Upgraded Python Tests GA to setup-uv

Removed system from uv pip Installing Python is not explicit Added glob cache Add flake8 to dev requirements Removed pyflake not installing to system Removed frozen Fixed syntax Moved benchmarking and publish to setup-uv Changed publish GA action Added lockfile Moved all actions to 3.13 Went back to python version via uv Uniformed GA
alcides · Dec 9, 2024 · 8f5bd25 · 8f5bd25
1 parent fb1ad24
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diff --git a/.github/workflows/python-benchmarking.yml b/.github/workflows/python-benchmarking.yml
@@ -5,44 +5,52 @@ name: Python Benchmarking
 
 on:
   push:
-    branches: [ main ]
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
 
 jobs:
-  benchmark:
+  tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
-    - uses: actions/checkout@v4.1.1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-benchmark mypy
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-    - name: Check install
-      run: |
-        pip install -e .
-    - name: Test with pytest
-      run: |
-        pytest --benchmark-only --benchmark-json output.json
-    - name: Store benchmark result
-      uses: benchmark-action/github-action-benchmark@v1
-      with:
-        name: Python Benchmark with pytest-benchmark
-        tool: 'pytest'
-        output-file-path: output.json
-        # Use personal access token instead of GITHUB_TOKEN due to https://github.community/t/github-action-not-triggering-gh-pages-upon-push/16096
-        github-token: ${{ secrets.BENCHMARK_REPO_TOKEN }}
-        gh-repository: github.com/alcides/GeneticEngineBenchmarkResults
-        auto-push: true
-        # Show alert with commit comment on detecting possible performance regression
-        alert-threshold: '200%'
-        comment-on-alert: true
-        alert-comment-cc-users: '@alcides'
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv and set the python version
+        uses: astral-sh/setup-uv@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Create venv
+        run: |
+          uv venv
+      - name: Install dependencies
+        run: |
+          if [ -f requirements.txt ]; then uv pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then uv pip install -r requirements-dev.txt; fi
+      - name: Check install
+        run: |
+          uv pip install  -e .
+      - name: Test with pytest
+        run: |
+          uv run --frozen pytest --benchmark-only --benchmark-json output.json
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Python Benchmark with pytest-benchmark
+          tool: 'pytest'
+          output-file-path: output.json
+          # Use personal access token instead of GITHUB_TOKEN due to https://github.community/t/github-action-not-triggering-gh-pages-upon-push/16096
+          github-token: ${{ secrets.BENCHMARK_REPO_TOKEN }}
+          gh-repository: github.com/alcides/GeneticEngineBenchmarkResults
+          auto-push: true
+          # Show alert with commit comment on detecting possible performance regression
+          alert-threshold: '200%'
+          comment-on-alert: true
+          alert-comment-cc-users: '@alcides'
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -8,30 +8,42 @@
 
 name: Upload Python Package
 
-on: [push, pull_request]
+on:
+  push:
+    branches: ["main"]
 
-jobs:
-  deploy:
 
+jobs:
+  tests:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.13"]
 
     steps:
-    - uses: actions/checkout@v4.1.1
-    - name: Set up Python
-      uses: actions/setup-python@v5.0.0
-      with:
-        python-version: '3.x'
-    # - name: Set env
-    #   run: echo "VIRTUAL_ENV=$(python -c 'import sys; print(sys.prefix)')">> $GITHUB_ENV
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade uv
-        uv pip install  --system build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      if: github.repository == 'alcides/GeneticEngine' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv and set the python version
+        uses: astral-sh/setup-uv@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Create venv
+        run: |
+          uv venv
+      - name: Install dependencies
+        run: |
+          if [ -f requirements.txt ]; then uv pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then uv pip install -r requirements-dev.txt; fi
+      - name: Lint with mypy
+        run: |
+          uv run mypy --no-strict-optional --ignore-missing-imports --explicit-package-bases geneticengine
+      - name: Check install
+        run: |
+          uv pip install  -e .
+      - name: Build package
+        run: uv build
+      - name: Publish
+        run: uv publish -t ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml
@@ -5,48 +5,44 @@ name: Python Tests
 
 on:
   push:
-    branches: [main]
+    branches: ["*"]
   pull_request:
-    branches: [main]
+    branches: ["*"]
 
 jobs:
   tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4.1.1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv and set the python version
+        uses: astral-sh/setup-uv@v4
         with:
           python-version: ${{ matrix.python-version }}
-      # - name: Set env
-      #   run: echo "VIRTUAL_ENV=$(python -c 'import sys; print(sys.prefix)')">> $GITHUB_ENV
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Create venv
+        run: |
+          uv venv
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade uv
-          uv pip install --system flake8 pytest mypy
-          if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
-          if [ -f requirements-dev.txt ]; then uv pip install --system -r requirements-dev.txt; fi
+          if [ -f requirements.txt ]; then uv pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then uv pip install -r requirements-dev.txt; fi
       - name: Lint with mypy
         run: |
-          mypy --no-strict-optional --ignore-missing-imports --explicit-package-bases geneticengine
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          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=127 --statistics
+          uv run mypy --no-strict-optional --ignore-missing-imports --explicit-package-bases geneticengine
       - name: Check install
         run: |
-          uv pip install --system  -e .
+          uv pip install  -e .
       - name: Test with pytest
-        run: |
-          pytest --cov --benchmark-skip
+        run: uv run --frozen pytest --cov --benchmark-skip
       - name: Upload coverage reports to Codecov
-        if: ${{ (matrix.python-version == '3.11') }}
+        if: ${{ (matrix.python-version == '3.13') }}
         uses: codecov/codecov-action@v3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/run-examples.yml b/.github/workflows/run-examples.yml
@@ -14,25 +14,33 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
+
 
     steps:
-    - uses: actions/checkout@v4.1.1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    # - name: Set env
-    #   run: echo "VIRTUAL_ENV=$(python -c 'import sys; print(sys.prefix)')">> $GITHUB_ENV
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade uv
-        uv pip install --system flake8 pytest mypy
-        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
-        if [ -f requirements-dev.txt ]; then uv pip install --system -r requirements-dev.txt; fi
-    - name: Check install
-      run: |
-        uv pip install --system -e .
-    - name: Run Examples Bash
-      run: |
-        bash run_examples.sh
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv and set the python version
+        uses: astral-sh/setup-uv@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: |
+            **/requirements*.txt
+            **/pyproject.toml
+      - name: Create venv
+        run: |
+          uv venv
+      - name: Install dependencies
+        run: |
+          if [ -f requirements.txt ]; then uv pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then uv pip install -r requirements-dev.txt; fi
+      - name: Lint with mypy
+        run: |
+          uv run mypy --no-strict-optional --ignore-missing-imports --explicit-package-bases geneticengine
+      - name: Check install
+        run: |
+          uv pip install  -e .
+      - name: Run Examples Bash
+        run: |
+          source .venv/bin/activate
+          bash run_examples.sh
diff --git a/pyproject.toml b/pyproject.toml
@@ -20,6 +20,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
     'dill==0.3.9',

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -4,6 +4,6 @@ mypy==1.13.0
 pre-commit
 pycln
 pytest
-pytest-cov
 pytest-codspeed
+pytest-cov
 ruff