From 0a3286b18e5d25b1e5cb5828b8e8b99a7328581b Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 2 Sep 2024 12:12:29 +0000 Subject: [PATCH] [status] 2024-09-02 12:12:29 UTC --- README.md | 34 +-- index.html | 106 +++++---- repos.csv | 676 +++++++++++++++++++++++++++++++++++++++++++++++++++-- 3 files changed, 740 insertions(+), 76 deletions(-) diff --git a/README.md b/README.md index 6a2802c..50c5835 100644 --- a/README.md +++ b/README.md @@ -2,24 +2,26 @@ GitHub Dashboard ================ ![](https://github.com/gadenbuie/status/workflows/Render%20Status/badge.svg) -2024-09-01 12:10:45 UTC +2024-09-02 12:10:49 UTC | Repo | Stars | Subscribers | Issues | Forks | Status | Commit | |:----------------------------------------------------------------------------------------------|------:|------------:|-------:|------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 730 | 18 | 67 | 169 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535081) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535098) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535076) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535080) | 6461a5 | -| [theislab/scvelo](https://github.com/theislab/scvelo) | 407 | 13 | 61 | 103 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9892975902) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9892975897) | 3fbce6 | | [theislab/scvelo](https://github.com/theislab/scvelo) | 407 | 13 | 61 | 103 | [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/8317755189) | b2f31b | -| [theislab/cellrank](https://github.com/theislab/cellrank) | 338 | 9 | 19 | 47 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10239706729) | 43c32b | +| [theislab/scvelo](https://github.com/theislab/scvelo) | 407 | 13 | 61 | 103 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/10662690984) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/10662690982) | bef8f1 | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 338 | 9 | 17 | 47 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10239706729) | 43c32b | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 338 | 9 | 17 | 47 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10662281968) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10662281966) | 554f7c | | [theislab/scib](https://github.com/theislab/scib) | 287 | 14 | 37 | 61 | [![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/10287985783) | 5547cd | | [theislab/zellkonverter](https://github.com/theislab/zellkonverter) | 144 | 5 | 26 | 27 | [![](https://github.com/theislab/zellkonverter/workflows/.github/workflows/check-bioc.yml/badge.svg)](https://github.com/theislab/zellkonverter/actions/runs/9611012269) | 328e7e | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 18 | [![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) | 84d33c | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 18 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10306217903) | e0e081 | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 18 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10572979429) | faa668 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 17 | [![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) | 84d33c | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 17 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10306217903) | e0e081 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 136 | 5 | 43 | 17 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10572979429) | faa668 | | [theislab/sfaira](https://github.com/theislab/sfaira) | 134 | 8 | 167 | 11 | [![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/9457340256) | 55bcbb | | [theislab/sfaira](https://github.com/theislab/sfaira) | 134 | 8 | 167 | 11 | [![](https://github.com/theislab/sfaira/workflows/Build%20sfaira%20Package/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672388) [![](https://github.com/theislab/sfaira/workflows/Create%20sfaira%20data-loader%20templates/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672382) [![](https://github.com/theislab/sfaira/workflows/Run%20bandit/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672385) [![](https://github.com/theislab/sfaira/workflows/Run%20flake8%20linting/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672384) | 5fcf93 | | [theislab/sfaira](https://github.com/theislab/sfaira) | 134 | 8 | 167 | 11 | [![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) | ceb14c | | [theislab/anndata2ri](https://github.com/theislab/anndata2ri) | 124 | 7 | 13 | 16 | [![](https://github.com/theislab/anndata2ri/workflows/Unit%20Tests/badge.svg)](https://github.com/theislab/anndata2ri/actions/runs/10612463111) | 8a5238 | | [theislab/moscot](https://github.com/theislab/moscot) | 107 | 3 | 48 | 9 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/10212768708) | 36d93b | +| [theislab/moscot](https://github.com/theislab/moscot) | 107 | 3 | 48 | 9 | [![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/10658580460) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/10658520850) | 6e65ac | | [theislab/ncem](https://github.com/theislab/ncem) | 102 | 6 | 27 | 13 | [![](https://github.com/theislab/ncem/workflows/Labeler/badge.svg)](https://github.com/theislab/ncem/actions/runs/5392074704) | 216fd5 | | [theislab/ncem](https://github.com/theislab/ncem) | 102 | 6 | 27 | 13 | [![](https://github.com/theislab/ncem/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/ncem/actions/runs/6666317399) [![](https://github.com/theislab/ncem/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/ncem/actions/runs/6666317397) | d03a07 | | [theislab/destiny](https://github.com/theislab/destiny) | 74 | 5 | 32 | 12 | [![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) | 300eb2 | @@ -28,16 +30,16 @@ GitHub Dashboard | [theislab/hadge](https://github.com/theislab/hadge) | 24 | 3 | 13 | 6 | [![](https://github.com/theislab/hadge/workflows/pre-commit/badge.svg)](https://github.com/theislab/hadge/actions/runs/9366149796) [![](https://github.com/theislab/hadge/workflows/hadge%20test%20workflow/badge.svg)](https://github.com/theislab/hadge/actions/runs/9366149805) | 490a55 | | [theislab/mubind](https://github.com/theislab/mubind) | 23 | 3 | 31 | 0 | [![](https://github.com/theislab/mubind/workflows/Python%20package/badge.svg)](https://github.com/theislab/mubind/actions/runs/10632591185) | 3f62f8 | | [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 13 | 6 | [![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/10459161813) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/10459161788) | a78677 | -| [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 13 | 6 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/10649868280) | e8a37c | +| [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 13 | 6 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/10659212143) | e8a37c | | [theislab/geome](https://github.com/theislab/geome) | 16 | 3 | 3 | 4 | [![](https://github.com/theislab/geome/workflows/Test/badge.svg)](https://github.com/theislab/geome/actions/runs/10651185375) | 402a0a | | [theislab/multimil](https://github.com/theislab/multimil) | 15 | 5 | 3 | 1 | [![](https://github.com/theislab/multimil/workflows/Check%20Build/badge.svg)](https://github.com/theislab/multimil/actions/runs/10163998577) [![](https://github.com/theislab/multimil/workflows/Test/badge.svg)](https://github.com/theislab/multimil/actions/runs/10651190191) | 2bb4f9 | | [theislab/scanpydoc](https://github.com/theislab/scanpydoc) | 12 | 6 | 3 | 6 | [![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/10579066618) | 5a2797 | | [theislab/cellrank2_reproducibility](https://github.com/theislab/cellrank2_reproducibility) | 6 | 1 | 0 | 1 | [![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/9877064958) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/9877064964) | 9f82e8 | | [theislab/cellrank_notebooks](https://github.com/theislab/cellrank_notebooks) | 6 | 4 | 1 | 5 | [![](https://github.com/theislab/cellrank_notebooks/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank_notebooks/actions/runs/6686677756) | 677784 | -| [theislab/moscot_notebooks](https://github.com/theislab/moscot_notebooks) | 6 | 1 | 4 | 3 | [![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/10551326301) | 5b9d4e | +| [theislab/moscot_notebooks](https://github.com/theislab/moscot_notebooks) | 6 | 1 | 4 | 3 | [![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/10658611524) | 5b9d4e | | [theislab/ehrapy-datasets](https://github.com/theislab/ehrapy-datasets) | 5 | 2 | 0 | 2 | [![](https://github.com/theislab/ehrapy-datasets/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy-datasets/actions/runs/8356857136) | e441a5 | | [theislab/ehrdata](https://github.com/theislab/ehrdata) | 5 | 3 | 2 | 1 | [![](https://github.com/theislab/ehrdata/workflows/Test/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/10651206167) | 873411 | -| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 1 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/10653796401) | b36ef2 | +| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 1 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/10666737019) | 2f66ea | | [theislab/idtrack](https://github.com/theislab/idtrack) | 0 | 1 | 6 | 0 | [![](https://github.com/theislab/idtrack/workflows/Labeler/badge.svg)](https://github.com/theislab/idtrack/actions/runs/5369045662) | 12aa73 | | [theislab/idtrack](https://github.com/theislab/idtrack) | 0 | 1 | 6 | 0 | [![](https://github.com/theislab/idtrack/workflows/Build%20idtrack%20Package/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702245) [![](https://github.com/theislab/idtrack/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702249) [![](https://github.com/theislab/idtrack/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702241) [![](https://github.com/theislab/idtrack/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702236) [![](https://github.com/theislab/idtrack/workflows/Run%20idtrack%20Tests/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702246) | ec9e9f | @@ -45,15 +47,15 @@ GitHub Dashboard | Repo | Stars | Subscribers | Issues | Forks | |:------------------------------------------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:| -| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1346 | 30 | 21 | 449 | +| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1347 | 30 | 21 | 449 | | [theislab/scarches](https://github.com/theislab/scarches) | 328 | 13 | 45 | 51 | -| [theislab/scgen](https://github.com/theislab/scgen) | 259 | 9 | 25 | 53 | +| [theislab/scgen](https://github.com/theislab/scgen) | 259 | 9 | 25 | 52 | | [theislab/dca](https://github.com/theislab/dca) | 241 | 11 | 31 | 71 | | [theislab/paga](https://github.com/theislab/paga) | 198 | 10 | 23 | 33 | -| [theislab/diffxpy](https://github.com/theislab/diffxpy) | 190 | 6 | 108 | 23 | -| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 177 | 8 | 1 | 20 | +| [theislab/diffxpy](https://github.com/theislab/diffxpy) | 191 | 6 | 108 | 23 | +| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 179 | 8 | 1 | 20 | | [theislab/kBET](https://github.com/theislab/kBET) | 151 | 8 | 9 | 23 | -| [theislab/scCODA](https://github.com/theislab/scCODA) | 146 | 9 | 7 | 24 | +| [theislab/scCODA](https://github.com/theislab/scCODA) | 147 | 9 | 7 | 24 | | [theislab/sc-pert](https://github.com/theislab/sc-pert) | 141 | 5 | 6 | 10 | | [theislab/chemCPA](https://github.com/theislab/chemCPA) | 96 | 5 | 10 | 23 | | [theislab/cpa](https://github.com/theislab/cpa) | 80 | 5 | 20 | 18 | @@ -109,6 +111,7 @@ GitHub Dashboard | [theislab/cpa-reproducibility](https://github.com/theislab/cpa-reproducibility) | 7 | 2 | 1 | 1 | | [theislab/ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) | 7 | 3 | 0 | 2 | | [theislab/mouse_cross-condition_pancreatic_islet_atlas](https://github.com/theislab/mouse_cross-condition_pancreatic_islet_atlas) | 7 | 2 | 0 | 3 | +| [theislab/prophet](https://github.com/theislab/prophet) | 7 | 3 | 0 | 0 | | [theislab/scachepy](https://github.com/theislab/scachepy) | 7 | 5 | 3 | 1 | | [theislab/scatac_poisson_reproducibility](https://github.com/theislab/scatac_poisson_reproducibility) | 7 | 3 | 0 | 0 | | [theislab/spapros-pipeline](https://github.com/theislab/spapros-pipeline) | 7 | 2 | 0 | 0 | @@ -117,13 +120,12 @@ GitHub Dashboard | [theislab/intercode](https://github.com/theislab/intercode) | 6 | 3 | 1 | 1 | | [theislab/jump-cpg0016-segmentation](https://github.com/theislab/jump-cpg0016-segmentation) | 6 | 1 | 2 | 0 | | [theislab/pancreatic-endocrinogenesis](https://github.com/theislab/pancreatic-endocrinogenesis) | 6 | 3 | 0 | 6 | -| [theislab/prophet](https://github.com/theislab/prophet) | 6 | 3 | 0 | 0 | | [theislab/sfaira_tutorials](https://github.com/theislab/sfaira_tutorials) | 6 | 4 | 4 | 2 | | [theislab/theislab.github.io](https://github.com/theislab/theislab.github.io) | 6 | 2 | 9 | 0 | | [theislab/trVAE_reproducibility](https://github.com/theislab/trVAE_reproducibility) | 6 | 3 | 2 | 6 | | [theislab/atlas-feature-selection-benchmark](https://github.com/theislab/atlas-feature-selection-benchmark) | 5 | 2 | 0 | 0 | | [theislab/flowVI](https://github.com/theislab/flowVI) | 5 | 3 | 0 | 0 | -| [theislab/InterpretableAutoencoders](https://github.com/theislab/InterpretableAutoencoders) | 5 | 4 | 0 | 1 | +| [theislab/InterpretableAutoencoders](https://github.com/theislab/InterpretableAutoencoders) | 5 | 4 | 0 | 0 | | [theislab/kbranches](https://github.com/theislab/kbranches) | 5 | 7 | 0 | 0 | | [theislab/scanpy-demo-czbiohub](https://github.com/theislab/scanpy-demo-czbiohub) | 5 | 5 | 0 | 5 | | [theislab/singlecell_proteomics](https://github.com/theislab/singlecell_proteomics) | 5 | 5 | 6 | 3 | diff --git a/index.html b/index.html index 5b198a6..a5d6f79 100644 --- a/index.html +++ b/index.html @@ -49,7 +49,7 @@

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Repos without Github Actions

- + diff --git a/repos.csv b/repos.csv index e767249..2b76819 100644 --- a/repos.csv +++ b/repos.csv @@ -20,7 +20,7 @@ theislab,GoBI_single_cell,theislab/GoBI_single_cell,0,3,0,0,FALSE,https://github theislab,HPA_reproducibility,theislab/HPA_reproducibility,2,3,0,1,FALSE,https://github.com/theislab/HPA_reproducibility,2,NA,NA,NA theislab,HRCA-reproducibility,theislab/HRCA-reproducibility,2,4,0,1,FALSE,https://github.com/theislab/HRCA-reproducibility,2,NA,NA,NA theislab,IMPA,theislab/IMPA,9,2,0,1,FALSE,https://github.com/theislab/IMPA,9,NA,NA,NA -theislab,InterpretableAutoencoders,theislab/InterpretableAutoencoders,5,4,0,1,FALSE,https://github.com/theislab/InterpretableAutoencoders,5,NA,NA,NA +theislab,InterpretableAutoencoders,theislab/InterpretableAutoencoders,5,4,0,0,FALSE,https://github.com/theislab/InterpretableAutoencoders,5,NA,NA,NA theislab,LODE,theislab/LODE,4,2,9,0,FALSE,https://github.com/theislab/LODE,4,NA,NA,NA theislab,LineagePulse,theislab/LineagePulse,2,5,0,0,FALSE,https://github.com/theislab/LineagePulse,2,NA,NA,NA theislab,LungAgingAtlas,theislab/LungAgingAtlas,0,5,0,0,FALSE,https://github.com/theislab/LungAgingAtlas,0,NA,NA,NA @@ -42,7 +42,8 @@ theislab,batchglm,theislab/batchglm,27,3,47,9,FALSE,https://github.com/theislab/ theislab,bindome,theislab/bindome,1,3,5,1,FALSE,https://github.com/theislab/bindome,1,NA,NA,NA theislab,campa,theislab/campa,14,4,5,4,FALSE,https://github.com/theislab/campa,14,NA,NA,NA theislab,campa_ana,theislab/campa_ana,2,4,0,0,FALSE,https://github.com/theislab/campa_ana,2,NA,NA,NA -theislab,cellrank,theislab/cellrank,338,9,19,47,FALSE,https://github.com/theislab/cellrank,338,43c32bb904243bbfc9dba2b2faea3607d50c95a5,Remove numba cache (#1212),[![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10239706729) +theislab,cellrank,theislab/cellrank,338,9,17,47,FALSE,https://github.com/theislab/cellrank,338,43c32bb904243bbfc9dba2b2faea3607d50c95a5,Remove numba cache (#1212),[![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10239706729) +theislab,cellrank,theislab/cellrank,338,9,17,47,FALSE,https://github.com/theislab/cellrank,338,554f7c8645d2c88c6700025ac86ed1e3e20ce93b,Update CellRank 2 paper citation (#1217),[![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10662281968) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10662281966) theislab,cellrank2_reproducibility,theislab/cellrank2_reproducibility,6,1,0,1,FALSE,https://github.com/theislab/cellrank2_reproducibility,6,9f82e87ae090f08302b760ba13ec660b3d11ef5d,"Update `labeling_kernel/inference.ipynb` (#62) Specify initial parameter estimate as `None`.",[![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/9877064958) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/9877064964) @@ -62,15 +63,15 @@ theislab,dali,theislab/dali,0,7,0,1,FALSE,https://github.com/theislab/dali,0,NA, theislab,dca,theislab/dca,241,11,31,71,FALSE,https://github.com/theislab/dca,241,NA,NA,NA theislab,deepflow,theislab/deepflow,31,5,1,14,FALSE,https://github.com/theislab/deepflow,31,NA,NA,NA theislab,destiny,theislab/destiny,74,5,32,12,FALSE,https://github.com/theislab/destiny,74,300eb293fb773fb3d667818b946fdd3c62b0aa05,Fix sparse matrix cast and ggplot aes_string deprecations (#65),[![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) -theislab,diffxpy,theislab/diffxpy,190,6,108,23,FALSE,https://github.com/theislab/diffxpy,190,NA,NA,NA +theislab,diffxpy,theislab/diffxpy,191,6,108,23,FALSE,https://github.com/theislab/diffxpy,191,NA,NA,NA theislab,diffxpy_tutorials,theislab/diffxpy_tutorials,10,8,4,2,FALSE,https://github.com/theislab/diffxpy_tutorials,10,NA,NA,NA theislab,disent,theislab/disent,6,3,0,0,FALSE,https://github.com/theislab/disent,6,NA,NA,NA theislab,edgepy,theislab/edgepy,0,3,0,0,FALSE,https://github.com/theislab/edgepy,0,NA,NA,NA -theislab,ehrapy,theislab/ehrapy,136,5,43,18,FALSE,https://github.com/theislab/ehrapy,136,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows +theislab,ehrapy,theislab/ehrapy,136,5,43,17,FALSE,https://github.com/theislab/ehrapy,136,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows Signed-off-by: zethson ",[![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) -theislab,ehrapy,theislab/ehrapy,136,5,43,18,FALSE,https://github.com/theislab/ehrapy,136,e0e081a3308add30d6ba55fcd8b28566e35e9386,Update fig1,[![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10306217903) -theislab,ehrapy,theislab/ehrapy,136,5,43,18,FALSE,https://github.com/theislab/ehrapy,136,faa668c039458d7d2d37c78d7b449741d49a8c59,"[pre-commit.ci] pre-commit autoupdate (#793) +theislab,ehrapy,theislab/ehrapy,136,5,43,17,FALSE,https://github.com/theislab/ehrapy,136,e0e081a3308add30d6ba55fcd8b28566e35e9386,Update fig1,[![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10306217903) +theislab,ehrapy,theislab/ehrapy,136,5,43,17,FALSE,https://github.com/theislab/ehrapy,136,faa668c039458d7d2d37c78d7b449741d49a8c59,"[pre-commit.ci] pre-commit autoupdate (#793) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2) @@ -98,7 +99,7 @@ theislab,gastrulation_analysis,theislab/gastrulation_analysis,9,4,0,1,FALSE,http theislab,geome,theislab/geome,16,3,3,4,FALSE,https://github.com/theislab/geome,16,402a0a8cdb442fee8666416e5f163c4098fa0c07,"Merge pull request #55 from theislab/fix/toarray Fix Sparse "".A"" Not Found",[![](https://github.com/theislab/geome/workflows/Test/badge.svg)](https://github.com/theislab/geome/actions/runs/10651185375) -theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,b36ef26d87ee5e51c138601d6c1c1b0f7c1a723d,[status] 2024-08-31 12:11:39 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/10653796401) +theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,2f66eae28d34399865d3d9860da9726bdbbb7bb5,[status] 2024-09-01 12:12:59 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/10666737019) theislab,graph_abstraction,theislab/graph_abstraction,26,8,0,10,FALSE,https://github.com/theislab/graph_abstraction,26,NA,NA,NA theislab,graphcompass,theislab/graphcompass,26,2,2,0,FALSE,https://github.com/theislab/graphcompass,26,7c455146402592d7ba73173a72d2abc4d5f7737b,initial commit,[![](https://github.com/theislab/graphcompass/workflows/Labeler/badge.svg)](https://github.com/theislab/graphcompass/actions/runs/7630989244) [![](https://github.com/theislab/graphcompass/workflows/Release/badge.svg)](https://github.com/theislab/graphcompass/actions/runs/7630989237) theislab,greatpy,theislab/greatpy,8,3,4,0,FALSE,https://github.com/theislab/greatpy,8,NA,NA,NA @@ -127,12 +128,655 @@ theislab,masterpraktikum_ssl_segmentation,theislab/masterpraktikum_ssl_segmentat theislab,moscot,theislab/moscot,107,3,48,9,FALSE,https://github.com/theislab/moscot,107,36d93bf11a407023e622b21aabca032c1885d249,"Merge pull request #737 from theislab/fix/linting_attr Fixing Linting and Plotting Error",[![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/10212768708) +theislab,moscot,theislab/moscot,107,3,48,9,FALSE,https://github.com/theislab/moscot,107,6e65ac14dc98f36459caf7ad5b90580429893f95,"(feat): Linear GENOT (#662) + +* fix jaxsampler + +* fix jaxsampler + +* fix jaxsampler + +* fix tests + +* add plot_convergence + +* remove jit from _compute_unbalanced marginals + +* fix sinkhorn_divergence + +* adapt tox.ini file + +* shape mismatch fixed without precommit + +* remove print statement + +* finish merge + +* adapt callbacks and rename tag `cost` to `cost_matrix` (#426) + +* rename tag cost to cost_matrix + +* fix renaming + +* [CI skip], adapt callback + +* incorporate requested changes + +* add test for quad custom callback + +* adapt kwargs for callback + +* fix handle_joint_attr + +* incorporate requested changes + +* Feature/correlation test (#423) + +* fix test in FGWProblem + +* add correlation test + +* add first test for correlation computation + +* add more tests + +* fix tests + +* add tfs to compute_feature_correlation + +* add testing for no nans in compute_feature_correlation + +* incorporate requested changes + +* fix docstring + +* fix sankey return statement (#428) + +* fix sankey return statement + +* adapt test + +* adapt return_fig + +* Bump version: 0.1.0 → 0.1.1 + +* fix return statements + +* add save tests + +* fix return type in mpl (#432) + +* fix return type in mpl + +* change import acronyms + +* fix tests + +* Simplify linear operator (#431) + +* Simplify linear operator + +* Simplify `align`, fix test + +* Explicitly jit the solvers (#433) + +* Feature/interpolate colors sankey (#434) + +* fix return type in mpl + +* change import acronyms + +* fix tests + +* add interpolation option to sankey + +* add test to interpolate color + +* define colors for pull/push` + +* adapt tests + +* introduce axes in mpl.push/pull + +* incorporate requested changes + +* change default color + +* adapt plotting + +* introduce scaling + +* fix scale + +* make start/end categorical in plot + +* regenerate images + +* Remove `FGWSolver` (#437) + +* Remove `FGWSolver` + +* Fix `tox.ini` + +* Fix wrong shape check + +* Use pure GW in generic solver + +* Update tests + +* fix bug in SinkhornProblem (#442) + +* fix bug in SinkhornProblem + +* fix tox.ini + +* fix pre commits + +* make push/pull always use source/target (#443) + +* make push/pull always use source/target + +* fix bug in StarPolicy _apply + +* adapt plotting to source/target + +* fix strip plotting in sankey (#445) + +* fix strip plotting in sankey + +* simplify code + +* Feature/spearman correlation (#444) + +* add spearman correlation + +* add tests + +* adapt tests + +* Delete logo.png + +* Feature/plot order (#453) + +* make push/pull plot in good order + +* [CI skip], try setting adata.uns color explicitly + +* [CI skip], fix copying of adata + +* fix pre commits + +* fix bug + +* Expose marginal kwargs for `moscot.temporal` and check for numeric type of `temporal_key` (#449) + +* make marginal_kwargs explicit in temporal problems + +* introduce check for numeric dtype in temporal mixin + +* add alternative way for marginal prior + +* adapt tolerances in tests + +* correct docs + +* fix bug + +* Fix math rendering + +* fix test + + +Co-authored-by: Michal Klein <46717574+michalk8@users.noreply.github.com> + +* adapt plot_convergence (#454) + +* Bug/docs generic analysis mixin (#455) + +* adapt plot_convergence + +* remove temporal-alluding docs in generic analysis mixin + +* Docs/improvements (#456) + +* adapt plot_convergence + +* remove temporal-alluding docs in generic analysis mixin + +* docs suggestions + +* remove uns_key from set_plotting_vars (#458) + +* resolve `fig referenced before assignment` (#460) + +* move generic mixins tests to problems` (#461) + +* Tests/spatiotemporalproblem (#464) + +* add more tests for spatiotemporalProblem + +* move some functions from TemporalProblem to TemporalMixin + +* add tests LineageProblem + +* fix tests + +* Feature/move taggedarray (#457) + +* adapt plot_convergence + +* remove temporal-alluding docs in generic analysis mixin + +* docs suggestions + +* move tagged array + +* move taggedarray back to solvers + +* add marginal_kwargs to prepare method of TemporalNeuralProblem + +* fix to scaling in + +* Revert ""fix to scaling in"" + +This reverts commit 0a6f7dbdd70b954694f109456274febe6ee46c0c. + +* fix to scaling argument in marginal_kwargs + +* updated conditional not pipeline + +* merge into condot branch + +* incoporated comments + +* incoporated comments + +* incoporated comments + +* removed new_adata for push/pull + +* [ci skip] start docs + +* added temporal neural test + +* [ci skip] continue docs + +* continue docs + +* continue docs + +* change validation epsilon + +* fixed error when not computing wasserstein baseline + +* fixed error when not computing wasserstein baseline + +* correct typo + +* fix bug + +* added neural tests + +* [ci skip] draft CondNeuralOutput + +* include CondDualPotentials and CondDualSolver + +* fixes to main merge + +* fix test_cell_transition_subset_pipeline + +* fix tests + +* update conditionalDualPotentials + +* update conditionalDualPotentials + +* fix most pre-commit hooks and fix tests + +* fix pandas version to <2.0 + +* fix tests for non-conditional solvers + +* continue + +* fix + +* continue fixing + +* fix ICNN setup + +* fix tests + +* swap role of f and g, such that push/pull is correct again + +* [ci skip] restructure to include more general neural solvers + +* [ci skip] restructure ICNNs to allow passing instances of ICNN + +* adapt tests + +* Filled in Monge Gap structure + +* Added Monge Gap paper to documentation + +* Ammend PointCloud Import + +* Update _utils.py + +Ammend PointCloud import + +* Solve compatibility issue with ProblemKind + +* Solve missing Import + +* Fix call to deprecated function + +* Fix style and comment issues + +* add callback, swap f & g + +* add callback, swap f & g + +* add callback, swap f & g + +* intermediate save + +* intermediate save + +* intermediate save + +* [ci skip] fix merge conflicts + +* resolve conflict + +* remove pairwise policy + +* add neural dependencies + +* add neural dependencies + +* add flax + +* fix _call_kwargs + +* fix marginal kwargs + +* remove monge gap solver + +* clean condneuralsolver + +* [ci skip] introduce new data container for joint neural problems + +* add conditions in distirbutioncontainer + +* resolve unfreeze/freeze + +* enable pretraining and weight clipping + +* make dicts compatible with older python versions + +* resolve precommit errors partially + +* resolve precommit errors partially + +* adapt tests + +* [ci skip] draft unbalancedNeuralMixin + +* [ci skip] fix naming of posterior marginals + +* [ci skip] add MLP_marginals + +* adapt neural output to incorporate learnt rescaling functions + +* fix _solve in neuraldualsolver + +* incorporate feedback + +* fix distributioncollection class + +* unify _split_data + +* fix tests + +* fix some precommit hooks + +* make neural dependencies optional + +* make neural dependencies optional + +* delete old files + +* adapt pyproject.toml + +* adapt pyproject.toml + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* [ci skip] adjust _format_params + +* adapt neuraldualsolver to be more similar to ott-jax + +* adapt neuraldualsolver + +* TODO: make JaxSampler return conditions + +* add basic neural test + +* [ci skip] intermediate save + +* adapt neuraldualsolver and finish tests for neural backend + +* [ci skip] TODO: re-iterate on initialisation of neural solver + +* adapt distributioncontainer + +* fix dict bug + +* resolve passing of arguments in solver call methods + +* [ci skip] adapt `solve` in `CondOTProblem` + +* adapt tests and valid loader conditions + +* adapt neural backend tests + +* fix mypy errors + +* make basesolveroutput to basediscretesolveroutput + +* move `to` to BaseSolverOutput` +"" + +* adapt transport_matrix docs + +* adapt transport_matrix docs + +* adapt tests + +* adapt tests + +* update unbalancedness mixin + +* use implementation from moscot + +* uncomment unused code + +* before passing states to loss-fn + +* intermediate save + +* adapt neuraldualsolver + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* resolve some / not all pre commit errors + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* (wip): tests run, code swapped out for now + +* (wip): `NeuralSolver`s implemented minus quad/linear + +* (wip): begin more generic problem + +* (wip): more refactoring to pass arguments to GENOT + +* (chore): remove more kantorovich + +* (chore): update branch to moscot neural + first test moving to solving + +* (fix): split data remains in numpy + +* (fix): push/pull api + +* (fix): make push test work + +* (feat): allow for custom optimziers + +* (chore): remove unclear test + +* (refactor): change to composition API + +* (refactor): start towards model-specific problems + +* (chore): clean up all unnecessary classes + +* (chore): updating to moscot latest + +* Merge branch 'main' into ig/neural_solvers + +* (chore): remove (hopefully) final ICNN vestiges + +* (chore): more cleanup + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* (fix): pass pre-commit hooks + +* (chore): remove duplicatec docs + +* (chore): add torch for testing + +* (fix): add ott jax branch as dep + +* (fix): repo name + +* (chore): remove unbalanced, update api, fix tests + drive by typing fix + +* (feat): first pass at neural mixin + +* (chore): add my name to todos + +* (fix): conditions left out if not necessary + +* (feat): logs and fix conditional attr + +* (fix): add `seed` to call_kwargs so reproducibility works + +* (chore): remove `is_conditional` business + +* (fix): create hidden dims arg for velocity field + +* (chore): raise not implemented error for `pull` + +* (fix): default args + +* (fix): add explicit policy + +* (fix): allow iteration to continue + +* (chore): add star policy to GENOT + +* (chore): notebooks + +* (chore): remove deps + +* (chore): remove unnecessary spaces + +* (chore): simplify quad handling + +* (fix): need to require `optax`/`flax` + +* (fix): use `ott-jax[neural]` + +* (chore): fix docs + +* (fix): small test fixes + +* (chore): small notebook changes + +* (fix): broken link in citation + +* (chore): make notebook dependent on ci + +* (fix): small todos just to push something + +* (fix): variable is a string + +* (fix): pass environment variable to tox + +* (fix): actually pass through + +* (fix): hidden dims ci + +* (fix): re-add notebook + +* (chore): make`recall_target` and `aggregate_to_topk` + +* (chore): fix default arguments + +* (chore): `project_transport_matrix` -> `project_to_transport_matrix` + +* (fix): remove dead `NeuralAnalysisMixin` code + +* (feat): allow custom `data_match_fn` + +* (fix): inherit from `MutableMapping` instead of `dict` + +* (Fix): docs + +* (fix): notebooks + +* (fix): docs reference + +* (fix): remove `attr` + +* (fix): erroneous change + +* (fix): remove empty + +* (fix): notebooks again? + +* (chore): ok? + +--------- + +Co-authored-by: Dominik Klein +Co-authored-by: Dominik Klein +Co-authored-by: AlejandroTL +Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> +Co-authored-by: lucaeyring +Co-authored-by: gocato <104785310+gocato@users.noreply.github.com> +Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/10658580460) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/10658520850) theislab,moscot-framework_reproducibility,theislab/moscot-framework_reproducibility,3,2,1,0,FALSE,https://github.com/theislab/moscot-framework_reproducibility,3,NA,NA,NA theislab,moscot_benchmarks,theislab/moscot_benchmarks,2,2,1,0,FALSE,https://github.com/theislab/moscot_benchmarks,2,NA,NA,NA theislab,moscot_not,theislab/moscot_not,3,2,8,1,FALSE,https://github.com/theislab/moscot_not,3,NA,NA,NA theislab,moscot_notebooks,theislab/moscot_notebooks,6,1,4,3,FALSE,https://github.com/theislab/moscot_notebooks,6,5b9d4e07d7188b1c391ec47a1c5d957da1ab2bca,"attribute and argument fixes (#80) -Co-authored-by: Arina Danilina ",[![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/10551326301) +Co-authored-by: Arina Danilina ",[![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/10658611524) theislab,moslin,theislab/moslin,9,1,0,1,FALSE,https://github.com/theislab/moslin,9,NA,NA,NA theislab,mouse_cross-condition_pancreatic_islet_atlas,theislab/mouse_cross-condition_pancreatic_islet_atlas,7,2,0,3,FALSE,https://github.com/theislab/mouse_cross-condition_pancreatic_islet_atlas,7,NA,NA,NA theislab,mubind,theislab/mubind,23,3,31,0,FALSE,https://github.com/theislab/mubind,23,3f62f838470ebc499540ff54fb8d074363abd7b6,Dropbox URL (typo),[![](https://github.com/theislab/mubind/workflows/Python%20package/badge.svg)](https://github.com/theislab/mubind/actions/runs/10632591185) @@ -161,7 +805,7 @@ theislab,pdac_analysis,theislab/pdac_analysis,0,2,0,0,FALSE,https://github.com/t theislab,pertpy-datasets,theislab/pertpy-datasets,1,3,1,1,FALSE,https://github.com/theislab/pertpy-datasets,1,NA,NA,NA theislab,pertpy-reproducibility,theislab/pertpy-reproducibility,0,2,0,0,FALSE,https://github.com/theislab/pertpy-reproducibility,0,NA,NA,NA theislab,perturbation-metrics,theislab/perturbation-metrics,4,2,1,0,FALSE,https://github.com/theislab/perturbation-metrics,4,NA,NA,NA -theislab,prophet,theislab/prophet,6,3,0,0,FALSE,https://github.com/theislab/prophet,6,NA,NA,NA +theislab,prophet,theislab/prophet,7,3,0,0,FALSE,https://github.com/theislab/prophet,7,NA,NA,NA theislab,prophet-reproducibility,theislab/prophet-reproducibility,0,3,0,0,FALSE,https://github.com/theislab/prophet-reproducibility,0,NA,NA,NA theislab,pseudodynamics,theislab/pseudodynamics,39,7,0,6,FALSE,https://github.com/theislab/pseudodynamics,39,NA,NA,NA theislab,quasiSCVI,theislab/quasiSCVI,0,2,0,0,FALSE,https://github.com/theislab/quasiSCVI,0,NA,NA,NA @@ -171,7 +815,7 @@ theislab,sc-best-practices-ce,theislab/sc-best-practices-ce,8,8,2,3,FALSE,https: theislab,sc-pert,theislab/sc-pert,141,5,6,10,FALSE,https://github.com/theislab/sc-pert,141,NA,NA,NA theislab,scAnalysisTutorial,theislab/scAnalysisTutorial,10,3,0,3,FALSE,https://github.com/theislab/scAnalysisTutorial,10,NA,NA,NA theislab,scArches-reproducibility,theislab/scArches-reproducibility,33,5,5,0,FALSE,https://github.com/theislab/scArches-reproducibility,33,NA,NA,NA -theislab,scCODA,theislab/scCODA,146,9,7,24,FALSE,https://github.com/theislab/scCODA,146,NA,NA,NA +theislab,scCODA,theislab/scCODA,147,9,7,24,FALSE,https://github.com/theislab/scCODA,147,NA,NA,NA theislab,scCODA_reproducibility,theislab/scCODA_reproducibility,8,5,0,1,FALSE,https://github.com/theislab/scCODA_reproducibility,8,NA,NA,NA theislab,scPoli_legacy,theislab/scPoli_legacy,2,5,0,0,FALSE,https://github.com/theislab/scPoli_legacy,2,NA,NA,NA theislab,scPoli_reproduce,theislab/scPoli_reproduce,13,3,2,4,FALSE,https://github.com/theislab/scPoli_reproduce,13,NA,NA,NA @@ -196,7 +840,7 @@ Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.gi theislab,scarches,theislab/scarches,328,13,45,51,FALSE,https://github.com/theislab/scarches,328,NA,NA,NA theislab,scarches_notebooks,theislab/scarches_notebooks,0,3,0,0,FALSE,https://github.com/theislab/scarches_notebooks,0,NA,NA,NA theislab,scatac_poisson_reproducibility,theislab/scatac_poisson_reproducibility,7,3,0,0,FALSE,https://github.com/theislab/scatac_poisson_reproducibility,7,NA,NA,NA -theislab,scgen,theislab/scgen,259,9,25,53,FALSE,https://github.com/theislab/scgen,259,NA,NA,NA +theislab,scgen,theislab/scgen,259,9,25,52,FALSE,https://github.com/theislab/scgen,259,NA,NA,NA theislab,scgen-reproducibility,theislab/scgen-reproducibility,18,4,5,8,FALSE,https://github.com/theislab/scgen-reproducibility,18,NA,NA,NA theislab,scib,theislab/scib,287,14,37,61,FALSE,https://github.com/theislab/scib,NA,5547cd1f6b24eed7499c6492bf5c1ef4e2ef9f7a,"Skip labels before loop (#394) @@ -209,12 +853,10 @@ theislab,scib,theislab/scib,287,14,37,61,FALSE,https://github.com/theislab/scib, Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com>",[![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/10287985783) theislab,scib-pipeline,theislab/scib-pipeline,64,7,16,28,FALSE,https://github.com/theislab/scib-pipeline,64,NA,NA,NA theislab,scib-reproducibility,theislab/scib-reproducibility,52,6,3,14,FALSE,https://github.com/theislab/scib-reproducibility,52,NA,NA,NA -theislab,scvelo,theislab/scvelo,407,13,61,103,FALSE,https://github.com/theislab/scvelo,407,3fbce6ff6d644a44911091f498efa0c69f6b85b0,"Update densifying sparse array (#1263) - -Switch from `.A` to `.toarray()`",[![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9892975902) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9892975897) theislab,scvelo,theislab/scvelo,407,13,61,103,FALSE,https://github.com/theislab/scvelo,407,b2f31b345641efdccd39fbcb8c0beaa0014b4b88,"Update `pyproject.toml` (#1226) Fix package directory.",[![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/8317755189) +theislab,scvelo,theislab/scvelo,407,13,61,103,FALSE,https://github.com/theislab/scvelo,407,bef8f1c2044d65a6c6b11e2f519ffafbd7dc2b34,Remove numpy<2.0.0 pin (#1267),[![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/10662690984) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/10662690982) theislab,scvelo_notebooks,theislab/scvelo_notebooks,29,2,4,12,FALSE,https://github.com/theislab/scvelo_notebooks,29,NA,NA,NA theislab,sfaira,theislab/sfaira,134,8,167,11,FALSE,https://github.com/theislab/sfaira,134,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/9457340256) theislab,sfaira,theislab/sfaira,134,8,167,11,FALSE,https://github.com/theislab/sfaira,134,5fcf932c44613e6bf4063ef3075ad6062bf5d9a1,round restored counts in some affected datasets,[![](https://github.com/theislab/sfaira/workflows/Build%20sfaira%20Package/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672388) [![](https://github.com/theislab/sfaira/workflows/Create%20sfaira%20data-loader%20templates/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672382) [![](https://github.com/theislab/sfaira/workflows/Run%20bandit/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672385) [![](https://github.com/theislab/sfaira/workflows/Run%20flake8%20linting/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672384) @@ -301,8 +943,8 @@ Signed-off-by: zethson --------- Signed-off-by: zethson ",[![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535081) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535098) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535076) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/10316535080) -theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,177,8,1,20,FALSE,https://github.com/theislab/single-cell-transformer-papers,177,NA,NA,NA -theislab,single-cell-tutorial,theislab/single-cell-tutorial,1346,30,21,449,FALSE,https://github.com/theislab/single-cell-tutorial,1346,NA,NA,NA +theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,179,8,1,20,FALSE,https://github.com/theislab/single-cell-transformer-papers,179,NA,NA,NA +theislab,single-cell-tutorial,theislab/single-cell-tutorial,1347,30,21,449,FALSE,https://github.com/theislab/single-cell-tutorial,1347,NA,NA,NA theislab,singlecell_proteomics,theislab/singlecell_proteomics,5,5,6,3,FALSE,https://github.com/theislab/singlecell_proteomics,5,NA,NA,NA theislab,spapros,theislab/spapros,23,3,13,6,FALSE,https://github.com/theislab/spapros,23,a7867793a6b1f49047fe33377bc2ae523a7bee6c,"[DEPENDABOT]: Bump pynndescent from 0.5.11 to 0.5.13 in /docs @@ -320,7 +962,7 @@ updated-dependencies: Signed-off-by: dependabot[bot] ",[![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/10459161813) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/10459161788) theislab,spapros,theislab/spapros,23,3,13,6,FALSE,https://github.com/theislab/spapros,23,e8a37c9e78039920a0792fc04f426ab062dbbf88,"Merge pull request #321 from theislab/patch_precommit -pre commit correction of readthedocs.yml",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/10649868280) +pre commit correction of readthedocs.yml",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/10659212143) theislab,spapros-pipeline,theislab/spapros-pipeline,7,2,0,0,FALSE,https://github.com/theislab/spapros-pipeline,7,NA,NA,NA theislab,spapros-smk,theislab/spapros-smk,0,2,0,1,FALSE,https://github.com/theislab/spapros-smk,0,NA,NA,NA theislab,spapros_reproducibility,theislab/spapros_reproducibility,0,1,0,1,FALSE,https://github.com/theislab/spapros_reproducibility,0,NA,NA,NA
13 61 103 -3fbce6b2f31b
theislab/scvelo 13 61 103b2f31b +bef8f1
theislab/cellrank 338 91917 47 43c32b
theislab/cellrank33891747 +554f7c
theislab/scib 287 14 5547cd
theislab/zellkonverter 144 5 328e7e
theislab/ehrapy 136 5 431817 84d33c
theislab/ehrapy 136 5 431817 e0e081
theislab/ehrapy 136 5 431817 faa668
theislab/sfaira 134 8 55bcbb
theislab/sfaira 134 8 5fcf93
theislab/sfaira 134 8 ceb14c
theislab/anndata2ri 124 7 8a5238
theislab/moscot 107 3 36d93b
theislab/moscot1073489 +6e65ac
theislab/ncem 102 13 6 - e8a37c
1 4 3 5b9d4e
2 0 0b36ef22f66ea
theislab/idtrack
theislab/single-cell-tutorial13461347 30 21 449 259 9 255352
theislab/dca
theislab/diffxpy190191 6 108 23
theislab/single-cell-transformer-papers177179 8 1 20
theislab/scCODA146147 9 7 24 3
theislab/prophet7300
theislab/scachepy 7 5 3 1
theislab/scatac_poisson_reproducibility 7 3 0 0
theislab/spapros-pipeline 7 2 0 0
theislab/2018_Angelidis 6 4 0 6
theislab/disent 6 3 0 0
theislab/intercode 6 3 1 1
theislab/jump-cpg0016-segmentation 6 1 2 0
theislab/pancreatic-endocrinogenesis 6 3 0 6
theislab/prophet6300
theislab/sfaira_tutorials 6 5 4 010
theislab/kbranches