Cleanups, updates to documentation, UV, remove ununsed modules (#111)

Author: fsoubelet

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,28 +3,32 @@
 This package implements different workflows for CI.
 They are organised as follows.
 
-### Documentation
+## Documentation
 
-The `documentation` workflow triggers on any push to master, builds the documentation and pushes it to the `gh-pages` branch (if the build is successful).
-It runs on `ubuntu-latest` and `Python 3.9`.
+The `documentation` workflow builds the documentation.
+It runs on `ubuntu-latest` and the latest supported Python version.
+If the workflow is run from `master` it pushes the successfully build documentation to the `gh-pages` branch.
+If run from a `pull_request` the documentation is uploaded as an artifact to allow manual checks.
 
-### Testing Suite
+## Testing Suite
 
-Tests are ensured in the `tests` workflow, which triggers on all pushes.
-Tests run on a matrix of all GitHub Actions supported operating systems for all supported Python versions (currently `3.8+`).
+Tests are ensured in the `tests` workflow.
+Tests run on a matrix of all supported operating systems and all currently supported Python versions.
 
-### Test Coverage
+## Test Coverage
 
-Test coverage is calculated in the `coverage` wokflow, which triggers on pushes to `master` and any push to a `pull request`.
-It runs on `ubuntu-latest` and `Python 3.9`, and reports the coverage results of the test suite to `Codecov`.
+Test coverage is calculated in the `coverage` workflow.
+It runs on `ubuntu-latest` and our latest supported Python version, and reports the coverage results of the test suite to `Codecov`.
 
-### Regular Testing
+## Regular Testing
 
-A `cron` workflow triggers every Saturday at 12:00 (UTC time) and runs the full testing suite, on all GitHub Actions supported operating systems for all supported Python versions (currently `3.8+`).
-It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically detected and reported.
+A `cron` workflow triggers every Saturday at 12:00 (UTC time) and runs the full testing suite, on all supported operating systems and supported Python versions.
+It is very similar to the normal Testing Suite, but in addition also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically included.
 
-### Publishing
+## Publishing
 
-Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the GitHub repository and runs on `ubuntu-latest` and `Python 3.9`.
-It builds a source distribution (`tar.gz`) and a `wheel` of the package, and pushes to `PyPI` if the builds are successful.
-No matrix is needed for this build as `pyhdtoolkit` is a pure python package and generates `*-py3-none-any.whl` wheels.
+Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made on GitHub.
+It runs on `ubuntu-latest` and the latest supported Python version.
+
+It builds the package (source distribution and `wheel`), checks the created artifacts, and pushes to `PyPI` if checks are successful.
+No matrix is needed for this build as `pyhdtoolkit` is a pure python package and generates `*-py3-none-any.whl` wheels.

.github/workflows/README.md

@@ -20,24 +20,23 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ env.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ env.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/pyproject.toml'
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
 
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
+      - name: Set up Python ${{ env.python-version }}
+        run: uv python install ${{ env.python-version }}
 
       - name: Install package with test dependencies
-        run: python -m pip install ".[test]"
+        run: uv sync --all-extras --dev
 
       - name: Get acc-models-lhc
         run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
 
       - name: Run all tests
-        run: make alltests
+        run: make tests
 
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v4

.github/workflows/coverage.yml

@@ -22,21 +22,20 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/pyproject.toml'
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
-
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+  
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+  
       - name: Install package with test dependencies
-        run: python -m pip install ".[test]"
+        run: uv sync --all-extras --dev
 
       - name: Get acc-models-lhc
         run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
 
       - name: Run Tests
-        run: make alltests
+        run: make tests

.github/workflows/cron.yml

@@ -29,18 +29,17 @@ jobs:
       - name: Install optipng, dvipng and cm-super
         run: sudo apt-get install -y optipng dvipng cm-super
 
-      - name: Set up Python ${{ env.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ env.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/pyproject.toml'
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+  
+      - name: Set up Python ${{ env.python-version }}
+        run: uv python install ${{ env.python-version }}
 
-      - name: Install package with doc dependencies
-        run: python -m pip install ".[docs]"
+      - name: Install package with test dependencies
+        run: uv sync --all-extras --dev
 
       - name: Get acc-models-lhc
         run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1

.github/workflows/documentation.yml

@@ -19,8 +19,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install hatch
-        run: pipx install hatch
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+
+      - name: Set up Python ${{ env.python-version }}
+        run: uv python install ${{ env.python-version }}
 
       - name: Build wheels and sdist
         run: make build

.github/workflows/publish.yml

@@ -10,7 +10,7 @@ on:  # Runs on any push event to any branch except master (the coverage workflow
       - 'master'
 
 jobs:
-  quick_tests:
+  tests:
     name: ${{ matrix.os }} / ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -22,44 +22,17 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: '**/pyproject.toml'
-
-      - name: Install package with test dependencies
-        run: python -m pip install ".[test]"
-
-      - name: Run Tests
-        run: make quicktests
-
-  cpymad_tests:
-    needs: quick_tests
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-22.04, ubuntu-24.04, macos-latest, windows-latest]
-        python-version: ["3.10", 3.11, 3.12]
-      fail-fast: false
-
-    steps:
-      - uses: actions/checkout@v4
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: '**/pyproject.toml'
-
-      - name: Install package
-        run: python -m pip install ".[test]"
-
-      - name: Get acc-models-lhc
-        run: git clone -b 2022 https://gitlab.cern.ch/acc-models/acc-models-lhc.git --depth 1
+        run: uv python install ${{ matrix.python-version }}
+  
+      - name: Install package with test dependencies
+        run: uv sync --all-extras --dev
 
       - name: Run Tests
-        run: make slowtests
+        run: make tests

.github/workflows/tests.yml

@@ -12,34 +12,31 @@ D = \033[34m  # dark blue
 E = \033[0m  # end
 P = \033[95m  # pink
 R = \033[31m  # red
-# Y = \033[33m  # yellow
+Y = \033[33m  # yellow
 
-.PHONY : help build clean docker docs format install lines lint typing alltests quicktests slowtests
+.PHONY : help build clean docker docs format install lines lint typing tests
 
 all: install
 
 help:
 	@echo "Please use 'make $(R)<target>$(E)' where $(R)<target>$(E) is one of:"
-	@echo "  $(R) build $(E)  \t  to build wheel and source distribution with $(P)Hatch$(E)."
-	@echo "  $(R) clean $(E)  \t  to recursively remove build, run and bitecode files/dirs."
-	@echo "  $(R) docker $(E)  \t  to build a $(P)Docker$(E) container image replicating said environment (and other goodies)."
-	@echo "  $(R) docs $(E)  \t  to build the documentation for the package with $(P)Sphinx$(E)."
-	@echo "  $(R) format $(E)  \t  to recursively apply PEP8 formatting through the $(P)Black$(E) and $(P)isort$(E) cli tools."
-	@echo "  $(R) install $(E)  \t  to $(C)pip install$(E) this package into the current environment."
-	@echo "  $(R) lines $(E)  \t  to count lines of code with the $(P)tokei$(E) tool."
-	@echo "  $(R) lint $(E)  \t  to lint the code though $(P)Pylint$(E)."
-	@echo "  $(R) typing $(E)  \t  to run type checking on the codebase with $(P)MyPy$(E)."
-	@echo "  $(R) alltests $(E)  \t  to run the full test suite with $(P)pytest$(E)."
-	@echo "  $(R) quicktests $(E) \t  to run tests not involving $(D)pyhdtoolkit.cpymadtools$(E) with $(P)Pytest$(E)."
-	@echo "  $(R) slowtests $(E)  \t  to run tests involving $(D)pyhdtoolkit.cpymadtools$(E) with $(P)Pytest$(E)."
-
-
-# ----- Dev Tools Targets ----- #
+	@echo "  $(R) build $(E)   to build wheel and source distribution with $(P)uv$(E)."
+	@echo "  $(R) clean $(E)   to recursively remove build, run and bitecode files/dirs."
+	@echo "  $(R) docker $(E)  to build a $(P)Docker$(E) container image replicating said environment (and other goodies)."
+	@echo "  $(R) docs $(E)    to build the documentation for the package with $(P)Sphinx$(E)."
+	@echo "  $(R) format $(E)  to recursively apply PEP8 formatting through the $(P)Black$(E) and $(P)isort$(E) cli tools."
+	@echo "  $(R) install $(E) to install this package into the current environment (editable install)."
+	@echo "  $(R) lines $(E)   to count lines of code with the $(P)tokei$(E) tool."
+	@echo "  $(R) lint $(E)    to lint the code though $(P)Ruff$(E)."
+	@echo "  $(R) tests $(E)   to run the test suite with $(P)pytest$(E) (parallelized)."
+
+
+# ----- Dev Targets ----- #
 
 build:
 	@echo "Re-building wheel and dist"
 	@rm -rf dist
-	@hatch build --clean
+	@uv build
 	@echo "Created build is located in the $(C)dist$(E) folder."
 
 clean:
@@ -49,7 +46,7 @@ clean:
 	@echo "Cleaning up sphinx-gallery build artifacts."
 	@rm -rf docs/gallery
 	@rm -rf docs/gen_modules
-	@echo "Cleaning up distutils remains."
+	@echo "Cleaning up package build remains."
 	@rm -rf build
 	@rm -rf dist
 	@rm -rf pyhdtoolkit.egg-info
@@ -61,6 +58,7 @@ clean:
 	@echo "Cleaning up pytest cache & test artifacts."
 	@find . -type d -name '*.pytest_cache' -exec rm -rf {} + -o -type f -name '*.pytest_cache' -exec rm -rf {} +
 	@find . -type f -name 'fc.*' -delete -o -type f -name 'fort.*' -delete
+	@find . -type f -name 'checkpoint_restart.*' -delete -o -type f -name 'internal_mag_pot.*' -delete
 	@echo "Cleaning up mypy cache."
 	@find . -type d -name "*.mypy_cache" -exec rm -rf {} +
 	@echo "Cleaning up coverage reports."
@@ -75,41 +73,30 @@ docker:
 
 docs:
 	@echo "Building static pages with $(D)Sphinx$(E)."
-	@python -m sphinx -v -b html docs doc_build -d doc_build
+	@uv run python -m sphinx -v -b html docs doc_build -d doc_build
 
 format:
-	@echo "Formatting code to PEP8 with $(P)isort$(E) and $(P)Black$(E) for $(C)docs$(E), $(C)pyhdtoolkit$(E) and $(C)tests$(E) folders. Max line length is 120 characters."
-	@python -m isort . && black .
-	@echo "Formatting code to PEP8 with $(P)isort$(E) and $(P)Black$(E) for $(C)examples$(E) folder. Max line length is 95 characters."
-	@python -m isort examples && black -l 95 examples
-
-install: format clean
-	@echo "Installing (editable) with $(D)pip$(E) in the current environment."
-	@python -m pip install --editable . -v
-
-lines: format
+	@echo "Formatting code in $(C)docs$(E), $(C)tests$(E) and $(C)pyhdtoolkit$(E)."
+	@uvx isort docs && uvx black docs
+	@uvx isort tests && uvx black tests
+	@uvx isort pyhdtoolkit && uvx black pyhdtoolkit
+	@echo "Formatting code to PEP8 with $(P)isort$(E) and $(P)Black$(E) for $(C)examples$(E) folder."
+	@uvx isort examples && uvx black -l 95 examples
+
+install:
+	@echo "Installing (editable) the package in the current environment."
+	@uv pip install --editable .
+
+lines:
+	@echo "Counting lines of code with $(P)tokei$(E)."
 	@tokei .
 
-lint: format
-	@echo "Linting code with $(P)Pylint$(E)."
-	@python -m pylint pyhdtoolkit/
-
-typing: format
-	@echo "Checking code typing with $(P)mypy$(E)."
-	@python -m mypy pyhdtoolkit
-	@make clean
-
-
-# ----- Tests Targets ----- #
-
-quicktests:  # all tests not involving pyhdtoolkit.cpymadtools
-	@python -m pytest -k "not test_cpymadtools" -n auto -v
-
-slowtests:  # all tests for pyhdtoolkit.cpymadtools
-	@python -m pytest -k "test_cpymadtools" -n auto -v
+lint:
+	@echo "Linting code with $(P)Ruff$(E)."
+	@uvx ruff check pyhdtoolkit
 
-alltests:
-	@python -m pytest -n auto -v
+tests:
+	@uv run python -m pytest -n auto -v
 
 # Catch-all unknow targets without returning an error. This is a POSIX-compliant syntax.
 .DEFAULT: