Merge pull request #5 from nipype/nipype-auto-conv

Setting up nipype-auto-converter

.github/workflows/ci-cd.yaml

@@ -16,54 +16,55 @@ on:
     types: [create-release]
 
 jobs:
-
   nipype-conv:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      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@v4
+      uses: actions/setup-python@v5
     - 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
+      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
+    - uses: actions/upload-artifact@v4
       with:
         name: converted-nipype
-        path: pydra/tasks/anatomical/auto
+        path: pydra/tasks/mriqc
 
   devcheck:
     needs: [nipype-conv]
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']  # Check oldest and newest versions
+        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@v3
+      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@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
-        path: pydra/tasks/anatomical/auto
+        path: pydra/tasks/mriqc
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/pydra\/tasks\/anatomical\/auto/d' .gitignore
+        sed -i '/\/pydra/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -77,207 +78,104 @@ jobs:
         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.anatomical 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_anatomical as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-        python -c "import fileformats.extras.medimage_anatomical 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_anatomical as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-    - name: Test fileformats with pytest
-      run: |
-        cd ./fileformats
-        pytest -sv --cov fileformats.medimage_anatomical --cov fileformats.extras.medimage_anatomical --cov-report xml .
 
+  
   test:
-    needs: [nipype-conv, fileformats-test]
+    needs: [nipype-conv]
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.8']  # '3.11'
+        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"      
-    - name: Get Download cache Key
-      id: cache-key
-      run: echo "::set-output name=key::anatomical-linux-ubuntu22_amd64-7.4.1"
-    - name: Cache FreeSurfer
-      uses: actions/cache@v2
-      with:
-        path: $HOME/downloads/anatomical
-        key: ${{ steps.cache-key.outputs.key }}
-        restore-keys: |
-          anatomical-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/anatomical
-        curl -s -o $HOME/downloads/anatomical/anatomical-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/anatomical/7.4.1/anatomical-linux-ubuntu22_amd64-7.4.1.tar.gz
-      shell: bash
-    - name: Install Freesurfer
-      env:
-        FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
-      run: |
-        pushd $HOME/downloads/anatomical
-        tar -zxpf anatomical-linux-ubuntu22_amd64-7.4.1.tar.gz
-        mv anatomical $HOME/
-        popd
-        export FREESURFER_HOME=$HOME/anatomical
-        source $FREESURFER_HOME/SetUpFreeSurfer.sh
-        echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
-        export PATH=$FREESURFER_HOME/bin:$PATH
-    - uses: actions/checkout@v3
+        sudo rm -rf "$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@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
-        path: pydra/tasks/anatomical/auto
-    - name: Strip auto package from gitignore so it is included in package
+        path: pydra/tasks/mriqc
+
+    - name: Strip pydra package from gitignore so it is included in package
       run: |
-        sed -i '/\/src\/pydra\/tasks\/anatomical\/auto/d' .gitignore
+        sed -i '/\/pydra/d' .gitignore
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install build dependencies
       run: |
         python -m pip install --upgrade pip
+
     - name: Install task package
       run: |
-        pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
-        python -c "import pydra.tasks.anatomical as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        pip install ".[test]"
+        python -c "import pydra.tasks.mriqc as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+
+    - name: Install dev Pydra version for now until it is merged
+      run: pip install --upgrade git+https://github.com/nipype/pydra.git@typing-bugfixes
+
+    - name: Set environment variables required for mocking tools
+      run: |
+        echo "$(pwd)/mock-tools" >> $GITHUB_PATH
+        echo "export FSLDIR=$(pwd)/mock-tools" >> $GITHUB_ENV
+        echo "export FSLOUTPUTTYPE=NIFTI_GZ" >> $GITHUB_ENV
+
     - name: Test with pytest
       run: |
-        pytest -sv --doctest-modules ./pydra/tasks/anatomical \
-            --cov pydra.tasks.anatomical --cov-report xml
+        pytest -sv ./pydra --cov pydra.tasks.mriqc --cov-report xml
+
     - uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:
-        files: coverage.xml,./fileformats/coverage.xml
-        name: pydra-anatomical
-
-  deploy-fileformats:
-    needs: [devcheck, test]
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-        fetch-depth: 0 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.11'
-    - name: Install build tools
-      run: python -m pip install build twine
-    - name: Build source and wheel distributions
-      run: python -m build ./related-packages/fileformats
-    - name: Check distributions
-      run: twine check ./related-packages/fileformats/dist/*
-    - name: Check for PyPI token on tag
-      id: deployable
-      if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch'
-      env:
-        PYPI_API_TOKEN: "${{ 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 
+        files: coverage.xml
+        name: pydra-mriqc
 
   deploy:
-    needs: [deploy-fileformats-extras]
+    needs: [test]
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0
     - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
-        path: pydra/tasks/anatomical/auto
+        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.anatomical.auto._version import *; print(post_release)")
+        POST=$(python -c "from pydra.tasks.mriqc._post_release import *; print(post_release)")
         git checkout $TAG
-        git add -f pydra/tasks/anatomical/auto/_version.py
+        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@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install build tools
       run: python -m pip install build twine
-    - name: Strip auto package from gitignore so it is included in package
+    - name: Strip pydra package from gitignore so it is included in package
       run: |
-        sed -i '/\/pydra\/tasks\/anatomical\/auto/d' .gitignore
+        sed -i '/\/pydra/d' .gitignore
     - name: Build source and wheel distributions
       run: python -m build .
     - name: Check distributions
@@ -288,7 +186,7 @@ jobs:
         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'
+      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
@@ -302,4 +200,4 @@ jobs:
 # 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        
+# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter        

.gitignore

@@ -137,6 +137,4 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
-/pydra/tasks/mriqc/interfaces
-/pydra/tasks/mriqc/_version.py
-/pydra/tasks/mriqc/auto
+/pydra

AUTHORS

@@ -0,0 +1 @@
+# Enter list of names and emails of contributors to this package

NOTICE

@@ -0,0 +1,6 @@
+Pydra-mriqc
+Copyright 2024 Pydra Development Team
+
+The bases for the task interfaces defined in this package were semi-automatically converted
+from Nipype interfaces (https://github.com/nipy/nipype) using the Nipype2Pydra tool
+(https://github.com/nipype/nipype2pydra).