Merge develop => main

[ialarmedalien]

Description of PR purpose/changes

• Please include a summary of the change and which issue is fixed.
• Please also include relevant motivation and context.
• List any dependencies that are required for this change.

Testing Instructions

• Details for how to test the PR:

• Tests pass locally and in GitHub Actions

Dev Checklist:

• My code follows the guidelines at https://sites.google.com/lbl.gov/trussresources/home?authuser=0
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have run Ruff format to format my code
• I have run Ruff check and fixed any errors that it uncovered
• Any dependent changes have been merged and published in downstream modules

Updating Version and Release Notes (if applicable)

• Version has been bumped for each release.
• README has been updated for each release.

[codecov]

Codecov Report

❌ Patch coverage is 73.46774% with 329 lines in your changes missing coverage. Please review.
✅ Project coverage is 52.40%. Comparing base (7832989) to head (6eb97a6).
⚠️ Report is 84 commits behind head on main.

Files with missing lines	Patch %	Lines
src/cdm_data_loader_utils/utils/minio.py	15.88%	90 Missing ⚠️
src/cdm_data_loader_utils/utils/xml_utils.py	37.50%	60 Missing ⚠️
...cdm_data_loader_utils/pipelines/uniref_pipeline.py	0.00%	56 Missing ⚠️
...data_loader_utils/pipelines/uniprot_kb_pipeline.py	0.00%	54 Missing ⚠️
src/cdm_data_loader_utils/utils/spark_delta.py	82.41%	16 Missing ⚠️
...dm_data_loader_utils/parsers/uniprot/uniprot_kb.py	90.19%	15 Missing ⚠️
...cdm_data_loader_utils/parsers/uniprot/idmapping.py	79.54%	9 Missing ⚠️
src/cdm_data_loader_utils/utils/cdm_logger.py	79.06%	9 Missing ⚠️
.../cdm_data_loader_utils/parsers/uniprot/metalink.py	90.74%	5 Missing ⚠️
...rc/cdm_data_loader_utils/parsers/uniprot/uniref.py	91.66%	5 Missing ⚠️
... and 4 more

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #88       +/-   ##
===========================================
- Coverage   86.97%   52.40%   -34.57%     
===========================================
  Files           9       65       +56     
  Lines         599     3238     +2639     
===========================================
+ Hits          521     1697     +1176     
- Misses         78     1541     +1463     

Files with missing lines	Coverage Δ
src/cdm_data_loader_utils/audit/checkpoint.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/audit/metrics.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/audit/rejects.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/audit/run.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/audit/schema.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/core/constants.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/core/pipeline_run.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/parsers/checkm2.py	100.00% <100.00%> (ø)
...m_data_loader_utils/utils/download/async_client.py	100.00% <100.00%> (ø)
src/cdm_data_loader_utils/utils/download/core.py	100.00% <100.00%> (ø)
... and 18 more

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