Merge pull request #322 from effigies/ci/update_packages

CI: Switch to miniconda setup, install fsl tools through conda

Author: effigies

.github/workflows/unittests.yml

@@ -13,18 +13,18 @@ concurrency:
 permissions:
   contents: read
 
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   build-linux:
     if: "!contains(github.event.head_commit.message, '[skip ci]' && (github.event_name == 'push' || github.event.pull_request.head.repo.full_name != 'nipreps/sdcflows'))"
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       TEST_DATA_HOME: /home/runner/sdcflows-tests
-      FSLDIR: /usr/share/fsl/5.0
       FSLOUTPUTTYPE: NIFTI_GZ
       FSLMULTIFILEQUIT: TRUE
-      POSSUMDIR: /usr/share/fsl/5.0
-      FSLTCLSH: /usr/bin/tclsh
-      FSLWISH: /usr/bin/wish
       AFNI_HOME: /opt/afni
       AFNI_MODELPATH: /opt/afni/models
       AFNI_IMSAVE_WARNINGS: NO
@@ -34,15 +34,15 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9]
 
     steps:
     - uses: actions/cache@v3
       with:
         path: /var/lib/apt
-        key: apt-cache-v2
+        key: apt-cache-v3
         restore-keys: |
-          apt-cache-v2
+          apt-cache-v3
     - name: Install dependencies
       run: |
         sudo apt-get update
@@ -53,10 +53,6 @@ jobs:
                         libglu1-mesa-dev libglw1-mesa     \
                         libxm4 build-essential
 
-    - name: Install FSL
-      run: |
-        sudo apt-get install -y --no-install-recommends fsl
-
     - uses: actions/cache@v3
       with:
         path: /opt/afni
@@ -88,28 +84,36 @@ jobs:
         git config --global user.name 'NiPreps Bot'
         git config --global user.email '[email protected]'
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: conda-incubator/setup-miniconda@v2
       with:
+        auto-update-conda: true
+        auto-activate-base: true
         python-version: ${{ matrix.python-version }}
+        channels: anaconda,https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/,conda-forge
     - uses: actions/cache@v3
       id: conda
+      env:
+        CACHE_NUM: v4
       with:
         path: |
-          /usr/share/miniconda/pkgs
+          ~/conda_pkgs_dir
           /home/runner/.cache/pip
-        key: python-${{ matrix.python-version }}-v3
+        key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
         restore-keys: |
-          python-${{ matrix.python-version }}-v3
+          python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
     - name: Install DataLad
       run: |
-        $CONDA/bin/conda install -c conda-forge git-annex datalad pip
-        $CONDA/bin/pip install datalad-osf
+        conda install git-annex datalad pip
+        pip install datalad-osf
+    - name: Install fsl
+      run: |
+        conda install fsl-fugue fsl-topup
     - uses: actions/checkout@v3
     - name: Install minimal dependencies
       timeout-minutes: 5
       run: |
-        $CONDA/bin/pip install -r min-requirements.txt
-        $CONDA/bin/pip install .[tests]
+        pip install -r min-requirements.txt
+        pip install .[tests]
 
 
     - uses: actions/cache@v3
@@ -120,7 +124,7 @@ jobs:
           tf-cache-
     - name: Get TemplateFlow's required objects
       run: |
-        $CONDA/bin/python tools/cache_templateflow.py
+        python tools/cache_templateflow.py
 
     - uses: actions/cache@v3
       with:
@@ -130,7 +134,6 @@ jobs:
           data-cache-
     - name: Install test data
       run: |
-        export PATH=$CONDA/bin:$PATH
         mkdir -p ${{ env.TEST_DATA_HOME }}
         cd ${{ env.TEST_DATA_HOME }}
 
@@ -173,9 +176,9 @@ jobs:
       run: |
         export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
         export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
-        $CONDA/bin/pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows
+        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows
 
     - name: Submit code coverage
       run: |
-        $CONDA/bin/conda install codecov
-        $CONDA/bin/python -m codecov --flags travis --file cov.xml -e $GITHUB_RUN_NUMBER
+        pip install codecov
+        python -m codecov --flags travis --file cov.xml -e $GITHUB_RUN_NUMBER