Merge pull request #36 from nipype/fileformats-patch

Patch up fileformats description and CI/CD

.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_CHANGEME --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://git.luolix.topmunity/t/16928
+# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter

README.md

@@ -10,10 +10,15 @@ All tasks will be inserted into the `pydra.tasks.<yourtaskpackagename>` namespac
 1. Give your repo a name.
 1. Once the repo is created and cloned, search for CHANGEME (`grep -rn CHANGEME . `) and
    replace with appropriate name.
-1. Rename the following folders to replace `CHANGEME` with the name of the package:
+1. Rename the namespace package root directory to replace `CHANGEME` with the name of the package:
    * `src/pydra/tasks/CHANGEME`
-   * `fileformats/fileformats/medimage_CHANGEME`
-   * `fileformats/fileformats/extras/medimage_CHANGEME`
+1. If you are planning to define [fileformats](https://arcanaframework.github.io/fileformats/) classes specific
+   to the tools defined in the task package, then rename the base and "extras" packages using a
+   matching name to the package (if the tool is from in another field other than medical imaging,
+   also replace the `medimage` part). If you don't need to define and tool-specific fileformats you can delete
+   these packages and the .github/workflows/fileformats-ci-cd.yaml
+   * `related-packages/fileformats/fileformats/medimage_CHANGEME`
+   * `related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME`
 1. Under the newly renamed package (i.e. formerly CHANGEME) there is a directory named "v1",
    `src/pydra/tasks/<package-name>/v1`, change this to valid Python package name starting with
    'v' to indicate the version of the tool the Pydra interfaces will be designed for,