Merge pull request #35 from nipype/fix/modernize

MNT: Update Python requirements, CI workflows, add Pydra 0.23 compatibility

Author: effigies

.github/workflows/publish.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

.github/workflows/pythonpackage.yml

@@ -129,4 +129,4 @@ dmypy.json
 .pyre/
 
 # Generated by flit_scm
-_versions.py
+_version.py

.gitignore

@@ -0,0 +1,18 @@
+import sys
+from atexit import register
+from contextlib import ExitStack
+from functools import lru_cache
+
+
+if sys.version_info < (3, 9):
+    from importlib_resources import as_file, files
+else:
+    from importlib.resources import as_file, files
+
+_stack = ExitStack()
+register(_stack.close)
+
+
+@lru_cache
+def load_resource(anchor, *parts) -> str:
+    return str(_stack.enter_context(as_file(files(anchor).joinpath(*parts))))

pydra/tasks/nipype1/tests/__init__.py

@@ -1,6 +1,6 @@
 import pytest
 import shutil
-from pkg_resources import resource_filename
+from . import load_resource
 
 from nipype.interfaces import fsl
 import nipype.interfaces.utility as nutil
@@ -12,7 +12,7 @@
 def test_isolation(tmp_path):
     in_file = tmp_path / "orig/tpms_msk.nii.gz"
     in_file.parent.mkdir()
-    shutil.copyfile(resource_filename("nipype", "testing/data/tpms_msk.nii.gz"), in_file)
+    shutil.copyfile(load_resource("nipype", "testing/data/tpms_msk.nii.gz"), in_file)
 
     out_dir = tmp_path / "output"
     out_dir.mkdir()

pydra/tasks/nipype1/tests/test_nipype1task.py

@@ -11,7 +11,7 @@ def traitedspec_to_specinfo(traitedspec):
     return pydra.specs.SpecInfo(
         name="Inputs",
         fields=[
-            (name, attrs.field(metadata={"help_string": trait.desc}))
+            (name, attrs.field(metadata={"help_string": trait.desc}, type=ty.Any))
             for name, trait in traitedspec.traits().items()
             if name in trait_names
         ],
@@ -27,11 +27,11 @@ class Nipype1Task(pydra.engine.task.TaskBase):
     in Pydra Task outputs.
 
     >>> import pytest
-    >>> from pkg_resources import resource_filename
+    >>> from pydra.tasks.nipype1.tests import load_resource
     >>> from nipype.interfaces import fsl
     >>> if fsl.Info.version() is None:
     ...     pytest.skip()
-    >>> img = resource_filename('nipype', 'testing/data/tpms_msk.nii.gz')
+    >>> img = load_resource('nipype', 'testing/data/tpms_msk.nii.gz')
 
     >>> from pydra.tasks.nipype1.utils import Nipype1Task
     >>> thresh = Nipype1Task(fsl.Threshold())
@@ -68,7 +68,7 @@ def __init__(
         )
         self.output_spec = traitedspec_to_specinfo(interface._outputs())
 
-    def _run_task(self):
+    def _run_task(self, environment=None):
         inputs = attrs.asdict(self.inputs, filter=lambda a, v: v is not attrs.NOTHING)
         node = nipype.Node(self._interface, base_dir=self.output_dir, name=self.name)
         node.inputs.trait_set(**inputs)

pydra/tasks/nipype1/utils.py

@@ -6,7 +6,7 @@ build-backend = "flit_scm:buildapi"
 name = "pydra-nipype1"
 description = "Tools for importing nipype 1.x interfaces into Pydra"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 dependencies = [
     "pydra >=0.6.2",
     "nipype",