OmicsML Dance Versions Save

DANCE: a deep learning library and benchmark platform for single-cell analysis

v1.0.1

5 months ago

What's Changed

bump version: v1.0.0 -> v1.0.1-dev by @RemyLau in https://github.com/OmicsML/dance/pull/305
change python-igraph to igraph by @szhorvat in https://github.com/OmicsML/dance/pull/315
pin lower version of scipy and scikit-mis version for python 3.8 by @RemyLau in https://github.com/OmicsML/dance/pull/325
add 5 datasets by @xingzhongyu in https://github.com/OmicsML/dance/pull/328
add 4 clustering datasets by @xingzhongyu in https://github.com/OmicsML/dance/pull/331
fix deprecated option by @RemyLau in https://github.com/OmicsML/dance/pull/336
Preprocessing benchmarking by @xingzhongyu in https://github.com/OmicsML/dance/pull/337
expfeat: implement anndata transform adaptor by @RemyLau in https://github.com/OmicsML/dance/pull/341
upgrade tox test; create lint workflow by @RemyLau in https://github.com/OmicsML/dance/pull/349
fix: remove pyro-ppl from direct deps to prevent install torch early by @RemyLau in https://github.com/OmicsML/dance/pull/352
readme: action runner script with instruction by @RemyLau in https://github.com/OmicsML/dance/pull/353
fix readme: conda activation; closes #354 by @RemyLau in https://github.com/OmicsML/dance/pull/356
DANCE V1.0.0 benchmark production by @RemyLau in https://github.com/OmicsML/dance/pull/371
fix: rtd config by @RemyLau in https://github.com/OmicsML/dance/pull/372
fix: tests by @RemyLau in https://github.com/OmicsML/dance/pull/373
bumpversion: 1.0.1.dev -> 1.0.1 by @RemyLau in https://github.com/OmicsML/dance/pull/376

Dependencies

build(deps): bump pandas from 2.0.2 to 2.0.3 by @dependabot in https://github.com/OmicsML/dance/pull/304
build(deps): bump scipy from 1.10.1 to 1.11.1 by @dependabot in https://github.com/OmicsML/dance/pull/303
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/309
build(deps): bump leidenalg from 0.9.1 to 0.10.0 by @dependabot in https://github.com/OmicsML/dance/pull/308
build(deps): bump opencv-python from 4.7.0.72 to 4.8.0.74 by @dependabot in https://github.com/OmicsML/dance/pull/307
build(deps): bump scikit-learn from 1.2.2 to 1.3.0 by @dependabot in https://github.com/OmicsML/dance/pull/306
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/313
build(deps): bump threadpoolctl from 3.1.0 to 3.2.0 by @dependabot in https://github.com/OmicsML/dance/pull/314
build(deps-dev): bump tox from 4.6.3 to 4.6.4 by @dependabot in https://github.com/OmicsML/dance/pull/310
build(deps): bump scikit-misc from 0.2.0 to 0.3.0 by @dependabot in https://github.com/OmicsML/dance/pull/312
build(deps): bump torchnmf from 0.3.4 to 0.3.5 by @dependabot in https://github.com/OmicsML/dance/pull/311
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/318
build(deps): bump pyro-ppl from 1.8.5 to 1.8.6 by @dependabot in https://github.com/OmicsML/dance/pull/317
build(deps): bump leidenalg from 0.10.0 to 0.10.1 by @dependabot in https://github.com/OmicsML/dance/pull/316
build(deps-dev): bump tox from 4.6.4 to 4.8.0 by @dependabot in https://github.com/OmicsML/dance/pull/319
build(deps): bump tqdm from 4.65.0 to 4.66.1 by @dependabot in https://github.com/OmicsML/dance/pull/321
build(deps): bump opencv-python from 4.8.0.74 to 4.8.0.76 by @dependabot in https://github.com/OmicsML/dance/pull/320
build(deps-dev): bump tox from 4.6.4 to 4.9.0 by @dependabot in https://github.com/OmicsML/dance/pull/323
build(deps): bump scipy from 1.11.1 to 1.11.2 by @dependabot in https://github.com/OmicsML/dance/pull/322
build(deps): bump igraph from 0.10.1 to 0.10.6 by @dependabot in https://github.com/OmicsML/dance/pull/324
build(deps-dev): bump tox from 4.9.0 to 4.10.0 by @dependabot in https://github.com/OmicsML/dance/pull/327
build(deps): bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by @dependabot in https://github.com/OmicsML/dance/pull/326
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/330
build(deps): bump scanpy from 1.9.3 to 1.9.4 by @dependabot in https://github.com/OmicsML/dance/pull/329
build(deps-dev): bump pytest from 7.4.0 to 7.4.1 by @dependabot in https://github.com/OmicsML/dance/pull/335
build(deps-dev): bump pre-commit from 3.3.3 to 3.4.0 by @dependabot in https://github.com/OmicsML/dance/pull/333
build(deps): bump pandas from 2.0.3 to 2.1.0 by @dependabot in https://github.com/OmicsML/dance/pull/332
build(deps-dev): bump tox from 4.10.0 to 4.11.1 by @dependabot in https://github.com/OmicsML/dance/pull/334
build(deps-dev): bump tox from 4.11.1 to 4.11.3 by @dependabot in https://github.com/OmicsML/dance/pull/340
build(deps-dev): bump pytest from 7.4.1 to 7.4.2 by @dependabot in https://github.com/OmicsML/dance/pull/339
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/343
build(deps): bump igraph from 0.10.6 to 0.10.8 by @dependabot in https://github.com/OmicsML/dance/pull/342
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/347
build(deps): bump pandas from 2.1.0 to 2.1.1 by @dependabot in https://github.com/OmicsML/dance/pull/344
build(deps): bump scikit-learn from 1.3.0 to 1.3.1 by @dependabot in https://github.com/OmicsML/dance/pull/346
build(deps): bump scipy from 1.11.2 to 1.11.3 by @dependabot in https://github.com/OmicsML/dance/pull/348
build(deps): bump opencv-python from 4.8.0.76 to 4.8.1.78 by @dependabot in https://github.com/OmicsML/dance/pull/350
build(deps): bump scanpy from 1.9.4 to 1.9.5 by @dependabot in https://github.com/OmicsML/dance/pull/338
build(deps): bump tables from 3.8.0 to 3.9.1 by @dependabot in https://github.com/OmicsML/dance/pull/355
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/357
build(deps-dev): bump pre-commit from 3.4.0 to 3.5.0 by @dependabot in https://github.com/OmicsML/dance/pull/359
build(deps): bump h5py from 3.9.0 to 3.10.0 by @dependabot in https://github.com/OmicsML/dance/pull/360
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/OmicsML/dance/pull/368
build(deps): bump scikit-learn from 1.3.1 to 1.3.2 by @dependabot in https://github.com/OmicsML/dance/pull/366
build(deps): bump networkx from 3.1 to 3.2.1 by @dependabot in https://github.com/OmicsML/dance/pull/365

New Contributors

@szhorvat made their first contribution in https://github.com/OmicsML/dance/pull/315
@xingzhongyu made their first contribution in https://github.com/OmicsML/dance/pull/328

Full Changelog: https://github.com/OmicsML/dance/compare/v1.0.0...v1.0.1

v1.0.0

10 months ago

What's Changed

improve scmogcn sampling by @RemyLau in https://github.com/OmicsML/dance/pull/28
fix: scmogcn device by @RemyLau in https://github.com/OmicsML/dance/pull/30
create cell feature function (updated version of gen_batch_feature) by @RemyLau in https://github.com/OmicsML/dance/pull/39
fix copyright notices by @RemyLau in https://github.com/OmicsML/dance/pull/40
refactor data object and update svm by @RemyLau in https://github.com/OmicsML/dance/pull/56
refactor label adata processing to increase compatibility with user defined datasets by @RemyLau in https://github.com/OmicsML/dance/pull/57
matrix normalization utility by @RemyLau in https://github.com/OmicsML/dance/pull/58
refactor cell feat transform by @RemyLau in https://github.com/OmicsML/dance/pull/59
fix tox testing environment: install dev extra dependencies by @RemyLau in https://github.com/OmicsML/dance/pull/60
add shortcut properties for train/val/test index by @RemyLau in https://github.com/OmicsML/dance/pull/62
update actinn example script with new data object by @RemyLau in https://github.com/OmicsML/dance/pull/63
update data API by @RemyLau in https://github.com/OmicsML/dance/pull/64
update celltypist example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/72
update scDeepSort example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/75
update singlecellnet to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/77
fix: update data split index test by @RemyLau in https://github.com/OmicsML/dance/pull/78
update data object to support multiple feature by @RemyLau in https://github.com/OmicsML/dance/pull/79
support more channel types in data object by @RemyLau in https://github.com/OmicsML/dance/pull/80
fix: slice both columns and rows for pairwise features by @RemyLau in https://github.com/OmicsML/dance/pull/81
refactor graph transforms and rename Gene -> Feature by @RemyLau in https://github.com/OmicsML/dance/pull/82
fix: add missing mudata dependency by @RemyLau in https://github.com/OmicsML/dance/pull/84
refactor spagcn graph construct; use dance data object in the example spagcn script by @RemyLau in https://github.com/OmicsML/dance/pull/83
add more complex support to label channels; replace layer option with channel_type by @RemyLau in https://github.com/OmicsML/dance/pull/88
update babel example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/89
update card cell-type deconvolution example script using dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/93
update spatialdeconv to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/94
Update clustering examples to use data object by @WenzhuoTang in https://github.com/OmicsML/dance/pull/95
fix action dependency by @RemyLau in https://github.com/OmicsML/dance/pull/96
remove deprecated args by @RemyLau in https://github.com/OmicsML/dance/pull/102
update dstg example script to use dance data, refactor dstg graph construct by @RemyLau in https://github.com/OmicsML/dance/pull/103
implement AnnDataTransform interface by @RemyLau in https://github.com/OmicsML/dance/pull/106
update spotlight example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/107
fix typos in the code-base that remy has worked on by @RemyLau in https://github.com/OmicsML/dance/pull/111
Create CODE_OF_CONDUCT.md by @RemyLau in https://github.com/OmicsML/dance/pull/112
fix spotlight score function arg types by @RemyLau in https://github.com/OmicsML/dance/pull/113
use data load in dstg and update nx api call by @RemyLau in https://github.com/OmicsML/dance/pull/119
clean up spatial deconv datasets; improve ct_select alignment by @RemyLau in https://github.com/OmicsML/dance/pull/120
add contribution guidelines by @RemyLau in https://github.com/OmicsML/dance/pull/121
add support for single column feature retrieval from data object by @RemyLau in https://github.com/OmicsML/dance/pull/123
update louvain example script to use dance dataobject by @RemyLau in https://github.com/OmicsML/dance/pull/124
update stlearn example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/126
update stagate example script to use dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/127
fix typo in readme with other minor edits by @RemyLau in https://github.com/OmicsML/dance/pull/128
pydance -> dance when applicable for consistency by @RemyLau in https://github.com/OmicsML/dance/pull/129
unify cell-type annotation dataloader and example scripts format by @RemyLau in https://github.com/OmicsML/dance/pull/137
remove deprecated functions and improve url dict format by @RemyLau in https://github.com/OmicsML/dance/pull/138
remove unused params and transformations in celltypist by @RemyLau in https://github.com/OmicsML/dance/pull/139
add options to return predicted labels; improve log msg by @RemyLau in https://github.com/OmicsML/dance/pull/140
update checkout and setup-python actions versions by @RemyLau in https://github.com/OmicsML/dance/pull/141
add majority voting parser option to celltypist example; improve log msg by @RemyLau in https://github.com/OmicsML/dance/pull/142
format and docstring edits for spatial modules by @RemyLau in https://github.com/OmicsML/dance/pull/144
Aditya - Reproduction Info Updated by @adiark in https://github.com/OmicsML/dance/pull/145
implement BaseDataset object with caching option by @RemyLau in https://github.com/OmicsML/dance/pull/151
Aditya - Changing cell node initializing value from Nan to data index by @adiark in https://github.com/OmicsML/dance/pull/146
refactor scn preprocessing by @RemyLau in https://github.com/OmicsML/dance/pull/152
update readme by @RemyLau in https://github.com/OmicsML/dance/pull/153
upload scn_feature.py by @RemyLau in https://github.com/OmicsML/dance/pull/154
fix action and tests by @RemyLau in https://github.com/OmicsML/dance/pull/155
fix doc deps and create api pages by @RemyLau in https://github.com/OmicsML/dance/pull/156
format docstring, use auto doc typehints by @RemyLau in https://github.com/OmicsML/dance/pull/160
update twitter badge by @RemyLau in https://github.com/OmicsML/dance/pull/161
create BaseMethod abstraction and refactor models by @RemyLau in https://github.com/OmicsML/dance/pull/163
upload missing file by @RemyLau in https://github.com/OmicsML/dance/pull/164
refactor preprocessing pipelines for spatial_domain tasks by @RemyLau in https://github.com/OmicsML/dance/pull/165
install requirements automatically from install.sh by @RemyLau in https://github.com/OmicsML/dance/pull/169
remove unused libraries by @RemyLau in https://github.com/OmicsML/dance/pull/181
fix: torch installation and update dgl channel by @RemyLau in https://github.com/OmicsML/dance/pull/184
fix clustering example scripts code styles by @RemyLau in https://github.com/OmicsML/dance/pull/186
Reformat data for multimodality by @wehos in https://github.com/OmicsML/dance/pull/188
refactor: use dance transformations in clustering example scripts by @RemyLau in https://github.com/OmicsML/dance/pull/189
format: minor format fixes for multi modality modules and example scripts by @RemyLau in https://github.com/OmicsML/dance/pull/190
refactor: use dance transform in graphsc example scripts by @RemyLau in https://github.com/OmicsML/dance/pull/191
refactor: wrap method specific composed preprocessing pipelines for clustering examples by @RemyLau in https://github.com/OmicsML/dance/pull/192
refactor: sctag model -> BaseClusteringMethod by @RemyLau in https://github.com/OmicsML/dance/pull/193
fix: set edge weights for normalized adjacency in sctag by @RemyLau in https://github.com/OmicsML/dance/pull/194
refactor: adapt graph-sc to BaseClusteringMethod object by @RemyLau in https://github.com/OmicsML/dance/pull/195
refactor: adapt scdsc to BaseClusteringMethod class; create BasePretrain mixin by @RemyLau in https://github.com/OmicsML/dance/pull/198
refactor: adapt scdeepcluster to BaseClusteringMethod and TorchNNPretrain by @RemyLau in https://github.com/OmicsML/dance/pull/199
refactor: adapt scdcc to BaseClusteringMethod and TorchNNPretrain by @RemyLau in https://github.com/OmicsML/dance/pull/200
format: unify clustering example scripts formats by @RemyLau in https://github.com/OmicsML/dance/pull/201
refactor: adapt ClusteringDataset to BaseDataset by @RemyLau in https://github.com/OmicsML/dance/pull/202
update spatial domain modules to inherit from BaseClusteringMethod by @RemyLau in https://github.com/OmicsML/dance/pull/170
use logger; minor edits by @RemyLau in https://github.com/OmicsML/dance/pull/203
refactor: adapt Stagate to BasePretrain class; improve consistency by @RemyLau in https://github.com/OmicsML/dance/pull/204
feat: implement FilterGenesCommon gene selection transformation by @RemyLau in https://github.com/OmicsML/dance/pull/206
feat: add option to initialize splits from dict by @RemyLau in https://github.com/OmicsML/dance/pull/207
fix: update test bench cli arguments for clustering examples by @RemyLau in https://github.com/OmicsML/dance/pull/205
feat: implement append method to dance data object by @RemyLau in https://github.com/OmicsML/dance/pull/209
refactor: adapt CellTypeDeconvoDataset to BaseDataset class by @RemyLau in https://github.com/OmicsML/dance/pull/210
refactor: create preprocessing pipelines for Spotlight and SpatialDecon by @RemyLau in https://github.com/OmicsML/dance/pull/211
refactor: udpate dstg example script to use dance transforms by @RemyLau in https://github.com/OmicsML/dance/pull/212
refactor: update card to use dance transformations by @RemyLau in https://github.com/OmicsML/dance/pull/213
refactor: adapt cell type deconvolution modules to BaseRegressionMethod by @RemyLau in https://github.com/OmicsML/dance/pull/215
fix: remove unused; do not set mutable default kwargs by @RemyLau in https://github.com/OmicsML/dance/pull/217
refactor: DeepImput & GraphSCI imputation modules (dataset + transform) by @RemyLau in https://github.com/OmicsML/dance/pull/223
replace scGNN with scGNN2.0 by @RemyLau in https://github.com/OmicsML/dance/pull/225
fix: load FilterGenesMarker transform by @RemyLau in https://github.com/OmicsML/dance/pull/226
refactor: multiomics modules by @RemyLau in https://github.com/OmicsML/dance/pull/228
fix: divid x_norm by mean instead of sum as in the original implement… by @RemyLau in https://github.com/OmicsML/dance/pull/240
update installation script (pytorch 2.0, pyg2.3, dgl1.0) by @RemyLau in https://github.com/OmicsML/dance/pull/244
doc: update installation instructions on readme by @RemyLau in https://github.com/OmicsML/dance/pull/255
add dataset availability check function by @RemyLau in https://github.com/OmicsML/dance/pull/273
change get_available_data to class method by @RemyLau in https://github.com/OmicsML/dance/pull/274
expose main properties of anndata (or mudata) to base dance data by @RemyLau in https://github.com/OmicsML/dance/pull/282
clean up multi dataset objects by @RemyLau in https://github.com/OmicsML/dance/pull/283
refactor multi dataset object for predict modality tasks by @RemyLau in https://github.com/OmicsML/dance/pull/284
standardize AVAILABLE_DATA to list of strings or dicts by @RemyLau in https://github.com/OmicsML/dance/pull/285
add version by @RemyLau in https://github.com/OmicsML/dance/pull/286
update datasets doc struct and fix torchvision dep by @RemyLau in https://github.com/OmicsML/dance/pull/292
fix dataset class attr name: DATASETS -> AVAILABLE_DATA by @RemyLau in https://github.com/OmicsML/dance/pull/295
refactor multi dataset object for matching modality tasks by @RemyLau in https://github.com/OmicsML/dance/pull/296
hotfix: add additional channels depending on the input data type by @RemyLau in https://github.com/OmicsML/dance/pull/297
refactor multi dataset object for joint embedding tasks by @RemyLau in https://github.com/OmicsML/dance/pull/298
implement gex2adt_subset for modality prediction and matching tasks by @RemyLau in https://github.com/OmicsML/dance/pull/299
link to tutorial repo by @RemyLau in https://github.com/OmicsML/dance/pull/300
fix typo in function name by @RemyLau in https://github.com/OmicsML/dance/pull/301
release v1.0.0 by @RemyLau in https://github.com/OmicsML/dance/pull/302

New Contributors

@pre-commit-ci made their first contribution in https://github.com/OmicsML/dance/pull/61
@WenzhuoTang made their first contribution in https://github.com/OmicsML/dance/pull/95
@adiark made their first contribution in https://github.com/OmicsML/dance/pull/145
@wehos made their first contribution in https://github.com/OmicsML/dance/pull/188

Full Changelog: https://github.com/OmicsML/dance/compare/v1.0.0rc0...v1.0.0

v1.0.0rc0

1 year ago