updated ci-cd to use neurocommand

.github/workflows/ci-cd.yaml

@@ -25,10 +25,12 @@ permissions:
   contents: read
   pages: write
   id-token: write
-env: # Define environment variables
 
-  # Force tox and pytest to use color
+env: # Define environment variables
+  SCIGET_NAME: fsl
+  SCIGET_VERSION: 6.0.7.18
   FORCE_COLOR: true
+
 jobs:
 
   build:
@@ -62,46 +64,31 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v4
 
-    - name: Install Minconda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        auto-activate-base: true
-        activate-environment: ""
-
-    - name: Install fsl Packages
-      run: >-
-        conda install -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
-        ciftilib cli11 elc fsl-add_module fsl-armawrap fsl-asl_mfree fsl-avwutils fsl-base
-        fsl-basil fsl-basisfield fsl-baycest fsl-bet2 fsl-bianca fsl-biancadata fsl-bint
-        fsl-cluster fsl-copain fsl-cprob fsl-cudimot fsl-data_atlases
-        fsl-data_atlases_xtract fsl-data_first_models_317_bin fsl-data_first_models_336_bin fsl-data_linearmni
-        fsl-data_omm fsl-data_possum fsl-data_standard fsl-deface fsl-discreteopt fsl-dpm fsl-dwssfp
-        fsl-easyfeat fsl-eddy fsl-eddy_qc fsl-fabber_core fsl-fabber_models_asl fsl-fabber_models_cest
-        fsl-fabber_models_dce fsl-fabber_models_dsc fsl-fabber_models_dualecho fsl-fabber_models_dwi
-        fsl-fabber_models_pet fsl-fabber_models_qbold fsl-fabber_models_t1 fsl-fast4 fsl-fastpdlib
-        fsl-fdt fsl-feat5 fsl-film fsl-filmbabe fsl-first fsl-first_lib fsl-flameo
-        fsl-flirt fsl-fnirt fsl-fugue fsl-get_standard fsl-giftiio fsl-gps
-        fsl-gui-desktop fsl-installer fsl-lesions fsl-libgdc fsl-libmeshutils fsl-libvis fsl-load_dicom fsl-mcflirt
-        fsl-melodic fsl-meshclass fsl-misc_c fsl-misc_scripts fsl-misc_tcl fsl-miscmaths fsl-miscvis
-        fsl-mist fsl-mm fsl-msm fsl-msmreglib fsl-mvdisc fsl-nets fsl-newimage
-        fsl-newmesh fsl-newnifti fsl-newran fsl-oxford_asl fsl-possum fsl-ptx2 fsl-pyfeeds
-        fsl-pyfeeds-tests fsl-qboot fsl-randomise fsl-relax fsl-shapemodel fsl-siena fsl-slicetimer
-        fsl-sub fsl-sub-plugin-sge fsl-sub-plugin-slurm fsl-surface fsl-susan fsl-swe fsl-tbss
-        fsl-topup fsl-utils fsl-vbm fsl-verbena fsl-vtkio fsl-warpfns fsl-wire fsl-xtract fsl-xtract_data
-        fsl-znzlib fsl_mrs fsl_sub fsl_sub_plugin_sge fsl_sub_plugin_slurm
-
-    - name: Download tasks converted from Nipype
-      uses: actions/download-artifact@v4
-      with:
-        name: converted-nipype
-        path: pydra/tasks/fsl/auto
+    - name: Revert version to most recent version tag on Nipype or Nipype2Pydra update
+      if: github.event_name == 'repository_dispatch'
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
 
-    - name: Show the contents of the auto-generated tasks
-      run: tree pydra
+    - name: Install Apptainer and Lmod
+      run: |
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt-get update
+        sudo apt-get install -y lmod apptainer
 
-    - name: Strip auto package from gitignore so it is included in package
+    - name: Install Neurocommand
       run: |
-        sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore
+        git clone https://github.com/NeuroDesk/neurocommand.git
+        pushd neurocommand
+        pip3 install -r neurodesk/requirements.txt --user
+        bash build.sh --cli
+        echo "APPTAINER_BINDPATH=`pwd -P`" >> $GITHUB_ENV
+
+        source /etc/profile.d/lmod.sh
+        ./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}'
+        SCIGET_BUILDVERSION=$(./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}')
+
+        ./local/fetch_containers.sh ${{ env.SCIGET_NAME }} ${{ env.SCIGET_VERSION }} $SCIGET_BUILDVERSION
+        echo "SCIGET_BUILDVERSION=$SCIGET_BUILDVERSION" >> $GITHUB_ENV
+        popd
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -161,7 +148,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
 
     - name: Install build tools
       run: python -m pip install build twine
@@ -174,7 +161,7 @@ jobs:
 
     - name: Check for PyPI token on tag
       id: deployable
-      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
+      if: github.event_name == 'release'
       env:
         PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}"
       run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
@@ -200,7 +187,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.x'
 
     - name: Install build tools
       run: python -m pip install build twine
@@ -213,7 +200,7 @@ jobs:
 
     - name: Check for PyPI token on tag
       id: deployable
-      if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
+      if: github.event_name == 'release'
       env:
         PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}"
       run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
@@ -227,9 +214,8 @@ jobs:
         packages-dir: ./related-packages/fileformats-extras/dist
 
   deploy:
-    needs: [build, test]
+    needs: [build, test, deploy-fileformats, deploy-fileformats-extras]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release'
     permissions:
       attestations: write
       id-token: write
@@ -240,8 +226,10 @@ jobs:
         name: Packages
         path: dist
     - name: Upload to PyPI
+      if: github.event_name == 'release'
       uses: pypa/gh-action-pypi-publish@release/v1
 
+
 # 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

tox.ini

@@ -47,6 +47,9 @@ setenv =
   pre: UV_INDEX_STRATEGY=unsafe-best-match
 uv_resolution =
   min: lowest-direct
+deps =
+    -e ./related-packages/fileformats
+    -e ./related-packages/fileformats-extras
 
 commands =
   pytest pydra/tasks/fsl --cov=pydra.tasks.fsl --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}