From 700f2359694f5818a58504ff9b8681876baa51c5 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 3 Sep 2024 12:13:31 +0000 Subject: [PATCH] [status] 2024-09-03 12:13:31 UTC --- README.md | 37 ++- index.html | 312 ++++++++++++----------- repos.csv | 713 +++-------------------------------------------------- 3 files changed, 206 insertions(+), 856 deletions(-) diff --git a/README.md b/README.md index 50c5835..a4b23b8 100644 --- a/README.md +++ b/README.md @@ -2,44 +2,42 @@ GitHub Dashboard ================ ![](https://github.com/gadenbuie/status/workflows/Render%20Status/badge.svg) -2024-09-02 12:10:49 UTC +2024-09-03 12:11:09 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/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 731 | 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/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/8317755189) | b2f31b | | [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 | 17 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437241) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437233) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437231) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437236) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437242) | 568b67 | | [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/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/10678804508) | 15e8d6 | | [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 | -| [theislab/graphcompass](https://github.com/theislab/graphcompass) | 26 | 2 | 2 | 0 | [![](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) | 7c4551 | +| [theislab/graphcompass](https://github.com/theislab/graphcompass) | 27 | 2 | 2 | 0 | [![](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) | 7c4551 | | [theislab/hadge](https://github.com/theislab/hadge) | 24 | 3 | 13 | 6 | [![](https://github.com/theislab/hadge/workflows/sphinx-docs/badge.svg)](https://github.com/theislab/hadge/actions/runs/7569650236) | 1ed105 | | [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/10659212143) | e8a37c | +| [theislab/mubind](https://github.com/theislab/mubind) | 23 | 3 | 32 | 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/10671940759) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/10671940758) | 9354ed | +| [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/10675082118) | 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/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/10678804523) | 122b37 | | [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/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/10666737019) | 2f66ea | +| [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/10682498898) | 0a3286 | | [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 | @@ -47,30 +45,30 @@ GitHub Dashboard | Repo | Stars | Subscribers | Issues | Forks | |:------------------------------------------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:| -| [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/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1348 | 30 | 21 | 449 | +| [theislab/scarches](https://github.com/theislab/scarches) | 328 | 13 | 46 | 51 | | [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) | 191 | 6 | 108 | 23 | -| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 179 | 8 | 1 | 20 | +| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 180 | 8 | 1 | 21 | | [theislab/kBET](https://github.com/theislab/kBET) | 151 | 8 | 9 | 23 | | [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 | +| [theislab/cpa](https://github.com/theislab/cpa) | 81 | 5 | 20 | 18 | | [theislab/scib-pipeline](https://github.com/theislab/scib-pipeline) | 64 | 7 | 16 | 28 | | [theislab/AutoGeneS](https://github.com/theislab/AutoGeneS) | 54 | 6 | 6 | 8 | | [theislab/trVAE](https://github.com/theislab/trVAE) | 54 | 6 | 3 | 11 | | [theislab/scib-reproducibility](https://github.com/theislab/scib-reproducibility) | 52 | 6 | 3 | 14 | | [theislab/spatial_scog_workshop_2022](https://github.com/theislab/spatial_scog_workshop_2022) | 48 | 9 | 0 | 27 | -| [theislab/nicheformer](https://github.com/theislab/nicheformer) | 44 | 3 | 12 | 2 | +| [theislab/nicheformer](https://github.com/theislab/nicheformer) | 46 | 3 | 12 | 2 | | [theislab/pseudodynamics](https://github.com/theislab/pseudodynamics) | 39 | 7 | 0 | 6 | | [theislab/scTab](https://github.com/theislab/scTab) | 38 | 3 | 1 | 7 | | [theislab/tcellmatch](https://github.com/theislab/tcellmatch) | 37 | 9 | 3 | 7 | | [theislab/scArches-reproducibility](https://github.com/theislab/scArches-reproducibility) | 33 | 5 | 5 | 0 | | [theislab/deepflow](https://github.com/theislab/deepflow) | 31 | 5 | 1 | 14 | -| [theislab/scvelo_notebooks](https://github.com/theislab/scvelo_notebooks) | 29 | 2 | 4 | 12 | +| [theislab/scvelo_notebooks](https://github.com/theislab/scvelo_notebooks) | 30 | 2 | 4 | 12 | | [theislab/DeepRT](https://github.com/theislab/DeepRT) | 28 | 2 | 11 | 10 | | [theislab/batchglm](https://github.com/theislab/batchglm) | 27 | 3 | 47 | 9 | | [theislab/graph_abstraction](https://github.com/theislab/graph_abstraction) | 26 | 8 | 0 | 10 | @@ -124,6 +122,7 @@ GitHub Dashboard | [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/ehrdata](https://github.com/theislab/ehrdata) | 5 | 3 | 2 | 1 | | [theislab/flowVI](https://github.com/theislab/flowVI) | 5 | 3 | 0 | 0 | | [theislab/InterpretableAutoencoders](https://github.com/theislab/InterpretableAutoencoders) | 5 | 4 | 0 | 0 | | [theislab/kbranches](https://github.com/theislab/kbranches) | 5 | 7 | 0 | 0 | @@ -178,7 +177,7 @@ GitHub Dashboard | [theislab/MS_mv_modelling](https://github.com/theislab/MS_mv_modelling) | 1 | 2 | 0 | 1 | | [theislab/pertpy-datasets](https://github.com/theislab/pertpy-datasets) | 1 | 3 | 1 | 1 | | [theislab/sc_mae](https://github.com/theislab/sc_mae) | 1 | 2 | 0 | 0 | -| [theislab/tardis](https://github.com/theislab/tardis) | 1 | 1 | 0 | 0 | +| [theislab/tardis](https://github.com/theislab/tardis) | 1 | 1 | 0 | 1 | | [theislab/tissue](https://github.com/theislab/tissue) | 1 | 3 | 0 | 0 | | [theislab/tissue_reproducibility](https://github.com/theislab/tissue_reproducibility) | 1 | 3 | 0 | 0 | | [theislab/transcription_factor_activity](https://github.com/theislab/transcription_factor_activity) | 1 | 1 | 5 | 1 | diff --git a/index.html b/index.html index a5d6f79..ac8c55e 100644 --- a/index.html +++ b/index.html @@ -49,7 +49,7 @@

GitHub Dashboard


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+ + + + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + diff --git a/repos.csv b/repos.csv index 2b76819..0aceb4b 100644 --- a/repos.csv +++ b/repos.csv @@ -29,7 +29,12 @@ theislab,MS_mv_modelling,theislab/MS_mv_modelling,1,2,0,1,FALSE,https://github.c theislab,MetaMap,theislab/MetaMap,12,7,0,8,FALSE,https://github.com/theislab/MetaMap,12,NA,NA,NA theislab,MetaMap-web,theislab/MetaMap-web,0,4,2,0,FALSE,https://github.com/theislab/MetaMap-web,0,NA,NA,NA theislab,PathReg,theislab/PathReg,8,3,0,0,FALSE,https://github.com/theislab/PathReg,8,NA,NA,NA 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theislab,archmap_doc,theislab/archmap_doc,0,3,0,0,FALSE,https://github.com/theislab/archmap_doc,0,NA,NA,NA theislab,astrocytes_reprogramming_analysis,theislab/astrocytes_reprogramming_analysis,1,5,0,0,FALSE,https://github.com/theislab/astrocytes_reprogramming_analysis,1,NA,NA,NA @@ -56,7 +61,7 @@ theislab,consensus-clustering-evaluation,theislab/consensus-clustering-evaluatio theislab,countae,theislab/countae,1,4,0,0,FALSE,https://github.com/theislab/countae,1,NA,NA,NA theislab,covid-perturbation,theislab/covid-perturbation,4,3,0,0,FALSE,https://github.com/theislab/covid-perturbation,4,NA,NA,NA theislab,covid_macrophages_integration,theislab/covid_macrophages_integration,2,5,0,5,FALSE,https://github.com/theislab/covid_macrophages_integration,2,NA,NA,NA -theislab,cpa,theislab/cpa,80,5,20,18,FALSE,https://github.com/theislab/cpa,80,NA,NA,NA +theislab,cpa,theislab/cpa,81,5,20,18,FALSE,https://github.com/theislab/cpa,81,NA,NA,NA theislab,cpa-reproducibility,theislab/cpa-reproducibility,7,2,1,1,FALSE,https://github.com/theislab/cpa-reproducibility,7,NA,NA,NA theislab,cross_system_integration,theislab/cross_system_integration,10,2,10,1,FALSE,https://github.com/theislab/cross_system_integration,10,NA,NA,NA theislab,dali,theislab/dali,0,7,0,1,FALSE,https://github.com/theislab/dali,0,NA,NA,NA @@ -67,17 +72,16 @@ theislab,diffxpy,theislab/diffxpy,191,6,108,23,FALSE,https://github.com/theislab 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,136,5,43,17,FALSE,https://github.com/theislab/ehrapy,136,568b67f0b5e15d54ed6e9ce1f8360bac93d426d3,"[pre-commit.ci] pre-commit autoupdate (#795) + +updates: +- [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3) + +Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437241) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437233) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437231) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437236) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10682437242) 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,136,5,43,17,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) -- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.11.2) - -Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/10572979429) theislab,ehrapy-cli,theislab/ehrapy-cli,1,3,0,0,FALSE,https://github.com/theislab/ehrapy-cli,1,NA,NA,NA theislab,ehrapy-datasets,theislab/ehrapy-datasets,5,2,0,2,FALSE,https://github.com/theislab/ehrapy-datasets,5,e441a5d0912396064360799f10de973b377ba6a5,"Merge pull request #23 from theislab/diabetes-update @@ -85,9 +89,7 @@ change diabetes dataset doc",[![](https://github.com/theislab/ehrapy-datasets/wo theislab,ehrapy-reproducibility,theislab/ehrapy-reproducibility,0,1,1,0,FALSE,https://github.com/theislab/ehrapy-reproducibility,0,NA,NA,NA theislab,ehrapy-site,theislab/ehrapy-site,1,2,0,0,FALSE,https://github.com/theislab/ehrapy-site,1,NA,NA,NA theislab,ehrapy-tutorials,theislab/ehrapy-tutorials,7,3,0,2,FALSE,https://github.com/theislab/ehrapy-tutorials,7,NA,NA,NA -theislab,ehrdata,theislab/ehrdata,5,3,2,1,FALSE,https://github.com/theislab/ehrdata,5,87341182cdee7438ca9647ff8f17baa2f45e6ba0,"Merge pull request #17 from theislab/pre-commit-ci-update-config - -[pre-commit.ci] pre-commit autoupdate",[![](https://github.com/theislab/ehrdata/workflows/Test/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/10651206167) +theislab,ehrdata,theislab/ehrdata,5,3,2,1,FALSE,https://github.com/theislab/ehrdata,5,NA,NA,NA theislab,enrichment_analysis_celltype,theislab/enrichment_analysis_celltype,9,5,0,4,FALSE,https://github.com/theislab/enrichment_analysis_celltype,9,NA,NA,NA theislab,epicardiods_analysis,theislab/epicardiods_analysis,2,2,1,0,FALSE,https://github.com/theislab/epicardiods_analysis,2,NA,NA,NA theislab,expiMap_reproducibility,theislab/expiMap_reproducibility,9,5,3,4,FALSE,https://github.com/theislab/expiMap_reproducibility,9,NA,NA,NA @@ -99,9 +101,9 @@ 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,1,2f66eae28d34399865d3d9860da9726bdbbb7bb5,[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,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,0a3286b18e5d25b1e5cb5828b8e8b99a7328581b,[status] 2024-09-02 12:12:29 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/10682498898) 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,graphcompass,theislab/graphcompass,27,2,2,0,FALSE,https://github.com/theislab/graphcompass,27,7c455146402592d7ba73173a72d2abc4d5f7737b,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 theislab,gut_lineage,theislab/gut_lineage,2,3,0,3,FALSE,https://github.com/theislab/gut_lineage,2,NA,NA,NA theislab,hadge,theislab/hadge,24,3,13,6,FALSE,https://github.com/theislab/hadge,24,1ed105ed192e66898ff7a305a2c21f5b8c81bcf7,fix gdown bug,[![](https://github.com/theislab/hadge/workflows/sphinx-docs/badge.svg)](https://github.com/theislab/hadge/actions/runs/7569650236) @@ -128,649 +130,6 @@ 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 @@ -779,7 +138,7 @@ theislab,moscot_notebooks,theislab/moscot_notebooks,6,1,4,3,FALSE,https://github 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) +theislab,mubind,theislab/mubind,23,3,32,0,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) theislab,mubind-benchmark,theislab/mubind-benchmark,0,2,19,0,FALSE,https://github.com/theislab/mubind-benchmark,0,NA,NA,NA theislab,multicpa,theislab/multicpa,13,2,1,2,FALSE,https://github.com/theislab/multicpa,13,NA,NA,NA theislab,multicpa-reproducibility,theislab/multicpa-reproducibility,0,2,0,0,FALSE,https://github.com/theislab/multicpa-reproducibility,0,NA,NA,NA @@ -796,7 +155,7 @@ theislab,ncem,theislab/ncem,102,6,27,13,FALSE,https://github.com/theislab/ncem,1 theislab,ncem_benchmarks,theislab/ncem_benchmarks,8,4,4,2,FALSE,https://github.com/theislab/ncem_benchmarks,8,NA,NA,NA theislab,ncem_tutorials,theislab/ncem_tutorials,11,4,6,0,FALSE,https://github.com/theislab/ncem_tutorials,11,NA,NA,NA theislab,neural_organoid_atlas,theislab/neural_organoid_atlas,10,4,2,1,FALSE,https://github.com/theislab/neural_organoid_atlas,10,NA,NA,NA -theislab,nicheformer,theislab/nicheformer,44,3,12,2,FALSE,https://github.com/theislab/nicheformer,44,NA,NA,NA +theislab,nicheformer,theislab/nicheformer,46,3,12,2,FALSE,https://github.com/theislab/nicheformer,46,NA,NA,NA theislab,organoid_dexamethason_stimulation,theislab/organoid_dexamethason_stimulation,0,3,0,1,FALSE,https://github.com/theislab/organoid_dexamethason_stimulation,0,NA,NA,NA theislab,paga,theislab/paga,198,10,23,33,FALSE,https://github.com/theislab/paga,198,NA,NA,NA theislab,pancreas-targeted_pharmacology,theislab/pancreas-targeted_pharmacology,0,7,0,2,FALSE,https://github.com/theislab/pancreas-targeted_pharmacology,0,NA,NA,NA @@ -830,14 +189,13 @@ theislab,scanpy-in-R,theislab/scanpy-in-R,13,3,1,0,FALSE,https://github.com/thei theislab,scanpy.org,theislab/scanpy.org,0,7,1,0,FALSE,https://github.com/theislab/scanpy.org,0,NA,NA,NA theislab,scanpy_neighbors,theislab/scanpy_neighbors,0,3,0,1,FALSE,https://github.com/theislab/scanpy_neighbors,0,NA,NA,NA theislab,scanpy_squidpy_demo_2021,theislab/scanpy_squidpy_demo_2021,2,4,0,1,FALSE,https://github.com/theislab/scanpy_squidpy_demo_2021,2,NA,NA,NA -theislab,scanpydoc,theislab/scanpydoc,12,6,3,6,FALSE,https://github.com/theislab/scanpydoc,12,5a27971e33cfe9534bb724511cc1b72be9c692e5,"[pre-commit.ci] pre-commit autoupdate (#167) +theislab,scanpydoc,theislab/scanpydoc,12,6,3,6,FALSE,https://github.com/theislab/scanpydoc,12,122b37783308b6b523277ca58bc4fe35244b6918,"[pre-commit.ci] pre-commit autoupdate (#168) 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) -- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.11.2) +- [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3) -Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/10579066618) -theislab,scarches,theislab/scarches,328,13,45,51,FALSE,https://github.com/theislab/scarches,328,NA,NA,NA +Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/10678804523) +theislab,scarches,theislab/scarches,328,13,46,51,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,259,9,25,52,FALSE,https://github.com/theislab/scgen,259,NA,NA,NA @@ -857,7 +215,7 @@ theislab,scvelo,theislab/scvelo,407,13,61,103,FALSE,https://github.com/theislab/ 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,scvelo_notebooks,theislab/scvelo_notebooks,30,2,4,12,FALSE,https://github.com/theislab/scvelo_notebooks,30,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) theislab,sfaira,theislab/sfaira,134,8,167,11,FALSE,https://github.com/theislab/sfaira,134,ceb14c946f699c38d18a32192b76d4639caf845e,fix download links,[![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) @@ -866,7 +224,7 @@ theislab,sfaira-site,theislab/sfaira-site,0,4,0,0,FALSE,https://github.com/theis theislab,sfaira_benchmarks,theislab/sfaira_benchmarks,0,3,0,0,FALSE,https://github.com/theislab/sfaira_benchmarks,0,NA,NA,NA theislab,sfaira_extension,theislab/sfaira_extension,0,3,1,0,FALSE,https://github.com/theislab/sfaira_extension,0,NA,NA,NA theislab,sfaira_tutorials,theislab/sfaira_tutorials,6,4,4,2,FALSE,https://github.com/theislab/sfaira_tutorials,6,NA,NA,NA -theislab,single-cell-best-practices,theislab/single-cell-best-practices,730,18,67,169,FALSE,https://github.com/theislab/single-cell-best-practices,730,6461a5c0c8f797ed3ace9909e3e66348d9aef78b,"Fix integration environments (#292) +theislab,single-cell-best-practices,theislab/single-cell-best-practices,731,18,67,169,FALSE,https://github.com/theislab/single-cell-best-practices,731,6461a5c0c8f797ed3ace9909e3e66348d9aef78b,"Fix integration environments (#292) * New mamba action @@ -943,26 +301,27 @@ 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,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,single-cell-transformer-papers,theislab/single-cell-transformer-papers,180,8,1,21,FALSE,https://github.com/theislab/single-cell-transformer-papers,180,NA,NA,NA +theislab,single-cell-tutorial,theislab/single-cell-tutorial,1348,30,21,449,FALSE,https://github.com/theislab/single-cell-tutorial,1348,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 +theislab,spapros,theislab/spapros,23,3,13,6,FALSE,https://github.com/theislab/spapros,23,9354edf6b59a6536cd4e68e99604db06860beb11,"[DEPENDABOT]: Bump contourpy from 1.2.0 to 1.3.0 -Bumps [pynndescent](https://github.com/lmcinnes/pynndescent) from 0.5.11 to 0.5.13. -- [Release notes](https://github.com/lmcinnes/pynndescent/releases) -- [Commits](https://github.com/lmcinnes/pynndescent/compare/release-0.5.11...release-0.5.13) +Bumps [contourpy](https://github.com/contourpy/contourpy) from 1.2.0 to 1.3.0. +- [Release notes](https://github.com/contourpy/contourpy/releases) +- [Changelog](https://github.com/contourpy/contourpy/blob/main/docs/changelog.rst) +- [Commits](https://github.com/contourpy/contourpy/compare/v1.2.0...v1.3.0) --- updated-dependencies: -- dependency-name: pynndescent +- dependency-name: contourpy dependency-type: direct:production - update-type: version-update:semver-patch + update-type: version-update:semver-minor ... -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) +Signed-off-by: dependabot[bot] ",[![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/10671940759) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/10671940758) 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/10659212143) +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/10675082118) 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 @@ -972,7 +331,7 @@ theislab,squidpy_reproducibility,theislab/squidpy_reproducibility,8,2,0,7,FALSE, theislab,ssl_in_scg,theislab/ssl_in_scg,4,1,0,1,FALSE,https://github.com/theislab/ssl_in_scg,4,NA,NA,NA theislab,superexacttestpy,theislab/superexacttestpy,9,2,3,0,FALSE,https://github.com/theislab/superexacttestpy,9,NA,NA,NA theislab,svaeligr,theislab/svaeligr,2,3,0,0,FALSE,https://github.com/theislab/svaeligr,2,NA,NA,NA 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theislab/moscot 36d93b
theislab/moscot1073489 -6e65ac
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theislab/ncem 102 6 d03a07
theislab/destiny 74 5 300eb2
theislab/graphcompass2627 2 2 0 7c4551
theislab/hadge 24 3 1ed105
theislab/hadge 24 3 490a55
theislab/mubind 23 33132 0 3f62f8
theislab/spapros 23 3 13 6 -a78677 +9354ed
theislab/spapros 23 3 13 6 - e8a37c
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theislab/ehrapy-datasets 5 2 e441a5
theislab/ehrdata5321873411
theislab/gh-dashboard 1 2 0 02f66ea0a3286
theislab/idtrack
theislab/single-cell-tutorial13471348 30 21 449 theislab/scarches 328 134546 51
theislab/single-cell-transformer-papers179180 8 12021
theislab/kBET
theislab/cpa8081 5 20 18
theislab/nicheformer4446 3 12 2
theislab/scvelo_notebooks2930 2 4 12 0
theislab/ehrdata5321
theislab/flowVI 5 3 0 0
theislab/InterpretableAutoencoders 5 4 0 0
theislab/kbranches 5 7 0 0
theislab/scanpy-demo-czbiohub 5 5 0 5
theislab/singlecell_proteomics 5 5 6 3
theislab/2022_Tritschler_pancreas_cross_species 4 3 0 1
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