Changelog#

TODO List#

  • Multiple ambient profiles

  • Batch processing

  • Transfer learning

  • Early stopping

  • Plotting functionality

  • Reporting functionality

v0.5.2 (2023-05-02)#

Feature#

Fix#

  • scar: Raise MPS NotImplementedError (838981e)

Documentation#

Chore#

  • scar: add loss in progression bar (#65) (37e95ea)

v0.5.1 (2023-03-01)#

Feature#

  • Update dependencies (40e906e)

  • Default clip_to_obs to False, as it leads to overall over-correction (944f09a)

  • Support AnnData object as the input (24a1ab6)

  • Print message (7659672)

  • Print message (203687f)

  • Estimate the ambient profile for all features all together, add ambient_profile_all to adata.uns (e1913fd)

Fix#

  • setup: Change sample and n_batch parameters to allow using all droplets by default (4f5e05f)

  • setup: Fix setupdata (63afe9d)

Documentation#

  • tutorials: Update tutorials (a21e2ec)

v0.5.0 (2023-02-04)#

Feature#

  • *: Remove tensorboard parameter (98717e7)

  • model: Add an option to clip the prediction (b250ebf)

v0.4.4 (2022-08-09)#

Documentation#

  • Update dependency (03cf19e)

  • Update dependencies (9bd7f1c)

  • Update documentations (418996c)

  • Update dependencies (1bde351)

  • main: Add link to anndata and scanpy (8436e05)

  • main: Update dependencies (984df35)

  • main: Update documentation for .h5 file (2a309e0)

  • Add a link of binary installers (2faed3e)

  • Update documentations (e26a6e9)

  • Add competing methods (8564b2b)

  • scar: Add versionadded directives for parameter sparsity and round_to_int (33e35ca)

  • Update docs (a4da539)

  • Update introduction (a036b24)

  • Change readthedocs template (421e52f)

  • data_generator: Update docs (1f8f668)

  • data_generator: Re-style docs (afef9fb)

  • *: Re-style docs (2d550fa)

Performance#

  • main: Command line tool supports a new input: filtered_feature_bc_matrix.h5 (73bc13e)

  • setup: Add an error raise statement (f4fb1a8)

v0.4.3 (2022-06-15)#

Fix#

  • setup: Fix a bug to allow sample reasonable numbers of droplets (ef6f7e4)

  • main: Fix a bug in main to set default NN number (794ff17)

Documentation#

  • main: Add scanpy as dependency (252a492)

Performance#

  • main: Set a separate batchsize_infer parameter for inference (8727f04)

  • setup: Add an option of random sampling droplets to speed up calculation (ce042dd)

  • setup: Enable manupulate large-scale emptydroplets (15f1840)

v0.4.2 (2022-06-07)#

Documentation#

Performance#

  • Add a setup_anndata method (#54) (923b1e5)

  • Change sparsity to 1 for scCRISPR-seq and cell indexing (d4b2c3d)

v0.4.1 (2022-05-19)#

Feature#

  • inference: add a round_to_int parameter to round the counts (float) for easy interpretation and better integration into other methods (#47) (902a2b9) (8694239)

Build#

  • setup: replace setup.py with setup.cfg and pyproject.toml (#51) (3dc999a)

Chore#

Documentation#

  • readthedocs: add scAR_logo image (#51) (c34f362)

  • tutorials: add ci=None to speed up plotting (#51) (902a2b9)

v0.4.0 (2022-05-05)#

Feature#

  • _scar.py: add a sparsity parameter to control data sparsity (#44) (0c30046) (cd33fdd)

  • _activation_functions.py: rewrite activation functions (f19faa5)

Documentation#

Chore#

  • Pylint: disable R and C message classes (9eaaa76)

  • Pylint: enable pylint to recognize torch members (5970702)

  • _scar.py: use plot directive in docstring (927b4b6)

  • _data_generator.py: use plot directive in docstring (927b4b6)

v0.3.5 (2022-05-03)#

Documentation#

  • docs: delete API.rst (497b080)

  • main(): update autodoc for the command line interface (5ad9986)

  • tutorials: update colab links in tutorial notebooks (5ad9986)

  • _data_generator.py: add documentations (11fa2b8)

  • _scar.py: update documentation of Python API (11fa2b8)

Refactor#

  • _data_generator.py: rename class, uppercase –> lowercase (5ad9986)

v0.3.4 (2022-05-01)#

Fix#

  • setup.py: importing modules of scar in setup.py fails. Change it back to exec(open(“scar/main/version.py”).read()) (3e9d7c3)

Style#

  • docstring: google style –> numpy style (cb20b2a)

Documentation#

  • main(): autodoc command line interface (cb20b2a)

v0.3.3 (2022-05-01)#

Documentation#

0.3.2 (2022-04-29)#

Feature#

  • GitHub Action: Add python semantic release (#36) (e794242)

Documentation#

0.3.0 (2022-04-27)#

0.2.3 (2022-04-19)#

0.2.2 (2022-04-04)#

pre-release#

0.2.1-beta (2022-04-01)#

0.2.0-beta (2022-04-01)#

0.1.6-beta (2022-02-17)#

0.1.5-beta (2022-02-08)#

0.1.4-beta (2022-02-03)#

0.1.3-beta (2022-02-03)#

0.1.2-beta (2022-02-03)#

0.1.1-beta (2022-02-03)#

0.1.0-beta (2022-01-30)#

Reverts#

  • Revert “unknow changes” (460add0)