CI: Rework CI to use conda-installed Python/FSL

Author: effigies

.github/workflows/pythonpackage.yml

@@ -6,28 +6,37 @@ name: Python package
 # Set once
 env:
   SUBPACKAGE: nipype1
+  FSLCONDA: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -el {0}
 
 jobs:
   devcheck:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.7', '3.11' ]  # Check oldest and newest versions
-        pip-flags: [ '', '--editable' ]
+        python-version: ["3.8", "3.12"] # Check oldest and newest versions
+        pip-flags: ["", "--editable"]
         pydra:
-          - 'pydra'
-          - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
+          - "pydra"
+          - "--editable git+https://github.com/nipype/pydra.git#egg=pydra"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install build dependencies
@@ -47,19 +56,24 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Set up NeuroDebian
-        run: bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
+          mamba-version: "*"
+          channels: ${{ env.FSLCONDA }},conda-forge,defaults
+          channel-priority: true
       - name: Install FSL
-        run: sudo apt-get install -y fsl
-      - name: Install build dependencies
+        run: |
+          mamba install fsl-avwutils
+          mamba env config vars set FSLDIR="$CONDA_PREFIX" FSLOUTPUTTYPE="NIFTI_GZ"
+          # Hack because we're not doing a full FSL install
+          echo "6.0.7.9" > $CONDA_PREFIX/etc/fslversion
+      - name: Upgrade pip
         run: |
           python -m pip install --upgrade pip
       - name: Install task package
@@ -69,34 +83,31 @@ jobs:
           python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
       - name: Test with pytest
         run: |
-          source /etc/fsl/fsl.sh
           pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \
               --cov pydra.tasks.$SUBPACKAGE --cov-report xml
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         if: ${{ always() }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
-  deploy:
-    needs: [ devcheck, test ]
+  build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.9' ]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install build tools
-        run: python -m pip install build twine
-      - name: Build source and wheel distributions
-        run: python -m build
-      - name: Check distributions
-        run: twine check dist/*
-      - uses: actions/upload-artifact@v2
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  deploy:
+    needs: [build, devcheck, test]
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    if: github.repository_owner == 'nipype' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v4
         with:
-          name: distributions
-          path: dist/
+          name: Packages
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1