| 23ac336 | Philipp A | 15 November 2019, 12:32:42 UTC | Link to tutorials | 15 November 2019, 12:32:42 UTC |
| 5d6f276 | Philipp A | 13 November 2019, 17:13:25 UTC | fix link | 13 November 2019, 17:13:32 UTC |
| 259bdb2 | Philipp A | 13 November 2019, 16:51:36 UTC | Mention regress_out limitations Closes #526 | 13 November 2019, 16:51:36 UTC |
| 9a06922 | Philipp A | 13 November 2019, 16:46:43 UTC | Add issue role | 13 November 2019, 16:48:43 UTC |
| d39cd39 | Philipp A | 13 November 2019, 12:17:00 UTC | Now that I know how contact links look, this makes more sense. | 13 November 2019, 12:17:00 UTC |
| e88814d | Philipp A | 13 November 2019, 12:14:12 UTC | Create issue templates (#886) | 13 November 2019, 12:14:12 UTC |
| 64f04d8 | Philipp A | 08 November 2019, 12:18:24 UTC | Use immutable defaults (#908) | 08 November 2019, 12:18:24 UTC |
| 0200814 | Gert Hulselmans | 06 November 2019, 10:36:22 UTC | Allow specifying chromosome name when retrieving mitochondrial genes. (#902) Some organisms use a different chromosome name than "MT". | 06 November 2019, 10:36:22 UTC |
| 19d7cd2 | Philipp A | 06 November 2019, 10:21:38 UTC | remove text box border | 06 November 2019, 10:21:38 UTC |
| da0ffd7 | Gökçen Eraslan | 05 November 2019, 02:36:34 UTC | Switch to normalize_total in sc.pl.highest_expr_genes (#901) * Switch to normalize_total in sc.pl.highest_expr_genes * Fix log argument type * Add missing import * Blacken | 05 November 2019, 02:36:34 UTC |
| c02d285 | Fidel Ramirez | 30 October 2019, 16:35:52 UTC | Merge pull request #899 from theislab/layer_to_violin add 'layer' option to sc.pl.violin | 30 October 2019, 16:35:52 UTC |
| fdbff3f | Fidel Ramírez | 30 October 2019, 10:35:21 UTC | updated test image; fixed black | 30 October 2019, 10:35:21 UTC |
| 723766b | Fidel Ramírez | 30 October 2019, 10:18:15 UTC | updated violin test image for notebook related to the new default cut=0 | 30 October 2019, 10:18:15 UTC |
| 948895f | Fidel Ramírez | 30 October 2019, 10:02:56 UTC | added violin test image with layer | 30 October 2019, 10:02:56 UTC |
| fabe118 | Fidel Ramírez | 30 October 2019, 10:02:33 UTC | added violin test with layer | 30 October 2019, 10:02:33 UTC |
| 770de20 | Fidel Ramírez | 30 October 2019, 10:01:59 UTC | added support for layers to sc.pl.violin. Added cut=0 as default, similar to stacked_violin | 30 October 2019, 10:01:59 UTC |
| 6f72225 | Philipp A | 29 October 2019, 21:35:08 UTC | Inherit main requirements (#898) | 29 October 2019, 21:35:08 UTC |
| 784387e | Scott Gigante | 29 October 2019, 20:20:05 UTC | Update MAGIC API and docs (#896) | 29 October 2019, 20:20:05 UTC |
| 27115e3 | Fidel Ramirez | 29 October 2019, 13:15:32 UTC | Fix plot issues (#893) * fix error in stacked_violin plots when order is given and swap_axes=False * fix #891. when groups is given to an embedding, sort the cell belonging to groups on top. * Improve plot_embedding docstring: `size` can also be a sequence of sizes for each cell. | 29 October 2019, 13:15:32 UTC |
| 48a11bc | Philipp A | 25 October 2019, 17:44:16 UTC | Fix remaining docs (#894) | 25 October 2019, 17:44:16 UTC |
| b3933ac | Philipp A | 25 October 2019, 09:35:28 UTC | Unify fontsize/weight params (#892) | 25 October 2019, 09:35:28 UTC |
| 1611d63 | Philipp A | 24 October 2019, 15:40:21 UTC | Fix mnn_correct for degenerate case | 24 October 2019, 15:40:21 UTC |
| e6e08e5 | Philipp A | 20 October 2019, 11:31:23 UTC | Link to matrixplot | 20 October 2019, 11:31:23 UTC |
| 07d1b4c | Philipp A | 20 October 2019, 11:21:33 UTC | Export dendrogram | 20 October 2019, 11:22:19 UTC |
| 5f84ab3 | Philipp A | 19 October 2019, 23:23:39 UTC | Fix the rest of the docs (#881) | 19 October 2019, 23:23:39 UTC |
| dd892fa | Philipp A | 19 October 2019, 18:59:42 UTC | tl doc fixes (#880) | 19 October 2019, 18:59:42 UTC |
| 2cb54f0 | Philipp A | 19 October 2019, 17:21:21 UTC | Update pp docs (#879) | 19 October 2019, 17:21:21 UTC |
| f112719 | Philipp A | 19 October 2019, 14:12:02 UTC | Add and use bright logo | 19 October 2019, 14:12:02 UTC |
| 5dd8a72 | Philipp A | 18 October 2019, 18:12:55 UTC | Style | 18 October 2019, 18:12:55 UTC |
| 18fd777 | Philipp A | 18 October 2019, 18:11:05 UTC | Install typing_extensions in docs | 18 October 2019, 18:11:05 UTC |
| 7fec83f | Philipp A | 18 October 2019, 15:52:38 UTC | First docstring line can’t contain references | 18 October 2019, 15:52:38 UTC |
| 172a1a4 | Philipp A | 18 October 2019, 15:15:49 UTC | Fixed scvelo inventory URL | 18 October 2019, 15:15:49 UTC |
| f539870 | Philipp A | 18 October 2019, 15:12:14 UTC | Use typing.Literal (#878) | 18 October 2019, 15:12:14 UTC |
| ffb0685 | Philipp A | 18 October 2019, 11:17:52 UTC | Low hanging formatting fruit (#877) | 18 October 2019, 11:17:52 UTC |
| 724da7d | Fidel Ramirez | 10 October 2019, 14:47:54 UTC | Merge pull request #869 from fidelram/fix_pl_paga Fix pl paga when adata.uns color list was not set | 10 October 2019, 14:47:54 UTC |
| f572f88 | Fidel Ramírez | 10 October 2019, 11:07:20 UTC | remove unneeded imports and added a couple of lines before functions to fulfull Pep8 | 10 October 2019, 11:07:20 UTC |
| 2cc2e82 | Fidel Ramírez | 10 October 2019, 10:47:50 UTC | fix test errors | 10 October 2019, 10:47:50 UTC |
| 5ed73b0 | Fidel Ramírez | 10 October 2019, 09:31:22 UTC | update paga test | 10 October 2019, 09:31:22 UTC |
| f5e4ae9 | Fidel Ramírez | 10 October 2019, 09:28:48 UTC | remove redundant code in _utils and move code from scatterplots to _utils. Rename color by the current number of colors | 10 October 2019, 09:28:48 UTC |
| e4dd5ee | Fidel Ramirez | 09 October 2019, 14:56:24 UTC | Merge pull request #867 from fidelram/fix_density_title fix repeated title when plotting multiple panels | 09 October 2019, 14:56:24 UTC |
| 61e6460 | Fidel Ramírez | 09 October 2019, 14:40:43 UTC | fix repeated title when plotting multiple panels | 09 October 2019, 14:40:43 UTC |
| be2401e | Isaac Virshup | 08 October 2019, 02:50:59 UTC | Change _get_mean_var dispatch * Changed to @flying-sheep's implementation * Added axis argument to _get_mean_var * Added test cases for other axes | 08 October 2019, 08:34:48 UTC |
| 0f9f71e | Isaac Virshup | 01 October 2019, 07:46:43 UTC | Revert dense mean var, format, & simplify | 08 October 2019, 08:34:48 UTC |
| 135bed1 | Isaac Virshup | 01 October 2019, 05:30:01 UTC | Improve accuracy and speed of _get_meanvar | 08 October 2019, 08:34:48 UTC |
| e46f89b | Krzysztof Polanski | 07 October 2019, 10:11:54 UTC | update bbknn reference (#861) | 07 October 2019, 10:11:54 UTC |
| d8f32c0 | Fabian Rost | 02 October 2019, 10:17:13 UTC | update ValueError message in pca (#858) replaced the deprecated filter_gene_dispersion with highly_variable_genes | 02 October 2019, 10:17:13 UTC |
| 76b5a28 | Philipp A | 02 October 2019, 09:46:43 UTC | better link in readme | 02 October 2019, 09:46:43 UTC |
| d9c6f0a | Tom White | 25 September 2019, 16:31:32 UTC | Add ability to run nearest neighbors, umap and louvain on a GPU using RAPIDS (#830) | 25 September 2019, 16:31:32 UTC |
| b9dbe36 | Isaac Virshup | 23 September 2019, 09:02:09 UTC | Add note about compilation time to qc metrics | 25 September 2019, 09:06:25 UTC |
| 3a6c9db | Isaac Virshup | 17 September 2019, 11:07:57 UTC | Add warning for qc_metric parallel | 25 September 2019, 09:06:25 UTC |
| 0e6c66e | Isaac Virshup | 16 September 2019, 05:21:38 UTC | Use cacheing and parallelism for qc metrics | 25 September 2019, 09:06:25 UTC |
| 0612475 | Philipp A | 23 September 2019, 11:51:04 UTC | Fix badge | 23 September 2019, 11:51:04 UTC |
| fd7df3e | Philipp A | 23 September 2019, 11:37:15 UTC | Better conda badge | 23 September 2019, 11:37:15 UTC |
| e890764 | Philipp A | 18 September 2019, 20:43:40 UTC | Cleaned up unused utils | 18 September 2019, 20:43:40 UTC |
| cd69440 | Philipp A | 18 September 2019, 13:30:15 UTC | Fix many plotting idiosyncrasies. Fixes #850 | 18 September 2019, 13:30:15 UTC |
| 44320ea | Philipp A | 17 September 2019, 10:16:27 UTC | Add cache_compression setting (#847) | 17 September 2019, 10:16:27 UTC |
| 1ec61f4 | Koncopd | 17 September 2019, 08:34:41 UTC | fix zheng17 and recipe_seurat (#816) | 17 September 2019, 08:34:41 UTC |
| ee1f2c6 | Isaac Virshup | 17 September 2019, 03:58:57 UTC | Fix h5py doc link h5py docs don't do https. | 17 September 2019, 04:04:45 UTC |
| b073cb8 | Philipp A | 16 September 2019, 14:41:01 UTC | Added h5py intersphinx link | 16 September 2019, 14:41:01 UTC |
| 1875df1 | Philipp A | 16 September 2019, 12:28:49 UTC | added cache_compression kwarg to read() (#831) | 16 September 2019, 12:28:49 UTC |
| 5b5cc08 | Isaac Virshup | 16 September 2019, 11:14:09 UTC | Run static analysis concurrently with tests (#846) | 16 September 2019, 11:14:09 UTC |
| 3c585f7 | Isaac Virshup | 16 September 2019, 06:11:43 UTC | Add release note for queries Additionally some module doc updates. | 16 September 2019, 06:45:59 UTC |
| 178a098 | Philipp A | 14 September 2019, 15:02:33 UTC | blacken everything without too many line changes (#841) | 14 September 2019, 15:02:33 UTC |
| be420bc | Philipp A | 14 September 2019, 14:48:46 UTC | Don’t error if n_top_genes > n_var (#835) * Don’t error if n_top_genes > n_var * Whoops | 14 September 2019, 14:48:46 UTC |
| bb62b33 | Philipp A | 14 September 2019, 12:21:28 UTC | Unify all isinstance calls (#839) | 14 September 2019, 12:21:28 UTC |
| b07d455 | Philipp A | 13 September 2019, 10:09:19 UTC | Added CSS colors | 13 September 2019, 10:09:19 UTC |
| 52e25b5 | Philipp A | 12 September 2019, 13:05:40 UTC | sphinx-autodoc-typehints is fixed | 12 September 2019, 13:05:40 UTC |
| d69832a | MalteDLuecken | 11 September 2019, 15:49:40 UTC | highly_variable_gene batch_key variant fix (#824) | 11 September 2019, 15:49:40 UTC |
| b181ae0 | Gökcen Eraslan | 11 September 2019, 03:55:47 UTC | Add forgotten test image | 11 September 2019, 03:55:47 UTC |
| 6ff5b2c | Gökcen Eraslan | 11 September 2019, 03:49:47 UTC | Fix fontoutline variable overwrite and add tests. | 11 September 2019, 03:49:47 UTC |
| 2060dc4 | Gökçen Eraslan | 10 September 2019, 14:59:21 UTC | Rotate only xticks in sc.pl.violin (#825) | 10 September 2019, 14:59:21 UTC |
| e63c2df | Philipp A | 10 September 2019, 11:20:40 UTC | Added verbosity override | 10 September 2019, 11:20:40 UTC |
| 928d475 | Isaac Virshup | 09 September 2019, 02:07:58 UTC | Don't allow h5py 2.10.0 | 09 September 2019, 02:22:42 UTC |
| 2e1e69b | Philipp A | 06 September 2019, 17:43:38 UTC | Fix matplotlib links | 06 September 2019, 17:43:38 UTC |
| 02140a8 | Philipp A | 06 September 2019, 17:40:42 UTC | Fix weird discrepancy between travis and local | 06 September 2019, 17:40:42 UTC |
| 1bcf492 | Philipp A | 06 September 2019, 17:28:23 UTC | Link to stable AnnData | 06 September 2019, 17:28:44 UTC |
| 1b6d35e | Philipp A | 06 September 2019, 16:55:43 UTC | Adapt to anndata style | 06 September 2019, 16:55:43 UTC |
| 1a5defb | Philipp A | 06 September 2019, 15:01:14 UTC | Adopt changes from PR (Fixes #656) | 06 September 2019, 15:01:14 UTC |
| 26fd770 | Philipp A | 06 September 2019, 14:54:12 UTC | Renamed all used utils to _* | 06 September 2019, 14:54:12 UTC |
| 1851232 | Philipp A | 06 September 2019, 13:12:42 UTC | Better test IDs | 06 September 2019, 13:13:19 UTC |
| 27765ad | Philipp A | 06 September 2019, 13:04:04 UTC | Reenable docs tests | 06 September 2019, 13:04:04 UTC |
| b45e3b0 | Philipp A | 06 September 2019, 12:09:53 UTC | Harmonized docs and params of embedding_density and the embedding plots | 06 September 2019, 12:09:53 UTC |
| 262c9c7 | Philipp A | 06 September 2019, 10:55:33 UTC | Remove defunct _top_genes_visual.py | 06 September 2019, 10:55:33 UTC |
| dff94a5 | Philipp A | 06 September 2019, 10:51:49 UTC | Simplify scatter and its docs | 06 September 2019, 10:52:32 UTC |
| b3921ae | Philipp A | 06 September 2019, 10:47:31 UTC | Fix performance regression caused by | 06 September 2019, 10:47:31 UTC |
| 56e0cb4 | Philipp A | 06 September 2019, 10:43:52 UTC | Only make broken links cause a doc build failure when on readthedocs Errors cause cache invalidation, making sphinx very slow on repeated builds. We want the docs to fail building on rtd (to see errors) but locally warnings are sufficient. | 06 September 2019, 10:43:52 UTC |
| f4d2e91 | Gokcen Eraslan | 06 September 2019, 02:27:58 UTC | Do not overwrite cax variable and add another paga plotting test. | 06 September 2019, 02:27:58 UTC |
| 525c96a | Gokcen Eraslan | 06 September 2019, 01:44:03 UTC | Add obs_key support to PAGA plots and fix the cax parameter. | 06 September 2019, 01:44:03 UTC |
| e657134 | Gökçen Eraslan | 05 September 2019, 14:17:58 UTC | Fix clustermap error due to fillna call in seaborn. (#809) | 05 September 2019, 14:17:58 UTC |
| 0bc37ee | Philipp A | 05 September 2019, 14:11:09 UTC | Completed docs for external module, rm’d defunct rtools, moved external | 05 September 2019, 14:11:09 UTC |
| 320561e | Philipp A | 05 September 2019, 13:49:34 UTC | Moved things belonging to external.pp into there | 05 September 2019, 13:49:34 UTC |
| df5df93 | Philipp A | 05 September 2019, 12:23:55 UTC | Moved external tools to scanpy.external.tl (#814) | 05 September 2019, 12:23:55 UTC |
| 7982dc2 | Philipp A | 05 September 2019, 11:10:31 UTC | Fixed style and docs for datasets | 05 September 2019, 11:10:31 UTC |
| 9275ad3 | Philipp A | 04 September 2019, 21:32:42 UTC | scanpydoc 0.4 | 04 September 2019, 21:32:54 UTC |
| 33e0236 | Félix Raimundo | 04 September 2019, 13:49:27 UTC | Make the dca learning rate accessible from scanpy. (#813) | 04 September 2019, 13:49:27 UTC |
| a194993 | Philipp A | 04 September 2019, 09:49:23 UTC | ranking style fix | 04 September 2019, 09:49:23 UTC |
| e042513 | Philipp A | 04 September 2019, 09:35:01 UTC | Style | 04 September 2019, 09:35:01 UTC |
| eb37b97 | Philipp A | 04 September 2019, 09:23:09 UTC | Adapt coding style guidelines | 04 September 2019, 09:23:09 UTC |
| f7dc704 | Gökçen Eraslan | 04 September 2019, 00:33:12 UTC | Show PCA loadings for genes with lowest loadings (#805) * Add include_lowest option to pca_loadings which allows us to plot genes with negative loadings * Hide xticks if include_lowest is given * Add test. * Fix string components and extend the test * Fix pca_loadsings test after making include_lowest True by default | 04 September 2019, 00:33:12 UTC |
| 0951fa5 | Gökcen Eraslan | 04 September 2019, 00:07:32 UTC | Add PAGA plotting tests | 04 September 2019, 00:14:19 UTC |
