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Merge branch 'main' into window_by
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‎.cirun.yml

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# Self-Hosted Github Action Runners on GCP via Cirun.io
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# Reference: https://docs.cirun.io/reference/yaml.html
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runners:
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- name: gpu-runner
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# Cloud Provider: GCP
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cloud: gcp
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# Cheapest GPU on GCP
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gpu: nvidia-tesla-t4
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# Cheapest VM on GCP, with GPU attachable
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instance_type: n1-standard-1
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# Ubuntu-20.4, can be seen from "gcloud compute images list"
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machine_image: ubuntu-minimal-2004-lts
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# preemptible instances seems quite less reliable.
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preemptible: false
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# Path of the relevant workflow file
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workflow: .github/workflows/build-gpu.yml
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# Number of runners to provision on every trigger on Actions job
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# 3 because testing on Python 3.7, 3.8, 3.9
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# See .github/workflows/build-gpu.yml
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count: 3
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# Adding the GPU label, this matches the runs-on param from .github/workflows/build-gpu.yml
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# So that this runner is selected for running .github/workflows/build-gpu.yml
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labels:
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- gpu

‎.github/scripts/test_sgkit.py

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import sgkit as sg
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if __name__ == "__main__":
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ds = sg.simulate_genotype_call_dataset(n_variant=100, n_sample=50, n_contig=23)
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print(ds)

‎.github/scripts/test_sgkit_bgen.py

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import urllib.request
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from sgkit.io.bgen import read_bgen
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if __name__ == "__main__":
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urllib.request.urlretrieve(
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"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/bgen/data/example.bgen",
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"example.bgen",
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)
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ds = read_bgen("example.bgen")
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print(ds)

‎.github/scripts/test_sgkit_plink.py

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import urllib.request
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from sgkit.io.plink import read_plink
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if __name__ == "__main__":
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for ext in (".bed", ".bim", ".fam"):
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urllib.request.urlretrieve(
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f"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/plink/data/plink_sim_10s_100v_10pmiss{ext}",
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f"plink_sim_10s_100v_10pmiss{ext}",
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)
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ds = read_plink(path="plink_sim_10s_100v_10pmiss")
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print(ds)

‎.github/scripts/test_sgkit_vcf.py

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import urllib.request
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import xarray as xr
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from sgkit.io.vcf import vcf_to_zarr
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if __name__ == "__main__":
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for ext in (".gz", ".gz.tbi"):
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urllib.request.urlretrieve(
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f"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/vcf/data/sample.vcf{ext}",
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f"sample.vcf{ext}",
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)
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vcf_to_zarr("sample.vcf.gz", "out")
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ds = xr.open_zarr("out") # type: ignore[no-untyped-call]
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print(ds)

‎.github/workflows/build-gpu.yml

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name: Build GPU
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on:
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workflow_dispatch:
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push:
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branches:
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- main
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jobs:
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build:
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runs-on: [self-hosted, gpu]
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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- uses: actions/checkout@v2
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- name: Run Nvidia-smi
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run: |
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nvidia-smi
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- name: Set up Python
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uses: conda-incubator/setup-miniconda@v2
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env:
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CONDA: /home/runnerx/miniconda3
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with:
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python-version: ${{ matrix.python-version }}
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miniconda-version: "latest"
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- name: Install dependencies
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run: |
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conda install -c anaconda cudatoolkit
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pip install -r requirements.txt -r requirements-dev.txt
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- name: Run GPU tagged tests
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run: |
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pytest -m gpu -v

‎.github/workflows/wheels.yml

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name: Wheels
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on:
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push:
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branches:
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- main
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- test
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tags:
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- '*'
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release:
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types: [published]
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jobs:
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build:
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# This workflow only runs on the origin org
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if: github.repository_owner == 'pystatgen'
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install setuptools twine wheel
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- name: Build a source distribution and a wheel
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run: |
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python setup.py sdist bdist_wheel
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python -m twine check --strict dist/*
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- name: Upload artifacts
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uses: actions/upload-artifact@v2
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with:
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path: dist
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unix-test:
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# This workflow only runs on the origin org
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if: github.repository_owner == 'pystatgen'
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needs: ['build']
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: [3.7, 3.8, 3.9]
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runs-on: ${{ matrix.os }}
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steps:
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# checkout repo to subdirectory to get access to scripts
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- uses: actions/checkout@v2
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with:
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path: sgkit-copy
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- name: Download artifacts
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uses: actions/download-artifact@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install wheel and test
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run: |
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python -VV
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# Install the local wheel
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wheel=$(ls artifact/sgkit-*.whl)
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pip install ${wheel} ${wheel}[bgen] ${wheel}[plink] ${wheel}[vcf]
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python sgkit-copy/.github/scripts/test_sgkit.py
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python sgkit-copy/.github/scripts/test_sgkit_bgen.py
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python sgkit-copy/.github/scripts/test_sgkit_plink.py
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python sgkit-copy/.github/scripts/test_sgkit_vcf.py
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# Windows doesn't support vcf
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windows-test:
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# This workflow only runs on the origin org
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if: github.repository_owner == 'pystatgen'
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runs-on: windows-latest
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needs: ['build']
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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steps:
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# checkout repo to subdirectory to get access to scripts
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- uses: actions/checkout@v2
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with:
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path: sgkit-copy
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- name: Download artifacts
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uses: actions/download-artifact@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install wheel and test
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run: |
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python -VV
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# Install the local wheel
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$env:wheel = $(ls artifact/sgkit-*.whl)
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pip install $env:wheel "$env:wheel[bgen]" "$env:wheel[plink]"
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python sgkit-copy/.github/scripts/test_sgkit.py
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python sgkit-copy/.github/scripts/test_sgkit_bgen.py
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python sgkit-copy/.github/scripts/test_sgkit_plink.py
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pypi-upload:
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if: github.repository_owner == 'pystatgen'
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runs-on: ubuntu-latest
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needs: ['unix-test', 'windows-test']
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steps:
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- name: Download all
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uses: actions/download-artifact@v2
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- name: Move to dist
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run: |
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mkdir dist
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cp */*.{whl,gz} dist/.
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- name: Publish package to TestPyPI
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if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.TEST_PYPI_API_TOKEN }}
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repository_url: https://test.pypi.org/legacy/
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- name: Publish package to PyPI
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if: github.event_name == 'release'
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎conftest.py

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# Ignore VCF files during pytest collection, so it doesn't fail if cyvcf2 isn't installed.
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collect_ignore_glob = ["sgkit/io/vcf/*.py"]
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collect_ignore_glob = ["sgkit/io/vcf/*.py", ".github/scripts/*.py"]
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def pytest_configure(config) -> None: # type: ignore

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