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Update coverage workflow to Python 3.10 and adjust numcodecs constraint
Align coverage workflow with test matrix baseline: Coverage Workflow Changes: - Change Python version from 3.12 to 3.10 for consistency - Ensures coverage runs on same baseline as tests - Reformatted YAML for consistency (auto-formatted) Dependency Adjustment: - numcodecs: >=0.15,<0.16 → >=0.13,<0.16 (broader stable range) - Maintains NumPy 1.26.4 baseline compatibility Rationale: - Coverage must match test matrix baseline (Python 3.10) - Prevents dependency resolution mismatches - Ensures all CI workflows use stable ecosystem
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.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: actions/setup-python@v5
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with:
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python-version: "3.10"
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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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- 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: 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

pyproject.toml

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scipy = "*"
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pandas = "*"
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zarr = ">=2.18.3, <3.0.0"
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numcodecs = ">=0.15, <0.16"
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numcodecs = ">=0.13, <0.16"
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dask = {version="*", extras=["array"]}
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distributed = "*"
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fsspec = "*"

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