[CLEANUP] Repo hygiene: pyproject-only dependencies, no environment.yml, coverage floor

[eleanorfrajka]

Summary

Repo hygiene: dependencies are declared once, in pyproject.toml; the root environment.yml and both requirements*.txt files are gone; CI enforces a coverage floor. No change to standardised output, variable names, attributes, or any public call — this is a packaging and tooling branch only.

What's changed

• Dependencies moved into pyproject.toml: [project] dependencies holds the runtime pins, and [project.optional-dependencies] adds test, docs, and dev (where dev = test + docs + ruff/jupyterlab/pygmt); dynamic is now ["version"] only.
• Deleted requirements.txt, requirements-dev.txt, and the root environment.yml; install for development with pip install -e ".[dev]".
• Docs workflows (docs.yml, docs_deploy.yml) no longer use conda/micromamba: they run on actions/setup-python, install pandoc with apt-get, and install the package with pip install -e ".[docs]".
• tests.yml matrix now runs Ubuntu on Python 3.10–3.13 and macOS and Windows on 3.12; installs pip install -e ".[test]"; and gates coverage at --cov-fail-under=55 on the Ubuntu 3.12 cell only (every other cell runs --no-cov).
• The Python 3.13 cell is marked experimental (continue-on-error) and fail-fast is off, so a missing 3.13 wheel fails softly without cancelling the supported cells; drop the experimental flag once the dependency stack has 3.13 wheels.
• The docs extra includes ipython, which provides the ipython3 Pygments lexer nbsphinx needs to render the notebook cells.
• Prose updated to the extras model across README, docs/source/about.rst, faq.md, the developer guides, and both CONTRIBUTING files.
• Added a .mailmap collapsing the Isabelle1299 and Isabelle commit identities to Isabelle Schmitz.
• CHANGELOG [Unreleased] written up for the changes merged since 0.4.0 ([DOC] add Zenodo DOI badge and CITATION doi #178–[FEAT] Add the SCOTIA overturning reader (neutral-density space) #184), including a Breaking changes section for [FEAT] amocvocab controlled vocabulary + OceanSITES format reset #181 (standardised output moved to the amocvocab + OceanSITES convention) and [CLEANUP] Repo and docs cleanup: regenerate reports, dedupe autodoc, ruff-only linting, drop dead AC1 writer #182 (writers.save_AC1_dataset() removed), plus the packaging change on this branch.

Breaking changes

None for a user of the package: no output, attribute, variable name, or public call changes on this branch. (The CHANGELOG's Breaking changes section documents #181 and #182, which are already on main and ship in the next release.)

Tests

pip install -e ".[test]" in a clean virtualenv, then pytest -m "not slow" — 434 passed, 1 skipped, coverage 58.18% (≥ 55 floor); pip check clean; docs build with .[docs] succeeds with 2 (pre-existing) warnings.

Notes

pyudunits2[xml] and jsonschema are test-only (lazy imports in the vocabulary validator) and live in the test extra, not runtime; pygmt stays dev-only. Please delete the merged branches docs/add-zenodo-doi, fix/time-epoch-and-attr-strip, and rel-v0.4.0 when merging this.

[Copilot]

🟡 Changes recommended

The dev extra in pyproject.toml is self-referential (amocatlas[test,docs]) and can break or mis-resolve pip install -e ".[dev]" in editable installs.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

Consolidates dependency and tooling configuration around pyproject.toml (including extras), removes redundant environment/requirements files, and updates CI/docs guidance to use pip-based installs while adding a CI coverage floor.

Changes:

• Move runtime/test/docs/dev dependencies into pyproject.toml with test/docs/dev extras; remove requirements*.txt and environment.yml.
• Update GitHub Actions workflows to install via extras and gate coverage on a single matrix cell; remove conda/micromamba from docs workflows.
• Refresh README/docs/CONTRIBUTING/CHANGELOG guidance to match the extras-based development workflow; add .mailmap.

File summaries

File	Description
tests/test_sf2021.py	Formatting-only change to a monkeypatch lambda for readability.
requirements.txt	Deleted in favor of [project] dependencies in pyproject.toml.
requirements-dev.txt	Deleted in favor of dev/test/docs extras in pyproject.toml.
README.md	Update install and docs-build instructions to use `pip install -e ".[dev
pyproject.toml	Define runtime deps and test/docs/dev extras; add Python 3.13 classifier.
environment.yml	Deleted; docs/test workflows no longer use conda/micromamba.
docs/source/faq.md	Update install/test instructions to remove requirements file installs.
docs/source/developers/housekeeping.md	Update dependency-management guidance to point to pyproject.toml extras.
docs/source/developers/git_beginners_guide.md	Update CI/test dependency explanation to reference .[test].
docs/source/developers/developer_guide.md	Update dev environment setup instructions to use .[dev].
docs/source/developers/actions.md	Update workflow descriptions and local commands to use extras-based installs.
docs/source/archive/developer_guide_original.md	Minor formatting update in a code block.
docs/source/about.rst	Update contribution install instructions to use .[dev].
CONTRIBUTING.md	Update docs build instructions to use pandoc + .[docs].
CHANGELOG.md	Document unreleased changes including the packaging/CI hygiene updates.
amocatlas/data_sources/wh41n.py	Formatting-only change to multi-line lambdas for readability.
.mailmap	Add canonical author mappings for consistent git history attribution.
.github/workflows/tests.yml	Switch to pip install -e ".[test]", expand matrix, and enforce a coverage floor on one cell.
.github/workflows/docs.yml	Switch docs build from micromamba to actions/setup-python + pip install -e ".[docs]" + apt pandoc.
.github/workflows/docs_deploy.yml	Same as docs.yml, for deployment workflow.
.github/CONTRIBUTING.md	Update quick-start contribution instructions to use .[dev].

Review details

• Files reviewed: 20/21 changed files
• Comments generated: 2
• Review effort level: Lite

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