task_cyto_batch_integration x.y.z

BREAKING CHANGES

NEW FUNCTIONALITY

Initialised repository with API files, readme, and a few test resources.
Added methods/harmonypy component (PR #3).
Added methods/limma_remove_batch_effect component (PR #7).
Added three negative control methods (PR #8):
- control_methods/shuffle_integration
- control_methods/shuffle_integration_by_batch
- control_methods/shuffle_integration_by_cell_type
Added metrics/emd_per_samples component (PR #9).

MAJOR CHANGES

Updated file schema (PR #18):
- Add is_control obs to indicate whether a cell should be used as control when correcting batch effect.
- Removed donor_id obs from unintegrated censored.
- Removed to_correct var from everything except common_dataset. All datasets now will only contain markers that need to be corrected.
Reupdated the file schema (PR #19):
- Included changes in PR #21: data Processor component partitions cells between unintegrated(censored) and validation.
- Add back to_correct var to every file except integrated to reflect the real world batch correction workflow better.
- Reverted PR #18 to retain only the 1st two changes (add is_control and remove donor_id from unintegrated_censored).

MINOR CHANGES

Enabled unit tests (PR #2).
Added integrated test resource (PR #5).
Updated file description in yaml file (PR #15).

BUGFIXES