WIP: Implement Pydra code-generators #33

Workflow file for this run

.github/workflows/package-pydra.yml at 8fa2030

	#This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	# For deployment, it will be necessary to create a PyPI API token and store it as a secret
	# https://docs.github.com/en/actions/reference/encrypted-secrets

	name: Pydra

	on:
	push:
	branches: [ master ]
	tags: [ '*' ]
	pull_request:
	branches:
	- master
	- dev

	jobs:

	generate-pydra:

	runs-on: ubuntu-latest

	env:
	CFLAGS: -Werror
	QT_SELECT: qt5
	SCCACHE_GHA_ENABLED: "true"
	SCCACHE_CACHE_SIZE: "2G"
	CXX_COMPILER_LAUNCHER: sccache

	steps:
	- uses: actions/checkout@v1

	- name: Install MRtrix dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install clang libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev
	- name: Run sccache-cache
	uses: mozilla-actions/sccache-action@v0.0.3
	- name: Configure MRtrix
	run: ./configure -assert \|\| { cat configure.log; false; }
	- name: Build MRtrix
	run: ./build -nowarnings -persistent -nopaginate \|\| { cat build.log; false; }
	- name: Set PATH Variable
	run: echo "PATH=$PATH:$(pwd)/bin" >> $GITHUB_ENV
	- name: Set LD_LIBRARY_PATH Variable
	run: echo "LD_LIBRARY_PATH=$(pwd)/lib" >> $GITHUB_ENV
	- name: Set up Python
	uses: actions/setup-python@v2
	- name: Install Python build dependencies
	run: \|
	python -m pip install --upgrade pip
	- name: Install pydra-auto-gen requirements
	run: \|
	pip install -r pydra/fileformats-mrtrix
	pip install -r pydra/fileformats-mrtrix-extras
	pip install -r pydra/requirements.txt
	- name: Generate task specifications
	run: \|
	python pydra/pydra-auto-gen.py
	- name: Upload auto-gen pydra
	uses: actions/upload-artifact@v2
	with:
	name: AutoGen
	path: pydra/src/pydra/tasks/mrtrix3/latest

	devcheck:
	needs: [generate-pydra]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.8, 3.11] # Check oldest and newest versions
	pip-flags: ['', '--editable']
	pydra:
	- 'pydra'
	- '--editable git+https://github.com/nipype/pydra.git#egg=pydra'

	steps:
	- uses: actions/checkout@v2
	- name: Download auto-gen pydra
	uses: actions/download-artifact@v2
	with:
	name: AutoGen
	path: pydra/src/pydra/tasks/mrtrix3/latest
	- 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 }} "pydra/src[dev]"
	python -c "import pydra.tasks.mrtrix3 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:
	# needs: [generate]
	# runs-on: ubuntu-latest
	# strategy:
	# matrix:
	# python-version: [3.8, 3.11]
	# defaults:
	# run:
	# shell: bash -l {0}
	# steps:
	# - uses: actions/checkout@v2
	# - name: Install Minconda
	# uses: conda-incubator/setup-miniconda@v2
	# with:
	# auto-activate-base: true
	# activate-environment: ""
	# - name: Install MRtrix via Conda
	# run: \|
	# conda install -c mrtrix3 mrtrix3
	# mrconvert --version
	# - 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 task package
	# run: \|
	# pip install ".[test]"
	# python -c "import pydra.tasks.mrtrix3 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/mrtrix3 \
	# --cov pydra.tasks.mrtrix3 --cov-report xml
	# - uses: codecov/codecov-action@v1
	# if: ${{ always() }}


	deploy:
	needs: [devcheck] # , test]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.11]
	steps:
	- uses: actions/checkout@v2
	- name: Download auto-gen pydra
	uses: actions/download-artifact@v2
	with:
	name: AutoGen
	path: pydra/src/pydra/tasks/mrtrix3/latest
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install build tools
	run: python -m pip install --upgrade pip twine build
	- name: Build source and wheel distributions
	working-directory: ./pydra/src
	run: python -m build
	- name: Check distributions
	run: twine check pydra/src/dist/*
	- name: Upload sdist
	uses: actions/upload-artifact@v2
	with:
	name: SDist
	path: pydra/src/dist/*.tar.gz
	# Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
	# Secrets are not accessible in the if: condition [0], so set an output variable [1]
	# [0] https://github.community/t/16928
	# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter
	- name: Check for PyPI token on tag
	id: deployable
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
	env:
	PYPI_API_TOKEN: "${{ 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@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}
	packages-dir: pydra/src/dist/

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WIP: Implement Pydra code-generators #33

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WIP: Implement Pydra code-generators #33

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