refactor: migrate to uv

.github/workflows/coverage.yml

@@ -15,17 +15,17 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Set up Python 3.11
+      - name: Set up Python 3.13
         uses: actions/setup-python@v3
         with:
-          python-version: '3.11'
+          python-version: '3.13'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest
-          pip install -e '.[dev]'
+          pip install uv
+          uv sync
       - name: Test Coverage
         run: |-
-          pytest --junitxml=pytest.xml --cov-report=term-missing --cov=src tests/*/test_integration_*.py | tee pytest-coverage.txt
+          uv run pytest --junitxml=pytest.xml --cov-report=term-missing --cov=src tests/*/test_integration_*.py | tee pytest-coverage.txt
       - name: Comment coverage
         uses: coroo/pytest-coverage-commentator@v1.0.2

.github/workflows/python_tests.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-versions: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-versions: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -26,19 +26,19 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest
-          pip install -e '.[dev]'
+          pip install uv
+          uv sync
       - name: Test with pytest
         run: |
-          pytest src/*/test_*.py
+          uv run pytest src tests/*/test_unit_*.py
   integration_tests:
     runs-on: ubuntu-latest
     needs: unit_tests
     strategy:
       fail-fast: true
       matrix:
-        # no 3.11 as it's covered by the Coverage job.
-        python-versions: ['3.8', '3.9', '3.10', '3.12']
+        # no 3.12 as it's covered by the Coverage job.
+        python-versions: ['3.8', '3.9', '3.10', '3.11', '3.13', '3.14']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -48,18 +48,18 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          pip install -e '.[dev]'
+          pip install uv
+          uv sync
       - name: Test with pytest
         run: |
-          pytest tests/*/test_integration_*.py
+          uv run pytest tests/*/test_integration_*.py
   system_tests:
     needs: integration_tests
     runs-on: ubuntu-latest
     strategy:
       fail-fast: true
       matrix:
-        python-versions: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-versions: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -69,30 +69,27 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          pip install -e '.[dev]'
+          pip install uv
+          uv sync
       - name: Test with pytest
         run: |
-          pytest tests/*/test_system_*.py
+          uv run pytest tests/*/test_system_*.py
   style:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.10
+      - name: Set up Python
         uses: actions/setup-python@v3
-      - uses: psf/black@stable
         with:
-          options: --check --verbose
-          src: ./src
-          version: ~= 22.0
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
-          pip install flake8
-      - name: Lint with flake8
+          pip install uv
+          uv sync
+      - name: Lint with ruff
         run: |-
           # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          uv run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --statistics
+          uv run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --statistics

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ exclude: |
 repos:
   # GENERAL PURPOSE  ##################################################################
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: [--maxkb=500]
@@ -37,34 +37,49 @@ repos:
       - id: check-executables-have-shebangs
       - id: check-shebang-scripts-are-executable
 
-  # - repo: https://github.com/commitizen-tools/commitizen
-  #   rev: v4.1.0
-  #   hooks:
-  #     - id: commitizen
+  # Enforce conventional commit messages
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v4.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
 
+  # Spellchecking
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         args: [-w]
+        exclude: uv.lock
 
   - repo: https://github.com/BenjaminMummery/pre-commit-hooks
-    rev: v2.6.0
+    rev: v2.8.0
     hooks:
       - id: add-copyright
+        exclude: .github/|README.md
       - id: add-msg-issue
       - id: update-copyright
       - id: sort-file-contents
         files: .gitignore
 
+  # update the uv lock
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: '0.10.0'
+    hooks:
+      - id: uv-lock
+
+  # Unify dependencies between pre-commit hooks.
+  - repo: https://github.com/pre-commit/sync-pre-commit-deps
+    rev: v0.0.3
+    hooks:
+      - id: sync-pre-commit-deps
+
   # C++ ###############################################################################
   - repo: https://github.com/pocc/pre-commit-hooks
     rev: 'v1.3.5'
     hooks:
       - id: clang-format
         args: [-i]
-      # - id: clang-tidy
-      #   args: [--fix-errors]
       - id: cppcheck
       - id: cpplint
 
@@ -83,58 +98,76 @@ repos:
 
   # PYTHON  ###########################################################################
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
       - id: check-docstring-first
       - id: debug-statements
-      - id: fix-encoding-pragma
-        args: [--remove]
       - id: requirements-txt-fixer
 
+  - repo: https://github.com/asottile/pyupgrade
+    rev: 'v3.21.2'
+    hooks:
+      - id: pyupgrade
+
+  # Remove unused imports
   - repo: https://github.com/hadialqattan/pycln
-    rev: v2.4.0
+    rev: v2.6.0
     hooks:
       - id: pycln
         exclude: __init__.py
 
+  # Sort imports
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 7.0.0
     hooks:
       - id: isort
         args: [--profile, black]
 
+  # Remove unneeded f-strings
   - repo: https://github.com/dannysepler/rm_unneeded_f_str
     rev: v0.2.0
     hooks:
       - id: rm-unneeded-f-str
 
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black
-
-  # - repo: https://github.com/PyCQA/flake8
-  #   rev: 7.1.1
+  # Lint with black
+  # - repo: https://github.com/psf/black
+  #   rev: 26.1.0
   #   hooks:
-  #     - id: flake8
-  #       entry: pflake8
-  #       additional_dependencies: [pyproject-flake8]
+  #     - id: black
 
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v1.13.0
-  #   hooks:
-  #     - id: mypy
-  #       additional_dependencies: ["types-all"]
+  # Static type checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.19.1
+    hooks:
+    -   id: mypy
 
+  # Detect missing docstrings
   - repo: https://github.com/econchick/interrogate # flags up missing docstrings
     rev: 1.7.0
     hooks:
       - id: interrogate
         args: [--config=pyproject.toml]
         exclude: test_.*\.py|conftest.py
 
+  # docstring checking
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        args: [--config=pyproject.toml, --count]
+        exclude: ^tests/|conftest.py
+
+  # Lint and format with ruff
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.15.0'
+    hooks:
+      - id: ruff
+        args: [--config=pyproject.toml]
+      - id: ruff-format
+        args: [--config=pyproject.toml]
+
   # - repo: https://github.com/pycqa/pydocstyle
   #   rev: 6.3.0
   #   hooks:
@@ -143,14 +176,27 @@ repos:
   #     additional_dependencies: [tomli]
   #     exclude: test_.*\.py|conftest.py
 
+  # JUPYTER NOPEBOOKS  ################################################################
+
+  # remove outputs from jupyter notebooks.
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        files: \.ipynb$
+        stages: [pre-commit]
+        language: system
+        entry: poetry run jupyter nbconvert --ClearOutputPreprocessor.enabled=True --ClearMetadataPreprocessor.enabled=True --inplace examples/*.ipynb
+
+
   # YAML  #############################################################################
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
 
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.17.0
+    rev: 1.19.1
     hooks:
       - id: yamlfix
         exclude: .pre-commit-config.yaml