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Merge pull request #36 from nipype/fileformats-patch
Patch up fileformats description and CI/CD
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‎.github/workflows/fileformats-ci-cd.yaml

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name: CI/CD
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on:
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push:
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branches: [ main, develop ]
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pull_request:
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branches: [ main, develop ]
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release:
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types: [published]
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defaults:
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run:
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shell: bash
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jobs:
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test:
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.8", "3.12"]
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fail-fast: false
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Unset header
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: git config --local --unset http.https://github.com/.extraheader
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- name: Fetch tags
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run: git fetch --prune --unshallow
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- name: Disable etelemetry
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run: echo "NO_ET=TRUE" >> $GITHUB_ENV
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- name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Update build tools
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run: python3 -m pip install --upgrade pip
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- name: Install Package
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run: python3 -m pip install -e related-packages/fileformats[test] -e related-packages/fileformats-extras[test]
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- name: Pytest
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run: pytest -vvs --cov fileformats.medimage_CHANGEME --cov-config .coveragerc --cov-report xml .
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v2
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with:
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fail_ci_if_error: true
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token: ${{ secrets.CODECOV_TOKEN }}
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build:
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needs: [test]
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runs-on: ubuntu-latest
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strategy:
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matrix:
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pkg:
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- ["main", "related-packages/fileformats"]
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- ["extras", "related-packages/fileformats-extras"]
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steps:
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- uses: actions/checkout@v3
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Unset header
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# checkout@v2 adds a header that makes branch protection report errors
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# because the Github action bot is not a collaborator on the repo
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run: git config --local --unset http.https://github.com/.extraheader
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.12'
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- name: Install build tools
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run: python3 -m pip install build twine
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- name: Build source and wheel distributions
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run: python3 -m build ${{ matrix.pkg[1] }}
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- name: Check distributions
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run: twine check ${{ matrix.pkg[1] }}/dist/*
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- uses: actions/upload-artifact@v3
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with:
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name: built-${{ matrix.pkg[0] }}
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path: ${{ matrix.pkg[1] }}/dist
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deploy:
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needs: [build]
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runs-on: ubuntu-latest
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steps:
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- name: Download build
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uses: actions/download-artifact@v3
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with:
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name: built-main
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path: dist
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- name: Check for PyPI token on tag
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id: deployable
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if: github.event_name == 'release'
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env:
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PYPI_API_TOKEN: "${{ secrets.FILEFORMATS_PYPI_API_TOKEN }}"
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run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
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- name: Upload to PyPI
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if: steps.deployable.outputs.DEPLOY
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.FILEFORMATS_PYPI_API_TOKEN }}
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deploy-extras:
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needs: [build, deploy]
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runs-on: ubuntu-latest
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steps:
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- name: Download build
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uses: actions/download-artifact@v3
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with:
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name: built-extras
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path: dist
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- name: Check for PyPI token on tag
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id: deployable
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if: github.event_name == 'release'
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env:
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EXTRAS_PYPI_API_TOKEN: "${{ secrets.FILEFORMATS_EXTRAS_PYPI_API_TOKEN }}"
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run: if [ -n "$EXTRAS_PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
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- name: Upload to PyPI
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if: steps.deployable.outputs.DEPLOY
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.FILEFORMATS_EXTRAS_PYPI_API_TOKEN }}
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# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
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# Secrets are not accessible in the if: condition [0], so set an output variable [1]
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# [0] https://github.community/t/16928
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# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter

‎README.md

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

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