Merge branch 'main' into fix/no_mutate_on_run

.editorconfig

@@ -0,0 +1,24 @@
+# EditorConfig <editorconfig.org>
+
+# This is the top-most EditorConfig file.
+root = true
+
+# Use Unix-style newlines with a newline ending for all files.
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+# Use 4-space indentation for Python.
+[*.py]
+indent_size = 4
+indent_style = space
+
+# Use 4-space indentation for TOML.
+[*.toml]
+indent_size = 4
+indent_style = space
+
+# Use 2-space indentation for YAML.
+[*.{yml,yaml}]
+indent_size = 2
+indent_style = space

.github/workflows/pythonpackage.yml

@@ -6,114 +6,112 @@ name: Python package
 # Set once
 env:
   SUBPACKAGE: nipype1
+  FSLCONDA: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
 
 on:
   push:
-    branches: [ main ]
-    tags: [ '*' ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+  release:
+    types:
+      - published
+
+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, 3.9]  # 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
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-    - name: Install Pydra
-      run: |
-        pip install ${{ matrix.pydra }}
-        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-    - name: Install task package
-      run: |
-        pip install ${{ matrix.pip-flags }} ".[dev]"
-        python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-        python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        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: |
+          pip install ${{ matrix.pydra }}
+          python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+      - name: Install task package
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev]"
+          python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+          python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
 
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Set up NeuroDebian
-      run: bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-    - name: Install FSL
-      run: sudo apt-get install -y fsl
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-    - name: Install task package
-      run: |
-        pip install ".[test]"
-        python -c "import pydra.tasks.$SUBPACKAGE 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: |
-        source /etc/fsl/fsl.sh
-        pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \
-            --cov pydra.tasks.$SUBPACKAGE --cov-report xml
-    - uses: codecov/codecov-action@v1
-      if: ${{ always() }}
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: ${{ env.FSLCONDA }},conda-forge,defaults
+          channel-priority: true
+      - name: Install FSL
+        run: |
+          mamba install fsl-avwutils
+          mamba env config vars set FSLDIR="$CONDA_PREFIX" FSLOUTPUTTYPE="NIFTI_GZ"
+          # Hack because we're not doing a full FSL install
+          echo "6.0.7.9" > $CONDA_PREFIX/etc/fslversion
+      - name: Upgrade pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Install task package
+        run: |
+          pip install ".[test]"
+          python -c "import pydra.tasks.$SUBPACKAGE 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/$SUBPACKAGE \
+              --cov pydra.tasks.$SUBPACKAGE --cov-report xml
+      - uses: codecov/codecov-action@v4
+        if: ${{ always() }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
 
   deploy:
-    needs: [devcheck, test]
+    needs: [build, devcheck, test]
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.9]
+    permissions:
+      id-token: write
+    if: github.repository_owner == 'nipype' && github.event.action == 'published'
+    environment: Publish
     steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: recursive
-        fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install build tools
-      run: python -m pip install --upgrade pip setuptools wheel twine
-    - name: Build source and wheel distributions
-      run: python setup.py sdist bdist_wheel
-    - name: Check distributions
-      run: twine check dist/*
-    - uses: actions/upload-artifact@v2
-      with:
-        name: distributions
-        path: dist/
-    # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
-    # Secrets are not accessible in the if: condition [0], so set an output variable [1]
-    # [0] https://github.community/t/16928
-    # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
-    - name: Check for PyPI token on tag
-      id: deployable
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      env:
-        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
-      run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi
-    - name: Upload to PyPI
-      if: steps.deployable.outputs.DEPLOY
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29  # v1.4.2
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Generated by flit_scm
+_version.py

.pre-commit-config.yaml

@@ -2,13 +2,13 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.3.0
     hooks:
     -   id: black

CHANGELOG.md

@@ -1,4 +1,52 @@
-0.1.0 (9 April 2021)
-====================
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.3.0] - 2024-03-22
+
+### Changed
+
+* Pydra 0.23+ compatibility
+* Drop Python 3.7 compatibility, test Python 3.12
+* Updates to CI workflows
+
+## [0.2.2] – 2022-11-22
+
+### Changed
+
+- Set Nipype developers as maintainers.
+
+## [0.2.1] – 2022-11-22
+
+### Added
+
+- Publish package automatically on release.
+
+### Fixed
+
+- Update project metadata.
+
+## [0.2.0] – 2022-11-21
+
+### Added
+
+- Expose `Nipype1Task` to the root of the package.
+
+### Changed
+
+- Use modern `attrs` namespace instead of `attr`.
+- Migrate project to `flit_scm`.
+
+### Fixed
+
+- Keep collection types in wrapped interfaces.
+
+## [0.1.0] – 2021-04-09
 
 - Initial release for PyPI
+
+[0.3.0]: https://github.com/nipype/pydra-nipype1/compare/0.2.2...0.3.0
+[0.2.2]: https://github.com/nipype/pydra-nipype1/compare/0.2.1...0.2.2
+[0.2.1]: https://github.com/nipype/pydra-nipype1/compare/0.2.0...0.2.1
+[0.2.0]: https://github.com/nipype/pydra-nipype1/compare/0.1.0...0.2.0
+[0.1.0]: https://github.com/nipype/pydra-nipype1/releases/tag/0.1.0

pydra/tasks/nipype1/__init__.py

@@ -1,4 +1,13 @@
-from ._version import get_versions
+"""
+>>> from pydra import ShellCommandTask
+>>> import pydra.tasks.nipype1
+"""
 
-__version__ = get_versions()["version"]
-del get_versions
+try:
+    from ._version import __version__
+except ImportError:
+    pass
+
+from .utils import Nipype1Task
+
+__all__ = ["Nipype1Task"]