[WIP] Sydneyimaging t1 preproc #3

Workflow file for this run

	# This workflows will upload a Python Package using Twine when a release is created
	# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

	name: CI/CD

	on:
	push:
	branches: [ main, develop ]
	tags: [ '*' ]
	pull_request:
	branches: [ main, develop ]
	release:
	types: [published]
	workflow_dispatch: # Allow manual triggering by a user with write access to this repo

	defaults:
	run:
	shell: bash

	jobs:
	test-python:
	strategy:
	matrix:
	os: [macos-latest, ubuntu-latest, windows-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 ./src[test]
	- name: Pytest
	run: pytest -vvs --cov australianimagingservice_community --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-python:
	needs: [test-python]
	runs-on: ubuntu-latest
	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 ./src
	- name: Check distributions
	run: twine check ./dist/*
	- uses: actions/upload-artifact@v3
	with:
	name: built-python
	path: ./dist

	build-docs:
	runs-on: ubuntu-20.04
	steps:
	- name: Checkout repository
	uses: actions/checkout@v2
	with:
	submodules: recursive # Fetch Hugo themes (true OR recursive)
	fetch-depth: 1 # Fetch all history for .GitInfo and .Lastmod
	# TODO: Need a unique key we can pass, but as we're targeting
	# arcana@master, this is not trivial.
	#
	# - name: Cache dependencies
	# uses: actions/cache@v1
	# with:
	# path: ~/.local/lib
	# key: ${{ runner.os }}-python-${{ hashFiles('**/package-lock.json') }}
	# restore-keys: \|
	# ${{ runner.os }}-python-
	- name: Setup Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.11' # Version range or exact version of a Python version to use, using SemVer'
	- name: Install python dependencies
	run: pip install -r ./requirements.txt
	- name: Generate pipeline docs
	run: arcana deploy make-docs specs/australian-imaging-service-community docs/pipelines --flatten --default-data-space arcana.common:Clinical
	- uses: actions/upload-artifact@v3
	with:
	name: built-docs
	path: docs/build/html

	deploy-python:
	needs: [build-python, build-docs]
	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: "${{ secrets.PYPI_API_TOKEN }}"
	run: if [ -n "$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.PYPI_API_TOKEN }}

	build-deploy-pipelines:
	needs: [deploy-python]
	runs-on: ubuntu-latest
	steps:
	- name: Remove unnecessary tools to free space
	run: \|
	sudo rm -rf /usr/share/dotnet
	sudo rm -rf "$AGENT_TOOLSDIRECTORY"
	- name: Checkout
	uses: actions/checkout@v2
	- name: Get release tag
	run: \|
	git fetch --prune --unshallow
	echo "RELEASE=`echo $(git describe --tags --abbrev=0)`" >> $GITHUB_ENV
	- 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@v2
	with:
	python-version: '3.11'
	- name: Update build tools
	run: python -m pip install --upgrade pip
	- name: Install dependencies
	run: pip install -r requirements.txt
	- uses: docker/login-action@v2
	with:
	registry: ghcr.io
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }} # - must be in GitHub Secrets!
	- name: Check for tagged release
	id: deployable
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
	run: echo "PUSH=--push" >> $GITHUB_ENV
	- name: Build and push container images
	run: >
	arcana deploy make-app specs/australian-imaging-service-community xnat:XnatApp
	--registry ghcr.io --check-registry --clean-up --tag-latest --loglevel info
	--release pipelines-community-metapackage $RELEASE $PUSH

	deploy-docs:
	needs: [build-docs, build-deploy-pipelines]
	runs-on: ubuntu-latest
	steps:
	- name: Download built docs
	uses: actions/download-artifact@v3
	with:
	name: built-docs
	path: docs/build/html
	- name: Remove /docs/pipelines/ from .gitignore
	run: sed -i 's%^/docs/pipelines/\*$%%' .gitignore
	- name: Check for GHPAGES_DEPLOY_KEY token on tag
	id: deployable
	if: github.event_name == 'release'
	env:
	GHPAGES_DEPLOY_KEY: "${{ secrets.GHPAGES_DEPLOY_KEY }}"
	run: if [ -n "$GHPAGES_DEPLOY_KEY" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
	- name: Deploy docs
	uses: peaceiris/actions-gh-pages@v3
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	publish_dir: .
	publish_branch: docs
	enable_jekyll: true # This branch isn't actually fed to GH pages
	# It's possible, likely even, that we'll trigger unnecessary docs
	# rebuilds with this. Running this properly as a separate workflow
	# only when real docs changes occur would require using a PAT.
	- name: Trigger rebuild of docs
	uses: peter-evans/repository-dispatch@v1
	if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
	with:
	token: ${{ secrets.GITHUBPAGES_KEY }}
	repository: Australian-Imaging-Service/Australian-Imaging-Service.github.io
	event-type: Rebuild docs

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[WIP] Sydneyimaging t1 preproc #3

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[WIP] Sydneyimaging t1 preproc #3

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Workflow file for this run