CHANGELOG#

v0.6.0 (2024-05-25)#

Feature#

  • feat(scar): support MPS, but not recommend due to lower speed than CPU on Mac (9c3145c)

Unknown#

  • Develop (#75)

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg

  • chore: update workflow file

  • refactor codes (#73) (#74)

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg (4d4ea48)

  • refactor codes (#73)

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg

  • fix: refactor pyproject.toml file, delete setup.cfg (830677b)

v0.5.5 (2024-05-24)#

Unknown#

  • fix a dependency issue and make a new release (401da53)

  • Update pyproject.toml

require setuptools >= 68.1.2 to be compatible with the new version of pytorch-cuda12 (d08ff9a)

v0.5.4 (2024-05-23)#

Unknown#

update python version (86b948d)

  • Update requirements.txt

remove sphinx (bb633db)

  • Develop (#71)

  • fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update version for scanpy and anndata

  • fix: version conflict between anndata and scanpy

  • fix: remove anndata dependency (e8ed18c)

  • Develop (#70)

  • fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update version for scanpy and anndata (d8d12ed)

v0.5.3 (2024-05-23)#

Documentation#

  • docs(release_note): update release notes (7e76f32)

Fix#

  • fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict (#69)

  • fix: update python=3.8.6 -> python=3.10 to fix numpy & pandas conflict

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file

  • fix: update the action file (ffc4091)

Unknown#

  • Develop (#67)

  • revise log info

  • update reference

  • update reference in introduction (14b430b)

v0.5.2 (2023-05-02)#

Feature#

  • feat: add a feature/tutorial for denoising scATACseq (#65)

  • feat: add a feature/tutorial for denoising scATACseq

  • fix(scar): raise MPS NotImplementedError

  • chore(scar): add loss in progression bar

  • chore(gitignore): ignore count matrix data

  • style(main): refactor logging message

  • style: refactor main.py

  • style(_scar): add logging message for device

  • chore(_scar.py): clear progressbar

  • docs(tutorials): update tutorials

Co-authored-by: EC2 Default User <ec2-user@ip-172-16-91-220.us-east-2.compute.internal> (f8432f3)

Unknown#

  • Update version.py (292a916)

  • Merge branch ‘develop’ of github.com:Novartis/scar into develop (44920dc)

v0.5.1 (2023-03-02)#

Chore#

  • chore(release_note): manually add release note (54c0c64)

Documentation#

  • docs(tutorial): update hyperlinks for tutorials (8db27b6)

  • docs(tutorials): update tutorials (a21e2ec)

Feature#

  • feat(setup): change sample and n_batch parameters (4f5e05f)

  • feat: support AnnData object as the input (24a1ab6)

  • feat: print message (7659672)

  • feat: print message (203687f)

  • feat: estimate ambient_profile_all (e1913fd)

Fix#

Unknown#

  • Default clip_to_obs to False (#63)

  • docs: update documentations

  • docs: add a link of binary installers

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

  • docs(main): update documentation for .h5 file

  • docs(main): update dependencies

  • docs(main): add link to anndata and scanpy

  • docs: update dependencies

  • docs: update documentations

  • docs: update dependencies

  • docs: update dependency

  • add myst_parser

  • add sphinx_tabs

  • autodocsumm==0.2.8

  • 0.4.4

Automatically generated by python-semantic-release

  • chore: add an option to support Mac M1 and M2 processors

You need to install Mac specific version of Pytorch to allow M1/M2 acceleration. Though, support for this accelerator is still experimental in Pytorch, set device=’cpu’ upon any errors.

  • chore(docs): correct a wrong link

  • chore(docs): fix a typo

  • feat(model): add an option to clip the prediction

  • chore(docs):revise the docs

  • feat(*): remove tensorboard parameter

  • remove tensorboard from the command line tool

  • change email address, change default training epochs to 400

  • 0.5.0

Automatically generated by python-semantic-release

  • feat: estimate ambient_profile_all

  • fix: fix setupdata

  • feat: print message

  • feat: print message

  • feat: support AnnData object as the input

  • default clip_to_obs to False, as it leads to overall over-correction

  • default clip_to_obs to False, as it leads to overall over-correction, change docs

  • default clip_to_obs to False, as it leads to overall over-correction, change main.py

  • Update python-semantic-release

  • 0.6.0

Automatically generated by python-semantic-release

  • make a new release 0.5.1

  • feat(setup): change sample and n_batch parameters

  • docs(tutorials): update tutorials

  • chore(release_note): manually add release note

  • docs(tutorial): update hyperlinks for tutorials

Co-authored-by: Sheng, Caibin <caibin.sheng@novartis.com> Co-authored-by: github-actions <action@github.com> Co-authored-by: Caibin Sheng <caibin@Caibins-MBP.fritz.box> Co-authored-by: github-actions <github-actions@github.com> (3e66569)

  • make a new release 0.5.1 (dffbd5d)

  • make a new release 0.5.1 (6922c56)

  • Update python-semantic-release (40e906e)

  • update python-semantic-release (77559cd)

  • Merge branch ‘main’ into develop (af55f8b)

  • default clip_to_obs to False, as it leads to overall over-correction, change main.py (a527017)

  • default clip_to_obs to False, as it leads to overall over-correction, change docs (92c433b)

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

  • new release (#61)

  • docs: update documentations

  • docs: add a link of binary installers

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

  • docs(main): update documentation for .h5 file

  • docs(main): update dependencies

  • docs(main): add link to anndata and scanpy

  • docs: update dependencies

  • docs: update documentations

  • docs: update dependencies

  • docs: update dependency

  • add myst_parser

  • add sphinx_tabs

  • autodocsumm==0.2.8

  • 0.4.4

Automatically generated by python-semantic-release

  • chore: add an option to support Mac M1 and M2 processors

You need to install Mac specific version of Pytorch to allow M1/M2 acceleration. Though, support for this accelerator is still experimental in Pytorch, set device=’cpu’ upon any errors.

  • chore(docs): correct a wrong link

  • chore(docs): fix a typo

  • feat(model): add an option to clip the prediction

  • chore(docs):revise the docs

  • feat(*): remove tensorboard parameter

  • remove tensorboard from the command line tool

  • change email address, change default training epochs to 400

  • 0.5.0

Automatically generated by python-semantic-release

Co-authored-by: Sheng, Caibin <caibin.sheng@novartis.com> Co-authored-by: github-actions <action@github.com> Co-authored-by: Caibin Sheng <caibin@Caibins-MBP.fritz.box> (3f25b4e)

v0.5.0 (2023-02-04)#

Chore#

  • chore(docs): fix a typo (e7e6dd9)

  • chore(docs): correct a wrong link (7c7deda)

  • chore: add an option to support Mac M1 and M2 processors

You need to install Mac specific version of Pytorch to allow M1/M2 acceleration. Though, support for this accelerator is still experimental in Pytorch, set device=’cpu’ upon any errors. (38031ab)

Feature#

  • feat(*): remove tensorboard parameter (98717e7)

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

  • feat(main): support .h5 files by the command line tool (#57)

  • docs: update documentations

  • docs: add a link of binary installers

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

  • docs(main): update documentation for .h5 file

  • docs(main): update dependencies

  • docs(main): add link to anndata and scanpy

  • docs: update dependencies

  • docs: update documentations

  • docs: update dependencies

  • docs: update dependency

  • add myst_parser

  • add sphinx_tabs

  • autodocsumm==0.2.8

  • 0.4.4

Automatically generated by python-semantic-release

Co-authored-by: github-actions <action@github.com> (311ed92)

Unknown#

  • clip the predicted ambient counts (#60)

  • docs: update documentations

  • docs: add a link of binary installers

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

  • docs(main): update documentation for .h5 file

  • docs(main): update dependencies

  • docs(main): add link to anndata and scanpy

  • docs: update dependencies

  • docs: update documentations

  • docs: update dependencies

  • docs: update dependency

  • add myst_parser

  • add sphinx_tabs

  • autodocsumm==0.2.8

  • 0.4.4

Automatically generated by python-semantic-release

  • chore: add an option to support Mac M1 and M2 processors

You need to install Mac specific version of Pytorch to allow M1/M2 acceleration. Though, support for this accelerator is still experimental in Pytorch, set device=’cpu’ upon any errors.

  • chore(docs): correct a wrong link

  • chore(docs): fix a typo

  • feat(model): add an option to clip the prediction

  • chore(docs):revise the docs

  • feat(*): remove tensorboard parameter

  • remove tensorboard from the command line tool

  • change email address, change default training epochs to 400

Co-authored-by: Sheng, Caibin <caibin.sheng@novartis.com> Co-authored-by: github-actions <action@github.com> Co-authored-by: Caibin Sheng <caibin@Caibins-MBP.fritz.box> (76c3e6e)

  • Merge branch ‘main’ into develop (b524e44)

  • change email address, change default training epochs to 400 (dabd5a2)

  • remove tensorboard from the command line tool (6f70fdd)

  • chore(docs):revise the docs (5b15106)

v0.4.4 (2022-08-09)#

Chore#

  • chore: fix a typo (6ddcd8f)

  • chore: update docs (faf454c)

  • chore: update docs (d7c3dbd)

  • chore: add a dependency (a396a73)

  • chore(data_generator): sort synthetic data (ca52a81)

  • chore(data_generator): set rasterized=True for heatmaps (fd7f794)

Documentation#

  • docs: update dependency (03cf19e)

  • docs: update dependencies (9bd7f1c)

  • docs: update documentations (418996c)

  • docs: update dependencies (1bde351)

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

  • docs(main): update dependencies (984df35)

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

  • docs: add a link of binary installers (2faed3e)

  • docs: update documentations (e26a6e9)

  • docs: add competing methods (8564b2b)

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

  • docs: update docs (a4da539)

  • docs: update introduction (a036b24)

  • docs: change readthedocs template (421e52f)

  • docs(data_generator): update docs (1f8f668)

  • docs(data_generator): re-style docs (afef9fb)

  • docs(*): re-style docs (2d550fa)

Performance#

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

  • perf(setup): add an error raise statement (f4fb1a8)

Unknown#

  • autodocsumm==0.2.8 (22420ba)

  • add sphinx_tabs (4241244)

  • add myst_parser (a0e8897)

  • Merge branch ‘develop’ into main (f4db01e)

  • Merge branch ‘develop’ into main (d600009)

  • Merge branch ‘develop’ into main (0a039a7)

  • Develop (#56)

  • perf(main): set a separate batchsize_infer parameter for inference

  • docs(main): add scanpy as dependency

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

  • chore(_scar): convert non-str index to str

  • 0.4.3

Automatically generated by python-semantic-release

Co-authored-by: github-actions <action@github.com> (ab5437e)

v0.4.3 (2022-06-15)#

Chore#

  • chore(_scar): convert non-str index to str (aeb3ea2)

Documentation#

  • docs(main): add scanpy as dependency (252a492)

Fix#

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

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

Performance#

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

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

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

Unknown#

  • Merge branch ‘develop’ into main (8232ada)

  • Merge branch ‘develop’ into main (53335e5)

  • merge develop to main (#55)

  • chore(main): change assigned null sgrna to empty string

  • perf: add a setup_anndata method (#54)

  • perf: add a setup_anndata method

  • fix(docs): downgrade protobuf to allow success when building docs

  • chore(setup): refactor codes

  • chore(docs): add anndata dependency to docs

  • chore(docs): fix wrong hyperlinks of notebooks

  • build: downgrade python-semantic-release version

  • 0.4.2

Automatically generated by python-semantic-release

Co-authored-by: github-actions <action@github.com> (4132481)

v0.4.2 (2022-06-07)#

Build#

  • build: downgrade python-semantic-release version (569b011)

Chore#

  • chore(docs): fix wrong hyperlinks of notebooks (f06726a)

  • chore(docs): add anndata dependency to docs (e5efca8)

  • chore(main): change assigned null sgrna to empty string (e81cfc3)

Documentation#

Performance#

  • perf: add a setup_anndata method (#54)

  • perf: add a setup_anndata method

  • fix(docs): downgrade protobuf to allow success when building docs

  • chore(setup): refactor codes (923b1e5)

  • perf: change sparsity to 1 for scCRISPR-seq and cell indexing (d4b2c3d)

Unknown#

  • update readme (70b77c0)

  • rename logo file (7afd964)

  • Merge branch ‘develop’ into main (03881cb)

  • Merge branch ‘develop’ into main (f68b594)

  • Merge branch ‘main’ into develop (af8f574)

v0.4.1 (2022-05-19)#

Chore#

  • chore: refactor setup files (c30f4f0)

Ci#

  • ci(inference): round the counts using stochastic rounding (#50)

  • Add option for stochastic rounding to integer (#48)

  • ci(inference): add round_to_int parameters in several places

Co-authored-by: mdmanurung <10704760+mdmanurung@users.noreply.github.com> (bf6e226)

Documentation#

  • docs(readme): add bionconda badge

add badge of “install with bioconda” (d807404)

  • docs: update Changelog.md (8764941)

Unknown#

  • merge develop into main (#51)

  • Chore(main): refactor device

  • Chore(test): modify unittest

  • Chore: add scAR logo in documentation

  • Chore: introduce ci=None to speed up kneeplot

  • chore: refactor setup files

  • ci(inference): round the counts using stochastic rounding (#50)

  • Add option for stochastic rounding to integer (#48)

  • ci(inference): add round_to_int parameters in several places

Co-authored-by: mdmanurung <10704760+mdmanurung@users.noreply.github.com>

  • make a new release

Co-authored-by: mdmanurung <10704760+mdmanurung@users.noreply.github.com> (ad76c1c)

  • make a new release (4ae8e14)

  • Chore: introduce ci=None to speed up kneeplot (3dc999a)

  • Chore: add scAR logo in documentation (902a2b9)

  • Chore(test): modify unittest (c34f362)

  • Chore(main): refactor device (a597c5f)

  • Merge branch ‘develop’ into main (e0cd40a)

  • Chore(datasets): delete dataset folder (#45)

  • docs: modify Changlog.md

  • Chore(datasets): delete datasets

  • Chore(github action): update semantic release conditioning

  • Chore(contributing): merge branch ‘main’ into develop

  • 0.4.0

Automatically generated by python-semantic-release

  • Test(test_scar.py): increase epochs to allow convergence

Co-authored-by: github-actions <action@github.com> (241aaca)

  • Test(test_scar.py): increase epochs to allow convergence (dfe61e6)

v0.4.0 (2022-05-05)#

Documentation#

  • docs(contributing): add contributing guidelines

add contributing guidelines (b77967b)

  • docs: modify Changlog.md (deb920c)

  • docs: update documentation of Python API (#42)

  • docs: update documentations

update documentation of Python API add documentation of synthetic data

  • docs: update documentations

update Python API update command line interface update colab links in tutorial notebooks rename class in _data_generator.py

  • 0.3.5

Automatically generated by python-semantic-release

Co-authored-by: github-actions <action@github.com> (39880f1)

Feature#

  • feat(scar.model): addition of a sparsity parameter (#44)

  • disable C and R message classes

  • enable pylint to recognize torch members

  • use plot directive in docstring

  • feat(scar.main): introduce a sparsity parameter

  • rewrite custom activation functions

  • update data_generator

  • update sparsity parameter (#43)

  • update activation function and sparsity parameters

  • update tutorials

  • fix a bug

  • update pylint score to 8.5

  • fix a bug in unit test

  • update command line tool for sparsity parameter

  • add black style badge, readthedocs maxdepth: 3 ->1

  • add functional test

  • fix a bug in functional testing

  • manually update Changelog (0c30046)

  • feat(scar.main): introduce a sparsity parameter

1, introduce a sparsity parameter to control data sparsity 2, rewrite custom activation functions (cd33fdd)

Unknown#

  • Chore(contributing): merge branch ‘main’ into develop (25cc8a5)

  • Update README.md (f9ef8d4)

  • Update CONTRIBUTING.md (ae92a67)

  • Test(Github Action): test semantic release conditioning (2fa5661)

  • Test(Github Action): test semantic release conditioning (70813e3)

  • Test(Github Action): test semantic release conditioning (8096278)

  • Test(Github Action): test semantic release conditioning (04a754b)

  • Chore(Github Action): update semantic release conditioning (52aa26f)

  • Chore(Github Action): update semantic release conditioning (c290c08)

  • Chore(Github Action): update semantic release conditioning (5e81d73)

  • Chore(Github Action): update semantic release conditioning (d06ec3b)

  • Chore(github action): update semantic release conditioning (207a6b2)

  • Chore(datasets): delete datasets (5a90e8c)

  • update Changlog, update semantic release conditional branch to develop (e673d22)

  • Merge branch ‘main’ into develop after pull request (42aeadf)

  • manually update Changelog (c2fee96)

  • fix a bug in functional testing (d463328)

  • add functional test (270f10d)

  • add black style badge, readthedocs maxdepth: 3 ->1 (0c6d96e)

  • update sparsity parameter (#43)

  • update activation function and sparsity parameters

  • update tutorials

  • fix a bug

  • update pylint score to 8.5

  • fix a bug in unit test

  • thank Will

  • update command line tool for sparsity parameter (0f29c2a)

  • update data_generator (bcee0c3)

  • use plot directive in docstring (f19faa5)

  • enable pylint to recognize torch members (927b4b6)

  • disable C and R message classes (5970702)

  • Merge branch ‘develop’ into main

Conflicts: docs/usages/index.rst docs/usages/processing.rst docs/usages/synthetic_dataset.rst scar/main/_data_generater.py (9eaaa76)

  • Merge branch ‘develop’ of https://github.com/Novartis/scAR into develop (d6961f9)

v0.3.5 (2022-05-03)#

Documentation#

  • docs: update documentation for data_generator

update docstring for modules of data_generator update sphinx documentation for data_generator (7268ede)

  • docs: delete API.rst (497b080)

  • docs: update documentations

update Python API update command line interface update colab links in tutorial notebooks rename class in _data_generator.py (5ad9986)

  • docs: update documentations update documentation of Python API add documentation of synthetic data (11fa2b8)

Unknown#

  • Merge branch ‘main’ into develop (4890828)

  • Update version.py

bump to 0.3.4 (7dacee8)

v0.3.4 (2022-05-01)#

Documentation#

  • docs: autodoc command line interface (#40)

  • docs: autodoc command line interface

style: docstring from google to numpy style docs: autodoc command line interface refactor: command line interface test: semantic release on pull_request opened fix a bug for semantic release bump to version 0.3.3

Automatically generated by python-semantic-release

Co-authored-by: github-actions <action@github.com> (e89cf54)

Fix#

Unknown#

  • Merge branch ‘main’ into develop (3e9d7c3)

v0.3.3 (2022-05-01)#

Documentation#

  • docs: autodoc command line interface

style: docstring from google to numpy style docs: autodoc command line interface refactor: command line interface (0efae6c)

Test#

  • test: semantic release on pull_request opened (57aba29)

Unknown#

  • fix a bug for semantic release (cb20b2a)

  • fix a bug for semantic release (ed1b8a5)

  • refactor codes (37074e9)

  • Merge branch ‘main’ into develop (cd1807e)

  • Update conf.py

update conf.py (a627895)

  • Update setup.py

update setup (aeb5e27)

  • Update semantic-release.yaml

change semantic release to be triggered when opening a PR (36a083d)

  • Update setup.cfg

change github action to happen on develop branch (a743000)

  • update Release_notes.md (b0df98d)

  • Merge branch ‘main’ into develop (121577d)

  • update Release_notes.md (4f6f245)

v0.3.2 (2022-04-29)#

Fix#

  • fix(*): semantic release bugs (#36)

  • additions of docstring, autodocs, reference (#30)

  • conf for autodocs

  • add numpy for autodocs

  • add pip install in requirements for sphinx autodocs

  • feature semantic release (#31)

  • feat(*) addition of semantic releasing

  • fix(*): addition of semantic releasing

  • 0.3.1

Automatically generated by python-semantic-release

  • fix: changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes

  • fix semantic release

  • style: semantic release.yaml

Co-authored-by: github-actions <action@github.com>

  • update setup.cfg

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

  • fix a bug in setup.cfg

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

  • Release_notes.md

Co-authored-by: github-actions <action@github.com> (e794242)

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release (b9171a3)

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release (44a4409)

Unknown#

  • Release_notes.md (72c32b0)

  • fix a bug (4d81bde)

  • test semantic release (#34)

  • additions of docstring, autodocs, reference (#30)

  • conf for autodocs

  • add numpy for autodocs

  • add pip install in requirements for sphinx autodocs

  • feature semantic release (#31)

  • feat(*) addition of semantic releasing

  • fix(*): addition of semantic releasing

  • 0.3.1

Automatically generated by python-semantic-release

  • fix: changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes

  • fix semantic release

  • style: semantic release.yaml

Co-authored-by: github-actions <action@github.com>

  • update setup.cfg

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

  • fix a bug in setup.cfg

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

Co-authored-by: github-actions <action@github.com> (f26a35e)

  • Merge branch ‘develop’ of https://github.com/Novartis/scAR into develop (9e010f1)

  • fix a bug in setup.cfg (0afe77b)

  • bump to version 0.3.2 (#33)

  • additions of docstring, autodocs, reference (#30)

  • conf for autodocs

  • add numpy for autodocs

  • add pip install in requirements for sphinx autodocs

  • feature semantic release (#31)

  • feat(*) addition of semantic releasing

  • fix(*): addition of semantic releasing

  • 0.3.1

Automatically generated by python-semantic-release

  • fix: changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes

  • fix semantic release

  • style: semantic release.yaml

Co-authored-by: github-actions <action@github.com>

  • update setup.cfg

  • fix(*): changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes fix semantic release

Co-authored-by: github-actions <action@github.com> (34b711c)

  • Merge branch ‘main’ into develop (f8eab47)

  • additions semantic release and docstring (#32)

  • additions of docstring, autodocs, reference (#30)

  • conf for autodocs

  • add numpy for autodocs

  • add pip install in requirements for sphinx autodocs

  • feature semantic release (#31)

  • feat(*) addition of semantic releasing

  • fix(*): addition of semantic releasing

  • 0.3.1

Automatically generated by python-semantic-release

  • fix: changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes

  • fix semantic release

  • style: semantic release.yaml

  • update setup.cfg

Co-authored-by: github-actions <action@github.com> (f1c0ab8)

  • update setup.cfg (2eed2d9)

  • feature semantic release (#31)

  • feat(*) addition of semantic releasing

  • fix(*): addition of semantic releasing

  • 0.3.1

Automatically generated by python-semantic-release

  • fix: changelog docs: adding docstring in documentation docs: adding Release notes in documentation docs: adding docstring in documentation test: adding semantic release refactor: further refactoring codes

  • fix semantic release

  • style: semantic release.yaml

Co-authored-by: github-actions <action@github.com> (ae49ba2)

  • add pip install in requirements for sphinx autodocs (c0201f7)

  • add numpy for autodocs (c1299eb)

  • conf for autodocs (711689d)

  • additions of docstring, autodocs, reference (#30) (d93970a)

  • git revert commit (7869cab)

  • merge main into development (d190876)

v0.3.0 (2022-04-27)#

Unknown#

  • remove datsets to CaibinSh/scAR-reproducibility/data (070bf45)

  • tutorials bugs fixed (cf8dc02)

  • colab bugs fixed (d9b31db)

  • colab bugs fixed (01693b6)

  • harmonize development and main branches (#29)

  • New release (#26)

  • Add github action to publish package to PyPi

  • Feature GitHub action conda build (#1)

  • Add conda github action that builds the package with conda. It is triggered on pull request.

  • Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

  • Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

  • Feature - Add basic unit tests to cover activation_functions.py (#3)

  • adding first unit tests

  • Format conda-build YAML file

  • Update action name

  • Fix path to version

  • Test commit - Trigger workflow

  • Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

  • Feature clean helper functions (#4)

  • delete _helper_functions.py

  • delete _hyperparams_optimization.py

  • delete plot_every_epoch function

  • delete import _helper_functions

  • delete gpyopt dependency

  • edit only README

  • Add pylint github action

  • Remove pypi github action (#9)

  • support CPU, modify README (#10)

  • support CPU, modify README

  • shorten the import, add model to init

  • More lenient scar installation specifications (#8)

  • Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.

  • More lenient installation specifications.

  • Bump version to 0.2.0

  • fix a typo, reorganise init.py

  • fix bugs

  • add synthetic data for integration test (#13)

  • add synthetic data for integration test

  • change paths

  • change paths

  • Remove torchaudio. Bump version to 0.2.2 (#14)

  • Remove torchaudio

  • Bump version to 0.2.2

  • Update readme (#16)

  • update README

  • Black github action (#17)

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (–diff), but returns exit code 0, even if errors are observed.

  • Addition of integration test (#18)

  • Add integration test as unit test

  • update version

  • loweercase module name

  • lowercase module name

  • Update black.yaml

lowercase module name

  • Update python-conda-build.yaml

lowercase module name

  • lowercase module name

  • Update scar-gpu.yml

  • Update scar-cpu.yml

  • Update init.py

lowercase module name

  • refactor versioning (#21)

  • refactor versioning

  • refactor versioning

  • update .gitignore

  • fix a bug

  • fix bugs

  • Documentation with readthedocs (#22)

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update requirements.txt

  • Create README.md

  • Create conf.py

  • Update requirements.txt

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update conf.py

  • Update .readthedocs.yaml

  • add documentations

  • fix a bug

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update

  • update

  • fix a bug

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update document

  • update README.md

  • upadte documentations

  • update documentations

  • update documentations

  • Update .readthedocs.yaml

  • Update README.md

  • update documentations

  • add comments

  • add comments

  • update comment functionality

  • update documentation

  • add documentations via readthedocs (#23)

  • fix a bug

  • update documentation – denoising mRNAs

  • update documentations – CITEseq tutorials

  • update documentations – identity barcodes & sgRNA assignment

  • Update README.md

add Git Action Badge

  • Update README.md

  • Update README.md

Update Git Action Badge to default branch and default events

  • Black_formatting (#24)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml

  • further code refactoring (#25)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml

  • refactor _scar.py and _vae.py

  • code refactoring

  • fix a bug

  • fix a bug

  • fix a bug

  • fix a bug

  • increase pylint score from 0.5 to 6

  • bump version to 0.2.4

  • update tutorials

  • optimize command line

  • bump version to 0.3.0

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com> Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com> Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

  • delete scAR/test

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com> Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com> Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com> (2720895)

  • delete scAR/test (dbf61eb)

  • New release (#26)

  • Add github action to publish package to PyPi

  • Feature GitHub action conda build (#1)

  • Add conda github action that builds the package with conda. It is triggered on pull request.

  • Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

  • Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

  • Feature - Add basic unit tests to cover activation_functions.py (#3)

  • adding first unit tests

  • Format conda-build YAML file

  • Update action name

  • Fix path to version

  • Test commit - Trigger workflow

  • Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

  • Feature clean helper functions (#4)

  • delete _helper_functions.py

  • delete _hyperparams_optimization.py

  • delete plot_every_epoch function

  • delete import _helper_functions

  • delete gpyopt dependency

  • edit only README

  • Add pylint github action

  • Remove pypi github action (#9)

  • support CPU, modify README (#10)

  • support CPU, modify README

  • shorten the import, add model to init

  • More lenient scar installation specifications (#8)

  • Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.

  • More lenient installation specifications.

  • Bump version to 0.2.0

  • fix a typo, reorganise init.py

  • fix bugs

  • add synthetic data for integration test (#13)

  • add synthetic data for integration test

  • change paths

  • change paths

  • Remove torchaudio. Bump version to 0.2.2 (#14)

  • Remove torchaudio

  • Bump version to 0.2.2

  • Update readme (#16)

  • update README

  • Black github action (#17)

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (–diff), but returns exit code 0, even if errors are observed.

  • Addition of integration test (#18)

  • Add integration test as unit test

  • update version

  • loweercase module name

  • lowercase module name

  • Update black.yaml

lowercase module name

  • Update python-conda-build.yaml

lowercase module name

  • lowercase module name

  • Update scar-gpu.yml

  • Update scar-cpu.yml

  • Update init.py

lowercase module name

  • refactor versioning (#21)

  • refactor versioning

  • refactor versioning

  • update .gitignore

  • fix a bug

  • fix bugs

  • Documentation with readthedocs (#22)

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update requirements.txt

  • Create README.md

  • Create conf.py

  • Update requirements.txt

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update conf.py

  • Update .readthedocs.yaml

  • add documentations

  • fix a bug

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update

  • update

  • fix a bug

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update document

  • update README.md

  • upadte documentations

  • update documentations

  • update documentations

  • Update .readthedocs.yaml

  • Update README.md

  • update documentations

  • add comments

  • add comments

  • update comment functionality

  • update documentation

  • add documentations via readthedocs (#23)

  • fix a bug

  • update documentation – denoising mRNAs

  • update documentations – CITEseq tutorials

  • update documentations – identity barcodes & sgRNA assignment

  • Update README.md

add Git Action Badge

  • Update README.md

  • Update README.md

Update Git Action Badge to default branch and default events

  • Black_formatting (#24)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml

  • further code refactoring (#25)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml

  • refactor _scar.py and _vae.py

  • code refactoring

  • fix a bug

  • fix a bug

  • fix a bug

  • fix a bug

  • increase pylint score from 0.5 to 6

  • bump version to 0.2.4

  • update tutorials

  • optimize command line

  • bump version to 0.3.0

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com> Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com> Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com> (7376aab)

  • bump version to 0.3.0 (20ab02e)

  • Merge branch ‘main’ into develop

Conflicts: .github/workflows/black.yaml README.md scar/main/init.py (e020108)

  • further code refactoring (#25)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml

  • refactor _scar.py and _vae.py

  • code refactoring

  • fix a bug

  • fix a bug

  • fix a bug

  • fix a bug

  • increase pylint score from 0.5 to 6

  • bump version to 0.2.4

  • update tutorials

  • optimize command line (4385b22)

  • Black_formatting (#24)

  • black_formatting

  • Pylint checking

  • optimize activation function and add docstring

  • fix a bug

  • fix a bug for activation functions

  • update import torch in activation functions

  • refactor _scar.py

  • refactor _loss_functions.py

  • refactor _vae.py

  • refactor main.py

  • refactor _data_generater.py

  • refactor__version__.py

  • Pylint formatting

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

  • Update scar-cpu.yml

restrict setuptools<=59.5.0

  • Update scar-cpu.yml (d6e8b73)

  • Update README.md

Update Git Action Badge to default branch and default events (47fbb2a)

  • Update README.md (dc127db)

  • Update README.md

add Git Action Badge (5a6680d)

  • add documentations via readthedocs (#23)

  • fix a bug

  • update documentation – denoising mRNAs

  • update documentations – CITEseq tutorials

  • update documentations – identity barcodes & sgRNA assignment (88ba2e5)

  • Documentation with readthedocs (#22)

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update requirements.txt

  • Create README.md

  • Create conf.py

  • Update requirements.txt

  • Update .readthedocs.yaml

  • Update .readthedocs.yaml

  • Update requirements.txt

  • Update conf.py

  • Update .readthedocs.yaml

  • add documentations

  • fix a bug

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update documentations

  • update

  • update

  • fix a bug

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update

  • update document

  • update README.md

  • upadte documentations

  • update documentations

  • update documentations

  • Update .readthedocs.yaml

  • Update README.md

  • update documentations

  • add comments

  • add comments

  • update comment functionality

  • update documentation (c4832ba)

  • fix bugs (26dc46d)

  • fix a bug (b1534fc)

  • solve conflict (1e54316)

  • update .gitignore (441a59d)

  • refactor versioning (#21)

  • refactor versioning

  • refactor versioning (1502294)

  • Update init.py

lowercase module name (0766f9f)

  • Update scar-cpu.yml (ba51efe)

  • Update scar-gpu.yml (a77b6bd)

  • Merge branch ‘lowcase_package_name’ of https://github.com/Novartis/scAR into lowcase_package_name (fccbc11)

  • lowercase module name (7931b98)

  • Update python-conda-build.yaml

lowercase module name (f982eef)

  • Update black.yaml

lowercase module name (21c4689)

v0.2.3 (2022-04-19)#

Unknown#

  • Develop (#19)

  • Add github action to publish package to PyPi

  • Feature GitHub action conda build (#1)

  • Add conda github action that builds the package with conda. It is triggered on pull request.

  • Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

  • Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

  • Feature - Add basic unit tests to cover activation_functions.py (#3)

  • adding first unit tests

  • Format conda-build YAML file

  • Update action name

  • Fix path to version

  • Test commit - Trigger workflow

  • Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

  • Feature clean helper functions (#4)

  • delete _helper_functions.py

  • delete _hyperparams_optimization.py

  • delete plot_every_epoch function

  • delete import _helper_functions

  • delete gpyopt dependency

  • edit only README

  • Add pylint github action

  • Remove pypi github action (#9)

  • support CPU, modify README (#10)

  • support CPU, modify README

  • shorten the import, add model to init

  • More lenient scar installation specifications (#8)

  • Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.

  • More lenient installation specifications.

  • Bump version to 0.2.0

  • fix a typo, reorganise init.py

  • fix bugs

  • add synthetic data for integration test (#13)

  • add synthetic data for integration test

  • change paths

  • change paths

  • Remove torchaudio. Bump version to 0.2.2 (#14)

  • Remove torchaudio

  • Bump version to 0.2.2

  • Update readme (#16)

  • update README

  • Black github action (#17)

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (–diff), but returns exit code 0, even if errors are observed.

  • Addition of integration test (#18)

  • Add integration test as unit test

  • update version

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com> Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com> Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com> (45cbeec)

  • Merge branch ‘main’ into develop (c26be41)

  • update version (f6283c3)

  • Addition of integration test (#18)

  • Add integration test as unit test (ef7bfb4)

  • Black github action (#17)

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (–diff), but returns exit code 0, even if errors are observed. (7a61e7f)

  • Update readme (#16)

  • update README (6018a26)

v0.2.2 (2022-04-05)#

Unknown#

  • Remove torchaudio, add test data and bump version to 0.2.2 (#15)

  • Add synthetic data for integration test

  • Remove torchaudio

  • Bump version to 0.2.2

Co-authored-by: Sheng, Caibin <caibin.sheng@novartis.com> (e432ad1)

  • Merge branch ‘main’ into develop (3bef86e)

  • Remove torchaudio. Bump version to 0.2.2 (#14)

  • Remove torchaudio

  • Bump version to 0.2.2 (e41e343)

  • add synthetic data for integration test (#13)

  • add synthetic data for integration test

  • change paths

  • change paths (1805102)

  • Develop (#12)

  • fix a typo in scAR-gpu.yml

  • reorganise init.py files (0f973b5)

  • Merge branch ‘main’ into develop (fe5d4ca)

  • fix bugs (fbd5a94)

  • fix a typo, reorganise init.py (2880cfa)

  • 0.2.0-release (#11)

  • Support for training of the model with CPUs

  • Addition of two yaml files for CPU/GPU installation

  • Refactor of setup.py and structure of the package

  • Addition of tests with pytest

  • Addition of lint checks

  • Automate build with github actions (install package and run lint checks and pytest)

  • Update documentation

  • Version 0.2.0

Co-authored-by: Caibin Sheng <43896555+CaibinSh@users.noreply.github.com> Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com> Co-authored-by: Sheng, Caibin <caibin.sheng@novartis.com> Co-authored-by: Ternent, Tobias <tobias.ternent@novartis.com> (61b9782)

  • More lenient scar installation specifications (#8)

  • Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.

  • More lenient installation specifications.

  • Bump version to 0.2.0 (a6ee6dd)

  • support CPU, modify README (#10)

  • support CPU, modify README

  • shorten the import, add model to init (97292da)

  • Remove pypi github action (#9) (8bea098)

  • Merge pull request #7 from Novartis/pylint-github-action

Add pylint github action (c1331e0)

  • Add pylint github action (38fc141)

  • edit only README (71a3d5b)

  • Feature clean helper functions (#4)

  • delete _helper_functions.py

  • delete _hyperparams_optimization.py

  • delete plot_every_epoch function

  • delete import _helper_functions

  • delete gpyopt dependency (501de71)

  • Feature GitHub action conda build (#1)

  • Add conda github action that builds the package with conda. It is triggered on pull request.

  • Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

  • Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

  • Feature - Add basic unit tests to cover activation_functions.py (#3)

  • adding first unit tests

  • Format conda-build YAML file

  • Update action name

  • Fix path to version

  • Test commit - Trigger workflow

  • Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com> (23ee354)

  • Merge pull request #6 from CaibinSh/feature-pypi-github-action

Add github action to publish package to PyPi (a22c86f)

  • Add github action to publish package to PyPi (959ec7f)

  • fix a misleading annotation for scCRISPRseq (547a7b6)

  • update README, add single cell CRISPR tutorial (ee507ea)

  • update commond line tool for guide assignment output (bb23a07)

  • integrate sgRNA/identity-barcode assignment module (464abbc)

  • update README, add docs for scAR (232343d)

  • fix a bug for loss function (6e5751c)

  • adding parameter options for command line tool (2859ad9)

  • add count adjust options for guide assignment (0bac46f)

  • cleanning (0c5b19d)

  • fix a bug (4ae5e41)

  • adding ZeroInflatedPoisson as an option of count model (8d02b84)

  • optimize guide assignment by adding error term (dbae1a6)

  • Update _vae.py

add an error term (82d2236)

  • Update _vae.py

add an error term in inference (1b93952)

  • Update main.py

fix a bug (03e04ac)

  • fix a bug for commond line tool, add an error term for BayesFactor computation (4e73932)

  • add # -- coding: utf-8 -- to the first lines of relavant *.py files (a8547d3)

  • update README file (5148832)

  • delete a citeseq data (6d16c11)

  • update README (0eb64b3)

  • change to ReLU for CITEseq (1ff6268)

  • update tutorial (a442a79)

  • update README (81bbe46)

  • Merge branch ‘main’ of https://github.com/CaibinSh/scAR into main (634c050)

  • update readme (e22505e)

  • add a tutorial (7fc4bef)

  • Update requirements.txt (a21ee16)

  • Update requirements.txt (07007ca)

  • Update requirements.txt (7ee76f7)

  • Update requirements.txt (a6e421a)

  • update for readthedocs (d43ba5c)

  • update inference (fce1358)

  • rename scar.readthedocs.yaml (2ea19c1)

  • add readthedocs config (ab3f7bc)

  • move requirements.txt under docs (cce0773)

  • add scanpy and anndata in scAR.yml env file (a179c6d)

  • update README file (b5f3671)

  • Merge pull request #1 from CaibinSh/dev

Dev (447987b)

  • update env yml file (28c0ab7)

  • modify dataloader to improve efficiency (c7a356a)

  • improve Dataset and DataLoader to allow more efficient memory usage (0d62d53)

  • add runtime (8d6b21e)

  • updating dependencies (fb53f90)

  • Revert “unknow changes”

This reverts commit 8ae88f67e01a424b60d8dfe722f107194e93ae77. (460add0)

  • unknow changes (8ae88f6)

  • fix bugs (85351e6)

  • allow both package and command line tool (37fd473)

  • split off the simulation modules from _data_loader (7c1fc0f)

  • rename *.py files (d574eee)

  • split out reproducibility to a separate repo (ee554c1)

  • update dependencies (dfa59ac)

  • update Readme (60de3cc)

  • Update README.md (9bc33eb)

  • Update README.md (5db8071)

  • modify img: overview_scAR.png (6f56471)

  • Update README.md (6d2be13)

  • Update README.md (4a775ee)

  • Update README.md (0b1dad3)

  • update reproducibility (a6de7be)

  • update reproducibility notebooks (0e9eac6)

  • update Readme file (f232e76)

  • Add files via upload

initial submission (4e71a2a)

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