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Pull request overview
This PR removes several benchmark components (two control methods and two disabled metrics) from the repository and updates the dependency pinning for the lisi metric component.
Changes:
- Removed
shuffle_integration_within_batchandshuffle_integration_within_cell_typecontrol methods and dropped them from the run_benchmark workflow/dependencies and HPC image list. - Deleted the (previously
status: disabled) metric componentsn_inconsistent_peaksandbras. - Bumped the
anndatadependency inmetrics/lisifrom~0.11.0to~0.12.0.
Reviewed changes
Copilot reviewed 13 out of 13 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| src/workflows/run_benchmark/main.nf | Removes two control methods from the benchmark method list. |
| src/workflows/run_benchmark/config.vsh.yaml | Removes corresponding workflow dependencies for the deleted control methods. |
| src/metrics/n_inconsistent_peaks/script.py | Deletes disabled metric implementation. |
| src/metrics/n_inconsistent_peaks/helper.py | Deletes helper code for disabled metric. |
| src/metrics/n_inconsistent_peaks/config.vsh.yaml | Deletes disabled metric component config. |
| src/metrics/lisi/config.vsh.yaml | Updates anndata package pin to ~0.12.0. |
| src/metrics/bras/script.py | Deletes disabled metric implementation. |
| src/metrics/bras/config.vsh.yaml | Deletes disabled metric component config. |
| src/control_methods/shuffle_integration_within_cell_type/script.py | Deletes control method implementation. |
| src/control_methods/shuffle_integration_within_cell_type/config.vsh.yaml | Deletes control method component config. |
| src/control_methods/shuffle_integration_within_batch/script.py | Deletes control method implementation. |
| src/control_methods/shuffle_integration_within_batch/config.vsh.yaml | Deletes control method component config. |
| scripts/run_benchmark/wehi_hpc/images.txt | Removes deleted control-method container images from HPC image list. |
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| // construct list of methods and control methods | ||
| methods = [ | ||
| shuffle_integration_globally, | ||
| shuffle_integration_within_batch, | ||
| shuffle_integration_within_cell_type, | ||
| no_integration, | ||
| perfect_integration, |
4 tasks
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Proposed changes are described in the CHANGELOG.md
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