Fastsurfer Singularity workflow to quick test new code before merging #496
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Removed extra workflows used for local testing Removed extra files used for local testing documentation for the fastsurfer singularity test workflow Delete test/__pycache__ directory Update fastsurfer_singularity.yaml converting tests to run on singularity Switching from Docker to Singularity changed runner to ci-gpu Deleted old action files Changed the name of FastSurfer actions to differentiate between Docker and Singularity Resolved issues from code review added fastsurfer_singularity.yaml to run FastSurfer in singularity container fixed issues in test_file_existence completed implementation of tests through command line arguments instead of yaml files Taking yaml files using command line arguments Implemented script to check for errors in log files Adding a file existence test to make sure all the files that are supposed to be in the results are actually there. making jobs sequential by adding dependencies Added environment variables for MRI data and output renaming the workflow to 'FastSurfer Docker Image Build' Building GPU FastSurfer Image and running analysis simple workflow to test if self hosted runner 'dirac' is running correctly
m-reuter
reviewed
Mar 25, 2024
m-reuter
reviewed
Mar 25, 2024
dkuegler
requested changes
Mar 25, 2024
- added errors and whitelists QUICKTEST.md: - renamed from singularity_workflow.md quicktest.yaml: - renamed from singularity_workflow.md - fixed typo test_errors.py: - using pathlib.Path instead of os.path - added context for errors - improved error output to give more information about the errors test_file_existence.py: - using pathlib.Path instead of os.path in test-error-messages: - changed file name to test/quick_test/test_errors.py
- replacing hardcoded 'stable' branch with the current working branch so docs point to current branch code
This reverts commit 813be12.
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This PR adds a workflow to test new code inside a Singularity container, running on a local runner, before it is merged into the
devbranch. It also adds some quick tests to evaluate the new code and includes documentation for how to set up and run the workflow and tests..github/workflows/
fastsurfer_singularity.yaml
singularity_workflow.md
test/
quick_test/
test_file_existence.py
test_errors.py
data/
files.yaml
errors.yaml
Switching from Docker to Singularity:
The workflow originally used Docker but was switched to Singularity later on.