Add github action for installing python and poetry

Some of the workflows were installing the dependencies using pip,
which always grabs the latest allowed package version. This was
causing subtle failures in some cases since the new versions may not
be compatible (e.g. numpy 2) or have bugs (e.g. pandas). This adds a
re-usable action so all the workflows setup python in the same way,
and install packages with poetry (which will follow the lock file).

Author: Jacob Garber

.github/actions/setup-python/action.yaml

@@ -0,0 +1,22 @@
+name: 'Setup python and poetry'
+inputs:
+  python-version:
+    required: true
+runs:
+  using: "composite"
+  steps:
+    - name: Install poetry
+      shell: bash
+      run: pipx install poetry
+
+    - name: Setup python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ inputs.python-version }}
+        cache: poetry
+
+    - name: Install packages
+      shell: bash
+      run: |
+        poetry env use ${{ inputs.python-version }}
+        poetry install --extras dev

.github/workflows/coverage.yml

@@ -16,16 +16,12 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup python
-        uses: actions/setup-python@v5
+        uses: ./.github/actions/setup-python
         with:
-          python-version: "3.10"
-          cache: "pip"
-
-      - name: Install package
-        run: pip install .[dev]
+          python-version: "3.12"
 
       - name: Run unit tests with coverage
-        run: pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml
+        run: poetry run pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v3

.github/workflows/integration_tests.yml

@@ -21,13 +21,9 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup python
-        uses: actions/setup-python@v5
+        uses: ./.github/actions/setup-python
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
-
-      - name: Install package
-        run: pip install .[dev]
 
       - id: 'auth'
         name: 'Set up Google Cloud authentication'
@@ -50,7 +46,7 @@ jobs:
           key: gcs_cache_integration_tests_20240922
 
       - name: Run integration tests
-        run: pytest --durations=20 -v tests/integration
+        run: poetry run pytest --durations=20 -v tests/integration
 
       - name: Save GCS cache
         uses: actions/cache/save@v3

.github/workflows/latest_docs.yml

@@ -12,20 +12,14 @@ jobs:
       - name: Check out source 🛒
         uses: actions/checkout@v4
 
-      - name: Set up Python 🐍
-        uses: actions/setup-python@v5
+      - name: Setup python 🐍
+        uses: ./.github/actions/setup-python
         with:
           python-version: '3.12'
 
-      - name: Install poetry
-        run: pipx install poetry==1.8.3
-
       - name: Eyeball native environment 👀
         run: python --version ; pip --version ; poetry --version ; pwd ; ls -la
 
-      - name: Install package dependencies 📜
-        run: poetry install
-
       - name: Build HTML 🏗️
         run: poetry run sphinx-build -b html docs/source docs/build/html
 

.github/workflows/linting.yml

@@ -16,17 +16,12 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Setup python
-              uses: actions/setup-python@v5
+              uses: ./.github/actions/setup-python
               with:
                   python-version: '3.12'
-                  cache: 'pip'
 
             - name: Run pre-commit checks
               uses: pre-commit/action@v3.0.0
 
-            - name: Install package
-              run: pip install .[dev]
-
             - name: Run mypy
-              run: |
-                  mypy malariagen_data tests --ignore-missing-imports
+              run: poetry run mypy malariagen_data tests --ignore-missing-imports

.github/workflows/notebooks.yml

@@ -17,13 +17,9 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup python
-        uses: actions/setup-python@v5
+        uses: ./.github/actions/setup-python
         with:
           python-version: "3.12"
-          cache: "pip"
-
-      - name: Install package
-        run: pip install .[dev]
 
       - id: 'auth'
         name: 'Set up Google Cloud authentication'
@@ -46,7 +42,7 @@ jobs:
           key: gcs_cache_notebooks_20240922
 
       - name: Run notebooks
-        run: jupyter nbconvert --execute notebooks/*.ipynb --inplace
+        run: poetry run jupyter nbconvert --execute notebooks/*.ipynb --inplace
 
       - name: Save GCS cache
         uses: actions/cache/save@v3

.github/workflows/release.yml

@@ -10,14 +10,10 @@ jobs:
             - name: Checkout source
               uses: actions/checkout@v4
 
-            - name: Install poetry
-              run: pipx install poetry==1.8.3
-
             - name: Setup python
-              uses: actions/setup-python@v5
+              uses: ./.github/actions/setup-python
               with:
                   python-version: '3.12'
-                  cache: 'poetry'
 
             - name: Configure poetry
               run: |

.github/workflows/tagged_docs.yml

@@ -24,20 +24,14 @@ jobs:
         with:
           ref: ${{ env.VERSION_TAG }}
 
-      - name: Set up Python 🐍
-        uses: actions/setup-python@v5
+      - name: Setup python 🐍
+        uses: ./.github/actions/setup-python
         with:
           python-version: '3.12'
 
-      - name: Install poetry
-        run: pipx install poetry==1.8.3
-
       - name: Eyeball native environment 👀
         run: python --version ; pip --version ; poetry --version ; pwd ; ls -la
 
-      - name: Install package dependencies 📜
-        run: poetry install
-
       - name: Build HTML 🏗️
         run: poetry run sphinx-build -b html docs/source docs/build/html
 

.github/workflows/tests.yml

@@ -11,25 +11,20 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.10"]
-        numpy-version: ["numpy==1.26.4"]
+        python-version: ["3.10", "3.11", "3.12"]
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout source
         uses: actions/checkout@v4
 
       - name: Setup python
-        uses: actions/setup-python@v5
+        uses: ./.github/actions/setup-python
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
-
-      - name: Install package
-        run: pip install "${{ matrix.numpy-version }}" .[dev]
 
       - name: Verify NumPy version
-        run: python -c "import numpy; print('NumPy version:', numpy.__version__)"
+        run: poetry run python -c "import numpy; print('NumPy version:', numpy.__version__)"
 
       - name: Run unit tests
-        run: pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph
+        run: poetry run pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph