Merge pull request #4 from nipype/develop

Debugging GH actions for auto-conversion from Nipype

.github/workflows/ci-cd.yaml

@@ -107,77 +107,68 @@ jobs:
         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 .
+        pytest ./related-packages -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
 
   test:
     needs: [nipype-conv, fileformats-test]
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.8']  # '3.11'
+        python-version: ['3.8', '3.11']
     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:$PATH
-    - uses: actions/checkout@v3
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+    - name: Checkout repo
+      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: Install AFNI
+      run: |
+        curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_22_64_a_admin.txt
+        curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_22_64_b_user.tcsh
+        sudo bash OS_notes.linux_ubuntu_22_64_a_admin.txt 2>&1 | tee o.ubuntu_22_a.txt
+    
     - name: Download tasks converted from Nipype 
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
+
+    - name: Show the contents of the auto-generated tasks
+      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
       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 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
-    - uses: codecov/codecov-action@v3
+        pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
+
+    - name: Upload to CodeCov
+      uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:
         files: coverage.xml,./fileformats/coverage.xml

README.rst

@@ -1,11 +1,11 @@
-===============================
+===========================
 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
-.. .. image:: https://codecov.io/gh/nipype/pydra-afni/branch/main/graph/badge.svg?token=UIS0OGPST7
-..    :target: https://codecov.io/gh/nipype/pydra-afni
+.. image:: https://codecov.io/gh/nipype/pydra-afni/branch/main/graph/badge.svg?token=UIS0OGPST7
+   :target: https://codecov.io/gh/nipype/pydra-afni
 .. image:: https://img.shields.io/pypi/pyversions/pydra-afni.svg
    :target: https://pypi.python.org/pypi/pydra-afni/
    :alt: Supported Python versions
@@ -14,10 +14,10 @@ Pydra task package for afni
    :alt: Latest Version
 
 
-This package contains a collection of Pydra task interfaces for the afni toolkit.
-The basis of this collection has been formed by the semi-automatic conversion of
-existing `Nipype <https://github.com/nipy/nipype>`__ interfaces to Pydra using the
-`Nipype2Pydra <https://github.com/nipype/nipype2pydra>`__ tool
+This package contains a collection of Pydra task interfaces for the `AFNI <https://afni.nimh.nih.gov/>`__
+software toolkit. The basis of this collection has been formed by the semi-automatic
+conversion of existing `Nipype <https://github.com/nipy/nipype>`__ interfaces to Pydra
+using the `Nipype2Pydra <https://github.com/nipype/nipype2pydra>`__ tool
 
 
 Automatically-generated vs manually-curated tasks
@@ -26,8 +26,7 @@ Automatically-generated vs manually-curated tasks
 Automatically generated tasks can be found in the `pydra.tasks.afni.auto` package.
 These packages should be treated with extreme caution as they likely do not pass testing.
 Generated tasks that have been edited and pass testing are imported into one or more of the
-`pydra.tasks.afni.v*` packages, corresponding to the version of the afni toolkit
-they are designed for. 
+`pydra.tasks.afni.v*` packages, corresponding to the version of AFNI they are designed for. 
 
 Tests
 -----
@@ -39,7 +38,8 @@ the necessary dependencies to run the tests
 
    $ pip install -e .[test]
 
-Then the tests, including `doctests` <https://docs.python.org/3/library/doctest.html>`__, can be launched using
+Then the tests, including `doctests` <https://docs.python.org/3/library/doctest.html>`__,
+can be launched using
 
 .. code-block::
 
@@ -71,14 +71,22 @@ Contributing to this package
 Developer installation
 ~~~~~~~~~~~~~~~~~~~~~~
 
+Install the `fileformats <https://arcanaframework.github.io/fileformats/>`__ packages
+corresponding to AFNI specific file formats
+
+
+.. code-block::
+
+   $ pip install -e ./related-packages/fileformats[dev]
+   $ pip install -e ./related-packages/fileformats-extras[dev]
 
 Install repo in developer mode from the source directory and install pre-commit to
 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

pydra/tasks/afni/latest.py

@@ -1,3 +1,3 @@
-PACKAGE_VERSION = "v1"
+PACKAGE_VERSION = "v24_0_12"
 
-from .v1 import *  # noqa
+from .v24_0_12 import *  # noqa

related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 import typing as ty
 from random import Random
-from fileformats.core import FileSet
+from fileformats.core import FileSet, SampleFileGenerator
 from fileformats.medimage_afni import (
     OneD,
     Head,
@@ -16,58 +16,46 @@
 @FileSet.generate_sample_data.register
 def gen_sample_oned_data(
     oned: OneD,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
 def gen_sample_head_data(
     head: Head,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
 def gen_sample_all1_data(
     all1: All1,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
 def gen_sample_r1_data(
     r1: R1,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
 def gen_sample_threed_data(
     threed: ThreeD,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
 def gen_sample_dset_data(
     dset: Dset,
-    dest_dir: Path,
-    seed: ty.Union[int, Random] = 0,
-    stem: ty.Optional[str] = None,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     raise NotImplementedError