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Develop => main#194

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ialarmedalien merged 18 commits into
mainfrom
develop
Jun 18, 2026
Merged

Develop => main#194
ialarmedalien merged 18 commits into
mainfrom
develop

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@ialarmedalien

@ialarmedalien ialarmedalien commented Jun 18, 2026

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Develop => main for v0.1.10

ialarmedalien and others added 18 commits June 16, 2026 10:33
Merge version bump into dev
Co-authored-by: i alarmed alien <ialarmedalien@users.noreply.github.com>
Co-authored-by: Matt Dawson <mattldawson@gmail.com>
Switch to __name__ logger; rename/moved file batcher
updating slack messaging to be a bit more circumspect
…ke account of root logger init code in the cli_app initialisation.
Add in root logger configuration
Version bump to v0.1.10
@ialarmedalien ialarmedalien merged commit c7c9c1a into main Jun 18, 2026
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@codecov

codecov Bot commented Jun 18, 2026

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Codecov Report

❌ Patch coverage is 95.04505% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 66.91%. Comparing base (e8fdf1f) to head (c7d3ebd).
⚠️ Report is 19 commits behind head on main.

Files with missing lines Patch % Lines
src/cdm_data_loaders/utils/s3.py 27.27% 8 Missing ⚠️
src/cdm_data_loaders/parsers/uniprot/idmapping.py 81.81% 2 Missing ⚠️
src/cdm_data_loaders/utils/xml_utils.py 66.66% 1 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #194      +/-   ##
==========================================
- Coverage   67.06%   66.91%   -0.16%     
==========================================
  Files          72       72              
  Lines        4424     4413      -11     
==========================================
- Hits         2967     2953      -14     
- Misses       1457     1460       +3     
Files with missing lines Coverage Δ
src/cdm_data_loaders/audit/checkpoint.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/audit/metrics.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/audit/rejects.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/audit/run.py 100.00% <100.00%> (ø)
src/cdm_data_loaders/ncbi_ftp/assembly.py 90.36% <100.00%> (ø)
src/cdm_data_loaders/ncbi_ftp/manifest.py 92.98% <100.00%> (ø)
src/cdm_data_loaders/ncbi_ftp/metadata.py 91.56% <100.00%> (ø)
src/cdm_data_loaders/ncbi_ftp/promote.py 89.95% <100.00%> (ø)
.../cdm_data_loaders/parsers/gene_association_file.py 61.73% <100.00%> (-0.33%) ⬇️
src/cdm_data_loaders/parsers/uniprot/metalink.py 90.74% <100.00%> (ø)
... and 23 more

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