Skip to content

Commit

Permalink
updated ci to pull in github tags for python versioning
Browse files Browse the repository at this point in the history
  • Loading branch information
@tclose
tclose committed Sep 10, 2024
1 parent e03104d commit 9db3f2d
Show file tree
Hide file tree
Showing 2 changed files with 8 additions and 76 deletions.
79 changes: 6 additions & 73 deletions .github/workflows/ci-cd.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,23 +45,18 @@ jobs:
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
Expand All @@ -71,10 +66,8 @@ jobs:
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 $MRTRIX_HOME/src
Expand All @@ -88,40 +81,31 @@ jobs:
-D CMAKE_C_COMPILER=clang \
-D CMAKE_CXX_COMPILER=clang++ \
-D CMAKE_INSTALL_PREFIX=$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
Expand All @@ -130,22 +114,18 @@ jobs:
$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:
Expand All @@ -165,40 +145,32 @@ jobs:

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"
Expand All @@ -221,100 +193,84 @@ jobs:
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: Install dev branch of pydra until bugfix
run: pip install --upgrade git+https://github.com/nipype/pydra.git@typing-bugfixes

- 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
Expand All @@ -327,33 +283,26 @@ jobs:
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
Expand All @@ -367,73 +316,58 @@ jobs:
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
Expand All @@ -444,7 +378,6 @@ jobs:
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
Expand Down
5 changes: 2 additions & 3 deletions pyproject.toml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ description = "pydra-mrtrix3 contains Pydra task specifications for MRtrix3 tool
readme = "README.rst"
requires-python = ">=3.8"
dependencies = [
"fileformats-medimage_mrtrix3 >=3.0.4a4",
"fileformats-medimage_mrtrix3 >=3.0.4a7",
"numpy",
"pydra >=0.23",
]
Expand Down Expand Up @@ -36,8 +36,7 @@ dev = [
"click >=8.1.3",
"tqdm",
"attrs >=23.1.0",
"fileformats >= 0.8",
"fileformats-extras >= 0.2.1",
"fileformats-extras >= 0.12.1",
]
doc = [
"packaging",
Expand Down

0 comments on commit 9db3f2d

Please sign in to comment.