Merge pull request #7 from openproblems-bio/doc/no-ref/add-changelog

Add changelog

CHANGELOG.md

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+# denoising 0.1.0
+
+## BREAKING CHANGES
+
+* Update to viash 0.9.0 RC6
+
+* Directory structure has been updated.
+
+## NEW FUNCTIONALITY
+
+* Add `CHANGELOG.md` (PR #7)
+
+## transfer from openproblems-v2 repository
+
+### NEW FUNCTIONALITY
+
+* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline.
+
+* `api/comp_*`: Created an api definition for the split, method and metric components.
+
+* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects.
+
+* `resources_test/denoising/pancreas` with `src/tasks/denoising/resources_test_scripts/pancreas.sh`.
+
+* `workflows/run`: Added nf-tower test script. (PR #205)
+
+### V1 MIGRATION
+
+* `control_methods/no_denoising`: Migrated from v1. Extracted from baseline method
+
+* `control_methods/perfect_denoising`: Migrated from v1.Extracted from baseline method
+
+* `methods/alra`: Migrated from v1. Changed from python to R and uses lg_cpm normalised data instead of L1 sqrt
+
+* `methods/dca`: Migrated and adapted from v1.
+
+* `methods/knn_smoothing`: Migrated and adapted from v1.
+
+* `methods/magic`: Migrated from v1.
+
+* `metrics/mse`: Migrated from v1.
+
+* `metrics/poisson`: Migrated from v1.
+
+### Changes from V1
+
+* Anndata layers are used to store data instead of obsm
+
+* extended the use of sparse data in methods unless it was not possible
+
+* process_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics.