diff --git a/.github/scripts/upstream_install.py b/.github/scripts/upstream_install.py deleted file mode 100644 index 9b367f040..000000000 --- a/.github/scripts/upstream_install.py +++ /dev/null @@ -1,60 +0,0 @@ -import subprocess -import sys -from pathlib import Path - -from packaging.requirements import Requirement -from packaging.specifiers import SpecifierSet -from packaging.utils import canonicalize_name - - -def install_deps() -> None: - install_cmd = ( - sys.executable, - "-m", - "pip", - "install", - "--upgrade", - ) - upstream_deps = ( - "dask[array,dataframe] @ git+https://github.com/dask/dask.git", - "pandas @ git+https://github.com/pandas-dev/pandas.git", - "rechunker @ git+https://github.com/pangeo-data/rechunker.git", - "xarray @ git+https://github.com/pydata/xarray.git", - # Rechunker requires Zarr < 3; test the maintained Zarr 2 branch. - "zarr @ git+https://github.com/zarr-developers/zarr-python.git@support/v2", - ) - upstream_names = {canonicalize_name(Requirement(dep).name) for dep in upstream_deps} - req_deps = [] - for filename in ("requirements.txt", "requirements-dev.txt"): - for line in Path(filename).read_text().splitlines(): - dep = line.partition(" #")[0].strip() - if dep and not dep.startswith("#"): - requirement = Requirement(dep) - if canonicalize_name(requirement.name) in upstream_names: - continue - # Remove version bounds while preserving extras and platform markers. - requirement.specifier = SpecifierSet() - req_deps.append(str(requirement)) - # Resolve source and release dependencies in a single transaction. - full_cmd = install_cmd + upstream_deps + tuple(dict.fromkeys(req_deps)) - print(f"Install upstream test environment via: {full_cmd}", flush=True) - subprocess.check_call(full_cmd) - - -def install_self() -> None: - install_cmd = ( - sys.executable, - "-m", - "pip", - "install", - "--no-deps", - "-e", - ".", - ) - print(f"Install sgkit via: `{install_cmd}`") - subprocess.check_call(install_cmd) - - -if __name__ == "__main__": - install_deps() - install_self() diff --git a/.github/workflows/build-gpu.yml b/.github/workflows/build-gpu.yml index 5be4d20e4..fcb021b89 100644 --- a/.github/workflows/build-gpu.yml +++ b/.github/workflows/build-gpu.yml @@ -34,6 +34,12 @@ jobs: python-version: ${{ matrix.python-version }} miniconda-version: "latest" + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + enable-cache: true + - name: Conda info run: | conda info @@ -42,7 +48,8 @@ jobs: - name: Installing cudatoolkit and dependencies run: | conda install -c nvidia cudatoolkit - pip install -r requirements.txt -r requirements-dev.txt + # Avoid building SciPy from source in CI. + uv pip install --only-binary scipy --python "$CONDA_PREFIX/bin/python" -e ".[bgen,plink]" --group test - name: Numba Information run: | diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 897bbbdf5..805c0b74a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -22,15 +22,20 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt + uv sync --locked --all-extras --group test --group lint --no-default-groups --python "${{ matrix.python-version }}" - name: Run pre-commit - uses: pre-commit/action@v3.0.1 + run: uv run --no-sync pre-commit run --all-files - name: Test with pytest and coverage run: | - pytest -v --cov=sgkit --cov-report=term-missing + uv run --no-sync pytest -v --cov=sgkit --cov-report=term-missing - name: Upload coverage to Codecov uses: codecov/codecov-action@v7 with: @@ -49,14 +54,19 @@ jobs: - uses: actions/setup-python@v7 with: python-version: '3.11' + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: '3.11' + enable-cache: true - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt + uv sync --locked --all-extras --group test --no-default-groups --python 3.11 - name: Install zarr${{ matrix.zarr }} run: | - python -m pip install --pre 'zarr${{ matrix.zarr }}' - python -m pip uninstall -y bio2zarr # TODO: remove when bio2zarr supports Zarr Python 3 + uv pip install --python .venv/bin/python --pre 'zarr${{ matrix.zarr }}' + uv pip uninstall --python .venv/bin/python bio2zarr # TODO: remove when bio2zarr supports Zarr Python 3 - name: Run tests run: | - pytest + uv run --no-sync pytest diff --git a/.github/workflows/check-docs.yml b/.github/workflows/check-docs.yml index 5dd07237a..fae957f54 100644 --- a/.github/workflows/check-docs.yml +++ b/.github/workflows/check-docs.yml @@ -22,19 +22,25 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install dependencies run: | sudo apt update -y sudo apt install graphviz # Needed for documentation - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt - pip install -U dask distributed # need latest versions to successully build docs + uv sync --locked --all-extras --group docs --group lint --no-default-groups --python "${{ matrix.python-version }}" + # Use newer Dask for task-graph rendering with NumPy 2. + uv pip uninstall --python .venv/bin/python dask-expr + uv pip install --python .venv/bin/python 'dask==2026.8.0' - name: Run pre-commit - uses: pre-commit/action@v3.0.1 + run: uv run --no-sync pre-commit run --all-files - name: Check for Sphinx doc warnings run: | - cd docs - make html SPHINXOPTS="-W --keep-going -n" + make -C docs html SPHINXOPTS="-W --keep-going -n" - uses: actions/upload-artifact@v7 if: failure() with: diff --git a/.github/workflows/cubed.yml b/.github/workflows/cubed.yml index 03a40b153..00337411a 100644 --- a/.github/workflows/cubed.yml +++ b/.github/workflows/cubed.yml @@ -21,16 +21,24 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install deps and sgkit run: | - python -m pip install --upgrade pip - python -m pip install -r requirements.txt -r requirements-dev.txt - python -m pip install -U git+https://github.com/cubed-dev/cubed.git -U git+https://github.com/cubed-dev/cubed-xarray.git -U git+https://github.com/pydata/xarray.git + uv sync --locked --all-extras --group test --no-default-groups --python "${{ matrix.python-version }}" + # Update the experimental packages without upgrading unrelated dependencies. + uv pip install --python .venv/bin/python \ + --upgrade-package cubed --upgrade-package cubed-xarray --upgrade-package xarray \ + git+https://github.com/cubed-dev/cubed.git git+https://github.com/cubed-dev/cubed-xarray.git git+https://github.com/pydata/xarray.git - name: Test with pytest run: | - pytest -v sgkit/tests/test_{aggregation,association,hwe,pca,window}.py \ + uv run --no-sync pytest -v sgkit/tests/test_{aggregation,association,hwe,pca,window}.py \ -k "test_count_call_alleles or \ test_gwas_linear_regression or \ test_hwep or \ diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 09d37efb9..c0ac7a390 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -12,21 +12,27 @@ jobs: steps: - uses: actions/checkout@v7 - - name: Set up Python ${{ matrix.python-version }} + - name: Set up Python 3.11 uses: actions/setup-python@v7 with: python-version: "3.11" + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: "3.11" + enable-cache: true - name: Install dependencies run: | sudo apt update -y sudo apt install graphviz # Needed for documentation - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt - pip install -U dask distributed # need latest versions to successully build docs + uv sync --locked --all-extras --group docs --no-default-groups --python "3.11" + # Use newer Dask for task-graph rendering with NumPy 2. + uv pip uninstall --python .venv/bin/python dask-expr + uv pip install --python .venv/bin/python 'dask==2026.8.0' - name: Build Sphinx documentation run: | - cd docs - make html SPHINXOPTS="-W --keep-going -n" + make -C docs html SPHINXOPTS="-W --keep-going -n" - name: Commit documentation changes to gh-pages branch run: | git clone https://github.com/sgkit-dev/sgkit.git --branch gh-pages --single-branch gh-pages diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml deleted file mode 100644 index 3eb33fe2e..000000000 --- a/.github/workflows/upstream.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Upstream - -on: - push: - # schedule: - # - cron: "0 1 * * *" - # manual trigger - workflow_dispatch: - -jobs: - build: - # This workflow only runs on the origin org - if: github.repository_owner == 'sgkit-dev' - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.12", "3.13"] - - steps: - - uses: actions/checkout@v7 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v7 - with: - python-version: ${{ matrix.python-version }} - - - name: Install deps and sgkit - run: | - python -m pip install --upgrade pip packaging - python .github/scripts/upstream_install.py - - - name: Test with pytest - run: | - python -m pip freeze - pytest -v diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml index 31c6f86ad..73efaa81c 100644 --- a/.github/workflows/wheels.yml +++ b/.github/workflows/wheels.yml @@ -22,18 +22,25 @@ jobs: steps: - uses: actions/checkout@v7 + with: + fetch-depth: 0 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install setuptools twine wheel build + uv sync --locked --only-group packaging --python "${{ matrix.python-version }}" - name: Build a source distribution and a wheel run: | - python -m build --sdist --wheel - python -m twine check --strict dist/* + uv build --no-sources --python "${{ matrix.python-version }}" + uv run --locked --only-group packaging twine check --strict dist/* - name: Upload artifacts uses: actions/upload-artifact@v7 with: @@ -62,15 +69,22 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install wheel and test run: | python -VV - # Install the local wheel + # Avoid building SciPy from source in CI. wheel=$(ls artifact/sgkit-*.whl) - pip install ${wheel} ${wheel}[bgen] ${wheel}[plink] - python sgkit-copy/.github/scripts/test_sgkit.py - python sgkit-copy/.github/scripts/test_sgkit_bgen.py - python sgkit-copy/.github/scripts/test_sgkit_plink.py + uv venv --python "${{ matrix.python-version }}" + uv pip install --python .venv/bin/python --only-binary scipy "${wheel}[bgen,plink]" + .venv/bin/python sgkit-copy/.github/scripts/test_sgkit.py + .venv/bin/python sgkit-copy/.github/scripts/test_sgkit_bgen.py + .venv/bin/python sgkit-copy/.github/scripts/test_sgkit_plink.py windows-test: # This workflow only runs on the origin org @@ -94,15 +108,22 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install wheel and test run: | python -VV - # Install the local wheel - $env:wheel = $(ls artifact/sgkit-*.whl) - pip install $env:wheel "$env:wheel[bgen]" "$env:wheel[plink]" - python sgkit-copy/.github/scripts/test_sgkit.py - python sgkit-copy/.github/scripts/test_sgkit_bgen.py - python sgkit-copy/.github/scripts/test_sgkit_plink.py + # Avoid building SciPy from source in CI. + $wheel = (Get-ChildItem artifact/sgkit-*.whl).FullName + uv venv --python "${{ matrix.python-version }}" + uv pip install --python .venv/Scripts/python.exe --only-binary scipy "${wheel}[bgen,plink]" + .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit.py + .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit_bgen.py + .venv/Scripts/python.exe sgkit-copy/.github/scripts/test_sgkit_plink.py pypi-upload: @@ -118,14 +139,14 @@ jobs: - name: Move to dist run: | mkdir dist - cp */*.{whl,gz} dist/. + cp ./*/*.{whl,gz} dist/. - name: Publish package to TestPyPI if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ password: ${{ secrets.TEST_PYPI_API_TOKEN }} - repository_url: https://test.pypi.org/legacy/ + repository-url: https://test.pypi.org/legacy/ - name: Publish package to PyPI if: github.event_name == 'release' uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 8b1d9687e..669ce9def 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -22,13 +22,18 @@ jobs: uses: actions/setup-python@v7 with: python-version: ${{ matrix.python-version }} + - name: Set up uv + uses: astral-sh/setup-uv@v10.0.1 + with: + version: "0.12.10" + python-version: ${{ matrix.python-version }} + enable-cache: true - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt + uv sync --locked --all-extras --group test --no-default-groups --python "${{ matrix.python-version }}" - name: Test with pytest # To avoid: 'UserWarning: KMeans is known to have a memory leak on Windows with MKL, when there are less chunks than available threads. You can avoid it by setting the environment variable OMP_NUM_THREADS=1' env: OMP_NUM_THREADS: 1 run: | - pytest -v + uv run --no-sync pytest -v diff --git a/.gitignore b/.gitignore index 66ff71dd3..4b322ed5e 100644 --- a/.gitignore +++ b/.gitignore @@ -82,8 +82,7 @@ target/ profile_default/ ipython_config.py -# pyenv -.python-version +# Python version is tracked for uv contributor environments. # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. @@ -105,6 +104,7 @@ celerybeat.pid # Environments .env .venv +.venv-*/ env/ venv/ ENV/ diff --git a/.python-version b/.python-version new file mode 100644 index 000000000..e4fba2183 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3760123b1..b470885a2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,3 +1,14 @@ All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome. For general information on how to contribute see https://sgkit-dev.github.io/sgkit/latest/contributing.html. + +For local development, install uv 0.12.10 or newer and run: + +```sh +uv sync +uv run pytest +uv run pre-commit install +``` + +See [the contributor guide](docs/contributing.rst) for dependency updates and documentation setup. +After preparing the documentation dependencies, build with `cd docs && make html`. diff --git a/README.md b/README.md index da7f259e2..d27828743 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,6 @@ [![Build](https://github.com/sgkit-dev/sgkit/actions/workflows/build.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/build.yml) [![Windows](https://github.com/sgkit-dev/sgkit/actions/workflows/windows.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/windows.yml) [![Docs](https://github.com/sgkit-dev/sgkit/actions/workflows/docs.yml/badge.svg)](https://sgkit-dev.github.io/sgkit/) -[![Upstream](https://github.com/sgkit-dev/sgkit/actions/workflows/upstream.yml/badge.svg)](https://github.com/sgkit-dev/sgkit/actions/workflows/upstream.yml) [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](http://numfocus.org) Sgkit is a Python package that provides a variety of analytical genetics methods through the use of diff --git a/docs/Makefile b/docs/Makefile index d8e6d74a0..959cde53c 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,12 +1,10 @@ # Minimal makefile for Sphinx documentation # -PYPATH=${PWD}/.. - # You can set these variables from the command line, and also # from the environment for the first two. SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build +SPHINXBUILD ?= uv run --no-sync sphinx-build SOURCEDIR = . BUILDDIR = _build @@ -24,4 +22,4 @@ clean: # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile - @PYTHONPATH=${PYPATH} $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/contributing.rst b/docs/contributing.rst index a72be4219..737e34ae0 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -88,15 +88,15 @@ Contributions to *sgkit* can then be made by submitting pull requests on GitHub. Install ~~~~~~~ -You can install the necessary requirements using pip:: +Install `uv `_ +(version 0.12.10 or newer), then create the development environment:: cd sgkit - pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt + uv sync - -Then install the `sgkit` in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs) - - pip install -e . +This installs sgkit in editable mode with the ``dev`` dependency group, including +the dependencies needed to test its optional I/O formats. Use ``uv run`` to run +commands in this environment without activating it. If you have a Nvidia GPU you will need to make sure that it is configured properly, @@ -104,9 +104,9 @@ as in you have cudatoolkit installed, the instructions for the same can be found `nvidia docs. `_ -Also install pre-commit, which is used to enforce coding standards:: +Install the pre-commit hook, which is used to enforce coding standards:: - pre-commit install + uv run pre-commit install Run tests @@ -115,7 +115,7 @@ Run tests *sgkit* uses pytest_ for testing. You can run tests from the main ``sgkit`` directory as follows:: - pytest + uv run pytest .. _pytest: https://docs.pytest.org/en/latest/ @@ -143,7 +143,7 @@ and for the future. Test coverage must be 100% for code to be accepted. You can measure the coverage on your local machine by running:: - pytest --cov=sgkit --cov-report=html + uv run pytest --cov=sgkit --cov-report=html A report will be written in the ``htmlcov`` directory that will show any lines that are not covered by tests. @@ -186,8 +186,8 @@ after the line. .. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard Docstrings are tested by CI. You can test them locally -by running ``pytest`` (this works because the ``--doctest-modules`` option is automatically added -in the *setup.cfg* file). +by running ``uv run pytest`` (this works because the ``--doctest-modules`` option is automatically added +in the *pyproject.toml* file). Coding standards @@ -207,11 +207,11 @@ if the change passes all the checks. It is also run for pull requests using CI. To manually enforce (or check) the source code adheres to our coding standards without doing a git commit, run:: - pre-commit run --all-files + uv run pre-commit run --all-files To run a specific tool (``black``/``flake8``/``isort``/``mypy`` etc):: - pre-commit run black --all-files + uv run pre-commit run black --all-files You can omit ``--all-files`` to only check changed files. @@ -241,18 +241,22 @@ and specifically a very handy `interactive rebase doc `_. -There is a `GitHub Action `_ that runs every night -against the main branches of our key upstream dependencies. This is useful for finding any breaking changes that would -affect *sgkit*, so we can report or try to fix the problem before the upstream library is released. +Dependencies for tests, documentation, linting, and packaging checks are listed in +the ``test``, ``docs``, ``lint``, and ``packaging`` groups in ``pyproject.toml``. +The ``dev`` group includes all four for local development. Build-system dependencies +are listed separately in ``[build-system].requires``. -Build dependencies are listed in ``requirements-dev.txt`` and ``requirements-doc.txt``. +.. _contributing_docs: Contributing to documentation @@ -266,21 +270,33 @@ and API documentation. Building the documentation requires the Graphviz ``dot`` executable, which you can install by following `these instructions `_. -You can build the documentation locally with ``make``:: +Documentation builds use the same ``.venv`` as development. Task-graph +visualization with NumPy 2 needs a newer Dask than the current runtime bound. +From the repository root, on macOS or Linux, prepare the environment and build +with ``make``:: + uv sync --locked + uv pip uninstall --python .venv/bin/python dask-expr + uv pip install --python .venv/bin/python 'dask==2026.8.0' cd docs make html -The resulting HTML files end up in the ``_build/html`` directory. +The old ``dask-expr`` package is removed because it pins the runtime Dask version. +The Makefile uses ``uv run --no-sync`` to preserve the Dask override during builds. +Docs CI applies the same override. -You can now make edits to ``.rst`` files and run ``make html`` again to update -the affected pages. +The resulting HTML files are in ``_build/html``. After editing documentation, +run ``make html`` again. -The documentation build is checked by CI to ensure that it builds -without warnings. You can do that locally with:: +CI checks documentation with warnings treated as errors. Run the same check +locally with:: make clean html SPHINXOPTS="-W --keep-going -n" +Before running tests, restore the locked development dependencies with +``uv sync --locked`` from the repository root. Repeat the Dask setup above when +you next build the documentation. + .. _Sphinx: https://www.sphinx-doc.org/ Review process diff --git a/pyproject.toml b/pyproject.toml index bac546e5a..92194c0c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,6 +56,61 @@ content-type = "text/x-rst" plink = ["partd", "bed-reader"] bgen = ["rechunker", "cbgen > 1.0.5"] +[dependency-groups] +test = [ + "packaging", + "callee", + "pytest", + "pytest-cov", + "pytest-datadir", + "pytest-mock", + "hypothesis", + "scikit-allel", + "statsmodels", + "msprime>=1.0", + "bio2zarr[vcf]; platform_system != \"Windows\"", + "yarl", + "matplotlib", + "networkx", + "aiohttp", + "requests", + "graphviz", + # Exercise both optional I/O formats with `uv run pytest`. + "partd", + "bed-reader", + "rechunker", + "cbgen > 1.0.5", +] +docs = [ + "graphviz", + "myst_nb", + "pydata-sphinx-theme", + "sphinx < 9.0.0", + "sphinx_autodoc_typehints", + "sphinx-copybutton", + "scanpydoc", + "ipython", + "matplotlib", + "seaborn", + "ablog!=0.10.27", + "pickleshare", +] +lint = [ + "pre-commit", +] +packaging = [ + "twine", +] +dev = [ + { include-group = "test" }, + { include-group = "docs" }, + { include-group = "lint" }, + { include-group = "packaging" }, +] + +[tool.uv] +required-version = ">=0.12.10" + [tool.setuptools] packages = ["sgkit"] zip-safe = false # https://mypy.readthedocs.io/en/latest/installed_packages.html diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index c733d611f..000000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,22 +0,0 @@ -callee -pre-commit -pytest -pytest-cov -pytest-datadir -pytest-mock -hypothesis -scikit-allel -statsmodels -msprime>=1.0 -scikit-learn -partd -bed-reader -rechunker -cbgen > 1.0.5 -bio2zarr[vcf]; platform_system != "Windows" -yarl -matplotlib -networkx -aiohttp -requests -graphviz diff --git a/requirements-doc.txt b/requirements-doc.txt deleted file mode 100644 index e0513f475..000000000 --- a/requirements-doc.txt 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