Updated with latest nipype auto converter templates

.github/workflows/fileformats-ci-cd.yaml

@@ -0,0 +1,132 @@
+name: CI/CD
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.12"]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+    - name: Fetch tags
+      run: git fetch --prune --unshallow
+    - name: Disable etelemetry
+      run:  echo "NO_ET=TRUE" >> $GITHUB_ENV
+    - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Update build tools
+      run: python3 -m pip install --upgrade pip
+    - name: Install Package
+      run: python3 -m pip install -e related-packages/fileformats[test] -e related-packages/fileformats-extras[test]
+    - name: Pytest
+      run: pytest -vvs --cov fileformats.medimage_afni --cov-config .coveragerc --cov-report xml .
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    needs: [test]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        pkg:
+          - ["main", "related-packages/fileformats"]
+          - ["extras", "related-packages/fileformats-extras"]
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+    - name: Install build tools
+      run: python3 -m pip install build twine
+    - name: Build source and wheel distributions
+      run: python3 -m build ${{ matrix.pkg[1] }}
+    - name: Check distributions
+      run: twine check ${{ matrix.pkg[1] }}/dist/*
+    - uses: actions/upload-artifact@v3
+      with:
+        name: built-${{ matrix.pkg[0] }}
+        path: ${{ matrix.pkg[1] }}/dist
+
+  deploy:
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Download build
+      uses: actions/download-artifact@v3
+      with:
+        name: built-main
+        path: dist
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'release'
+      env:
+        PYPI_API_TOKEN: "${{ secrets.FILEFORMATS_PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.FILEFORMATS_PYPI_API_TOKEN }}
+
+  deploy-extras:
+    needs: [build, deploy]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Download build
+      uses: actions/download-artifact@v3
+      with:
+        name: built-extras
+        path: dist
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'release'
+      env:
+        EXTRAS_PYPI_API_TOKEN: "${{ secrets.FILEFORMATS_EXTRAS_PYPI_API_TOKEN }}"
+      run: if [ -n "$EXTRAS_PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.FILEFORMATS_EXTRAS_PYPI_API_TOKEN }}
+
+# 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

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 build/
 develop-eggs/
+_version.py
 dist/
 downloads/
 eggs/
@@ -131,6 +132,9 @@ dmypy.json
 # Pycharm
 .idea
 
+# Vim
+.*.sw[op]
+
 # VS Code
 .vscode
 

nipype-auto-conv/generate

@@ -59,6 +59,7 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
     auto_init += f"from .{module_name} import {converter.task_name}\n"
     all_interfaces.append(converter.task_name)
 
+
 with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "_version.py", "w") as f:
     f.write(
         f"""# Auto-generated by {__file__}, do not edit as it will be overwritten
@@ -69,7 +70,7 @@ post_release = (nipype_version + nipype2pydra_version).replace(".", "")
 """
     )
 
-auto_init += "\n\n__all__ = [\n" + "\n".join(f"    \"{i}\"," for i in all_interfaces) + "\n]\n"    
+auto_init += "\n\n__all__ = [\n" + "\n".join(f"    \"{i}\"," for i in all_interfaces) + "\n]\n"
 
 with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
     f.write(auto_init)

nipype-auto-conv/specs/a_boverlap.yaml

@@ -41,9 +41,12 @@ inputs:
     # type=file|default=<undefined>: input file A
     in_file_b: medimage/nifti1
     # type=file|default=<undefined>: input file B
-    out_file: text/text-file
+    out_file: Path
     # type=file: output file
     # type=file|default=<undefined>: collect output to a file
+  callable_defaults:
+  # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py`
+  # to set as the `default` method of input fields
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
 outputs:
@@ -93,7 +96,7 @@ tests:
     environ:
     # type=dict|default={}: Environment variables
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   expected_outputs:
   # dict[str, str] - expected values for selected outputs, noting that tests will typically
@@ -114,11 +117,11 @@ tests:
     # type=file|default=<undefined>: input file A
     in_file_b:
     # type=file|default=<undefined>: input file B
-    out_file:
+    out_file: ' "out.mask_ae_overlap.txt"'
     # type=file: output file
     # type=file|default=<undefined>: collect output to a file
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   expected_outputs:
   # dict[str, str] - expected values for selected outputs, noting that tests will typically
@@ -143,11 +146,11 @@ doctests:
     # type=file|default=<undefined>: input file A
     in_file_b:
     # type=file|default=<undefined>: input file B
-    out_file:
+    out_file: ' "out.mask_ae_overlap.txt"'
     # type=file: output file
     # type=file|default=<undefined>: collect output to a file
   imports:
-  # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item
+  # list[nipype2pydra.task.base.importstatement] - list import statements required by the test, with each list item
   # consisting of 'module', 'name', and optionally 'alias' keys
   directive:
   # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS