Prepare Spezi Data Pipeline for PyPI Distribution

[Vicbi]

Prepare Spezi Data Pipeline for PyPI Distribution

♻️ Current situation & Problem

This PR addresses the necessary configuration and organization for distributing the Spezi Data Pipeline tool through PyPI Issue #13.

⚙️ Release Notes

• Develops comprehensive tests to ensure functionality.
• Implements Hatch as the package manager to handle project environments and dependencies.
• Reorganizes the project to adopt the standard Python package structure.

📚 Documentation

Documentation is updated.

✅ Testing

The testing suite has been expanded to cover most functionalities according to the coverage criteria set by CodeCov.

📝 Code of Conduct & Contributing Guidelines

By submitting creating this pull request, you agree to follow our Code of Conduct and Contributing Guidelines:

• I agree to follow the Code of Conduct and Contributing Guidelines.

[codecov]

Codecov Report

Attention: Patch coverage is 83.22148% with 75 lines in your changes are missing coverage. Please review.

Project coverage is 78.06%. Comparing base (9d25173) to head (72dfd46).

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #14       +/-   ##
===========================================
+ Coverage   44.48%   78.06%   +33.58%     
===========================================
  Files          10       15        +5     
  Lines         796     1180      +384     
===========================================
+ Hits          354      921      +567     
+ Misses        442      259      -183     

Flag	Coverage Δ
unittests	78.06% <83.23%> (+33.58%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
..._pipeline/data_access/firebase_fhir_data_access.py	79.29% <100.00%> (ø)
...peline/data_flattening/fhir_resources_flattener.py	92.44% <100.00%> (ø)
...pezi_data_pipeline/data_processing/code_mapping.py	100.00% <100.00%> (ø)
...zi_data_pipeline/data_processing/data_processor.py	70.77% <100.00%> (ø)
tests/test_data_access.py	99.09% <100.00%> (+4.09%)	⬆️
tests/test_data_exploration.py	97.37% <100.00%> (ø)
...c/spezi_data_pipeline/data_export/data_exporter.py	78.27% <80.00%> (ø)
tests/test_data_process.py	98.12% <98.12%> (ø)
tests/test_data_export.py	94.60% <94.60%> (ø)
scripts/update_authors.py	82.61% <82.61%> (ø)
... and 5 more

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[PSchmiedmayer]

Thank you for all the improvement @Vicbi!

I looked at the different changes and improvements and added comments throughout the code. Mostly around the automation setup and elements around this.

Thank you for adding so many tests in this PR; provides tremendous value!

[PSchmiedmayer]

Thank you for all the improvements @Vicbi! I only had a few comments on restructuring the GitHub Actions and when the different scripts should be called.

Feel free to merge the PR once these elements are addressed, thank you for all the work that went into the PR, the improvements in test coverage are really nice 🚀