Correct the dev dependency table PEP 735

.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/[email protected]
+          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:

.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/[email protected]
+          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"

.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

.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

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"