AB#525 Consolidated setup in pyproject.toml and updated GH-actions ve…

…rsions.

.github/workflows/CI_pull_request.yml

@@ -24,9 +24,9 @@ jobs:
             singularity-version: "3.9.2"
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Attempt to restore Singularity/Apptainer installer from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache-singularity-installer
         with:
           path: ./singularity_installer.deb
@@ -45,19 +45,22 @@ jobs:
           sudo apt install ./singularity_installer.deb
           singularity --version
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-          cache-dependency-path: "**/test-requirements.txt"
+          cache-dependency-path: |
+            **/pyproject.toml
+            **/tests/__init__.py  # Make cache key depend on test file to differentiate from docs cache
       - name: Install test dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install -r test-requirements.txt
+          python3 -m pip install flit>=3.4
+          flit install --only-deps --extras=test
       - name: Run test suite via pytest
         run: pytest -vv --junitxml=pytest_junit_out.xml
       - name: Archive the test results and coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: test-results-and-coverage_python${{ matrix.python-version }}_${{ matrix.singularity-provider }}${{ matrix.singularity-version }}
           path: |

.github/workflows/CI_push.yml

@@ -15,16 +15,19 @@ jobs:
         python-version: ["3.9", "3.11"]
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-          cache-dependency-path: "**/test-requirements.txt"
+          cache-dependency-path: |
+            **/pyproject.toml
+            **/tests/__init__.py  # Make cache key depend on test file to differentiate from docs cache
       - name: Install test dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install -r test-requirements.txt
+          python3 -m pip install flit>=3.4
+          flit install --only-deps --extras=test
       - name: Run unittests via pytest
         run: pytest -vv -m "not endtoend and not singularity_integration and not conda_integration"

.github/workflows/SCHED_docs_linkcheck.yml

@@ -9,17 +9,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.x'
           cache: pip
-          cache-dependency-path: "**/docs-requirements.txt"
+          cache-dependency-path: |
+            **/pyproject.toml
+            **/doc/conf.py  # Make cache key depend on docs file to differentiate from test cache
       - name: Install docs dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install -r docs-requirements.txt
+          python3 -m pip install flit>=3.4
+          flit install --only-deps --extras=docs
       - name: Build documentation
         run: |
           make -C doc apidoc

.readthedocs.yml

@@ -8,12 +8,11 @@ build:
     python: "3"
   jobs:
     pre_build:
+      - python3 -m pip install flit>=3.4
+      - flit install --only-deps --extras=docs
       - make -C doc apidoc
       - make -C doc relnotes
 sphinx:
   builder: html
   configuration: doc/conf.py
   fail_on_warning: true
-python:
-  install:
-  - requirements: docs-requirements.txt

pyproject.toml

@@ -0,0 +1,63 @@
+[build-system]
+requires = ["flit_core >=3.4,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "cotainr"
+authors = [{name = "DeiC, deic.dk"}]
+readme = "README.md"
+dynamic = ["version", "description"]
+requires-python = ">=3.8"  # Synchronize this with _minimum_dependency_version in __init__.py
+maintainers = [
+    {name = "Christian Schou Oxvig"},
+    {name = "Eske Christiansen"}]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",  # Synchronize this with _minimum_dependency_version in __init__.py and the CI setup
+    "Topic :: Scientific/Engineering",
+]
+keywords = ["container", "singularity", "apptainer"]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6.0",
+    "pytest-cov>=2.10",
+]
+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",
+]
+
+[project.urls]
+Documentation = "https://cotainr.readthedocs.io"
+Source = "https://github.com/DeiC-HPC/cotainr"
+Issues = "https://github.com/DeiC-HPC/cotainr/issues"
+
+[project.scripts]
+cotainr = "cotainr.cli:main"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-ra -l --cov --cov-report=term-missing --cov-report=html"
+testpaths = ["cotainr/tests"]
+junit_suite_name = "cotainr_test_suite"
+markers = [
+    "conda_integration: marks tests of integration with conda/mamba",
+    "endtoend: marks end-to-end test cases",
+    "singularity_integration: marks tests of integration with singularity",
+]
+
+[tool.coverage.run]
+source = ["cotainr"]
+omit = ["cotainr/tests/*"]
+branch = true