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deploy.yaml
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name: Build and upload to PyPI
on:
pull_request:
branches:
- "package-*"
push:
branches:
- "package-*"
tags:
- "package-*"
release:
types:
- published
schedule:
# 3 am Tuesdays and Fridays
- cron: "0 3 * * 2,5"
concurrency:
group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
cancel-in-progress: true
defaults:
run:
shell: bash -l {0}
jobs:
build_wheels:
if: "github.repository == 'MDAnalysis/mdanalysis'"
name: Build wheels
runs-on: ${{ matrix.buildplat[0] }}
timeout-minutes: 15
strategy:
fail-fast: false
matrix:
buildplat:
- [ubuntu-22.04, manylinux_x86_64, x86_64]
- [macos-11, macosx_*, x86_64]
- [windows-2019, win_amd64, AMD64]
- [macos-14, macosx_*, arm64]
python: ["cp39", "cp310", "cp311", "cp312"]
defaults:
run:
working-directory: ./package
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Build wheels
uses: pypa/[email protected]
with:
package-dir: package
env:
CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}
CIBW_ARCHS: ${{ matrix.buildplat[2] }}
CIBW_BUILD_VERBOSITY: 1
- name: upload artifacts
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
with:
path: wheelhouse/*.whl
retention-days: 7
build_sdist:
if: "github.repository == 'MDAnalysis/mdanalysis'"
name: build package source distribution
runs-on: ubuntu-latest
timeout-minutes: 10
defaults:
run:
working-directory: ./package
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Build sdist
run: pipx run build --sdist
- name: upload artifacts
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
with:
path: package/dist/*.tar.gz
retention-days: 7
build_sdist_tests:
if: "github.repository == 'MDAnalysis/mdanalysis'"
name: build test source distribution
runs-on: ubuntu-latest
timeout-minutes: 10
defaults:
run:
working-directory: ./testsuite
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Build sdist
run: pipx run build --sdist
- name: upload artifacts
if: |
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package')) ||
(github.event_name == 'release' && github.event.action == 'published')
uses: actions/upload-artifact@v4
with:
path: testsuite/dist/*.tar.gz
retention-days: 7
upload_testpypi_mdanalysis:
if: |
github.repository == 'MDAnalysis/mdanalysis' &&
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
name: testpypi_upload_mdanalysis
environment:
name: deploy
url: https://test.pypi.org/p/mdanalysis
permissions:
id-token: write
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
with:
name: artifact
path: dist
- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
- name: upload_source_and_wheels
uses: pypa/[email protected]
with:
skip_existing: true
repository_url: https://test.pypi.org/legacy/
upload_testpypi_mdanalysistests:
if: |
github.repository == 'MDAnalysis/mdanalysis' &&
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
name: testpypi_upload_mdanalysistests
environment:
name: deploy
url: https://test.pypi.org/p/mdanalysis
permissions:
id-token: write
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
with:
name: artifact
path: dist
- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
- name: upload_tests
uses: pypa/[email protected]
with:
packages_dir: testsuite/dist
skip_existing: true
repository_url: https://test.pypi.org/legacy/
upload_pypi_mdanalysis:
if: |
github.repository == 'MDAnalysis/mdanalysis' &&
github.event_name == 'release' && github.event.action == 'published'
name: pypi_upload_mdanalysis
environment:
name: deploy
url: https://pypi.org/p/mdanalysis
permissions:
id-token: write
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
with:
name: artifact
path: dist
- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
- name: upload_source_and_wheels
uses: pypa/[email protected]
upload_pypi_mdanalysistests:
if: |
github.repository == 'MDAnalysis/mdanalysis' &&
github.event_name == 'release' && github.event.action == 'published'
name: pypi_upload_mdanalysistests
environment:
name: deploy
url: https://pypi.org/p/mdanalysistests
permissions:
id-token: write
runs-on: ubuntu-latest
needs: [build_wheels, build_sdist, build_sdist_tests]
steps:
- uses: actions/download-artifact@v4
with:
name: artifact
path: dist
- name: move_test_dist
run: |
mkdir -p testsuite/dist
mv dist/MDAnalysisTests-* testsuite/dist
- name: upload_tests
uses: pypa/[email protected]
with:
packages_dir: testsuite/dist
check_testpypi:
if: |
github.repository == 'MDAnalysis/mdanalysis' &&
(github.event_name == 'push' && startsWith(github.ref, 'refs/tags/package'))
name: testpypi check
runs-on: ${{ matrix.os }}
timeout-minutes: 60
needs: [upload_testpypi_mdanalysis, upload_testpypi_mdanalysistests]
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.10", "3.11", "3.12"]
type: ["FULL", "MIN"]
exclude:
# Multiple deps don't like windows
- os: windows-latest
type: "FULL"
env:
MPLBACKEND: agg
steps:
- uses: actions/checkout@v4
- name: setup_micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-name: mda
create-args: >-
python=${{ matrix.python-version }}
packaging
pip
# jaime's shim to avoid pulling down the cudatoolkit
# bioconda for clustalw things
condarc: |
channels:
- jaimergp/label/unsupported-cudatoolkit-shim
- conda-forge
- bioconda
- name: install_full_deps
uses: ./.github/actions/setup-deps
if: "matrix.type == 'FULL'"
with:
micromamba: true
full-deps: true
- name: pip_install_mda
run: |
awk '/__version__ =/ {print $3; exit}' package/MDAnalysis/version.py | tr -d \" > version.dat
ver=$(python maintainer/norm_version.py --file version.dat)
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysis==$ver
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple MDAnalysisTests==$ver
- name: install_min_deps
if: "matrix.type == 'MIN'"
run: |
pip install pytest-xdist pytest-timeout
- name: run_tests
run: |
pytest --timeout=200 -n auto --pyargs MDAnalysisTests