| 705b64a | falexwolf | 16 April 2018, 20:27:40 UTC | updated setup to contain versioneer cmdclass and display proper version numbers again | 16 April 2018, 20:27:40 UTC |
| 6ba0615 | falexwolf | 16 April 2018, 17:44:48 UTC | set _sdist to versioneer | 16 April 2018, 17:44:48 UTC |
| 5679f7b | falexwolf | 16 April 2018, 16:39:57 UTC | added statsmodels to conda install | 16 April 2018, 16:40:10 UTC |
| f6726f0 | Alex Wolf | 16 April 2018, 15:43:13 UTC | Merge pull request #124 from gokceneraslan/patch-4 Do not use paga in draw_graph, if use_paga is False | 16 April 2018, 15:43:13 UTC |
| 3160697 | Gökçen Eraslan | 16 April 2018, 15:20:33 UTC | Do not use paga is use_paga is False This fixes the exception that happens in following scenario: sc.tl.louvain(adata) sc.tl.paga(adata) sc.pl.paga(adata) sc.tl.draw_graph(adata) Since there is no else statement for use_paga check, ig_layout is not defined. | 16 April 2018, 15:20:33 UTC |
| 33bccc7 | falexwolf | 11 April 2018, 08:51:00 UTC | clarified UMAP docs | 11 April 2018, 08:56:47 UTC |
| e78062a | falexwolf | 10 April 2018, 08:20:55 UTC | added more extensive explanation on diffusion maps | 10 April 2018, 08:20:55 UTC |
| 182d7e2 | falexwolf | 09 April 2018, 13:19:35 UTC | fix paga auxiliary functions | 09 April 2018, 13:19:35 UTC |
| 24395dc | falexwolf | 09 April 2018, 13:09:09 UTC | fixed bug just introduced for dense matrices | 09 April 2018, 13:09:09 UTC |
| f27a69e | falexwolf | 09 April 2018, 12:25:23 UTC | fix array shape bug for neighbors method=='gauss' and large matries | 09 April 2018, 12:25:23 UTC |
| 073b3e6 | falexwolf | 09 April 2018, 11:12:57 UTC | added a few additional colors and a check for that these are used | 09 April 2018, 11:12:57 UTC |
| 683e1f0 | falexwolf | 09 April 2018, 07:59:53 UTC | updated DPT distance docs | 09 April 2018, 07:59:53 UTC |
| 3e8d390 | falexwolf | 08 April 2018, 22:21:44 UTC | updated docs | 08 April 2018, 22:21:44 UTC |
| 36bb3ba | falexwolf | 08 April 2018, 22:04:55 UTC | removed aga reexports | 08 April 2018, 22:04:55 UTC |
| 83e16c3 | falexwolf | 08 April 2018, 22:02:47 UTC | removed 'recompute' occurances from scanpy | 08 April 2018, 22:02:47 UTC |
| 72db9b7 | falexwolf | 08 April 2018, 21:59:43 UTC | remove redundant aga | 08 April 2018, 21:59:43 UTC |
| abb9c97 | falexwolf | 08 April 2018, 21:57:57 UTC | prettified docs and removed redundant parameters of pca | 08 April 2018, 21:57:57 UTC |
| 338bc37 | falexwolf | 08 April 2018, 20:38:37 UTC | updated numpydoc version | 08 April 2018, 20:38:37 UTC |
| aeec6a3 | falexwolf | 07 April 2018, 10:57:31 UTC | readded adjustment of dpi for saving figures | 07 April 2018, 10:57:31 UTC |
| 73fba0a | Alex Wolf | 07 April 2018, 07:39:55 UTC | Merge pull request #118 from iandriver/master savefig with bbox_inches = 'tight' | 07 April 2018, 07:39:55 UTC |
| dc1c49e | Ian Driver | 06 April 2018, 23:37:34 UTC | savefig with bbox_inches = 'tight' No longer cuts off figure text at edges | 06 April 2018, 23:37:34 UTC |
| c3c2df8 | Alex Wolf | 05 April 2018, 12:02:33 UTC | Merge pull request #116 from theislab/pypi-badge Update PyPI badge | 05 April 2018, 12:02:33 UTC |
| 2d86776 | Philipp A | 05 April 2018, 09:43:55 UTC | Update PyPI badge The new one is smaller, because it doesn’t say “package”. It’s also blue which shows it’s not a build status | 05 April 2018, 09:43:55 UTC |
| b52b41e | Alex Wolf | 03 April 2018, 08:28:55 UTC | Merge pull request #114 from gokceneraslan/master Make diffusion maps compatible with new Neighbors class | 03 April 2018, 08:28:55 UTC |
| 3633801 | Gökcen Eraslan | 01 April 2018, 11:18:19 UTC | Fix diffusion maps | 01 April 2018, 11:18:19 UTC |
| 207dbe4 | falexwolf | 31 March 2018, 17:10:20 UTC | added info about cachedir | 31 March 2018, 17:10:20 UTC |
| 024b5e1 | falexwolf | 31 March 2018, 16:48:02 UTC | updated release notes | 31 March 2018, 16:48:02 UTC |
| 0fd18c7 | falexwolf | 30 March 2018, 00:34:42 UTC | updated release notes | 30 March 2018, 00:34:42 UTC |
| 4f134f0 | falexwolf | 30 March 2018, 00:24:35 UTC | updated release notes | 30 March 2018, 00:24:35 UTC |
| 701aaec | falexwolf | 29 March 2018, 23:17:25 UTC | updated installation notes | 29 March 2018, 23:17:25 UTC |
| cf395be | falexwolf | 29 March 2018, 23:08:05 UTC | version 1.0 | 29 March 2018, 23:08:05 UTC |
| 16b4ee7 | falexwolf | 29 March 2018, 22:41:37 UTC | docs fixes | 29 March 2018, 22:41:37 UTC |
| 7975f07 | Alex Wolf | 29 March 2018, 22:32:06 UTC | Merge pull request #113 from theislab/version1 Version1 | 29 March 2018, 22:32:06 UTC |
| ffd78ae | falexwolf | 29 March 2018, 22:31:29 UTC | test release notes | 29 March 2018, 22:31:29 UTC |
| 5a41894 | falexwolf | 29 March 2018, 21:32:45 UTC | updated anndata requirement to 0.5.8 | 29 March 2018, 21:32:45 UTC |
| 42eb1a7 | falexwolf | 29 March 2018, 21:23:50 UTC | minor modifications | 29 March 2018, 21:23:50 UTC |
| 8be2e4b | falexwolf | 29 March 2018, 20:55:11 UTC | changed time formatting | 29 March 2018, 20:55:11 UTC |
| c2f6297 | falexwolf | 29 March 2018, 11:34:21 UTC | fixed bug in recipes | 29 March 2018, 11:34:21 UTC |
| ff06634 | falexwolf | 29 March 2018, 11:11:19 UTC | added timing to zheng17 recipe | 29 March 2018, 11:11:19 UTC |
| e0bb2bd | falexwolf | 29 March 2018, 10:38:13 UTC | renamed settings.savefigs to settings.autosave | 29 March 2018, 10:38:13 UTC |
| bfae2d2 | falexwolf | 29 March 2018, 10:27:55 UTC | prettified formatting of savefig | 29 March 2018, 10:27:55 UTC |
| 2bd3883 | falexwolf | 29 March 2018, 10:23:09 UTC | few fixes | 29 March 2018, 10:23:09 UTC |
| 2dbf2e7 | falexwolf | 29 March 2018, 10:04:51 UTC | check whether 'savefig.dpi' is integer | 29 March 2018, 10:04:51 UTC |
| eaa011f | falexwolf | 28 March 2018, 23:56:24 UTC | do not require psutil | 28 March 2018, 23:56:24 UTC |
| b3b1358 | falexwolf | 28 March 2018, 22:04:43 UTC | some fixes in plotting | 28 March 2018, 22:04:43 UTC |
| eaaa3a5 | falexwolf | 28 March 2018, 22:04:19 UTC | default n_neighbors to 15 | 28 March 2018, 22:04:19 UTC |
| f8c8665 | falexwolf | 28 March 2018, 21:04:33 UTC | fixed paga support of draw_graph | 28 March 2018, 21:04:33 UTC |
| 104a41d | falexwolf | 28 March 2018, 20:19:53 UTC | normalize with geom mean in paga | 28 March 2018, 20:19:53 UTC |
| e15f8c0 | falexwolf | 28 March 2018, 19:02:56 UTC | added random_state to neighbors | 28 March 2018, 19:02:56 UTC |
| 6bac486 | falexwolf | 28 March 2018, 17:09:38 UTC | fixed all paga related issues | 28 March 2018, 17:09:38 UTC |
| baf32de | falexwolf | 28 March 2018, 15:44:45 UTC | amended reclustering with louvain and restrict_to | 28 March 2018, 15:44:45 UTC |
| 338073d | falexwolf | 27 March 2018, 12:12:38 UTC | updated requirements | 27 March 2018, 12:12:38 UTC |
| 5627470 | falexwolf | 27 March 2018, 12:09:37 UTC | fixed two little bugs | 27 March 2018, 12:09:37 UTC |
| 7801a09 | Alex Wolf | 27 March 2018, 10:40:46 UTC | Merge pull request #112 from gokceneraslan/patch-3 Fix NoneType check in plotting/anndata.py | 27 March 2018, 10:40:46 UTC |
| 6901cf4 | Gökçen Eraslan | 27 March 2018, 10:03:54 UTC | Fix NoneType check in plotting/anndata.py `clustermap` raises an exception when an `obs_keys` argument is not provided, because None is not a type. | 27 March 2018, 10:03:54 UTC |
| 073bab6 | falexwolf | 27 March 2018, 09:00:23 UTC | cleaned up datasets | 27 March 2018, 09:00:23 UTC |
| db94dbd | falexwolf | 27 March 2018, 08:28:32 UTC | fixed interfaces of graph tools | 27 March 2018, 08:28:36 UTC |
| c5ff4fa | Alex Wolf | 27 March 2018, 08:28:00 UTC | Merge pull request #111 from gokceneraslan/master Fix dpt_scatter file saving. | 27 March 2018, 08:28:00 UTC |
| 723dc16 | Gökcen Eraslan | 26 March 2018, 18:52:43 UTC | Fix dpt_scatter file saving. | 26 March 2018, 18:52:43 UTC |
| fd9cb4c | falexwolf | 26 March 2018, 14:48:42 UTC | fixed tests | 26 March 2018, 14:48:42 UTC |
| cfef837 | falexwolf | 26 March 2018, 14:37:23 UTC | almost fixed tests | 26 March 2018, 14:37:23 UTC |
| 2e4b342 | falexwolf | 26 March 2018, 14:25:17 UTC | moved all rexports to api module | 26 March 2018, 14:25:17 UTC |
| f18def3 | falexwolf | 26 March 2018, 14:20:53 UTC | renamed sga to paga | 26 March 2018, 14:20:53 UTC |
| 1b92d5f | falexwolf | 23 March 2018, 20:20:06 UTC | large bunch of amendments | 23 March 2018, 20:20:06 UTC |
| e1737c5 | falexwolf | 23 March 2018, 16:30:40 UTC | fixed width of colorbars | 23 March 2018, 16:30:40 UTC |
| b44a119 | falexwolf | 22 March 2018, 15:16:11 UTC | harmonized knn: seurat, moignard, paul work | 22 March 2018, 15:16:11 UTC |
| 011bf6e | falexwolf | 22 March 2018, 14:53:11 UTC | harmonized knn treatment 2, beyond tests for large data | 22 March 2018, 14:53:11 UTC |
| 88e35be | falexwolf | 22 March 2018, 11:22:28 UTC | drafted release notes | 22 March 2018, 11:22:28 UTC |
| d9da9d8 | falexwolf | 22 March 2018, 11:22:15 UTC | harmonized knn treatment | 22 March 2018, 11:22:15 UTC |
| 781857f | falexwolf | 22 March 2018, 10:42:40 UTC | added tests for neighbors for gauss and umap methods | 22 March 2018, 10:42:40 UTC |
| ef8f4e8 | falexwolf | 21 March 2018, 12:53:05 UTC | hack anndata version for pytest | 21 March 2018, 12:53:05 UTC |
| 17aed47 | falexwolf | 21 March 2018, 11:06:41 UTC | prettified violin plots | 21 March 2018, 11:06:41 UTC |
| d8129ed | falexwolf | 21 March 2018, 10:28:36 UTC | fixed imports in umap copy | 21 March 2018, 10:28:36 UTC |
| d7d366c | falexwolf | 21 March 2018, 10:11:36 UTC | fixed conda ci setup | 21 March 2018, 10:11:36 UTC |
| f068937 | falexwolf | 21 March 2018, 02:04:36 UTC | removed cython, cleaned up setup.py | 21 March 2018, 02:04:36 UTC |
| b33aee8 | falexwolf | 21 March 2018, 01:58:06 UTC | added conda to travis ci | 21 March 2018, 01:58:06 UTC |
| abf6262 | falexwolf | 21 March 2018, 01:42:58 UTC | prettified docs of rank_genes_groups | 21 March 2018, 01:42:58 UTC |
| 196472d | falexwolf | 21 March 2018, 01:28:25 UTC | added numba install to travis | 21 March 2018, 01:28:25 UTC |
| 2fdc318 | falexwolf | 21 March 2018, 01:02:38 UTC | removed rexport of UMAP in __init__ | 21 March 2018, 01:02:38 UTC |
| 6f4da73 | falexwolf | 21 March 2018, 00:58:08 UTC | changed default key for louvain to \'louvain\' | 21 March 2018, 00:58:08 UTC |
| 57161ec | falexwolf | 21 March 2018, 00:48:40 UTC | scanpy no longer modifies rcParams upon import | 21 March 2018, 00:48:40 UTC |
| ad48860 | falexwolf | 19 March 2018, 17:09:07 UTC | towards scanpy 1.0 | 21 March 2018, 00:19:11 UTC |
| db515ab | falexwolf | 19 March 2018, 14:03:36 UTC | reintroduced n_pcs parameter | 21 March 2018, 00:19:11 UTC |
| a6cf100 | falexwolf | 19 March 2018, 12:55:44 UTC | amended use of UMAP as graph visualization | 21 March 2018, 00:19:11 UTC |
| a3dc072 | falexwolf | 19 March 2018, 00:56:42 UTC | restructured neighbors and all other tools to work with umap | 21 March 2018, 00:19:11 UTC |
| 6d735f5 | falexwolf | 19 March 2018, 00:56:17 UTC | added a copy of umap | 21 March 2018, 00:19:11 UTC |
| 9ec1e2c | falexwolf | 18 March 2018, 13:04:35 UTC | removed command-line interface | 21 March 2018, 00:19:11 UTC |
| 99c7869 | falexwolf | 14 March 2018, 22:05:43 UTC | added umap as an option for computing neighbors | 21 March 2018, 00:19:11 UTC |
| f075cda | falexwolf | 14 March 2018, 22:05:20 UTC | prettified logging module | 21 March 2018, 00:19:11 UTC |
| 3108f3e | falexwolf | 12 March 2018, 16:04:38 UTC | simplest model for sga | 21 March 2018, 00:19:11 UTC |
| e0075bb | falexwolf | 12 March 2018, 00:46:43 UTC | sga works for minimal examples | 21 March 2018, 00:19:11 UTC |
| 829fb5a | falexwolf | 11 March 2018, 21:59:06 UTC | update requirements | 21 March 2018, 00:19:11 UTC |
| 3ea2909 | falexwolf | 09 March 2018, 21:01:40 UTC | towards sga | 21 March 2018, 00:19:11 UTC |
| dd72539 | falexwolf | 09 March 2018, 19:42:41 UTC | updated choose_representation | 21 March 2018, 00:19:11 UTC |
| 490482d | falexwolf | 09 March 2018, 17:24:03 UTC | replaced option n_pcs with use_rep | 21 March 2018, 00:19:11 UTC |
| cb3ecc9 | falexwolf | 08 March 2018, 13:54:52 UTC | fixed trivial bug in neighbors | 21 March 2018, 00:19:11 UTC |
| 6098dad | falexwolf | 06 March 2018, 13:11:52 UTC | prettified Neighbors API | 21 March 2018, 00:19:11 UTC |
| f751451 | falexwolf | 06 March 2018, 11:43:12 UTC | fixes in aga_graph plotting | 21 March 2018, 00:19:11 UTC |
| 845e50e | falexwolf | 06 March 2018, 01:45:41 UTC | updated aga_graph | 21 March 2018, 00:19:11 UTC |
| 5007f97 | falexwolf | 06 March 2018, 00:30:29 UTC | added seurat preprocessing recipe | 21 March 2018, 00:19:11 UTC |
