Migrating Quicktest to PyTest and adding dockerized self hosted runner #22

Workflow file for this run

.github/workflows/quicktest_runner.yaml at 8ae2aec

	name: quicktest-runner

	# File: quicktest_runner.yaml
	# Author: Taha Abdullah
	# Created on: 2023-07-10
	# Functionality: This workflow runs FastSurfer on MRI data and runs pytest to check if the results are acceptable. It
	# also checks if the FastSurfer environment and output already exist, and if not, it creates them.
	# Usage: This workflow is triggered on a pull request to the dev and main branch. It can also be triggered manually
	# with workflow-dispatch.
	# Expected/Used Environment Variables:
	# - MAMBAPATH: Path to the micromamba binary.
	# - MAMBAROOT: Root path for micromamba.
	# - RUNNER_FS_OUTPUT: Path to the directory where FastSurfer output is stored.
	# - RUNNER_FS_MRI_DATA: Path to the directory where MRI data is stored.
	# - FREESURFER_HOME: Path to the freesurfer directory.
	# - FS_LICENSE: Path to the FreeSurfer license file.

	on:
	pull_request:
	branches:
	- dev
	- stable
	workflow_dispatch:

	jobs:
	# Checkout repo
	checkout:
	runs-on: self-hosted
	steps:
	- uses: actions/checkout@v2

	check-output:
	runs-on: self-hosted
	# outputs:
	# fastsurfer-output-exists: ${{ steps.check-fastsurfer-output.fastsurfer_output_exists }}
	needs: checkout
	steps:
	- name: Check FastSurfer Output Directory
	run: \|
	if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then
	echo "FastSurfer output directory for subject1 exists. Finishing job..."
	echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT
	exit 0
	else
	echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
	echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
	fi
	echo success
	id: check-fastsurfer-output

	# Create conda environment, install packages, and run Fastsurfer
	run-fastsurfer:
	runs-on: self-hosted
	needs: check-output
	if: needs.check-output.outputs.HAS_FASTSURFER == 'true'
	steps:
	# Check if the Environment Variables used in further steps are present
	- name: Check Environment Variables
	run: \|
	REQUIRED_ENV_VARS=(
	"MAMBAPATH"
	"MAMBAROOT"
	"RUNNER_FS_OUTPUT"
	"RUNNER_FS_MRI_DATA"
	"FREESURFER_HOME"
	"FS_LICENSE"
	)

	for VAR_NAME in "${REQUIRED_ENV_VARS[@]}"; do
	if [ -z "${!VAR_NAME}" ]; then
	echo "Error: Required environment variable $VAR_NAME is not set"
	exit 1
	fi
	done

	if [ ! -f "$FS_LICENSE" ]; then
	echo "Error: FreeSurfer license file does not exist at $FS_LICENSE"
	exit 1
	fi

	if [ ! -d "$FREESURFER_HOME" ]; then
	echo "Error: FreeSurfer installation directory does not exist at $FREESURFER_HOME"
	exit 1
	fi
	# Set up Python using setup-python@v3 action
	- name: Set up Python 3.10
	uses: actions/setup-python@v3
	with:
	python-version: "3.10"
	# Check if FastSurfer environment already exists
	- name: Check Environment
	run: \|
	if [ ! -f "$MAMBAPATH" ]; then
	echo "FastSurfer environment does not exist. Creating FastSurfer Environment..."
	echo "HAS_MAMBA=true" >> $GITHUB_OUTPUT
	else
	echo "FastSurfer environment exists. Skipping FastSurfer Environment creation..."
	echo "HAS_MAMBA=false" >> $GITHUB_OUTPUT
	fi
	id: check-environment
	# Create FastSurfer environment if it does not exist
	- name: Create FastSurfer Environment
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: env/fastsurfer.yml
	micromamba-root-path: $MAMBAROOT
	micromamba-binary-path: $MAMBAPATH
	cache-downloads: true
	cache-environment: true
	init-shell: none
	if: steps.check-environment.outputs.HAS_MAMBA == 'true'
	# Set up cache for python packages
	- name: Cache Python packages
	uses: actions/cache@v3
	with:
	path: /home/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	# Install required python packages
	- name: Install package
	run: \|
	python -m pip install --progress-bar off --upgrade pip \
	setuptools wheel
	python -m pip install --progress-bar off .[test]
	# Check if FastSurfer output already exists
	# - name: Check FastSurfer Output Directory
	# run: \|
	# if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then
	# echo "FastSurfer output directory for subject1 exists. Finishing job..."
	# echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT
	# exit 0
	# else
	# echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
	# echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
	#
	# fi
	# id: check-fastsurfer-output
	# Run FastSurfer
	- name: Run FastSurfer
	run: \|
	echo "Running FastSurfer..."
	export FREESURFER_HOME=/freesurfer
	source $FREESURFER_HOME/SetUpFreeSurfer.sh
	git config --global --add safe.directory \
	.
	./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \
	--sd $RUNNER_FS_OUTPUT \
	--parallel --threads 4 --3T --parallel_subjects surf
	# if: steps.check-fastsurfer-output.outputs.HAS_FASTSURFER == 'true'

	# Run pytest
	run-pytest:
	runs-on: self-hosted
	if: ${{ always() && contains(join(needs.*.result, ','), 'success') }}
	needs: [check-output, run-fastsurfer]
	steps:
	- name: Set up Python 3.10
	uses: actions/setup-python@v3
	with:
	python-version: "3.10"
	- name: Cache Python packages
	uses: actions/cache@v3
	with:
	path: /home/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	- name: Run pytest
	run: python -m pytest test/quick_test

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Migrating Quicktest to PyTest and adding dockerized self hosted runner #22

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Migrating Quicktest to PyTest and adding dockerized self hosted runner #22

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Workflow file for this run