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commented out read_array code that is causing error due to types #67

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commented out read_array code that is causing error due to types

commented out read_array code that is causing error due to types #67

Workflow file for this run

.github/workflows/ci-cd.yml at 4c7cec8
#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-release]
env:
MRTRIX_HOME: /opt/mrtrix3
MRTRIX_INSTALL: /opt/mrtrix3/install
MRTRIX_VERSION: 3.0.4
SUBPKG_NAME: v3_0
jobs:
generate:
runs-on: ubuntu-latest
env:
CFLAGS: -Werror
QT_SELECT: qt6
SCCACHE_GHA_ENABLED: "true"
SCCACHE_CACHE_SIZE: "2G"
steps:
- uses: actions/checkout@v1
with:
submodules: true
- name: Set Git User
# checkout@v2 adds a header that makes branch protection report errors
# because the Github action bot is not a collaborator on the repo
run: |
git config --global user.email "[email protected]"
git config --global user.name "Dummy User"
- name: install dependencies
run: |
sudo apt-get update
sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
- name: Run sccache-cache
uses: mozilla-actions/[email protected]
- name: Get CMake
uses: lukka/get-cmake@latest
with:
cmakeVersion: '3.16.3'
- name: Print CMake version
run: cmake --version
- name: Clone latest MRtrix and switch to latest tag
run: |
mkdir $MRTRIX_HOME
sudo chown -R $USER $MRTRIX_HOME
git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src
cd $MRTRIX_HOME/src
git checkout pydra-usage-python-cmd
git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-mrtrix3 release"
git describe --abbrev=0
# echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
# git checkout $MRTRIX_VERSION
- name: configure
run: |
cd $MRTRIX_HOME/src
cmake \
-B build \
-G Ninja \
-D CMAKE_BUILD_TYPE=Release \
-D MRTRIX_BUILD_TESTS=ON \
-D MRTRIX_STL_DEBUGGING=ON \
-D MRTRIX_WARNINGS_AS_ERRORS=ON \
-D CMAKE_C_COMPILER=clang \
-D CMAKE_CXX_COMPILER=clang++ \
-D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL
- name: Build Mrtrix
run: |
cd $MRTRIX_HOME/src
cmake --build build
- name: Install Mrtrix
run: |
cd $MRTRIX_HOME/src
cmake --install build
- name: Set PATH Variable
run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
- name: Set LD_LIBRARY_PATH Variable
run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
- name: Change back to the root directory
run: cd ..
- name: Set up Python
uses: actions/setup-python@v2
- name: Install Python build dependencies
run: |
python -m pip install --upgrade pip
- name: Install pydra-auto-gen requirements
run: >
pip install
-e related-packages/fileformats
-e related-packages/fileformats-extras
-e .[dev,test]
- name: Generate task specifications
run: >
./generate.py
$MRTRIX_INSTALL/bin
$(pwd)
$MRTRIX_VERSION
--log-errors
--latest
- name: Upload MRtrix3 install
uses: actions/upload-artifact@v2
with:
name: MRtrix3
path: ${{ env.MRTRIX_INSTALL}}
- name: Upload auto-gen pydra
uses: actions/upload-artifact@v2
with:
name: AutoGen
path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
- name: Write version file
run: echo $MRTRIX_VERSION > mrtrix3_version.txt
- name: Upload version file
uses: actions/upload-artifact@v2
with:
name: VersionFile
path: mrtrix3_version.txt
devcheck:
needs: [generate]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.11] # Check oldest and newest versions
pip-flags: ['', '--editable']
pydra:
- 'pydra'
- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
steps:
- uses: actions/checkout@v2
- name: Download version file
uses: actions/download-artifact@v2
with:
name: VersionFile
path: mrtrix3_version.txt
- name: Extract Mrtrix version
run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
- name: Download auto-gen pydra
uses: actions/download-artifact@v2
with:
name: AutoGen
path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install Pydra
run: |
pip install ${{ matrix.pydra }}
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Install task package
run: |
pip install ${{ matrix.pip-flags }} "related-packages/fileformats"
pip install ${{ matrix.pip-flags }} ".[dev]"
python -c "import pydra.tasks.mrtrix3 as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import pydra.tasks.mrtrix3.$SUBPKG_NAME"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
test:
needs: [generate]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.11]
defaults:
run:
shell: bash -l {0}
steps:
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
- name: Checkout code
uses: actions/checkout@v2
- name: Unset header
# checkout@v2 adds a header that makes branch protection report errors
# because the Github action bot is not a collaborator on the repo
run: git config --local --unset http.https://github.com/.extraheader
- name: Fetch tags
run: git fetch --prune --unshallow
- name: Download version file
uses: actions/download-artifact@v2
with:
name: VersionFile
path: mrtrix3_version.txt
- name: Extract Mrtrix version
run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
- name: Download auto-gen pydra
uses: actions/download-artifact@v2
with:
name: AutoGen
path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
- name: Download MRtrix3 install
uses: actions/download-artifact@v2
with:
name: MRtrix3
path: ${{ env.MRTRIX_INSTALL}}
- name: Make commands executable
run: chmod +x ${{ env.MRTRIX_INSTALL }}/bin/*
- name: Set PATH Variable
run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV
- name: Set LD_LIBRARY_PATH Variable
run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
- name: Install task package
run: >
pip install
-e ./related-packages/fileformats
-e ./related-packages/fileformats-extras
-e '.[test]'
- name: Test with pytest
run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
- uses: codecov/codecov-action@v1
if: ${{ always() }}
deploy-fileformats:
needs: [devcheck, test]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install build tools
run: python -m pip install build twine
- name: Build source and wheel distributions
run: python -m build ./related-packages/fileformats
- name: Check distributions
run: twine check ./related-packages/fileformats/dist/*
- name: Check for PyPI token on tag
id: deployable
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
packages-dir: ./related-packages/fileformats-extras/dist
deploy:
needs: [devcheck, test, deploy-fileformats, deploy-fileformats-extras]
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v2
- name: Set up Git user
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Action"
- name: Download version file
uses: actions/download-artifact@v2
with:
name: VersionFile
path: mrtrix3_version.txt
- name: Extract Mrtrix version
run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
- name: Download auto-gen pydra
uses: actions/download-artifact@v2
with:
name: AutoGen
path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
- name: Strip auto package from gitignore so it is included in package
run: |
sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
- name: Add auto-generated directory to git repo
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
run: |
git add pydra/tasks/mrtrix3/$SUBPKG_NAME
git commit -am"added auto-generated version to make new tag for package version"
git status
- 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: Overwrite the tag of release event with latest commit (i.e. including the auto directory)
if: github.event_name == 'release'
run: |
git tag -d ${{ steps.latest_tag.outputs.TAG }};
git tag -a ${{ steps.latest_tag.outputs.TAG }} -m"Tag used to create a pydra-mrtrix3 $MRTRIX_VERSION release";
- name: Set up Python 3.11
uses: actions/setup-python@v2
with:
python-version: 3.11
- name: Install build tools
run: python -m pip install --upgrade pip twine build
- name: Build source and wheel distributions
run: python -m build
- name: Check distributions
run: twine check dist/*
- name: Upload sdist
uses: actions/upload-artifact@v2
with:
name: SDist
path: dist/*.tar.gz
# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
# Secrets are not accessible in the if: condition [0], so set an output variable [1]
# [0] https://github.community/t/16928
# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
- name: Check for PyPI token on tag
id: deployable
if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
env:
PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; 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 }}
packages-dir: dist/