cokelaer / sequana / 33373264506

69%

master: 67%

Build Type

push

github

Committed by cokelaer

Commit Message

Remove accidentally committed generated artifacts and migration doc

- Remove HTML reports (bam.html, fastqc.html, summary.html, test.html, test_output.html, variant_calling.html)
- Remove MIGRATION_REPORT_REFACTOR.md

These were generated/temporary files that should not be in the repository.

Export common report modules for backward compatibility

Modules (FastQCModule, CutadaptModule, FastQStatsModule, PhixModule,
BWABAMtoFastQModule) moved back to sequana to resolve circular
dependencies.

Now exported from sequana.modules_report for external users (like pipelines).

Revert "Export common report modules for backward compatibility"

This reverts commit 2250d95d6.

Revert sequana_report migration to standby

- Restore original SequanaBaseModule in base_module.py
- Revert modules_report/__init__.py (remove sequana_report imports)
- Remove sequana_report dependency from pyproject.toml

Migration not working well; putting on standby for future work.

Remove sequana_report import from coverage.py and requirements.txt

- Remove unused sequana_report.config import from coverage.py
- Remove report_config.output_dir assignments (use config.output_dir directly)
- Clean up requirements.txt

Remove tmp file

Coverage Stats

92 of 141 new or added lines in 1 file covered. (65.25%)

26 existing lines in 1 file now uncovered.

17574 of 25433 relevant lines covered (69.1%)

1.38 hits per line