Run participant smoke test #627

Workflow file for this run

.github/workflows/smoke_test_participant.yml at fd4c83c

	# Copyright (C) 2022-2023 C-PAC Developers

	# This file is part of C-PAC.

	# C-PAC is free software: you can redistribute it and/or modify it under
	# the terms of the GNU Lesser General Public License as published by the
	# Free Software Foundation, either version 3 of the License, or (at your
	# option) any later version.

	# C-PAC is distributed in the hope that it will be useful, but WITHOUT
	# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
	# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
	# License for more details.

	# You should have received a copy of the GNU Lesser General Public
	# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
	name: Run participant smoke test

	on:
	workflow_call:
	workflow_dispatch:

	jobs:
	smoke_test_human:
	name: Human ${{ matrix.preconfig }} participant smoke tests
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	preconfig:
	- default
	- abcd-options
	- anat-only
	- benchmark-ANTS
	- benchmark-FNIRT
	- blank
	- ccs-options
	- fmriprep-options
	- fx-options
	- ndmg
	- preproc
	- rbc-options
	- regtest-1
	- regtest-2
	- regtest-3
	- regtest-4
	variant:
	- ''
	participant:
	- 1019436 2014113 3154996 3699991 3884955 NDARAA504CRN NDARAA947ZG5 NDARAB348EWR NDARAB458VK9 NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453
	include:
	- preconfig: default
	variant: lite
	participant: 1019436 2014113 3154996 3699991 3884955 NDARAA504CRN NDARAA947ZG5 NDARAB348EWR NDARAB458VK9 NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453
	- preconfig: abcd-options
	variant: ABCD-HCP
	participant: 1019436 2014113 3154996 3699991 3884955 NDARAA504CRN NDARAA947ZG5 NDARAB348EWR NDARAB458VK9 NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453
	- preconfig: fmriprep-options
	variant: fMRIPrep-LTS
	participant: 1019436 2014113 3154996 3699991 3884955 NDARAA504CRN NDARAA947ZG5 NDARAB348EWR NDARAB458VK9 NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453
	steps:
	- name: Get C-PAC
	run: \|
	if [[ "${{ matrix.variant }}" != "" ]]
	then
	VARIANT=-${{ matrix.variant }}
	fi
	GITHUB_BRANCH=$(echo ${GITHUB_REF} \| cut -d '/' -f 3-)
	if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=${GITHUB_BRANCH//\//_}
	elif [[ $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=nightly
	elif [[ $GITHUB_BRANCH == 'main' ]]
	then
	TAG=latest
	fi
	TAG=$TAG$VARIANT
	echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" \| tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
	cat $GITHUB_ENV
	- name: Run default smoke test
	if: ${{ matrix.preconfig == 'default' }}
	run: \|
	mkdir outputs
	docker run --rm \
	--user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \
	-v $PWD/outputs:/outputs \
	${{ env.DOCKER_TAG }} \
	/outputs /outputs test_config \
	--data_config_file /code/CPAC/resources/configs/test_configs/data-test_human.yml \
	--participant_label ${{ matrix.participant }} \
	--n_cpus 2
	- name: Run ${{ matrix.preconfig }} smoke test
	if: ${{ matrix.preconfig != 'default' }}
	run: \|
	mkdir outputs
	docker run --rm \
	--user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \
	-v $PWD/outputs:/outputs \
	${{ env.DOCKER_TAG }} \
	/outputs /outputs test_config \
	--data_config_file /code/CPAC/resources/configs/test_configs/data-test_human.yml \
	--participant_label ${{ matrix.participant }} \
	--preconfig ${{ matrix.preconfig }} \
	--n_cpus 2
	- uses: actions/upload-artifact@v3
	if: ${{ always() }}
	with:
	name: expectedOutputs human ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
	path: outputs/log/pipeline_//*_expectedOutputs.yml
	if-no-files-found: ignore
	smoke_test_nhp:
	name: Non-human primate ${{ matrix.preconfig }} participant smoke tests
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	preconfig:
	- monkey
	- nhp-macaque
	variant:
	- ''
	participant:
	- 032102 032106 032164 032167 032130 032128 2215 2312 032191 032195
	steps:
	- name: Get C-PAC
	run: \|
	if [[ "${{ matrix.variant }}" != "" ]]
	then
	VARIANT=-${{ matrix.variant }}
	fi
	GITHUB_BRANCH=$(echo ${GITHUB_REF} \| cut -d '/' -f 3-)
	if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=${GITHUB_BRANCH//\//_}
	elif [[ $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=nightly
	elif [[ $GITHUB_BRANCH == 'main' ]]
	then
	TAG=latest
	fi
	TAG=$TAG$VARIANT
	echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" \| tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
	cat $GITHUB_ENV
	- name: Set up datalad-OSF
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "Theodore (Machine User)"
	wget -O- http://neuro.debian.net/lists/focal.us-tn.libre \| sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
	sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
	sudo apt-get update
	sudo apt-get install datalad git-annex-standalone
	pip install datalad-osf
	- name: Get NHP test data
	run: \|
	datalad clone osf://xt93j test-data
	- name: Run ${{ matrix.preconfig }} smoke test
	run: \|
	mkdir outputs
	docker run --rm \
	--user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \
	-v $PWD/test-data:/test-data \
	-v $PWD/outputs:/outputs \
	${{ env.DOCKER_TAG }} \
	/test-data /outputs test_config \
	--preconfig ${{ matrix.preconfig }} \
	--participant_label ${{ matrix.participant }} \
	--n_cpus 2
	- uses: actions/upload-artifact@v3
	if: ${{ always() }}
	with:
	name: expectedOutputs nhp ${{ matrix.preconfig }} ${{ matrix.variant }} ${{ matrix.participant }}
	path: outputs/log/pipeline_//*_expectedOutputs.yml
	if-no-files-found: ignore
	smoke_test_rodent:
	name: Rodent participant smoke tests
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	variant:
	- ''
	steps:
	- name: Get C-PAC
	run: \|
	if [[ "${{ matrix.variant }}" != "" ]]
	then
	VARIANT=-${{ matrix.variant }}
	fi
	GITHUB_BRANCH=$(echo ${GITHUB_REF} \| cut -d '/' -f 3-)
	if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=${GITHUB_BRANCH//\//_}
	elif [[ $GITHUB_BRANCH == 'develop' ]]
	then
	TAG=nightly
	elif [[ $GITHUB_BRANCH == 'main' ]]
	then
	TAG=latest
	fi
	TAG=$TAG$VARIANT
	echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" \| tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
	cat $GITHUB_ENV
	- name: Set up datalad-OSF
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "Theodore (Machine User)"
	wget -O- http://neuro.debian.net/lists/focal.us-tn.libre \| sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
	sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
	sudo apt-get update
	sudo apt-get install datalad git-annex-standalone
	pip install datalad-osf
	- name: Get rodent test data
	run: \|
	datalad clone osf://uya3r test-data
	- name: Run rodent smoke test
	run: \|
	mkdir outputs
	docker run --rm \
	--user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \
	-v $PWD/test-data:/test-data \
	-v $PWD/outputs:/outputs \
	${{ env.DOCKER_TAG }} \
	/test-data /outputs test_config \
	--preconfig rodent \
	--n_cpus 2
	- uses: actions/upload-artifact@v3
	if: ${{ always() }}
	with:
	name: expectedOutputs rodent ${{ matrix.variant }}
	path: outputs/log/pipeline_//*_expectedOutputs.yml
	if-no-files-found: ignore

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Run participant smoke test #627

Workflow file

Run participant smoke test #627

Jobs

Run details

Workflow file for this run