diff --git a/.github/workflows/CI_pull_request.yml b/.github/workflows/CI_pull_request.yml index f801f575..311bd4d9 100644 --- a/.github/workflows/CI_pull_request.yml +++ b/.github/workflows/CI_pull_request.yml @@ -11,19 +11,33 @@ jobs: name: Lint and check formatting runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - name: Checkout code + uses: actions/checkout@v4 + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Verify the uv.lock is up-to-date + run: uv lock --check + - name: Install linting dependencies + run: uv sync --python 3.12 --managed-python --group=lint --frozen + - name: Restore pre-commit cache + uses: actions/cache@v4 with: - python-version: "3.x" - - uses: pre-commit/action@v3.0.1 + path: ~/.cache/pre-commit + key: pre-commit-3-${{ hashFiles('.pre-commit-config.yaml') }} + - name: Run pre-commit on all files + run: uv run pre-commit run --show-diff-on-failure --color=always --all-files build: name: Build package runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v5 - - run: uv build . - - uses: actions/upload-artifact@v4 + - name: Checkout code + uses: actions/checkout@v4 + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Build the Python Package + run: uv build + - name: Upload build artifacts for subsequent workflow steps + uses: actions/upload-artifact@v4 with: name: dist path: dist @@ -65,17 +79,14 @@ jobs: run: | sudo apt install ./singularity_installer.deb singularity --version - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: pip + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Install test dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install -e .[tests] + run: uv sync --python ${{ matrix.python-version }} --managed-python --group=tests --frozen + - name: Run test suite via pytest - run: pytest -vv --junitxml=pytest_junit_out.xml + run: uv run pytest -vv --junitxml=pytest_junit_out.xml - name: Archive the test results and coverage uses: actions/upload-artifact@v4 with: @@ -106,18 +117,13 @@ jobs: sudo apt update sudo apt install -y apptainer singularity --version - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: pip - cache-dependency-path: "**/test-requirements.txt" + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Install test dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install -r test-requirements.txt + run: uv sync --python ${{ matrix.python-version }} --managed-python --group=tests --frozen - name: Run test suite via pytest - run: pytest -vv --junitxml=pytest_junit_out.xml + run: uv run pytest -vv --junitxml=pytest_junit_out.xml - name: Archive the test results and coverage uses: actions/upload-artifact@v4 with: diff --git a/.github/workflows/CI_push.yml b/.github/workflows/CI_push.yml index 27ad1335..da312d13 100644 --- a/.github/workflows/CI_push.yml +++ b/.github/workflows/CI_push.yml @@ -10,11 +10,21 @@ jobs: name: Lint and check formatting runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 + - name: Checkout code + uses: actions/checkout@v4 + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Verify the uv.lock is up-to-date + run: uv lock --check + - name: Install linting dependencies + run: uv sync --python 3.12 --managed-python --group=lint --frozen + - name: Restore pre-commit cache + uses: actions/cache@v4 with: - python-version: "3.x" - - uses: pre-commit/action@v3.0.1 + path: ~/.cache/pre-commit + key: pre-commit-3-${{ hashFiles('.pre-commit-config.yaml') }} + - name: Run pre-commit on all files + run: uv run pre-commit run --show-diff-on-failure --color=always --all-files run-unittests: name: Run unittests runs-on: ubuntu-latest @@ -25,14 +35,10 @@ jobs: steps: - name: Checkout code uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: pip + - name: Set up uv + uses: astral-sh/setup-uv@v5 + - name: Install test dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install -e .[tests] + run: uv sync --python ${{ matrix.python-version }} --managed-python --group=tests --frozen - name: Run unittests via pytest - run: pytest -vv -m "not endtoend and not singularity_integration and not conda_integration" + run: uv run pytest -vv -m "not endtoend and not singularity_integration and not conda_integration" diff --git a/.github/workflows/SCHED_docs_linkcheck.yml b/.github/workflows/SCHED_docs_linkcheck.yml index f664c763..5673b869 100644 --- a/.github/workflows/SCHED_docs_linkcheck.yml +++ b/.github/workflows/SCHED_docs_linkcheck.yml @@ -13,21 +13,17 @@ jobs: steps: - name: Checkout code uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.x' - cache: pip - - name: Install docs dependencies - run: | - python3 -m pip install --upgrade pip - python3 -m pip install -e .[docs] + - name: Set up uv + uses: astral-sh/setup-uv@v5 + + - name: Install test dependencies + run: uv sync --python 3.12 --managed-python --group=docs --frozen - name: Build documentation run: | - make -C doc apidoc - make -C doc relnotes - make -C doc html + uv run make -C doc apidoc + uv run make -C doc relnotes + uv run make -C doc html - name: Run Sphinx linkcheck on documentation env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: make -C doc linkcheck + run: uv run make -C doc linkcheck diff --git a/.readthedocs.yml b/.readthedocs.yml index 8680d836..a2d88d18 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -3,19 +3,20 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: python: "3" jobs: + create_environment: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + install: + - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --frozen --group docs --link-mode=copy pre_build: - - make -C doc apidoc - - make -C doc relnotes + - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv run make -C doc apidoc + - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv run make -C doc relnotes sphinx: builder: html configuration: doc/conf.py fail_on_warning: true -python: - install: - - path: . - extra_requirements: - - docs diff --git a/pyproject.toml b/pyproject.toml index 8d2b3c71..b3985505 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,38 +39,30 @@ classifiers = [ "Programming Language :: Python :: 3.12", ] -[project.optional-dependencies] +[project.scripts] +cotainr = "cotainr.cli:main" + +[project.urls] +Documentation = "https://cotainr.readthedocs.io/en/stable/" +Repository = "https://github.com/DeiC-HPC/cotainr.git" +"Bug Tracker" = "https://github.com/DeiC-HPC/cotainr/issues" +Changelog = "https://cotainr.readthedocs.io/en/stable/release_notes/index.html" + +[dependency-groups] tests = [ "pytest-cov>=2.10", "pytest>=6.0" ] lint = [ - "cfgv>=3.4.0", - "distlib>=0.3.9", - "filelock>=3.17.0", - "identify>=2.6.6", - "nodeenv>=1.9.1", - "platformdirs>=4.3.6", "pre-commit>=4.1.0", - "virtualenv>=20.29.1", ] docs = [ - "numpydoc>=1.5.0", "pydata-sphinx-theme>=0.13.3", - "sphinx>=7.2.5", "sphinx-design>=0.5.0", "myst-parser>=2.0.0", + "numpydoc>=1.5.0" ] -dev = ["cotainr[tests,lint,docs]"] - -[project.scripts] -cotainr = "cotainr.cli:main" - -[project.urls] -Documentation = "https://cotainr.readthedocs.io/en/stable/" -Repository = "https://github.com/DeiC-HPC/cotainr.git" -"Bug Tracker" = "https://github.com/DeiC-HPC/cotainr/issues" -Changelog = "https://cotainr.readthedocs.io/en/stable/release_notes/index.html" +dev = [{include-group = "tests"}, {include-group = "lint"}, {include-group = "docs"}] [tool.hatch.version] path = "cotainr/__init__.py" diff --git a/uv.lock b/uv.lock index e027d339..7e5d1d1c 100644 --- a/uv.lock +++ b/uv.lock @@ -1,4 +1,5 @@ version = 1 +revision = 1 requires-python = ">=3.9" resolution-markers = [ "python_full_version >= '3.11'", @@ -170,46 +171,26 @@ wheels = [ name = "cotainr" source = { editable = "." } -[package.optional-dependencies] +[package.dev-dependencies] dev = [ - { name = "cfgv" }, - { name = "distlib" }, - { name = "filelock" }, - { name = "identify" }, { name = "myst-parser", version = "3.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "myst-parser", version = "4.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, - { name = "nodeenv" }, { name = "numpydoc" }, - { name = "platformdirs" }, { name = "pre-commit" }, { name = "pydata-sphinx-theme" }, { name = "pytest" }, { name = "pytest-cov" }, - { name = "sphinx", version = "7.4.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "sphinx", version = "8.1.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, - { name = "sphinx", version = "8.2.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, { name = "sphinx-design" }, - { name = "virtualenv" }, ] docs = [ { name = "myst-parser", version = "3.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, { name = "myst-parser", version = "4.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, { name = "numpydoc" }, { name = "pydata-sphinx-theme" }, - { name = "sphinx", version = "7.4.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" }, - { name = "sphinx", version = "8.1.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version == '3.10.*'" }, - { name = "sphinx", version = "8.2.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, { name = "sphinx-design" }, ] lint = [ - { name = "cfgv" }, - { name = "distlib" }, - { name = "filelock" }, - { name = "identify" }, - { name = "nodeenv" }, - { name = "platformdirs" }, { name = "pre-commit" }, - { name = "virtualenv" }, ] tests = [ { name = "pytest" }, @@ -217,107 +198,97 @@ tests = [ ] [package.metadata] -requires-dist = [ - { name = "cfgv", marker = "extra == 'dev'", specifier = ">=3.4.0" }, - { name = "cfgv", marker = "extra == 'lint'", specifier = ">=3.4.0" }, - { name = "distlib", marker = "extra == 'dev'", specifier = ">=0.3.9" }, - { name = "distlib", marker = "extra == 'lint'", specifier = ">=0.3.9" }, - { name = "filelock", marker = "extra == 'dev'", specifier = ">=3.17.0" }, - { name = "filelock", marker = "extra == 'lint'", specifier = ">=3.17.0" }, - { name = "identify", marker = "extra 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