * u.dimensionless_unscaled particle = "p+" - with pytest.warns( + with pytest.warns( # noqa: PT031 CouplingWarning, match="you might have strong coupling effects" ): blob = plasmablob.PlasmaBlob(T_e=T_e, n_e=n_e, Z=Z, particle=particle) diff --git a/tests/plasma/test_grids.py b/tests/plasma/test_grids.py index 983fb966bd..c261e4466b 100644 --- a/tests/plasma/test_grids.py +++ b/tests/plasma/test_grids.py @@ -3,6 +3,7 @@ """ import astropy.units as u +import matplotlib.pyplot as plt import numpy as np import pytest from astropy.tests.helper import assert_quantity_allclose @@ -513,7 +514,7 @@ def uniform_cartesian_grid(): 0.1 * u.cm, ], ) -def test_soften_edges(uniform_cartesian_grid, width): +def test_soften_edges(uniform_cartesian_grid, width) -> None: grid = uniform_cartesian_grid # Find the approximate center of the grid @@ -1010,7 +1011,6 @@ def debug_volume_avg_interpolator() -> None: Plot the comparison of the nearest neighbor interpolator and volume averaged interpolator for `~plasmapy.plasma.grids.CartesianGrid`. """ - import matplotlib.pyplot as plt grid = grids.CartesianGrid(-1 * u.cm, 1 * u.cm, num=24) diff --git a/tests/utils/decorators/test_checks.py b/tests/utils/decorators/test_checks.py index 05388055da..d90216ceb9 100644 --- a/tests/utils/decorators/test_checks.py +++ b/tests/utils/decorators/test_checks.py @@ -4,10 +4,12 @@ """ import inspect +from contextlib import nullcontext as does_not_raise from types import LambdaType from typing import Any from unittest import mock +import astropy import astropy.units as u import numpy as np import pytest @@ -28,10 +30,9 @@ RelativityWarning, ) +does_not_warn = does_not_raise + -# ---------------------------------------------------------------------------------------- -# Test Decorator class `CheckBase` -# ---------------------------------------------------------------------------------------- class TestCheckBase: """ Test for decorator class :class:`~plasmapy.utils.decorators.checks.CheckBase`. @@ -87,10 +88,24 @@ def foo_with_none(x: u.Quantity, y: u.cm = None): # noqa: ANN205 def test_inheritance(self) -> None: assert issubclass(CheckUnits, CheckBase) + @pytest.mark.parametrize( + "name", + [ + "_CheckUnits__check_defaults", + "_flatten_equivalencies_list", + "_condition_target_units", + "_normalize_equivalencies", + "_get_unit_checks", + "_check_unit", + "_check_unit_core", + ], + ) + def test_method_existence(self, name: str) -> None: + assert hasattr(CheckUnits, name) + def test_cu_default_check_values(self) -> None: """Test the default check dictionary for CheckUnits.""" cu = CheckUnits() - assert hasattr(cu, "_CheckUnits__check_defaults") assert isinstance(cu._CheckUnits__check_defaults, dict) _defaults = [ ("units", None), @@ -102,8 +117,6 @@ def test_cu_default_check_values(self) -> None: assert cu._CheckUnits__check_defaults[key] == val def test_cu_method__flatten_equivalencies_list(self) -> None: - assert hasattr(CheckUnits, "_flatten_equivalencies_list") - cu = CheckUnits() pairs = [([1, 2, 4], [1, 2, 4]), ([1, 2, (3, 4), [5, 6]], [1, 2, (3, 4), 5, 6])] for pair in pairs: @@ -111,7 +124,6 @@ def test_cu_method__flatten_equivalencies_list(self) -> None: def test_cu_method__condition_target_units(self) -> None: """Test method `CheckUnits._condition_target_units`.""" - assert hasattr(CheckUnits, "_condition_target_units") cu = CheckUnits() @@ -130,7 +142,6 @@ def test_cu_method__condition_target_units(self) -> None: def test_cu_method__normalize_equivalencies(self) -> None: """Test method `CheckUnits._normalize_equivalencies`.""" - assert hasattr(CheckUnits, "_normalize_equivalencies") cu = CheckUnits() @@ -181,90 +192,88 @@ def test_cu_method__normalize_equivalencies(self) -> None: with pytest.raises(ValueError): cu._normalize_equivalencies([("cm", u.cm)]) - def test_cu_method__get_unit_checks(self) -> None: - """ - Test functionality/behavior of the method `_get_unit_checks` on `CheckUnits`. - This method reviews the decorator `checks` arguments and wrapped function - annotations to build a complete checks dictionary. - """ - # methods must exist - assert hasattr(CheckUnits, "_get_unit_checks") - - # setup default checks - default_checks = { - **self.check_defaults.copy(), - "units": [self.check_defaults["units"]], - } - - # setup test cases - # 'setup' = arguments for `_get_unit_checks` - # 'output' = expected return from `_get_unit_checks` - # 'raises' = if `_get_unit_checks` raises an Exception - # 'warns' = if `_get_unit_checks` issues a warning - # - equivs = [ - # list of astropy Equivalency objects - [u.temperature_energy(), u.temperature()], - # list of equivalencies (pre astropy v3.2.1 style) - list(u.temperature()), - ] - _cases = [ - { - "description": "x units are defined via decorator kwarg of CheckUnits\n" - "y units are defined via decorator annotations, additional\n" - " checks thru CheckUnits kwarg", - "setup": { - "function": self.foo_partial_anno, + @pytest.mark.parametrize( + ("description", "setup", "expected", "warn_context", "raise_context"), + [ + ( + "x units are defined via decorator kwarg of CheckUnits " + "y units are defined via decorator annotations, additional " + "checks thru CheckUnits kwarg", + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, - "checks": {"x": {"units": [u.cm], "equivalencies": equivs[0][0]}}, + "checks": { + "x": { + "units": [u.cm], + "equivalencies": u.temperature_energy(), + }, + }, }, - "output": { - "x": {"units": [u.cm], "equivalencies": equivs[0][0]}, + { + "x": {"units": [u.cm], "equivalencies": u.temperature_energy()}, "y": {"units": [u.cm]}, }, - }, - { - "description": "x units are defined via decorator kwarg of CheckUnits\n" - "y units are defined via function annotations, additional\n" - " checks thru CheckUnits kwarg", - "setup": { - "function": self.foo_partial_anno, + does_not_warn(), + does_not_raise(), + ), + ( + "x units are defined via decorator kwarg of CheckUnits " + "y units are defined via function annotations, additional " + "checks thru CheckUnits kwarg", + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": { - "x": {"units": [u.cm], "equivalencies": equivs[0]}, + "x": { + "units": [u.cm], + "equivalencies": [ + u.temperature_energy(), + u.temperature(), + ], + }, "y": {"pass_equivalent_units": False}, }, }, - "output": { + { "x": { "units": [u.cm], - "equivalencies": equivs[0][0] + equivs[0][1], + "equivalencies": u.temperature_energy() + u.temperature(), }, "y": {"units": [u.cm], "pass_equivalent_units": False}, }, - }, - { - "description": "equivalencies are a list instead of astropy Equivalency objects", - "setup": { - "function": self.foo_no_anno, + does_not_warn(), + does_not_raise(), + ), + ( + "equivalencies are a list instead of astropy Equivalency objects", + { + "function": foo_no_anno, "args": (2 * u.K, 3 * u.K), "kwargs": {}, "checks": { - "x": {"units": [u.K], "equivalencies": equivs[1][0]}, - "y": {"units": [u.K], "equivalencies": equivs[1]}, + "x": { + "units": [u.K], + "equivalencies": next(iter(u.temperature())), + }, + "y": {"units": [u.K], "equivalencies": list(u.temperature())}, }, }, - "output": { - "x": {"units": [u.K], "equivalencies": [equivs[1][0]]}, - "y": {"units": [u.K], "equivalencies": equivs[1]}, + { + "x": { + "units": [u.K], + "equivalencies": [next(iter(u.temperature()))], + }, + "y": {"units": [u.K], "equivalencies": list(u.temperature())}, }, - }, - { - "description": "number of checked arguments exceed number of function arguments", - "setup": { - "function": self.foo_partial_anno, + does_not_warn(), + does_not_raise(), + ), + ( + "number of checked arguments exceed number of function arguments", + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": { @@ -273,13 +282,17 @@ def test_cu_method__get_unit_checks(self) -> None: "z": {"units": [u.cm]}, }, }, - "warns": PlasmaPyWarning, - "output": {"x": {"units": [u.cm]}, "y": {"units": [u.cm]}}, - }, - { - "description": "arguments passed via *args and **kwargs are ignored", - "setup": { - "function": self.foo_stars, + { + "x": {"units": [u.cm]}, + "y": {"units": [u.cm]}, + }, + pytest.warns(PlasmaPyWarning), + does_not_raise(), + ), + ( + "arguments passed via *args and **kwargs are ignored", + { + "function": foo_stars, "args": (2 * u.cm, "hello"), "kwargs": {"z": None}, "checks": { @@ -288,150 +301,200 @@ def test_cu_method__get_unit_checks(self) -> None: "z": {"units": [u.cm]}, }, }, - "warns": PlasmaPyWarning, - "output": {"x": {"units": [u.cm]}, "y": {"units": [u.cm]}}, - }, - { - "description": "arguments can be None values", - "setup": { - "function": self.foo_with_none, + { + "x": {"units": [u.cm]}, + "y": {"units": [u.cm]}, + }, + pytest.warns(PlasmaPyWarning), + does_not_raise(), + ), + ( + "arguments can be None values", + { + "function": foo_with_none, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"x": {"units": [u.cm, None]}}, }, - "output": { + { "x": {"units": [u.cm], "none_shall_pass": True}, "y": {"units": [u.cm], "none_shall_pass": True}, }, - }, - { - "description": "checks and annotations do not specify units", - "setup": { - "function": self.foo_no_anno, + does_not_warn(), + does_not_raise(), + ), + ( + "checks and annotations do not specify units", + { + "function": foo_no_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"x": {"pass_equivalent_units": True}}, }, - "raises": ValueError, - }, - { - "description": "units are directly assigned to the check kwarg", - "setup": { - "function": self.foo_partial_anno, + {}, + does_not_warn(), + pytest.raises(ValueError), + ), + ( + "units are directly assigned to the check kwarg", + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"x": u.cm}, }, - "output": {"x": {"units": [u.cm]}, "y": {"units": [u.cm]}}, - }, - { - "description": "return units are assigned via checks", - "setup": { - "function": self.foo_no_anno, + {"x": {"units": [u.cm]}, "y": {"units": [u.cm]}}, + does_not_warn(), + does_not_raise(), + ), + ( + "return units are assigned via checks", + { + "function": foo_no_anno, "args": (2 * u.km, 3 * u.km), "kwargs": {}, "checks": {"checks_on_return": u.km}, }, - "output": {"checks_on_return": {"units": [u.km]}}, - }, - { - "description": "return units are assigned via annotations", - "setup": { - "function": self.foo_return_anno, + {"checks_on_return": {"units": [u.km]}}, + does_not_warn(), + does_not_raise(), + ), + ( + "return units are assigned via annotations", + { + "function": foo_return_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {}, }, - "output": {"checks_on_return": {"units": [u.um]}}, - }, - { - "description": "return units are assigned via annotations and checks arg, but" + {"checks_on_return": {"units": [u.um]}}, + does_not_warn(), + does_not_raise(), + ), + ( + "return units are assigned via annotations and checks arg, but " "are not consistent", - "setup": { - "function": self.foo_return_anno, + { + "function": foo_return_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"checks_on_return": {"units": u.km}}, }, - "raises": ValueError, - }, - { - "description": "return units are not specified but other checks are", - "setup": { - "function": self.foo_no_anno, + {}, + does_not_warn(), + pytest.raises(ValueError), + ), + ( + "return units are not specified but other checks are", + { + "function": foo_no_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"checks_on_return": {"pass_equivalent_units": True}}, }, - "raises": ValueError, - }, - { - "description": "no parameter checks for x are defined, but a non-unit annotation" + {}, + does_not_warn(), + pytest.raises(ValueError), + ), + ( + "no parameter checks for x are defined, but a non-unit annotation " "is used", - "setup": { - "function": self.foo_partial_anno, + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {}, }, - "output": {"y": {"units": [u.cm]}}, - }, - { - "description": "parameter checks defined for x but unit checks calculated from" + {"y": {"units": [u.cm]}}, + does_not_warn(), + does_not_raise(), + ), + ( + "parameter checks defined for x but unit checks calculated from " "function annotations. Function annotations do NOT define " "a proper unit type.", - "setup": { - "function": self.foo_partial_anno, + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"x": {"pass_equivalent_units": True}}, }, - "raises": ValueError, - }, - { - "description": "parameter checks defined for return argument but unit checks " + {}, + does_not_warn(), + pytest.raises(ValueError), + ), + ( + "parameter checks defined for return argument but unit checks " "calculated from function annotations. Function annotations do " "NOT define a proper unit type.", - "setup": { - "function": self.foo_partial_anno, + { + "function": foo_partial_anno, "args": (2 * u.cm, 3 * u.cm), "kwargs": {}, "checks": {"checks_on_return": {"pass_equivalent_units": True}}, }, - "raises": ValueError, - }, - ] + {}, + does_not_warn(), + pytest.raises(ValueError), + ), + ], + ) + @pytest.mark.skipif(astropy.__version__ < "7", reason="see #3065") + def test_cu_method__get_unit_checks( + self, + description: str, + setup: dict[str, Any], + expected: dict[str, Any], + warn_context, + raise_context, + ) -> None: + """ + Test functionality/behavior of the method `_get_unit_checks` on `CheckUnits`. + This method reviews the decorator `checks` arguments and wrapped function + annotations to build a complete checks dictionary. + """ + + # setup default checks + default_checks = { + **self.check_defaults.copy(), + "units": [self.check_defaults["units"]], + } + + sig = inspect.signature(setup["function"]) + bound_args = sig.bind(*setup["args"], **setup["kwargs"]) # perform tests - for _ii, case in enumerate(_cases): - sig = inspect.signature(case["setup"]["function"]) - bound_args = sig.bind(*case["setup"]["args"], **case["setup"]["kwargs"]) + cu = CheckUnits(**setup["checks"]) + cu.f = setup["function"] + with warn_context, raise_context: + checks = cu._get_unit_checks(bound_args) - cu = CheckUnits(**case["setup"]["checks"]) - cu.f = case["setup"]["function"] - if "warns" in case: - with pytest.warns(case["warns"]): - checks = cu._get_unit_checks(bound_args) - elif "raises" in case: - with pytest.raises(case["raises"]): - cu._get_unit_checks(bound_args) - continue - else: - checks = cu._get_unit_checks(bound_args) + if not isinstance(raise_context, does_not_raise): + # method call raised except, no more tests needed + return - # only expected argument checks exist - assert sorted(checks.keys()) == sorted(case["output"].keys()) + # only expected argument checks exist + assert set(checks.keys()) == set(expected.keys()) - # if check key-value not specified then default is assumed - for arg_name in case["output"]: - arg_checks = checks[arg_name] + # if check key-value not specified then default is assumed + for arg_name, expected_checks in expected.items(): + for key in default_checks: # noqa: PLC0206 + _check = checks[arg_name][key] - for key, val in default_checks.items(): - if key in case["output"][arg_name]: - val = case["output"][arg_name][key] # noqa: PLW2901 - assert arg_checks[key] == val, ( - f"{case['description'] = }\n\n{arg_checks[key] = }\n\n{val = }" - ) + if key in expected_checks: + val = expected_checks[key] + else: + val = default_checks[key] + + if key == "equivalencies" and _check is not None and val is not None: + # Note: for some reason an equals comparison of an Equivalency + # and a list are not equal even if all the elements + # are equal. astropy.units.Equivalency is a subclass + # of a list...lets just do elementwise comparison instead + + assert all(_c == _v for _c, _v in zip(_check, val, strict=False)) + else: + assert _check == val, description def test_cu_method__check_unit(self) -> None: """ @@ -439,9 +502,6 @@ def test_cu_method__check_unit(self) -> None: on `CheckUnits`. These methods do the actual checking of the argument units and should be called by `CheckUnits.__call__()`. 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