[ENH] rerunning the app overrides old files and logs a warning #164

Workflow file for this run

	---
	on:
	push:
	branches:
	- main
	- maint/*
	tags:
	- '*'
	pull_request:
	branches:
	- main
	- maint/*

	defaults:
	run:
	shell: bash

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	permissions:
	contents: read

	jobs:
	check_skip_flags:
	name: Check skip flags
	runs-on: ubuntu-latest
	outputs:
	head-commit-message: ${{ steps.get_head_commit_message.outputs.headCommitMsg }}
	steps:
	- name: Get repo
	uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Print head git commit message
	id: get_head_commit_message
	run: echo "headCommitMsg=$(git show -s --format=%s)" >> $GITHUB_OUTPUT

	download-test-data:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v5
	- name: install tox
	run: pip install tox
	- uses: actions/cache@v3
	id: cache
	env:
	cache-name: ds000017
	with:
	path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
	key: ${{ env.cache-name }}

	- if: ${{ steps.cache.outputs.cache-hit != 'true' }}
	name: Download fmriprep derivative of ds000017
	id: download
	run: tox -e test_data

	build:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v5
	with:
	python-version: 3
	- run: pip install --upgrade build twine
	- name: Build sdist and wheel
	run: python -m build
	- run: twine check dist/*
	- name: Upload sdist and wheel artifacts
	uses: actions/upload-artifact@v3
	with:
	name: dist
	path: dist/
	- name: Build git archive
	run: mkdir archive && git archive -v -o archive/archive.tgz HEAD
	- name: Upload git archive artifact
	uses: actions/upload-artifact@v3
	with:
	name: archive
	path: archive/

	test-package:
	runs-on: ubuntu-latest
	needs: [build]
	strategy:
	matrix:
	package: [wheel, sdist, archive]
	steps:
	- name: Download sdist and wheel artifacts
	if: matrix.package != 'archive'
	uses: actions/download-artifact@v3
	with:
	name: dist
	path: dist/
	- name: Download git archive artifact
	if: matrix.package == 'archive'
	uses: actions/download-artifact@v3
	with:
	name: archive
	path: archive/
	- uses: actions/setup-python@v5
	with:
	python-version: 3
	- name: Display Python version
	run: python -c "import sys; print(sys.version)"
	- name: Update pip
	run: pip install --upgrade pip
	- name: Install wheel
	if: matrix.package == 'wheel'
	run: pip install dist/*.whl
	- name: Install sdist
	if: matrix.package == 'sdist'
	run: pip install dist/*.tar.gz
	- name: Install archive
	if: matrix.package == 'archive'
	run: pip install archive/archive.tgz

	test-coverage:
	runs-on: ubuntu-latest
	needs: [build, download-test-data, check_skip_flags]
	strategy:
	matrix:
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	- uses: actions/checkout@v4
	name: Set up Python ${{ matrix.python-version }}
	- uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Restore cached data ds000017
	id: cache
	uses: actions/cache/restore@v3
	with:
	path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
	key: ds000017

	- name: Install build dependencies
	run: python -m pip install --upgrade pip
	- name: Install task package
	run: pip install -e .[test]

	- name: Test with pytest - ignore smoke test.
	if: ${{ !contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }}
	run: \|
	pytest -m "not smoke" --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome

	- name: Full test - run all the test to generate accurate coverage report.
	if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} \|\| ${{ github.event.pull_request.merged }}
	run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome

	- uses: codecov/codecov-action@v3
	if: ${{ always() }}
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	docker:
	# build and test docker image
	if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }}
	runs-on: ubuntu-latest
	needs: [download-test-data, check_skip_flags]
	steps:
	- uses: actions/checkout@v4
	- name: Build the Docker image
	run: \|
	user_name="bids"
	docker build . --file Dockerfile --tag ${user_name}/giga_connectome
	mkdir -p "${HOME}/docker"
	docker save "${user_name}/giga_connectome" > "${HOME}/docker/image.tar"

	- name: Restore cached data ds000017
	id: cache
	uses: actions/cache/restore@v3
	with:
	path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
	key: ds000017

	- name: Test the Docker image
	run: \|
	docker load -i ${HOME}/docker/image.tar
	docker run --rm --read-only \
	-v /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data:/test_data \
	-v ./outputs:/outputs \
	-v ./outputs/working_dir:/work \
	bids/giga_connectome \
	/test_data/ds000017-fmriprep22.0.1-downsampled-nosurface \
	/outputs \
	participant \
	-w /work \
	--participant_label 1 \
	--reindex-bids

	- name: Upload output artifact
	uses: actions/upload-artifact@v3
	with:
	name: connectome
	path: ./outputs/
	- name: Upload docker image artifact
	uses: actions/upload-artifact@v3
	with:
	name: docker-image
	path: ${HOME}/docker/image.tar

	# publish:
	# runs-on: ubuntu-latest
	# needs: [test-package, test-coverage]
	# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
	# steps:
	# - uses: actions/download-artifact@v3
	# with:
	# name: dist
	# path: dist/
	# - uses: pypa/gh-action-pypi-publish@release/v1
	# with:
	# user: __token__
	# password: ${{ secrets.PYPI_API_TOKEN }}

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[ENH] rerunning the app overrides old files and logs a warning #164

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[ENH] rerunning the app overrides old files and logs a warning #164

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Workflow file for this run