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Decode BAM sequence with less code. Dispatch function at dynamic link time rather than at run time. #586

Decode BAM sequence with less code. Dispatch function at dynamic link time rather than at run time.

Decode BAM sequence with less code. Dispatch function at dynamic link time rather than at run time. #586

Workflow file for this run

name: CI
on: [push, pull_request]
jobs:
lint:
# Run for PRs only if they come from a forked repo (avoids duplicate runs)
if: >-
github.event_name != 'pull_request' ||
github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
timeout-minutes: 10
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.10"]
toxenv: [flake8, black, mypy, docs]
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: python -m pip install tox
- name: Run tox ${{ matrix.toxenv }}
run: tox -e ${{ matrix.toxenv }}
build:
if: >-
github.event_name != 'pull_request' ||
github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0 # required for setuptools_scm
- name: Build sdist and temporary wheel
run: pipx run build
- uses: actions/upload-artifact@v4
with:
name: sdist
path: dist/*.tar.gz
test:
if: >-
github.event_name != 'pull_request' ||
github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
timeout-minutes: 10
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
include:
- os: macos-13
python-version: "3.10"
- os: macos-14
python-version: "3.10"
- os: windows-latest
python-version: "3.10"
- os: ubuntu-latest
python-version: "3.10"
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: python -m pip install tox
- name: Test
run: tox -e py
- name: Upload coverage report
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
wheels:
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
needs: [lint, test]
timeout-minutes: 15
strategy:
matrix:
os: [ubuntu-latest, windows-latest, macos-13, macos-14]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0 # required for setuptools_scm
- name: Build wheels
uses: pypa/[email protected]
env:
CIBW_BUILD: "cp*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64"
CIBW_SKIP: "cp37-*"
CIBW_TEST_SKIP: "cp38-macosx_*:arm64"
- uses: actions/upload-artifact@v4
with:
name: wheels-${{ matrix.os }}
path: wheelhouse/*.whl
publish:
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
needs: [build, wheels]
runs-on: ubuntu-latest
steps:
- uses: actions/download-artifact@v4
with:
name: sdist
path: dist/
- uses: actions/download-artifact@v4
with:
pattern: wheels-*
path: dist/
merge-multiple: true
- name: Publish to PyPI
uses: pypa/[email protected]
with:
password: ${{ secrets.pypi_password }}
#password: ${{ secrets.test_pypi_password }}
#repository_url: https://test.pypi.org/legacy/