From db88b72b6b738d897965100e7fe4afbf83836228 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 14:52:37 +0100 Subject: [PATCH 01/10] Indents. --- .github/workflows/tests.yaml | 154 ++++++++++++++++++----------------- 1 file changed, 79 insertions(+), 75 deletions(-) diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index fa28dfa1..3e9fd780 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -1,78 +1,82 @@ name: Tests on: - push: - branches: - - main - pull_request: - workflow_dispatch: + push: + branches: + - main + pull_request: + workflow_dispatch: jobs: - ruff: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.10", "3.13"] - name: ruff on ${{ matrix.python-version }} - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: ruff check . - mypy: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.10", "3.13"] - name: mypy on ${{ matrix.python-version }} - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: mypy . - ruff-format: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.10", "3.13"] - name: ruff-format on ${{ matrix.python-version }} - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: ruff format --check . - pytest: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.10", "3.13"] - name: pytest on ${{ matrix.python-version }} - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: pytest --cov=src --cov-report term-missing - doctest: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.10", "3.13"] - name: doctest on ${{ matrix.python-version }} - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: make -C docs doctest + ruff: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.13"] + name: ruff on ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - run: pip install -e '.[dev]' + - run: ruff check . + + mypy: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.13"] + name: mypy on ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - run: pip install -e '.[dev]' + - run: mypy . + + ruff-format: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.13"] + name: ruff-format on ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - run: pip install -e '.[dev]' + - run: ruff format --check . + + pytest: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.13"] + name: pytest on ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - run: pip install -e '.[dev]' + - run: pytest --cov=src --cov-report term-missing + + doctest: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.13"] + name: doctest on ${{ matrix.python-version }} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + cache: "pip" + - run: pip install -e '.[dev]' + - run: make -C docs doctest From 01295d542af4909d4007a05c91ec4b1ce8d58039 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 14:58:53 +0100 Subject: [PATCH 02/10] Move to uv, change python version. --- justfile | 32 +- pyproject.toml | 2 +- uv.lock | 4252 ++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 4269 insertions(+), 17 deletions(-) create mode 100644 uv.lock diff --git a/justfile b/justfile index 9269edd3..200f1a04 100644 --- a/justfile +++ b/justfile @@ -2,15 +2,9 @@ default: @just --list -# Build docs. -docs: - rm -rf docs/build docs/source/_autosummary - make -C docs html - echo Docs are in $PWD/docs/build/html/index.html - # Do a dev install. -dev: - pip install -e '.[dev]' +setup: + uv sync --all-extras --dev # Run code checks. check: @@ -20,27 +14,33 @@ check: trap error=1 ERR echo - (set -x; ruff check . ) + ( set -x; uv run ruff check . ) echo - ( set -x; ruff format --check . ) + ( set -x; uv run ruff format --check . ) echo - ( set -x; mypy . ) + ( set -x; uv run mypy . ) echo - ( set -x; pytest --cov=src --cov-report term-missing ) + ( set -x; uv run pytest --cov=src --cov-report term-missing ) echo - ( set -x; make -C docs doctest ) + ( set -x; uv run make -C docs doctest ) test $error = 0 # Auto-fix code issues. fix: - ruff format . - ruff check --fix . + uv run ruff format . + uv run ruff check --fix . # Build a release. build: - python -m build + uv build + +# Build docs. +docs: + rm -rf docs/source/_autosummary + uv run make -C docs html + echo Docs are in $PWD/docs/build/html/index.html diff --git a/pyproject.toml b/pyproject.toml index f5d2ee5d..35eec468 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ dependencies = [ ] # Set by cpctools. -requires-python = ">=3.8" +requires-python = ">=3.9" dynamic = ["version"] readme = "README.rst" description = "Simplifies analysis of simulation and 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b/.github/workflows/publish_release.yaml index 16cc9c20..557e3663 100644 --- a/.github/workflows/publish_release.yaml +++ b/.github/workflows/publish_release.yaml @@ -9,14 +9,12 @@ jobs: env: VERSION: ${{ github.ref_name }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v5 with: - python-version: "3.10" - cache: "pip" - - run: pip install -e '.[dev]' - - run: python -m build - - run: twine upload - -u __token__ - -p ${{ secrets.PYPI_API_TOKEN }} - dist/* + enable-cache: true + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv build + - run: uv publish -u __token__ -p ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 3e9fd780..cea703aa 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -13,13 +13,16 @@ jobs: python-version: ["3.10", "3.13"] name: ruff on ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: + enable-cache: true python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: ruff check . + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv sync --all-extras --dev + - run: uv run ruff check . mypy: runs-on: ubuntu-latest @@ -28,13 +31,16 @@ jobs: python-version: ["3.10", "3.13"] name: mypy on ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: + enable-cache: true python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: mypy . + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv sync --all-extras --dev + - run: uv run mypy . ruff-format: runs-on: ubuntu-latest @@ -43,13 +49,16 @@ jobs: python-version: ["3.10", "3.13"] name: ruff-format on ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: + enable-cache: true python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: ruff format --check . + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv sync --all-extras --dev + - run: uv run ruff format --check . pytest: runs-on: ubuntu-latest @@ -58,13 +67,16 @@ jobs: python-version: ["3.10", "3.13"] name: pytest on ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: + enable-cache: true python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: pytest --cov=src --cov-report term-missing + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv sync --all-extras --dev + - run: uv run pytest doctest: runs-on: ubuntu-latest @@ -73,10 +85,13 @@ jobs: python-version: ["3.10", "3.13"] name: doctest on ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: + enable-cache: true python-version: ${{ matrix.python-version }} - cache: "pip" - - run: pip install -e '.[dev]' - - run: make -C docs doctest + - uses: actions/setup-python@v5 + with: + python-version-file: "pyproject.toml" + - run: uv sync --all-extras --dev + - run: uv run make -C docs doctest From 1c6826a9f6be3d316a808e420137b5c35a851c18 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:04:43 +0100 Subject: [PATCH 04/10] Update uv version, test matrix. --- .github/workflows/publish_release.yaml | 4 +--- .github/workflows/tests.yaml | 26 ++++++-------------------- 2 files changed, 7 insertions(+), 23 deletions(-) diff --git a/.github/workflows/publish_release.yaml b/.github/workflows/publish_release.yaml index 557e3663..4ab12090 100644 --- a/.github/workflows/publish_release.yaml +++ b/.github/workflows/publish_release.yaml @@ -10,11 +10,9 @@ jobs: VERSION: ${{ github.ref_name }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v5 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true - - uses: actions/setup-python@v5 - with: python-version-file: "pyproject.toml" - run: uv build - run: uv publish -u __token__ -p ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index cea703aa..42c0b5ea 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -5,6 +5,7 @@ on: - main pull_request: workflow_dispatch: + jobs: ruff: runs-on: ubuntu-latest @@ -14,13 +15,10 @@ jobs: name: ruff on ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v3 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-python@v5 - with: - python-version-file: "pyproject.toml" - run: uv sync --all-extras --dev - run: uv run ruff check . @@ -32,13 +30,10 @@ jobs: name: mypy on ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v3 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-python@v5 - with: - python-version-file: "pyproject.toml" - run: uv sync --all-extras --dev - run: uv run mypy . @@ -50,13 +45,10 @@ jobs: name: ruff-format on ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v3 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-python@v5 - with: - python-version-file: "pyproject.toml" - run: uv sync --all-extras --dev - run: uv run ruff format --check . @@ -68,13 +60,10 @@ jobs: name: pytest on ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v3 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-python@v5 - with: - python-version-file: "pyproject.toml" - run: uv sync --all-extras --dev - run: uv run pytest @@ -86,12 +75,9 @@ jobs: name: doctest on ${{ matrix.python-version }} steps: - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v3 + - uses: astral-sh/setup-uv@v6 with: enable-cache: true python-version: ${{ matrix.python-version }} - - uses: actions/setup-python@v5 - with: - python-version-file: "pyproject.toml" - run: uv sync --all-extras --dev - run: uv run make -C docs doctest From f17c6a8ed183bb3833ae89774efaf6643e04f973 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:21:38 +0100 Subject: [PATCH 05/10] Update install instructions. --- README.rst | 7 +++++-- docs/source/index.rst | 5 +++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index d909b678..1d8fe61d 100644 --- a/README.rst +++ b/README.rst @@ -43,7 +43,7 @@ How to get started ------------------ We suggest you give a read to the ``dynsight.trajectory`` module documentation, -which offers a compact and easy way of using most of the ``dynsight`` tools. +which offers a compact and easy way of using most of the ``dynsight`` tools. Also, the documentation offers some copiable Recipes and Examples for the most common analyses. @@ -60,14 +60,17 @@ Developer Setup --------------- #. Install `just`_. +#. Install `uv `_ #. In a new virtual environment run:: - $ just dev + $ just setup + #. Run code checks:: $ just check + .. _`just`: https://github.com/casey/just Examples diff --git a/docs/source/index.rst b/docs/source/index.rst index a52ae8ac..db761838 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -81,7 +81,7 @@ How to get started ------------------ We suggest you give a read to the ``dynsight.trajectory`` module documentation, -which offers a compact and easy way of using most of the ``dynsight`` tools. +which offers a compact and easy way of using most of the ``dynsight`` tools. Also, the documentation offers some copiable Recipes and Examples for the most common analyses. @@ -98,9 +98,10 @@ Developer Setup --------------- #. Install `just`_. +#. Install `uv `_ #. In a new virtual environment run:: - $ just dev + $ just setup #. Run code checks:: From 77ba1d6d7fda7ce1a778d63021904e25e5322098 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:21:52 +0100 Subject: [PATCH 06/10] Ruff fixes. --- src/dynsight/_internal/utilities/utilities.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/dynsight/_internal/utilities/utilities.py b/src/dynsight/_internal/utilities/utilities.py index 19f3b45f..5c616cee 100644 --- a/src/dynsight/_internal/utilities/utilities.py +++ b/src/dynsight/_internal/utilities/utilities.py @@ -1,7 +1,12 @@ from __future__ import annotations +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from collections.abc import Mapping, Sequence + from pathlib import Path -from typing import Callable, Literal, Mapping, Sequence +from typing import Callable, Literal import numpy as np import numpy.typing as npt From 5776f5cc0baba7901d672c701054dd20cecb4c72 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:29:27 +0100 Subject: [PATCH 07/10] Test rtd with uv. --- .readthedocs.yaml | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 4106f8a3..dbc7b625 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,16 +1,18 @@ version: 2 -build: - os: ubuntu-22.04 - tools: - python: "3.10" - sphinx: - configuration: docs/source/conf.py + configuration: docs/conf.py -python: - install: - - method: pip - path: . - extra_requirements: - - dev +build: + os: ubuntu-24.04 + tools: + python: "3.13" + jobs: + pre_create_environment: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + create_environment: + - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" + install: + - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group dev From 57483e38fb7701137239cefb377cf3afe8ba7866 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:30:53 +0100 Subject: [PATCH 08/10] Test rtd with uv. --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index dbc7b625..540c5464 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,4 +15,4 @@ build: create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group dev + - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --extra dev From bbe997ffcd359cdd241ad8b63c45abfa59c27b02 Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Wed, 1 Oct 2025 15:37:07 +0100 Subject: [PATCH 09/10] Fix conf.py location. --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 540c5464..99e280f7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,7 +1,7 @@ version: 2 sphinx: - configuration: docs/conf.py + configuration: docs/source/conf.py build: os: ubuntu-24.04 From bfe3aaac72b0e00e251c3fd9f07e74e9d1a1021f Mon Sep 17 00:00:00 2001 From: Andrew Tarzia Date: Thu, 2 Oct 2025 13:46:13 +0100 Subject: [PATCH 10/10] Modify numpy version. --- docs/source/_static/recipes/info_gain.py | 2 +- pyproject.toml | 2 +- uv.lock | 328 +++++------------------ 3 files changed, 68 insertions(+), 264 deletions(-) diff --git a/docs/source/_static/recipes/info_gain.py b/docs/source/_static/recipes/info_gain.py index 873839a0..82484cf7 100644 --- a/docs/source/_static/recipes/info_gain.py +++ b/docs/source/_static/recipes/info_gain.py @@ -63,7 +63,7 @@ def info_gain_with_onion( tmp_entr.append( dynsight.analysis.compute_shannon( selected_points, - data_range, + data_range, # type: ignore[arg-type] n_bins=n_bins, ) ) diff --git a/pyproject.toml b/pyproject.toml index 35eec468..b8570929 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ maintainers = [ ] dependencies = [ - "numpy", + "numpy<2", "dscribe", "tropea-clustering", "MDAnalysis", diff --git a/uv.lock b/uv.lock index 50996a89..59fe7ea4 100644 --- a/uv.lock +++ b/uv.lock @@ -4,13 +4,13 @@ requires-python = ">=3.9" resolution-markers = [ "python_full_version >= '3.12' and sys_platform == 'win32'", "python_full_version == '3.11.*' and sys_platform == 'win32'", + "python_full_version == '3.10.*' and sys_platform == 'win32'", "python_full_version >= '3.12' and sys_platform == 'darwin'", "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", "python_full_version == '3.11.*' and sys_platform == 'darwin'", "python_full_version == '3.11.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version == '3.11.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", - "python_full_version == '3.10.*' and sys_platform == 'win32'", "python_full_version == '3.10.*' and sys_platform == 'darwin'", "python_full_version == '3.10.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version == '3.10.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", @@ -54,13 +54,13 @@ source = { registry = "https://pypi.org/simple" } resolution-markers = [ "python_full_version >= '3.12' and sys_platform == 'win32'", "python_full_version == '3.11.*' and sys_platform == 'win32'", + "python_full_version == '3.10.*' and sys_platform == 'win32'", "python_full_version >= '3.12' and sys_platform == 'darwin'", "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", "python_full_version == '3.11.*' and sys_platform == 'darwin'", "python_full_version == '3.11.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version == '3.11.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", - "python_full_version == '3.10.*' and sys_platform == 'win32'", "python_full_version == '3.10.*' and sys_platform == 'darwin'", "python_full_version == '3.10.*' and platform_machine == 'aarch64' and sys_platform == 'linux'", "(python_full_version == '3.10.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", @@ -77,9 +77,7 @@ source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "matplotlib", version = "3.10.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, - { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, - { name = "numpy", version = "2.3.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy" }, { name = "scipy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, { name = "scipy", version = "1.16.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, @@ -314,7 +312,7 @@ resolution-markers = [ "(python_full_version < '3.10' and platform_machine != 'arm64' and sys_platform == 'darwin') or (python_full_version < '3.10' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.10' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", ] dependencies = [ - { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, + { name = "numpy", marker = "python_full_version < '3.10'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/f5/f6/31a8f28b4a2a4fa0e01085e542f3081ab0588eff8e589d39d775172c9792/contourpy-1.3.0.tar.gz", hash = "sha256:7ffa0db17717a8ffb127efd0c95a4362d996b892c2904db72428d5b52e1938a4", size = 13464370 } wheels = [ @@ -395,7 +393,7 @@ resolution-markers = [ "(python_full_version == '3.10.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.10.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", ] dependencies = [ - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, + { name = "numpy", marker = "python_full_version == '3.10.*'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/66/54/eb9bfc647b19f2009dd5c7f5ec51c4e6ca831725f1aea7a993034f483147/contourpy-1.3.2.tar.gz", hash = "sha256:b6945942715a034c671b7fc54f9588126b0b8bf23db2696e3ca8328f3ff0ab54", size = 13466130 } wheels = [ @@ -472,7 +470,7 @@ resolution-markers = [ "(python_full_version == '3.11.*' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'linux' and sys_platform != 'win32')", ] dependencies = [ - { name = "numpy", version = "2.3.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy", marker = "python_full_version >= '3.11'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/58/01/1253e6698a07380cd31a736d248a3f2a50a7c88779a1813da27503cadc2a/contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880", size = 13466174 } wheels = [ @@ -728,9 +726,7 @@ name = "deeptime" version = "0.4.5" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, - { name = "numpy", version = "2.3.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy" }, { name = "scikit-learn", version = "1.6.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "scikit-learn", version = "1.7.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "scipy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, @@ -778,9 +774,7 @@ source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "ase" }, { name = "joblib" }, - { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, - { name = "numpy", version = "2.3.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy" }, { name = "scikit-learn", version = "1.6.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "scikit-learn", version = "1.7.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "scipy", version = "1.13.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, @@ -843,9 +837,7 @@ dependencies = [ { name = "dscribe" }, { name = "mdanalysis", version = "2.7.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "mdanalysis", version = "2.9.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, - { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name 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