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Develop => main#186

Merged
ialarmedalien merged 171 commits into
mainfrom
develop
Jun 16, 2026
Merged

Develop => main#186
ialarmedalien merged 171 commits into
mainfrom
develop

Merge branch 'main' into develop

103b824
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Codecov / codecov/project succeeded Jun 16, 2026 in 1s

67.06% (+6.92%) compared to 21d3a6f

View this Pull Request on Codecov

67.06% (+6.92%) compared to 21d3a6f

Details

Codecov Report

❌ Patch coverage is 87.48906% with 143 lines in your changes missing coverage. Please review.
✅ Project coverage is 67.06%. Comparing base (21d3a6f) to head (103b824).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/cdm_data_loaders/utils/s3.py 57.51% 65 Missing ⚠️
src/cdm_data_loaders/ncbi_ftp/promote.py 89.95% 23 Missing ⚠️
src/cdm_data_loaders/ncbi_ftp/manifest.py 92.98% 19 Missing ⚠️
...rc/cdm_data_loaders/pipelines/ncbi_ftp_download.py 91.92% 13 Missing ⚠️
src/cdm_data_loaders/ncbi_ftp/assembly.py 90.36% 8 Missing ⚠️
src/cdm_data_loaders/utils/ftp_client.py 90.24% 8 Missing ⚠️
src/cdm_data_loaders/ncbi_ftp/metadata.py 91.56% 7 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #186      +/-   ##
==========================================
+ Coverage   60.13%   67.06%   +6.92%     
==========================================
  Files          64       72       +8     
  Lines        3339     4424    +1085     
==========================================
+ Hits         2008     2967     +959     
- Misses       1331     1457     +126     
Files with missing lines Coverage Δ
src/cdm_data_loaders/ncbi_ftp/constants.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/pipelines/all_the_bacteria.py 97.16% <ø> (ø)
src/cdm_data_loaders/pipelines/ncbi_rest_api.py 90.47% <100.00%> (+2.24%) ⬆️
src/cdm_data_loaders/utils/checksums.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/utils/gz.py 92.85% <100.00%> (+3.11%) ⬆️
src/cdm_data_loaders/utils/spark_delta.py 82.41% <100.00%> (ø)
src/cdm_data_loaders/ncbi_ftp/metadata.py 91.56% <91.56%> (ø)
src/cdm_data_loaders/ncbi_ftp/assembly.py 90.36% <90.36%> (ø)
src/cdm_data_loaders/utils/ftp_client.py 90.24% <90.24%> (ø)
...rc/cdm_data_loaders/pipelines/ncbi_ftp_download.py 91.92% <91.92%> (ø)
... and 3 more

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