| c9aaafd | Isaac Virshup | 12 November 2020, 12:30:38 UTC | release note | 12 November 2020, 12:31:21 UTC |
| 76cbc69 | Isaac Virshup | 12 November 2020, 07:17:45 UTC | Bump anndata required version for `anndata.concat` | 12 November 2020, 12:31:21 UTC |
| 5330a45 | Isaac Virshup | 12 November 2020, 11:27:46 UTC | formatting | 12 November 2020, 12:25:32 UTC |
| b0b746d | Isaac Virshup | 12 November 2020, 10:32:04 UTC | Update expected image for 3d plots | 12 November 2020, 12:25:32 UTC |
| dad8fca | Isaac Virshup | 12 November 2020, 10:24:26 UTC | Fixes for 3d plots | 12 November 2020, 12:25:32 UTC |
| a8ee1e0 | Daniel Strobl | 10 November 2020, 14:47:28 UTC | Fix download path of pbmc3k_processed (#1472) * Fix download path of pbmc3k_processed * Update release-latest.rst * Update release-latest.rst added newline in release-latest | 10 November 2020, 14:47:28 UTC |
| b7ebfa1 | Gökçen Eraslan | 10 November 2020, 05:30:23 UTC | Add dict input support to sc.queries.enrich (#1488) * Add dict support to sc.queries.enrich * Black | 10 November 2020, 05:30:23 UTC |
| 4b35178 | Corey J. Nolet | 06 November 2020, 05:17:00 UTC | Support random_state in rapids umap (#1474) | 06 November 2020, 05:17:00 UTC |
| 257ddcb | giovp | 03 November 2020, 17:02:41 UTC | add utils for basis key and invert coord for spatial (#1466) | 03 November 2020, 17:02:41 UTC |
| 460d670 | giovp | 02 November 2020, 13:50:39 UTC | update datasets (#1473) | 02 November 2020, 13:50:39 UTC |
| 49d4925 | Isaac Virshup | 30 October 2020, 10:00:42 UTC | Support dict for embedding palette argument (#1392) | 30 October 2020, 10:00:42 UTC |
| 0d25f45 | MalteDLuecken | 28 October 2020, 08:47:10 UTC | Fix default number of genes for marker_genes_overlap (#1464) * fix default of top_n_markers for marker_gene_overlap * don't explicitly set default to ensure adj_p_val and top_n_markers clashes are still dealt with consistently * remove pointless copied line * added release note | 28 October 2020, 08:47:10 UTC |
| 256f594 | Mukund Varma | 24 October 2020, 19:04:15 UTC | `groupby` is converted to a list before adding as dendrogram key (#1465) * don't add groupby as a list to key_added * Update _get_dendrogram_key * typo * Typo * add test * black * address PR remarks | 24 October 2020, 19:04:15 UTC |
| 95017dc | Volker Bergen | 23 October 2020, 09:19:05 UTC | fixes type bug, now tagging exactly n_top_genes (#1456) Due to type conversion, often 1999 genes gets tagged as 'highly_variable' even though n_top_genes is set to 2000. Now, this minor change guarantees that exactly (!) n_top_genes get tagged. | 23 October 2020, 09:19:05 UTC |
| 040e61f | Gregor Sturm | 12 October 2020, 08:28:54 UTC | Update ecosystem.rst | 20 October 2020, 14:40:45 UTC |
| dc9919e | Koncopd | 05 October 2020, 15:01:55 UTC | black test | 16 October 2020, 10:34:46 UTC |
| f82113f | Koncopd | 05 October 2020, 14:14:06 UTC | fix filter defaults in test | 16 October 2020, 10:34:46 UTC |
| 0e6bb91 | Koncopd | 05 October 2020, 12:11:27 UTC | format | 16 October 2020, 10:34:46 UTC |
| fb38f5f | Koncopd | 05 October 2020, 12:10:30 UTC | add test | 16 October 2020, 10:34:46 UTC |
| 711f3df | Koncopd | 05 October 2020, 11:21:57 UTC | rename to _calc_frac | 16 October 2020, 10:34:46 UTC |
| 2e60cdc | Koncopd | 05 October 2020, 11:04:17 UTC | fix raw | 16 October 2020, 10:34:46 UTC |
| 1fcb353 | Koncopd | 05 October 2020, 10:25:23 UTC | get rid of _prepare_dataframe | 16 October 2020, 10:34:46 UTC |
| fdbe840 | Rybakov | 25 August 2020, 14:41:31 UTC | filter_rank_genes_groups uses existing fractions, foldchanges | 16 October 2020, 10:34:46 UTC |
| 64e3ab8 | njbernstein | 09 October 2020, 06:17:19 UTC | Cell hashing method hashsolo for scanpy (#1432) * added hashsholo, a method to demultiplex single cell data, as an external scanpy tool (https://doi.org/10.1016/j.cels.2020.05.010) | 09 October 2020, 06:17:19 UTC |
| 1af9eca | Awni Mousa | 08 October 2020, 09:49:57 UTC | Phenograph supporting Leiden clustering (#1080) * Phenograph supporting Leiden clustering An updated new release of PhenoGraph package now supports Leiden algorithm for community detection. The suggested changes in scanpy/external/tl/_phenograph.py will make the new updates visible in Scanpy as well. Also, the suggested changes include a testing function in scanpy/tests/external/test_phenograph.py, and updated docs. * uodate exposed `n_iterations` for leiden algorithm. * uodate exposed `n_iterations` for leiden algorithm. * update pushing graph distances to `anndata.AnnData.obsp` instead of `uns` * fix docs indentation error * fix docs * update * read the docs fail * read the docs fail * update docs * update docs * update docs * update docs * update docs * update docs * black formatting * added docs/api/scanpy.external.rst | 08 October 2020, 09:49:57 UTC |
| 2bab494 | Awni Mousa | 06 October 2020, 12:54:31 UTC | Update palantir external (#1245) * New wrapper for Palantir * New wrapper for Palantir * New wrapper for Palantir add test * New wrapper for Palantir updates * New wrapper for Palantir data imputation made optional * fix to harmony time points dtype * fix to harmony time points dtype * update * added tl.palantir_results to the docs Co-authored-by: Alex Wolf <f.alex.wolf@gmx.de> Co-authored-by: Gökçen Eraslan <gokcen.eraslan@gmail.com> | 06 October 2020, 12:54:31 UTC |
| 746bc9a | Awni Mousa | 06 October 2020, 12:00:49 UTC | fix to harmony time points dtype (#1248) * fix to harmony time points dtype * fix to harmony time points dtype * Fix to 'time_points' as categorical data error. | 06 October 2020, 12:00:49 UTC |
| 8c88df6 | Philipp A | 05 October 2020, 07:28:25 UTC | Instructions zsh (#1444) | 05 October 2020, 07:28:25 UTC |
| 62bb643 | Fidel Ramirez | 24 September 2020, 06:43:43 UTC | Added missing documentation. Fixed option to set colorbar title. (#1425) | 24 September 2020, 06:43:43 UTC |
| 9df64be | Isaac Virshup | 24 September 2020, 05:25:25 UTC | Add importorskip to test_harmony_integrate | 24 September 2020, 06:36:47 UTC |
| 622895a | Isaac Virshup | 24 September 2020, 05:13:21 UTC | Directly use genome variable | 24 September 2020, 05:29:03 UTC |
| 826874a | Philipp Weiler | 02 September 2020, 10:45:03 UTC | Update readwrite.py Remove the chainging of `list`, `map` and `lambda`. Using `map` together with a `lambda` function and converting it to a list is slower than comparing directly to a `pandas.Series`. | 24 September 2020, 05:29:03 UTC |
| 66a7050 | Adam Gayoso | 23 September 2020, 19:28:47 UTC | update ecosystem (#1421) | 23 September 2020, 19:28:47 UTC |
| 1f02dbd | Philipp Weiler | 23 September 2020, 11:57:10 UTC | Replace `np.matrix` by `np.array` (#1424) The change suppresses PendingDeprecationWarning and follows numpys suggestion to not rely on `np.matrix`. | 23 September 2020, 11:57:10 UTC |
| aeeca1f | Philipp Weiler | 23 September 2020, 11:54:38 UTC | Fix docstrings for rank_genes_groups (#1417) Remove empty line which causes the example terminal commands to be displayed incorrectly. Also, three `>` are preprended to the comment. | 23 September 2020, 11:54:38 UTC |
| 705a14e | Philipp Weiler | 22 September 2020, 15:15:49 UTC | Fix / Unit tests `test_violin` and `test_pbmc3k` (#1422) When using `seaborn==0.11`, the vertical orientation is ignored when only `x` is specified. To orientate the violin plot vertically as before `seaborn.catplot` is used instead of `seaborn.FacetGrid`. | 22 September 2020, 15:15:49 UTC |
| f704f72 | Isaac Virshup | 31 August 2020, 10:28:32 UTC | Bugfix log1p for non-float dense arrays | 02 September 2020, 07:14:13 UTC |
| 43379e0 | Philipp A | 28 August 2020, 13:00:56 UTC | Utilize magic comma in new black update (#1394) | 28 August 2020, 13:00:56 UTC |
| 8829f2b | Isaac Virshup | 25 August 2020, 09:12:47 UTC | Fix docstrings for embedding wrappers | 25 August 2020, 09:56:47 UTC |
| 2679e45 | Isaac Virshup | 21 August 2020, 08:11:07 UTC | Response to feedback from Fidel | 25 August 2020, 09:56:47 UTC |
| 2c37a5c | Isaac Virshup | 21 August 2020, 05:09:49 UTC | Add na_color and na_in_legend parameters to embedding plots. | 25 August 2020, 09:56:47 UTC |
| b7efb0b | Isaac Virshup | 21 August 2020, 05:05:05 UTC | Update embedding plot tests (to squash before merge) | 25 August 2020, 09:56:47 UTC |
| 745f755 | Isaac Virshup | 20 August 2020, 11:47:33 UTC | Add tests for embedding plots with missing values It's quite a few. I might look into reducing the size of the plots/ storing them compressed. Also the test case is a bit cute. | 25 August 2020, 09:56:47 UTC |
| c1636fc | Isaac Virshup | 20 August 2020, 11:44:37 UTC | Fix handling of _missing_color for spatial plots | 25 August 2020, 09:56:47 UTC |
| cdd52af | Isaac Virshup | 19 August 2020, 09:56:42 UTC | Fixes for broken tests Had to make color palette getting work with masking. Led to creation of _get_palette function. | 25 August 2020, 09:56:47 UTC |
| 2f4b5c5 | Isaac Virshup | 19 August 2020, 08:40:13 UTC | Fix categorical legends when values are missing | 25 August 2020, 09:56:47 UTC |
| 80b92f7 | Isaac Virshup | 19 August 2020, 07:06:06 UTC | scatterplots: simplify group handling further | 25 August 2020, 09:56:47 UTC |
| 45b0862 | Isaac Virshup | 19 August 2020, 05:18:49 UTC | scatterplots: Have missing color be used when color=None | 25 August 2020, 09:56:47 UTC |
| 498b757 | Isaac Virshup | 18 August 2020, 05:18:53 UTC | Embeddings show nulls in continuous variables In embeddings this comes up as light gray points, in spatial plots these are transparent. This required adding explicit handling of the color map, and making sure we accepted `nan`s in a few more places. | 25 August 2020, 09:56:47 UTC |
| 785c59a | Isaac Virshup | 17 August 2020, 08:03:23 UTC | Plot missing values under present values in scatter plots This fixes issues with ordering when `groups` argument was used. This was done by consolidating the logic around ordering. Also includes a minor refactor of the code for choosing colors, mainly splitting it into two functions. | 25 August 2020, 09:56:47 UTC |
| a86370c | Isaac Virshup | 04 August 2020, 05:49:25 UTC | Make missing values lightgray in scatterplots | 25 August 2020, 09:56:47 UTC |
| 5c15aa1 | Gökçen Eraslan | 24 August 2020, 18:23:32 UTC | Use iloc for positional slicing in HVG (#1389) | 24 August 2020, 18:23:32 UTC |
| 912e7d0 | Philipp A | 24 August 2020, 14:37:42 UTC | Centralize setup information (#1381) | 24 August 2020, 14:37:42 UTC |
| c9fbe5c | Gökçen Eraslan | 20 August 2020, 22:41:32 UTC | Fix values_to_plot literal (#1384) | 20 August 2020, 22:41:32 UTC |
| 25836d1 | Isaac Virshup | 19 August 2020, 12:03:09 UTC | Temporarily revert flit commits (#1380) This reverts commits: f2efd3ad27ae7c461da2ef5dcd8a6129cd91ca19 4e9496baad3edac7243a0d62cb69a0dbd2b3f0e2 e06d921559b0aa15a9844c40ceb0d72a0ab0bc47 d66a5e4b9c816d526c939ef05b89d188fcfa1444 28aea53ac14e04d1683e6eda568b816977456b5a | 19 August 2020, 12:03:09 UTC |
| f2efd3a | Philipp A | 18 August 2020, 15:45:43 UTC | Add instructions for conda dev install (#1377) | 18 August 2020, 15:45:43 UTC |
| 4e9496b | Philipp A | 18 August 2020, 14:33:51 UTC | Allow JUST symlinking anndata installs (#1378) | 18 August 2020, 14:33:51 UTC |
| e06d921 | Philipp A | 18 August 2020, 08:44:01 UTC | Fix install (#1376) | 18 August 2020, 08:44:01 UTC |
| d66a5e4 | Philipp A | 17 August 2020, 20:50:19 UTC | pytest can also be configured in TOML! (#1375) | 17 August 2020, 20:50:19 UTC |
| 28aea53 | Philipp A | 17 August 2020, 19:20:56 UTC | Switch to flit (#1374) | 17 August 2020, 19:20:56 UTC |
| 5533b64 | Philipp A | 16 August 2020, 20:21:03 UTC | short version of print_versions and print_header (#1373) | 16 August 2020, 20:21:03 UTC |
| 6c16f31 | Alex Wolf | 15 August 2020, 22:27:03 UTC | version 1.6.0 (#1372) * streamline release latest * further fixes | 15 August 2020, 22:27:03 UTC |
| 8611dba | stuartarchibald | 07 August 2020, 13:43:46 UTC | Promote ns from machine int to int64. (#1359) Co-authored-by: Philipp A <flying-sheep@web.de> | 07 August 2020, 13:43:46 UTC |
| 090d577 | Chris Rands | 05 August 2020, 19:57:51 UTC | A few minor style changes via `pyupgrade` (#971) Co-authored-by: Philipp A <flying-sheep@web.de> | 05 August 2020, 19:57:51 UTC |
| f6212ce | Gökçen Eraslan | 01 August 2020, 19:41:24 UTC | Proper string comparison (#1350) | 01 August 2020, 19:41:24 UTC |
| e6474b5 | Joshua Gould | 01 August 2020, 18:52:26 UTC | added cirrocumulus (#1311) Co-authored-by: Gökçen Eraslan <gokcen.eraslan@gmail.com> | 01 August 2020, 18:52:26 UTC |
| b9f3257 | Philipp A | 01 August 2020, 13:40:45 UTC | `print_versions` outputs more, updated GH issue template (#1343) | 01 August 2020, 13:40:45 UTC |
| 2ea9f83 | Fidel Ramirez | 01 August 2020, 05:31:54 UTC | fix missing yticklabels (#1342) * fix missing yticklabels * added `yticklabels` parameter to `sc.pl.stacked_violin()`. * fixed problem with overlapping tick labels and legend * improved formatting of the tick labels | 01 August 2020, 05:31:54 UTC |
| 96bd59d | Philipp A | 31 July 2020, 15:28:28 UTC | Use theme from scanpydoc (#1349) | 31 July 2020, 15:28:28 UTC |
| 4856784 | Isaac Virshup | 31 July 2020, 09:52:47 UTC | Export concat (#1348) | 31 July 2020, 09:52:47 UTC |
| ab9247b | Isaac Virshup | 31 July 2020, 07:18:39 UTC | Shorten _download function | 31 July 2020, 07:54:32 UTC |
| 650c20d | Isaac Virshup | 30 July 2020, 09:19:24 UTC | Register internet test marker, gets rid of warnings | 31 July 2020, 07:54:32 UTC |
| 0da9559 | Isaac Virshup | 30 July 2020, 09:11:36 UTC | Update number of genes for test dataset | 31 July 2020, 07:54:32 UTC |
| 24f77fe | Isaac Virshup | 30 July 2020, 09:05:58 UTC | Rewrite _download As noted in #1334, visium downloads were broken. Setting a header on downloads seems to fix them. We can't use the solution suggested in #1334 since it modifies global state around `urllib`, which is asking for trouble. This unfortunatley means most of the method had to be reimplemeted. The new implementation is based on `urllib.requests.urlretrieve`, but with a modification to let us pass a header. I've also removed the automatic `mkdir(..., parents=True)` from `_download` since typos could result in very messy filesystems. | 31 July 2020, 07:54:32 UTC |
| fc01716 | Alex Wolf | 30 July 2020, 12:18:34 UTC | Organize news section (#1345) * briefer statement * add news file * less wordy * fix articles | 30 July 2020, 12:18:34 UTC |
| 2f160ea | Isaac Virshup | 30 July 2020, 06:16:09 UTC | Minor code cleanup for sc.pl.rank_genes_groups Mostly reducing flow control, moving similar statements together | 30 July 2020, 06:37:04 UTC |
| 4d08f5a | Isaac Virshup | 29 July 2020, 09:29:36 UTC | Update reference figures for tests | 30 July 2020, 06:37:04 UTC |
| 55a57db | Isaac Virshup | 29 July 2020, 07:42:59 UTC | Fix y-axis for rank_genes_groups * Previously min and max were set by full range of scores, not just the ones being plotted. * Also did some minor code simplification. | 30 July 2020, 06:37:04 UTC |
| dc70a14 | Koncopd | 29 July 2020, 20:26:34 UTC | expand test | 29 July 2020, 22:04:05 UTC |
| e95dbcf | Koncopd | 29 July 2020, 18:43:48 UTC | update release notes | 29 July 2020, 22:04:05 UTC |
| 182c245 | Rybakov | 23 July 2020, 14:58:03 UTC | fix test | 29 July 2020, 22:04:05 UTC |
| 29924bd | Rybakov | 23 July 2020, 12:55:11 UTC | test tie corrected pvals | 29 July 2020, 22:04:05 UTC |
| aefd687 | Rybakov | 23 July 2020, 12:19:45 UTC | default values for _RankGenes | 29 July 2020, 22:04:05 UTC |
| dda90b1 | Rybakov | 23 July 2020, 12:11:51 UTC | fix n_genes in correction | 29 July 2020, 22:04:05 UTC |
| 73d590a | Rybakov | 21 July 2020, 15:01:45 UTC | doc for tie_correct | 29 July 2020, 22:04:05 UTC |
| 846446e | Rybakov | 21 July 2020, 14:05:17 UTC | add tie correction | 29 July 2020, 22:04:05 UTC |
| cf98241 | Alex Wolf | 29 July 2020, 15:14:27 UTC | Clean up release notes for v1.6.0 (#1339) * clean up release notes * fix typo * add statement on original references * better wording | 29 July 2020, 15:14:27 UTC |
| d4d373e | Fidel Ramirez | 29 July 2020, 13:39:09 UTC | split BasePlot.show() into show and savefig to match matplotlib style (#1329) * separated functionality of BasePlot.show() as `savefig` and `show` which is more in-line with matplotlib way of working and modified visual parameters to avoid light colored elements to blend with background | 29 July 2020, 13:39:09 UTC |
| debf131 | Isaac Virshup | 29 July 2020, 05:50:31 UTC | Add hvg to release notes | 29 July 2020, 08:12:57 UTC |
| 4ef47fb | Isaac Virshup | 29 July 2020, 05:27:21 UTC | Update nonnegative integer check Minor update, just checking if the type is already an integer, and doing a faster check for positive values. | 29 July 2020, 08:12:57 UTC |
| c8be573 | adamgayoso | 30 June 2020, 05:40:01 UTC | fix nan handling | 29 July 2020, 08:12:57 UTC |
| 3b26ccf | adamgayoso | 30 June 2020, 05:20:54 UTC | better handle nan in merging hvgs in batches seurat v3 | 29 July 2020, 08:12:57 UTC |
| 5859327 | adamgayoso | 29 June 2020, 17:22:37 UTC | skmisc travis | 29 July 2020, 08:12:57 UTC |
| ce008b1 | adamgayoso | 29 June 2020, 16:52:07 UTC | gzip test file | 29 July 2020, 08:12:57 UTC |
| d091c82 | Isaac Virshup | 29 June 2020, 05:43:07 UTC | Fix formatting test | 29 July 2020, 08:12:57 UTC |
| 9a567be | adamgayoso | 17 June 2020, 18:17:19 UTC | update docstrings, uns key added, defaults | 29 July 2020, 08:12:57 UTC |
| c34b043 | adamgayoso | 17 June 2020, 18:07:09 UTC | add util test | 29 July 2020, 08:12:57 UTC |
| 0c0cc3a | adamgayoso | 17 June 2020, 06:37:53 UTC | fix merging with batch key, add batch test | 29 July 2020, 08:12:57 UTC |
| afa19d6 | adamgayoso | 16 June 2020, 22:47:13 UTC | fix plotting function | 29 July 2020, 08:12:57 UTC |
| fb63e4c | adamgayoso | 16 June 2020, 22:32:43 UTC | update check raw data util | 29 July 2020, 08:12:57 UTC |
