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Setting up nipype-auto-converter #28

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Setting up nipype-auto-converter

Setting up nipype-auto-converter #28

Workflow file for this run

.github/workflows/ci-cd.yaml at d782fec
#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 ]
tags: [ '*' ]
pull_request:
branches: [ main, develop ]
repository_dispatch:
types: [create-release]
jobs:
nipype-conv:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Revert version to most recent tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
- name: Show file tree
run: tree .
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
- name: Install build dependencies
run: python -m pip install --upgrade pip
- name: Install requirements
run: python -m pip install -r ./nipype-auto-conv/requirements.txt
- name: Run automatic Nipype > Pydra conversion
run: ./nipype-auto-conv/generate
- uses: actions/upload-artifact@v4
with:
name: converted-nipype
path: pydra/tasks/mriqc
devcheck:
needs: [nipype-conv]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.10', '3.12'] # 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@v4
- name: Revert version to most recent tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v4
with:
name: converted-nipype
path: pydra/tasks/mriqc
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra/d' .gitignore
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
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 ${{ matrix.pip-flags }} ".[dev]"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
test:
needs: [nipype-conv]
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: ['3.10', '3.12']
steps:
- name: Removed unnecessary tools to free space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- uses: actions/checkout@v4
- name: Revert version to most recent tag on upstream update
if: github.event_name == 'repository_dispatch'
run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v4
with:
name: converted-nipype
path: pydra/tasks/mriqc
- name: Strip pydra package from gitignore so it is included in package
run: |
sed -i '/\/pydra/d' .gitignore
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install ".[test]"
python -c "import pydra.tasks.mriqc as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Set environment variables required for mocking tools
run: |
export PATH=$(pwd)/mock-tools:$PATH
export FSLDIR=$(pwd)/mock-tools
- name: Test with pytest
run: |
pytest -sv ./pydra --cov pydra.tasks.mriqc --cov-report xml
- uses: codecov/codecov-action@v3
if: ${{ always() }}
with:
files: coverage.xml
name: pydra-mriqc
deploy:
needs: [test]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v4
with:
name: converted-nipype
path: pydra/tasks/mriqc
- name: Tag release with a post-release based on Nipype and Nipype2Pydra versions
if: github.event_name == 'repository_dispatch'
run: |
TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}')
POST=$(python -c "from pydra.tasks.mriqc._post_release import *; print(post_release)")
git checkout $TAG
git add -f pydra/tasks/mriqc/_version.py
git commit -am"added auto-generated version to make new tag for package version"
git tag ${TAG}post${POST}
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install build tools
run: python -m pip install build twine
- name: Strip pydra package from gitignore so it is included in package
run: |
sed -i '/\/pydra/d' .gitignore
- 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'
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 }}
# 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