Hackathon/dec23 #272
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Hackathon/dec23 #272
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Alternative approach to mock sqlalchemy engine for unittests
Update tests tree structure and docstrings
Hackathon/dec23
Co-authored-by: J. Alvarez-Jarreta <[email protected]>
Co-authored-by: J. Alvarez-Jarreta <[email protected]>
Mbarba/hack/fix fasta tests
Co-authored-by: Matthieu Barba <[email protected]>
Co-authored-by: Matthieu Barba <[email protected]>
Disha/genbank test update
Co-authored-by: J. Alvarez-Jarreta <[email protected]>
GFF3 modules tests
Add genome stats comparison tests
Resolve conflict to prepare merging hackathon/dec23 to main
MatBarba
requested review from
JAlvarezJarreta,
ens-LCampbell,
vsitnik and
Dishalodha
JAlvarezJarreta
approved these changes
Jan 18, 2024
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A net 1700+ new lines to include the first iteration of unit tests, increasing our coverage from 11% to 19%... Well done everyone!
Coverage information of the modules updated:
| Module | statements | missing | excluded | branches | partial | coverage |
|---|---|---|---|---|---|---|
| fasta/__init__.py | 2 | 0 | 0 | 0 | 0 | 100% |
| fasta/process.py | 42 | 1 | 11 | 18 | 1 | 97% |
| genbank/__init__.py | 3 | 0 | 0 | 0 | 0 | 100% |
| genbank/download.py | 23 | 0 | 11 | 2 | 0 | 100% |
| genbank/extract_data.py | 249 | 211 | 14 | 94 | 0 | 11% |
| genome_stats/__init__.py | 3 | 0 | 0 | 0 | 0 | 100% |
| genome_stats/compare.py | 68 | 0 | 10 | 24 | 0 | 100% |
| genome_stats/dump.py | 57 | 38 | 14 | 8 | 0 | 29% |
| gff3/__init__.py | 5 | 0 | 0 | 0 | 0 | 100% |
| gff3/extract_annotation.py | 101 | 8 | 0 | 34 | 2 | 91% |
| gff3/gene_merger.py | 69 | 8 | 0 | 24 | 3 | 86% |
| gff3/process.py | 7 | 0 | 28 | 0 | 0 | 100% |
| gff3/simplifier.py | 444 | 385 | 0 | 218 | 0 | 9% |
ens-LCampbell
approved these changes
Jan 23, 2024
Fix GFF3 parsing for naked transcripts and CDSs
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All hackathon commits from December 2023, adding lots of unit testing, with some code refactoring.