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‎.codecov.yml‎

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coverage:
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status:
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project:
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default:
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target: auto
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patch:
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default:
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target: 80%
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threshold: 0%

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

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

‎.github/workflows/coverage.yml‎

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name: coverage
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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coverage:
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strategy:
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fail-fast: true
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runs-on: ubuntu-latest
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steps:
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- name: Checkout source
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uses: actions/checkout@v4
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coverage:
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strategy:
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fail-fast: true
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runs-on: ubuntu-latest
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steps:
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- name: Checkout source
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: 'pip'
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- name: Setup python
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uses: ./.github/actions/setup-python
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with:
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python-version: "3.12"
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- name: Install package
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run: pip install .[dev]
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- name: Run unit tests with coverage
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run: poetry run pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml
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- name: Run unit tests with coverage
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run: pytest -v tests --ignore tests/integration --cov malariagen_data/anoph --cov-report=xml
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- name: Upload coverage report
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uses: codecov/codecov-action@v3
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with:
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files: ./coverage.xml
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verbose: true
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- name: Upload coverage report
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uses: codecov/codecov-action@v3
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with:
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files: ./coverage.xml
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verbose: true

‎.github/workflows/integration_tests.yml‎

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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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integration_tests:
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strategy:
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v5
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uses: ./.github/actions/setup-python
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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- name: Install package
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run: pip install .[dev]
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- id: 'auth'
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name: 'Set up Google Cloud authentication'
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key: gcs_cache_integration_tests_20240922
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- name: Run integration tests
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run: pytest --durations=20 -v tests/integration
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run: poetry run pytest --durations=20 -v tests/integration
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- name: Save GCS cache
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uses: actions/cache/save@v3

‎.github/workflows/latest_docs.yml‎

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- name: Check out source 🛒
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uses: actions/checkout@v4
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- name: Set up Python 🐍
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uses: actions/setup-python@v5
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- name: Setup python 🐍
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uses: ./.github/actions/setup-python
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with:
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python-version: '3.12'
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- name: Install poetry
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run: pipx install poetry==1.8.3
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- name: Eyeball native environment 👀
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run: python --version ; pip --version ; poetry --version ; pwd ; ls -la
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- name: Install package dependencies 📜
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run: poetry install
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- name: Build HTML 🏗️
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run: poetry run sphinx-build -b html docs/source docs/build/html
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- name: Deploy HTML to GitHub Pages 🚀
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uses: peaceiris/actions-gh-pages@v3.9.3
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uses: peaceiris/actions-gh-pages@v4
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/linting.yml‎

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

‎.github/workflows/notebooks.yml‎

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push:
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pull_request:
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- master
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jobs:
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notebooks:
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strategy:
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v5
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uses: ./.github/actions/setup-python
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with:
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python-version: "3.12"
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cache: "pip"
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- name: Install package
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run: pip install .[dev]
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- id: 'auth'
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key: gcs_cache_notebooks_20240922
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- name: Run notebooks
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run: jupyter nbconvert --execute notebooks/*.ipynb --inplace
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run: poetry run jupyter nbconvert --execute notebooks/*.ipynb --inplace
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- name: Save GCS cache
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uses: actions/cache/save@v3

‎.github/workflows/release.yml‎

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

‎.github/workflows/tagged_docs.yml‎

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

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fail-fast: true
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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numpy-version:
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- "numpy==1.26.4" # current colab version
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- "numpy~=2.0" # 2.0 series
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# numba (0.60.0) does not yet support numpy 2.1, disable this for now
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# - "numpy~=2.1" # 2.1 series
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numpy-spec:
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# Keep this aligned with pyproject.toml: numpy = ">=2.0.2,<2.1"
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- "==2.0.2" # locked baseline
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- ">=2.0.2,<2.1" # latest allowed in declared range
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runs-on: ubuntu-latest
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steps:
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- name: Checkout source
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v5
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uses: ./.github/actions/setup-python
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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- name: Install package
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run: pip install "${{ matrix.numpy-version }}" .[dev]
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- name: Install matrix NumPy version
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run: poetry run pip install --upgrade --no-deps "numpy${{ matrix.numpy-spec }}"
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- name: Verify NumPy version and spec
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env:
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NUMPY_SPEC: ${{ matrix.numpy-spec }}
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run: |
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poetry run python - <<'PY'
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import os
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import numpy
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from packaging.specifiers import SpecifierSet
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spec = SpecifierSet(os.environ["NUMPY_SPEC"])
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version = numpy.__version__
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if version not in spec:
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raise RuntimeError(
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f"NumPy version {version} does not satisfy matrix spec {spec}"
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)
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print("NumPy version:", version, "| spec:", spec)
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PY
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- name: Run unit tests
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run: pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph
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run: poetry run pytest -v tests --ignore tests/integration --typeguard-packages=malariagen_data,malariagen_data.anoph

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