Merge pull request #11 from nipype/develop

fixed up fileformats deps

Author: tclose

.github/workflows/ci-cd.yaml

@@ -9,31 +9,46 @@ name: CI/CD
 on:
   push:
     branches: [ main, develop ]
-    tags: [ '*' ]
   pull_request:
     branches: [ main, develop ]
+  release:
+    types: [published]
   repository_dispatch:
-    types: [create-release]
+    types: [create-post-release]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
 
 jobs:
 
   nipype-conv:
     runs-on: ubuntu-latest
     steps:
+
     - name: Checkout
-      uses: actions/checkout@v3
-    - name: Revert version to most recent tag on upstream update
+      uses: actions/checkout@v4
+
+    - name: Revert version to most recent version 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
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
     - 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 ./related-packages/fileformats
+
     - 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/afni/auto
@@ -43,43 +58,50 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']  # Check oldest and newest versions
+        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'
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
-    - name: Revert version to most recent tag on upstream update
+      uses: actions/checkout@v4
+
+    - 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 | tail -n 1 | awk -F post '{print $1}')    
-    - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Download tasks converted from Nipype
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
+        sed -i '/^_version.py/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 Pydra
       run: |
         pushd $HOME
         pip install ${{ matrix.pydra }}
         popd
         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.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
@@ -88,7 +110,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
@@ -106,77 +128,55 @@ jobs:
         pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
-      run: |
-        cd ./fileformats
-        pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
+      run: >-
+        pytest ./related-packages -sv --cov fileformats.medimage_afni
+        --cov fileformats.extras.medimage_afni --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: ['3.8', '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::afni-linux-ubuntu22_amd64-7.4.1"
-    - name: Cache FreeSurfer
-      uses: actions/cache@v2
-      with:
-        path: $HOME/downloads/afni
-        key: ${{ steps.cache-key.outputs.key }}
-        restore-keys: |
-          afni-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/afni
-        curl -s -o $HOME/downloads/afni/afni-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/afni/7.4.1/afni-linux-ubuntu22_amd64-7.4.1.tar.gz
-      shell: bash
-    - name: Install Freesurfer
-      env:
-        FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
-      run: |
-        pushd $HOME/downloads/afni
-        tar -zxpf afni-linux-ubuntu22_amd64-7.4.1.tar.gz
-        mv afni $HOME/
-        popd
-        export FREESURFER_HOME=$HOME/afni
-        source $FREESURFER_HOME/SetUpFreeSurfer.sh
-        echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
-        export PATH=$FREESURFER_HOME/bin:$PATH
-    - 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
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Download tasks converted from Nipype
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
+    - name: Show package contents
+      run: tree ./pydra
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
+        sed -i '/\/pydra\/tasks\/afni\/auto/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.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test with pytest
       run: |
-        pytest -sv --doctest-modules ./pydra/tasks/afni \
-            --cov pydra.tasks.afni --cov-report xml
+        pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
     - uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:
@@ -256,7 +256,7 @@ jobs:
         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/afni/auto
@@ -282,7 +282,7 @@ jobs:
       run: python -m build .
     - name: Check distributions
       run: twine check dist/*
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: distributions
         path: dist/

.gitignore

@@ -138,6 +138,5 @@ dmypy.json
 .DS_store
 
 /pydra/tasks/afni/auto
-/pydra/tasks/afni/nipype_ports
 /pydra/tasks/afni/_version.py
 /related-packages/**/_version.py

README.md

@@ -1,6 +1,6 @@
-===============================
+===========================
 Pydra task package for afni
-===============================
+===========================
 
 .. image:: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml/badge.svg
    :target: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml
@@ -78,7 +78,7 @@ ensure consistent code-style and quality.
 .. code-block::
 
    $ pip install -e .[test,dev]
-$ pre-commit install
+   $ pre-commit install
 
 Next install the requirements for running the auto-conversion script and generate the
 Pydra task interfaces from their Nipype counterparts

README.rst

@@ -49,7 +49,7 @@ inputs:
     # type=file|default=<undefined>: can include a whole brain mask within which to calculate correlation. Otherwise, data should be masked already
     weight_ts: generic/file
     # type=file|default=<undefined>: input a 1D file WTS of weights that will be applied multiplicatively to each ROI's average time series. WTS can be a column- or row-file of values, but it must have the same length as the input time series volume. If the initial average time series was A[n] for n=0,..,(N-1) time points, then applying a set of weights W[n] of the same length from WTS would produce a new time series:  B[n] = A[n] * W[n]
-    out_file: medimage-afni/ncorr
+    out_file: medimage-afni/n-corr
     # type=file|default=<undefined>: output file name part
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)

nipype-auto-conv/specs/interfaces/net_corr.yaml

@@ -5,6 +5,7 @@
 >>> import pydra.engine
 >>> import pydra.tasks.afni
 """
+
 from warnings import warn
 from pathlib import Path
 
@@ -19,15 +20,15 @@
     )
 if "nipype" not in __version__:
     try:
-        from .auto._version import nipype_version, nipype2pydra_version
+        from .auto._post_release import src_pkg_version, nipype2pydra_version
     except ImportError:
         warn(
             "Nipype interfaces haven't been automatically converted from their specs in "
             f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` "
             "to generated the converted Nipype interfaces in pydra.tasks.afni.auto"
         )
     else:
-        n_ver = nipype_version.replace(".", "_")
+        n_ver = src_pkg_version.replace(".", "_")
         n2p_ver = nipype2pydra_version.replace(".", "_")
         __version__ += (
             "_" if "+" in __version__ else "+"

pydra/tasks/afni/__init__.py

@@ -12,7 +12,8 @@ dependencies = [
     "fileformats >=0.8.3",
     "fileformats-datascience >=0.1",
     "fileformats-medimage >=0.4.1",
-    "fileformats-medimage-afni"
+    "fileformats-medimage-afni",
+    "looseversion"
 ]
 license = {file = "LICENSE"}
 authors = [{name = "Nipype developers", email = "[email protected]"}]
@@ -44,6 +45,7 @@ doc = [
     "sphinxcontrib-versioning",
 ]
 test = [
+    "nipype2pydra",
     "pytest >= 4.4.0",
     "pytest-cov",
     "pytest-env",