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Added in auto-generated nipype conversion templates #15

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Added in auto-generated nipype conversion templates

Added in auto-generated nipype conversion templates #15

Workflow file for this run

.github/workflows/ci-cd.yaml at 75c3299
#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@v3
- 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: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
- 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@v3
with:
name: converted-nipype
path: pydra/tasks/freesurfer/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 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@v3
with:
name: converted-nipype
path: pydra/tasks/freesurfer/auto
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/freesurfer\/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 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.freesurfer 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_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import fileformats.extras.medimage_freesurfer 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 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: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Test fileformats with pytest
run: |
cd ./related-packages
pytest -sv --cov fileformats.medimage_freesurfer --cov fileformats.extras.medimage_freesurfer --cov-report xml .
test:
needs: [nipype-conv, fileformats-test]
runs-on: ubuntu-22.04
strategy:
matrix:
python-version: ['3.8'] # '3.11'
steps:
- name: Removed unnecessary tools to free space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Get Download cache Key
id: cache-key
run: echo "::set-output name=key::freesurfer-linux-ubuntu22_amd64-7.4.1"
- name: Cache FreeSurfer
uses: actions/cache@v2
with:
path: $HOME/downloads/freesurfer
key: ${{ steps.cache-key.outputs.key }}
restore-keys: |
freesurfer-linux-ubuntu22_amd64-7.4.1
- name: Download FreeSurfer
if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key
run: |
mkdir -p $HOME/downloads/freesurfer
curl -s -o $HOME/downloads/freesurfer/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
shell: bash
- name: Install Freesurfer
env:
FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
run: |
pushd $HOME/downloads/freesurfer
tar -zxpf freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
mv freesurfer $HOME/
popd
export FREESURFER_HOME=$HOME/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
export PATH=$FREESURFER_HOME/bin:$PATH
- uses: actions/checkout@v3
- 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@v3
with:
name: converted-nipype
path: pydra/tasks/freesurfer/auto
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/src\/pydra\/tasks\/freesurfer\/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.freesurfer 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 --doctest-modules ./pydra/tasks/freesurfer \
--cov pydra.tasks.freesurfer --cov-report xml
- uses: codecov/codecov-action@v3
if: ${{ always() }}
with:
files: coverage.xml,./related-packages/coverage.xml
name: pydra-freesurfer
deploy-fileformats:
needs: [devcheck, test]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Build source and wheel distributions
run: python -m build ./related-packages/fileformats
- name: Check distributions
run: twine check ./related-packages/fileformats/dist/*
- name: Check for PyPI token on tag
id: deployable
if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
packages-dir: ./related-packages/fileformats/dist
deploy-fileformats-extras:
needs: [deploy-fileformats]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Build source and wheel distributions
run: python -m build ./related-packages/fileformats-extras
- name: Check distributions
run: twine check ./related-packages/fileformats-extras/dist/*
- name: Check for PyPI token on tag
id: deployable
if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
packages-dir: ./related-packages/fileformats-extras/dist
deploy:
needs: [deploy-fileformats-extras]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Download tasks converted from Nipype
uses: actions/download-artifact@v3
with:
name: converted-nipype
path: pydra/tasks/freesurfer/auto
- name: Tag release with a post-release based on Nipype and Nipype2Pydra versions
if: github.event_name == 'repository_dispatch'
run: |
TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}')
POST=$(python -c "from pydra.tasks.freesurfer.auto._version import *; print(post_release)")
git checkout $TAG
git add -f pydra/tasks/freesurfer/auto/_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@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\/freesurfer\/auto/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 == 'push' && startsWith(github.ref, 'refs/tags')) || 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 }}
# 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