DNACE 1.0.1: Bug fixes & new datasets

What's Changed

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

Dependencies

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

New Contributors

• @szhorvat made their first contribution in #315
• @xingzhongyu made their first contribution in #328

Full Changelog: v1.0.0...v1.0.1

DANCE v1.0.0 release

What's Changed

• improve scmogcn sampling by @RemyLau in #28
• fix: scmogcn device by @RemyLau in #30
• create cell feature function (updated version of gen_batch_feature) by @RemyLau in #39
• fix copyright notices by @RemyLau in #40
• refactor data object and update svm by @RemyLau in #56
• refactor label adata processing to increase compatibility with user defined datasets by @RemyLau in #57
• matrix normalization utility by @RemyLau in #58
• refactor cell feat transform by @RemyLau in #59
• fix tox testing environment: install dev extra dependencies by @RemyLau in #60
• add shortcut properties for train/val/test index by @RemyLau in #62
• update actinn example script with new data object by @RemyLau in #63
• update data API by @RemyLau in #64
• update celltypist example script to use dance data object by @RemyLau in #72
• update scDeepSort example script to use dance data object by @RemyLau in #75
• update singlecellnet to use dance data object by @RemyLau in #77
• fix: update data split index test by @RemyLau in #78
• update data object to support multiple feature by @RemyLau in #79
• support more channel types in data object by @RemyLau in #80
• fix: slice both columns and rows for pairwise features by @RemyLau in #81
• refactor graph transforms and rename Gene -> Feature by @RemyLau in #82
• fix: add missing mudata dependency by @RemyLau in #84
• refactor spagcn graph construct; use dance data object in the example spagcn script by @RemyLau in #83
• add more complex support to label channels; replace layer option with channel_type by @RemyLau in #88
• update babel example script to use dance data object by @RemyLau in #89
• update card cell-type deconvolution example script using dance data object by @RemyLau in #93
• update spatialdeconv to use dance data object by @RemyLau in #94
• Update clustering examples to use data object by @WenzhuoTang in #95
• fix action dependency by @RemyLau in #96
• remove deprecated args by @RemyLau in #102
• update dstg example script to use dance data, refactor dstg graph construct by @RemyLau in #103
• implement AnnDataTransform interface by @RemyLau in #106
• update spotlight example script to use dance data object by @RemyLau in #107
• fix typos in the code-base that remy has worked on by @RemyLau in #111
• Create CODE_OF_CONDUCT.md by @RemyLau in #112
• fix spotlight score function arg types by @RemyLau in #113
• use data load in dstg and update nx api call by @RemyLau in #119
• clean up spatial deconv datasets; improve ct_select alignment by @RemyLau in #120
• add contribution guidelines by @RemyLau in #121
• add support for single column feature retrieval from data object by @RemyLau in #123
• update louvain example script to use dance dataobject by @RemyLau in #124
• update stlearn example script to use dance data object by @RemyLau in #126
• update stagate example script to use dance data object by @RemyLau in #127
• fix typo in readme with other minor edits by @RemyLau in #128
• pydance -> dance when applicable for consistency by @RemyLau in #129
• unify cell-type annotation dataloader and example scripts format by @RemyLau in #137
• remove deprecated functions and improve url dict format by @RemyLau in #138
• remove unused params and transformations in celltypist by @RemyLau in #139
• add options to return predicted labels; improve log msg by @RemyLau in #140
• update checkout and setup-python actions versions by @RemyLau in #141
• add majority voting parser option to celltypist example; improve log msg by @RemyLau in #142
• format and docstring edits for spatial modules by @RemyLau in #144
• Aditya - Reproduction Info Updated by @adiark in #145
• implement BaseDataset object with caching option by @RemyLau in #151
• Aditya - Changing cell node initializing value from Nan to data index by @adiark in #146
• refactor scn preprocessing by @RemyLau in #152
• update readme by @RemyLau in #153
• upload scn_feature.py by @RemyLau in #154
• fix action and tests by @RemyLau in #155
• fix doc deps and create api pages by @RemyLau in #156
• format docstring, use auto doc typehints by @RemyLau in #160
• update twitter badge by @RemyLau in #161
• create BaseMethod abstraction and refactor models by @RemyLau in #163
• upload missing file by @RemyLau in #164
• refactor preprocessing pipelines for spatial_domain tasks by @RemyLau in #165
• install requirements automatically from install.sh by @RemyLau in #169
• remove unused libraries by @RemyLau in #181
• fix: torch installation and update dgl channel by @RemyLau in #184
• fix clustering example scripts code styles by @RemyLau in #186
• Reformat data for multimodality by @wehos in #188
• refactor: use dance transformations in clustering example scripts by @RemyLau in #189
• format: minor format fixes for multi modality modules and example scripts by @RemyLau in #190
• refactor: use dance transform in graphsc example scripts by @RemyLau in #191
• refactor: wrap method specific composed preprocessing pipelines for clustering examples by @RemyLau in #192
• refactor: sctag model -> BaseClusteringMethod by @RemyLau in #193
• fix: set edge weights for normalized adjacency in sctag by @RemyLau in #194
• refactor: adapt graph-sc to BaseClusteringMethod object by @RemyLau in #195
• refactor: adapt scdsc to BaseClusteringMethod class; create BasePretrain mixin by @RemyLau in #198
• refactor: adapt scdeepcluster to BaseClusteringMethod and TorchNNPretrain by @RemyLau in #199
• refactor: adapt scdcc to BaseClusteringMethod and TorchNNPretrain by @RemyLau in #200
• format: unify clustering example scripts formats by @RemyLau in #201
• refactor: adapt ClusteringDataset to BaseDataset by @RemyLau in #202
• update spatial domain modules to inherit from BaseClusteringMethod by @RemyLau in #170
• use logger; minor edits by @RemyLau in #203
• refactor: adapt Stagate to BasePretrain class; improve consistency by @RemyLau in #204
• feat: implement FilterGenesCommon gene selection transformation by @RemyLau in #206
• feat: add option to initialize splits from dict by @RemyLau in #207
• fix: update test bench cli arguments for clustering examples by @RemyLau in #205
• feat: implement append method to dance data object by @RemyLau in #209
• refactor: adapt CellTypeDeconvoDataset to BaseDataset class by @RemyLau in #210
• refactor: create preprocessing pipelines for Spotlight and SpatialDecon by @RemyLau in #211
• refactor: udpate dstg example script to use dance transforms by @RemyLau in https://github.com/OmicsML/d...

v1.0.0rc0

Add usage notes to README (#10)