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debugging deploy job in gha #59

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debugging deploy job in gha

debugging deploy job in gha #59

Workflow file for this run

.github/workflows/ci-cd.yaml at c52c429
#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
# For deployment, it will be necessary to create a PyPI API token and store it as a secret
# https://docs.github.com/en/actions/reference/encrypted-secrets
name: CI/CD
on:
push:
branches: [ main, develop ]
pull_request:
branches: [ main, develop ]
release:
types: [published]
repository_dispatch:
types: [create-post-release]
jobs:
nipype-conv:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Revert version to most recent version tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
- name: Set up Python
uses: actions/setup-python@v4
- name: Install build dependencies
run: python -m pip install --upgrade pip
- name: Install requirements
run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt
- name: Run automatic Nipype > Pydra conversion
run: ./nipype-auto-conv/generate
- uses: actions/upload-artifact@v3
with:
name: converted-nipype
path: pydra/tasks/afni/auto
devcheck:
needs: [nipype-conv]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.11'] # Check oldest and newest versions
pip-flags: ['', '--editable']
pydra:
- 'pydra'
- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Revert version to most recent version tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v3
with:
name: converted-nipype
path: pydra/tasks/afni/auto
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
sed -i '/^_version.py/d' .gitignore
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install Pydra
run: |
pushd $HOME
pip install ${{ matrix.pydra }}
popd
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Install task package
run: |
pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
pip install ${{ matrix.pip-flags }} ".[dev]"
python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
fileformats-test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.11']
steps:
- uses: actions/checkout@v3
- name: Revert version to most recent version tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Test fileformats with pytest
run: |
pytest ./related-packages -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
test:
needs: [nipype-conv, fileformats-test]
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: ['3.8', '3.11']
steps:
- name: Removed unnecessary tools to free space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Checkout repo
uses: actions/checkout@v3
- name: Revert version to most recent version tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
- name: Install AFNI
run: |
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_22_64_a_admin.txt
curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_22_64_b_user.tcsh
sudo bash OS_notes.linux_ubuntu_22_64_a_admin.txt 2>&1 | tee o.ubuntu_22_a.txt
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v3
with:
name: converted-nipype
path: pydra/tasks/afni/auto
- name: Show the contents of the auto-generated tasks
run: tree pydra
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Test with pytest
run: |
pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
- name: Upload to CodeCov
uses: codecov/codecov-action@v3
if: ${{ always() }}
with:
files: coverage.xml,./fileformats/coverage.xml
name: pydra-afni
deploy-fileformats:
needs: [devcheck, test, fileformats-test]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Build source and wheel distributions
run: python -m build ./related-packages/fileformats
- name: Check distributions
run: twine check ./related-packages/fileformats/dist/*
- name: Check for PyPI token on tag
id: deployable
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}"
run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
- name: Upload to PyPI
if: steps.deployable.outputs.DEPLOY
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
packages-dir: ./related-packages/fileformats/dist
deploy-fileformats-extras:
needs: [deploy-fileformats]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Build source and wheel distributions
run: python -m build ./related-packages/fileformats-extras
- name: Check distributions
run: twine check ./related-packages/fileformats-extras/dist/*
- name: Check for PyPI token on tag
id: deployable
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}"
run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
- name: Upload to PyPI
if: steps.deployable.outputs.DEPLOY
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
packages-dir: ./related-packages/fileformats-extras/dist
deploy:
needs: [nipype-conv, test, deploy-fileformats, deploy-fileformats-extras]
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Git user
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Action"
- name: Get latest version tag
id: latest_tag
run: |
git fetch --tags
echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT
- name: Revert to latest tag
if: github.event_name == 'repository_dispatch'
run: git checkout ${{ steps.latest_tag.outputs.TAG }}
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v3
with:
name: converted-nipype
path: pydra/tasks/afni/auto
- name: Show the contents of the auto-generated tasks
run: tree pydra
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
cat .gitignore
- name: Install task package to calculate post-release tag
run: |
pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
tree /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/pydra/
- name: Generate post-release tag based on Nipype and Nipype2Pydra versions
id: post_release_tag
run: |
POST=$(python -c "from pydra.tasks.afni.auto._version import *; print(post_release)")
echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT
- name: Add auto directory to git repo and tag it (overwriting previous tag if release event)
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
run: |
git add pydra/tasks/afni/auto
git commit -m"added auto-generated version to make new tag for package version"
if [ ${{ github.event_name }} == "release"]; then
git tag -d ${{ steps.latest_tag.outputs.TAG }};
git tag ${{ steps.latest_tag.outputs.TAG }};
else
git tag ${{ steps.post_release_tag.outputs.TAG }}
fi
- name: Build source and wheel distributions
run: python -m build .
- name: Check distributions
run: twine check dist/*
- uses: actions/upload-artifact@v3
with:
name: distributions
path: dist/
- name: Check for PyPI token on tag
id: deployable
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
- name: Upload to PyPI
if: steps.deployable.outputs.DEPLOY
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
# - name: Create post-release release for releases triggered by nipype2pydra dispatches
# if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch'
# uses: actions/create-release@v1
# env:
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
# with:
# tag_name: ${{ steps.post_release_tag.outputs.TAG }}
# release_name: Release ${{ steps.post_release_tag.outputs.TAG }}
# draft: false
# prerelease: false
# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
# Secrets are not accessible in the if: condition [0], so set an output variable [1]
# [0] https://github.community/t/16928
# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter