Moving GA to setup-uv instead of setup-python

.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'

.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 }}

.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 }}

.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

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',

requirements-dev.txt

@@ -4,6 +4,6 @@ mypy==1.13.0
 pre-commit
 pycln
 pytest
-pytest-cov
 pytest-codspeed
+pytest-cov
 ruff