denoising v1.0.0

BREAKING CHANGES

• Update to viash 0.9.0 RC6

• Directory structure has been updated.

• Update to viash 0.9.0 (PR #13).

NEW FUNCTIONALITY

• Add CHANGELOG.md (PR #7).

• Update process_dataset component to subsample large datasets (PR #14).

• Add the scPRINT method (PR #25)

MAJOR CHANGES

• Revamp scripts directory (PR #13).

• Relocated process_datasets to data_processors/process_datasets (PR #13).

MINOR CHANGES

• Remove dtype parameter in .Anndata() (PR #6).

• Fix target_sum deprecation warning in mse mmetric (PR #8).

• Update task_name variable to denoising in component scripts (PR #9).

• Update docker containers used in components (PR #12).

• Set numpy<2 for some failing methods (PR #13).

• Small changes to api file names (PR #13).

• Update test_resources path in components (PR #18).

• Update workflows to use core repository dependency (PR #20).

• Update the common submodule (PR #24)

• Use the common checkItemAllowed() for the method check in the benchmark workflow (PR #24)

• Use the cxg_immune_cell_atlas dataset instead of the cxg_mouse_pancreas_atlas for testing (PR #24)

• Update README (PR #24)

• Add a base method API schema (PR #24)

• Add dataset_organism to training input files (PR #24)

BUG FIXES

• Update the nextflow workflow dependencies (PR #17).

• Fix paths in scripts (PR #18).

• Subsample datasets by batch if batch is defined (PR #22).