DAFNI Workflow Enhancements

[f-allian]

Enhancements to the DAFNI workflow that enables better usability and reproducibility. These include:

• Removed variables.json as an argument. The variables can now be stored as metadata attributes in the dot file produced by the user.
• Developing a local test suite to ensure the entrypoint works as expected.
• Turned main_dafni.py into a module, which improves the modularity and testability of the entrypoint in the test suite.
• CI/CD workflows have also been updated.

[github-actions]

🦙 MegaLinter status: ✅ SUCCESS

Descriptor	Linter	Files	Fixed	Errors	Elapsed time
✅ PYTHON	black	31		0	0.96s
✅ PYTHON	pylint	31		0	6.07s

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.84%. Comparing base (cdbaf1c) to head (40faa83).
Report is 29 commits behind head on main.

Additional details and impacted files

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  Coverage   93.84%   93.84%           
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  Files          27       27           
  Lines        1593     1593           
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  Hits         1495     1495           
  Misses         98       98           

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[Copilot]

Pull Request Overview

This PR introduces enhancements to the DAFNI workflow to improve usability and reproducibility. Key changes include:

• Storing variable metadata directly in the dot file and removing the standalone variables.json argument.
• Converting main_dafni.py into a module to facilitate local testing.
• Updating CI/CD workflows and docker-compose configurations for improved build and test processes.

Reviewed Changes

Copilot reviewed 5 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
dafni/model_definition.yaml	Updated metadata with additional attributes and a modified URL.
dafni/main_dafni.py	Removed the standalone entry point to favor modular testing.
dafni/docker-compose.yaml	Adjusted the Dockerfile path and volume mount changes.
dafni/README.md	Revised directory hierarchy documentation to reflect changes.
.github/workflows/publish-to-dafni.yaml	Added dependency installation and test execution steps prior to container build.

Files not reviewed (5)

• dafni/Dockerfile: Language not supported
• dafni/data/inputs/causal_tests.json: Language not supported
• dafni/data/inputs/dag.dot: Language not supported
• dafni/data/inputs/variables.json: Language not supported
• dafni/data/outputs/causal_tests_results.json: Language not supported

Comments suppressed due to low confidence (1)

dafni/model_definition.yaml:2

• The updated URL now includes a percent-encoded space. Please verify that this is the intended URL and that it resolves correctly.

+# https://docs.secure.dafni.rl.ac.uk/docs/How%20to/how-to-write-a-model-definition-file