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 #212
• refactor: update card to use dance transformations by @RemyLau in #213
• refactor: adapt cell type deconvolution modules to BaseRegressionMethod by @RemyLau in #215
• fix: remove unused; do not set mutable default kwargs by @RemyLau in #217
• refactor: DeepImput & GraphSCI imputation modules (dataset + transform) by @RemyLau in #223
• replace scGNN with scGNN2.0 by @RemyLau in #225
• fix: load FilterGenesMarker transform by @RemyLau in #226
• refactor: multiomics modules by @RemyLau in #228
• fix: divid x_norm by mean instead of sum as in the original implement… by @RemyLau in #240
• update installation script (pytorch 2.0, pyg2.3, dgl1.0) by @RemyLau in #244
• doc: update installation instructions on readme by @RemyLau in #255
• add dataset availability check function by @RemyLau in #273
• change get_available_data to class method by @RemyLau in #274
• expose main properties of anndata (or mudata) to base dance data by @RemyLau in #282
• clean up multi dataset objects by @RemyLau in #283
• refactor multi dataset object for predict modality tasks by @RemyLau in #284
• standardize AVAILABLE_DATA to list of strings or dicts by @RemyLau in #285
• add version by @RemyLau in #286
• update datasets doc struct and fix torchvision dep by @RemyLau in #292
• fix dataset class attr name: DATASETS -> AVAILABLE_DATA by @RemyLau in #295
• refactor multi dataset object for matching modality tasks by @RemyLau in #296
• hotfix: add additional channels depending on the input data type by @RemyLau in #297
• refactor multi dataset object for joint embedding tasks by @RemyLau in #298
• implement gex2adt_subset for modality prediction and matching tasks by @RemyLau in #299
• link to tutorial repo by @RemyLau in #300
• fix typo in function name by @RemyLau in #301
• release v1.0.0 by @RemyLau in #302

New Contributors

• @pre-commit-ci made their first contribution in #61
• @WenzhuoTang made their first contribution in #95
• @adiark made their first contribution in #145
• @wehos made their first contribution in #188

Full Changelog: v1.0.0rc0...v1.0.0