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12 June 2023, 04:30:47 UTC
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00cc0cf MeeseeksMachine 24 February 2021, 07:21:27 UTC Backport PR #1683: Update release notes for 1.7.1 (#1686) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 24 February 2021, 07:21:27 UTC
df06682 MeeseeksMachine 24 February 2021, 05:43:17 UTC Backport PR #1655: Drop passing of **kwds (#1681) Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 24 February 2021, 05:43:17 UTC
65b8a29 MeeseeksMachine 22 February 2021, 14:37:22 UTC Backport PR #1676: More twitter handles in key_contributors (#1677) Co-authored-by: Gökçen Eraslan <gokcen.eraslan@gmail.com> 22 February 2021, 14:37:22 UTC
fe3cd51 MeeseeksMachine 22 February 2021, 10:10:29 UTC Backport PR #1659: Fix passing of arguments between scrublet routines (#1674) Co-authored-by: Jonathan Manning <jmanning@ebi.ac.uk> 22 February 2021, 10:10:29 UTC
7954e6b MeeseeksMachine 19 February 2021, 06:11:12 UTC Backport PR #1654: Fix timeseries plot traceback (#1668) 19 February 2021, 06:11:12 UTC
53f7dba MeeseeksMachine 19 February 2021, 04:09:20 UTC Backport PR #1628: Release notes reorganization (#1665) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 19 February 2021, 04:09:20 UTC
8685872 MeeseeksMachine 10 February 2021, 09:32:56 UTC Backport PR #1638: Fix failing CI for scanorama and python3.6 (#1641) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 10 February 2021, 09:32:56 UTC
4dddeb3 MeeseeksMachine 10 February 2021, 09:18:11 UTC Backport PR #1637: Fix sc.get.obs_df when keys not passed (#1639) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 10 February 2021, 09:18:11 UTC
96ccd02 MeeseeksMachine 10 February 2021, 07:07:43 UTC Backport PR #1614: fixes dendrogram issue #1228 (#1635) Co-authored-by: Fidel Ramirez <fidel.ramirez@gmail.com> 10 February 2021, 07:07:43 UTC
242ada2 MeeseeksMachine 03 February 2021, 05:39:29 UTC Backport PR #1623: Release note for #1583 and update release date (#1624) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 03 February 2021, 05:39:29 UTC
9571356 Isaac Virshup 02 February 2021, 10:43:16 UTC Merge pull request #1622 from meeseeksmachine/auto-backport-of-pr-1621-on-1.7.x Backport PR #1621 on branch 1.7.x (Get cleanup) 02 February 2021, 10:43:16 UTC
eea2af2 Isaac Virshup 02 February 2021, 10:30:15 UTC Backport PR #1621: Get cleanup 02 February 2021, 10:30:26 UTC
0591634 Isaac Virshup 02 February 2021, 03:53:36 UTC Backport ingest fix (#1618) * fix ingest for umap 0.5 * rm block on umap 0.5 * add fix to release notes * fix formatting * Release note Co-authored-by: Koncopd <koncopd@gmail.com> 02 February 2021, 03:53:36 UTC
fad82a0 MeeseeksMachine 02 February 2021, 02:55:37 UTC Backport PR #1583: Allow plots to use adata.obs index as groupby (#1617) Co-authored-by: Fidel Ramirez <fidel.ramirez@gmail.com> 02 February 2021, 02:55:37 UTC
e1ed250 MeeseeksMachine 27 January 2021, 12:39:26 UTC Backport PR #1603: Address issues with heatmaps reported in #1591 (#1610) Co-authored-by: Fidel Ramirez <fidel.ramirez@gmail.com> 27 January 2021, 12:39:26 UTC
764619d MeeseeksMachine 27 January 2021, 10:51:07 UTC Backport PR #1608: Remove dependency on scvelo for doc builds (#1609) 27 January 2021, 10:51:07 UTC
1069451 MeeseeksMachine 25 January 2021, 03:40:15 UTC Backport PR #1602: add twine check to azure CI + 3.8 matrix (#1607) Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> 25 January 2021, 03:40:15 UTC
ac89e59 MeeseeksMachine 19 January 2021, 11:29:07 UTC Backport PR #1589: fix sc.tl.umap for umap-0.5 (#1598) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 19 January 2021, 11:29:07 UTC
edc868c MeeseeksMachine 19 January 2021, 03:23:09 UTC Backport PR #1595: Update sam params (#1597) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 19 January 2021, 03:23:09 UTC
12f4999 Isaac Virshup 17 January 2021, 11:27:38 UTC Backport #1592 (#1594) 17 January 2021, 11:27:38 UTC
6055f44 Isaac Virshup 14 January 2021, 05:41:40 UTC Add note about `twine check` to release guide 14 January 2021, 06:10:30 UTC
0a68287 Isaac Virshup 14 January 2021, 05:35:45 UTC Fix authors field in pyproject.toml pypi doesn't like it when authors (or anything before long_description) has new lines. toml has different rules for single and double tick strings. Can't escape in single tick strings. 14 January 2021, 06:10:30 UTC
546f206 Isaac Virshup 14 January 2021, 04:12:53 UTC Prep 1.7.0rc1 (#1582) * Update release note * bump date for rebuild 14 January 2021, 04:12:53 UTC
1878644 Isaac Virshup 13 January 2021, 07:54:15 UTC Remember to close figures, and not show them 13 January 2021, 09:40:05 UTC
51fb1f9 Isaac Virshup 13 January 2021, 07:03:51 UTC Fix section heading 13 January 2021, 09:40:05 UTC
a4bc6ad Isaac Virshup 13 January 2021, 06:38:55 UTC Updated other embedding plot tests 13 January 2021, 09:40:05 UTC
fd1f956 Isaac Virshup 13 January 2021, 05:11:34 UTC Update parameterized plotting results (oof) 13 January 2021, 09:40:05 UTC
7b0fc2b Isaac Virshup 13 January 2021, 04:19:02 UTC Docs 13 January 2021, 09:40:05 UTC
0f55122 Isaac Virshup 12 January 2021, 08:59:31 UTC Many orthogonality tests for sc.pl.spatial * Test that manually providing arguments is equivalent to extracting them * Tests for na_color argument behaviour * Test crop_coord behaves equivalenlty with different scale factors * Move spatial plot tests to test_embedding_plots * Existing spatial plot tests (with saved examples) need to be updated still. This is due to the change in how crop_coord is handled. 13 January 2021, 09:40:05 UTC
ef62e93 Isaac Virshup 12 January 2021, 08:55:07 UTC Simplify argument handling a bit more, enable scaling of crop_coord * crop_coord now scaled by scale factor * "lightgray" no longer disallowed for na_color when there is an image being plotted * Handling of library id, spatial_data moved into checking function * Fixed bug where `basis` argument was no actually used 13 January 2021, 09:40:05 UTC
3e02a27 Isaac Virshup 12 January 2021, 05:57:32 UTC Initial argument handling refactor for sc.pl.spatial * New argument `size_spot`, required if the spot size cannot be determined from metadata * Instead of one large argument validation function, I've split it out into multiple checks. Each check should have a smaller required set of arguments. * Refactored how crop_coords works so the size_factor will effect it. This currently is disabled so tests don't break. Changes how coordinates are cropped by default to defer to matplotlib, and makes crop_coords behave consistently across img resolutions. 13 January 2021, 09:40:05 UTC
10dff0a giovp 06 January 2021, 12:00:42 UTC black 13 January 2021, 09:40:05 UTC
b6320c0 giovp 06 January 2021, 10:47:19 UTC black 13 January 2021, 09:40:05 UTC
566180d giovp 06 January 2021, 09:47:46 UTC add test for ext image 13 January 2021, 09:40:05 UTC
46278fb giovp 06 January 2021, 09:27:44 UTC minor fix docs 13 January 2021, 09:40:05 UTC
cad0612 giovp 06 January 2021, 09:25:20 UTC add docs 13 January 2021, 09:40:05 UTC
55a5b42 giovp 23 December 2020, 15:05:49 UTC minor change names 13 January 2021, 09:40:05 UTC
97648b1 giovp 23 December 2020, 14:53:55 UTC refactoring, bring process image outside embedding 13 January 2021, 09:40:05 UTC
6c07990 giovp 19 December 2020, 09:44:34 UTC comments 13 January 2021, 09:40:05 UTC
307a953 giovp 18 December 2020, 22:10:34 UTC fixed logic, _process_image outside embedding, handle reverse axis 13 January 2021, 09:40:05 UTC
f29df59 giovp 09 December 2020, 10:35:16 UTC fix docs 13 January 2021, 09:40:05 UTC
4f40e40 giovp 09 December 2020, 10:33:34 UTC update on logic and tests 13 January 2021, 09:40:05 UTC
f6b2580 giovp 07 December 2020, 11:20:55 UTC fix #1534 , improve logic and add tests 13 January 2021, 09:40:05 UTC
7180440 giovp 07 December 2020, 09:18:37 UTC fix logic to account for visium and non visium 13 January 2021, 09:40:05 UTC
1b0d39e giovp 27 November 2020, 17:41:38 UTC add error in case adata.uns[spatial] is not empty because of graph construction 13 January 2021, 09:40:05 UTC
ce0ee87 giovp 27 November 2020, 15:23:45 UTC check for spatial and not onyl for library id 13 January 2021, 09:40:05 UTC
7d2cb65 giovp 27 November 2020, 14:17:51 UTC add comments to code to explain logic 13 January 2021, 09:40:05 UTC
5d94d6a giovp 27 November 2020, 14:14:03 UTC fix logic for empty library_id and images 13 January 2021, 09:40:05 UTC
f3db32a Isaac Virshup 12 January 2021, 01:58:35 UTC Add verioning/ backporting docs (#1575) 12 January 2021, 01:58:35 UTC
0042449 Isaac Virshup 12 January 2021, 01:57:57 UTC Update release notes for 1.7.0 (#1569) * Update release notes for 1.7.0 Co-authored-by: giovp <giov.pll@gmail.com> 12 January 2021, 01:57:57 UTC
cea278d Alex Wolf 07 January 2021, 09:38:42 UTC Update the News section (#1571) * Update news.rst * fixed typos * updated styling * only first 3 news sections * add news to index * simplify heading of contributing * update index * add heading * changed order 07 January 2021, 09:38:42 UTC
e60c7cb Galen Xing 05 January 2021, 09:21:58 UTC add deprecation warning for scvi and pin version (#1554) * add deprecation warning and update min version scvi * change to futurewarning * Release note Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 05 January 2021, 09:21:58 UTC
b87ccb1 Isaac Virshup 05 January 2021, 08:40:10 UTC Better CI test results (#1564) Make azure testing better * Stop getting all the warning pollution from pytest-azurepipelines * Generate and upload test results manually * Generate test coverage * typo * pytest colors on azure 05 January 2021, 08:40:10 UTC
6ab348d Isaac Virshup 17 December 2020, 07:25:42 UTC Regression test for when use_raw=None with sc.pl.violin 05 January 2021, 07:16:23 UTC
1da9e9c Isaac Virshup 17 December 2020, 07:04:05 UTC Normalize how `use_raw` argument is checked 05 January 2021, 07:16:23 UTC
b29be66 Isaac Virshup 17 December 2020, 07:02:54 UTC Remove checks for use_raw when it's not needed In these cases it's checked downstream anyways (though it might be best to check these things upstream) 05 January 2021, 07:16:23 UTC
b069254 brianhie 05 January 2021, 07:12:05 UTC Add Scanorama integration to external API (#1332) * adding modified files following harmony example * add numpy import * fix docstring * make suggested reformatting changes * make requested changes * fix text * add github link to docstring * change test to smaller dataset * Add scanorama to azure testing * Scrublet for azurepipelines Co-authored-by: Brian Hie <brianhie@mit.edu> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 05 January 2021, 07:12:05 UTC
b9b4b93 Koncopd 24 December 2020, 17:25:19 UTC delete cached rp_forest 04 January 2021, 16:16:52 UTC
1c924db Isaac Virshup 04 January 2021, 04:14:54 UTC Accommodate pandas 1.2.0 in matrix plot test (#1562) 04 January 2021, 04:28:58 UTC
54351c0 Isaac Virshup 04 January 2021, 03:49:33 UTC Show installed versions on azure 04 January 2021, 04:28:58 UTC
ff9a9b5 Isaac Virshup 04 January 2021, 03:43:25 UTC Update github-based contributing docs 04 January 2021, 04:28:58 UTC
17338fd Isaac Virshup 04 January 2021, 03:38:47 UTC Release note 04 January 2021, 04:28:58 UTC
97870ad Isaac Virshup 04 January 2021, 03:26:38 UTC Double backtick to single + minor doc workflow additions 04 January 2021, 04:28:58 UTC
e40c29d Alex Wolf 21 December 2020, 09:27:10 UTC Update index.rst 04 January 2021, 04:28:58 UTC
0133fa2 Isaac Virshup 21 December 2020, 08:50:02 UTC Fix some organization in testing docs 04 January 2021, 04:28:58 UTC
7a60e2b Isaac Virshup 21 December 2020, 08:45:12 UTC Add dev environment instructions 04 January 2021, 04:28:58 UTC
85046a4 Isaac Virshup 21 December 2020, 08:19:51 UTC Added to documentation guide 04 January 2021, 04:28:58 UTC
4e2884a Isaac Virshup 21 December 2020, 07:40:38 UTC Added contributing workflow, added to associated content 04 January 2021, 04:28:58 UTC
1168869 Isaac Virshup 13 December 2020, 09:24:06 UTC typo in release.rst 04 January 2021, 04:28:58 UTC
709161c Isaac Virshup 13 December 2020, 09:11:57 UTC Initial dev-docs commit (very WIP) 04 January 2021, 04:28:58 UTC
0b3a048 Gökçen Eraslan 24 December 2020, 02:52:14 UTC Remove sklearn testing module references (#1557) 24 December 2020, 02:52:14 UTC
ad1bf14 Isaac Virshup 22 December 2020, 08:48:12 UTC Add scrublet to external (#1555) * Add Scrublet as an external tool * Docstring fixes * Apply black formatting * Think the CI might want some full stops * strip colons and defaults from parameter docs * Try imposing line width limit * Remove problematic spaces Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Move scrublet plot to plotting module, add 'see also', call scrublet calling function from outer function only * Add Scrublet tests * Rename _call_doublets * Apply black formatting * Add scrublet install to testing * Match parameter with scanpy conventions Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Use _get_obs_rep() * Black again... * Update doublet score check Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * update predicted doublet check Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Remove section per previous commits Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * fix simulate_doublets arg in tests * Fix indent Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Add scrublet to extras_require * Import _get_obs_rep correctly * Black again... * yet more black * Simplifies the assignment a bit, and allows adata_sim to not have scrublet parameters Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * adata_sim parameter simplfication Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Apply forgotten updates Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Syntax fix + rst cleanup * release note Co-authored-by: Jonathan Manning <jmanning@ebi.ac.uk> 22 December 2020, 08:48:12 UTC
b4234d8 Hannah Spitzer 17 December 2020, 08:34:51 UTC Option for downloading tissue image for spatial visium dataset (#1506) * allow downloading tissue image from visium dataset * add image path to adata.uns instead of returning * store image path with correct sample_id * modify read_visium to add path to tif image to adata * remove print in test * rename argument, add tissue_image_path * fix formatting * rename arguments, remove guessing tiff file name * Apply suggestions from code review Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * add release note * Move change note to "features" section * Typo, sample_id -> library_id Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 17 December 2020, 08:34:51 UTC
8610b76 Isaac Virshup 17 December 2020, 06:31:05 UTC Simplify _is_run_from_ipython + release note 17 December 2020, 07:10:01 UTC
5cc5c01 Isaac Virshup 17 December 2020, 06:09:00 UTC Fix ipython check in settings + format 17 December 2020, 07:10:01 UTC
8eeb3fc njbernstein 17 December 2020, 04:48:05 UTC Addresses hashsolo pre_existing_cluster bugs (#1483) Fixed pre_existing_clusters argument Fixed hashsolo example to include columns * spelling * adding hashsolo to docs * fixing docs * getting rid of slash * removed typing from docstring * docs * spacing 17 December 2020, 04:48:05 UTC
a33cb93 Jonathan Manning 17 December 2020, 04:36:08 UTC Require a minimum groupsize for marker detection to prevent division by zero errors (#1490) * Require a minimum groupsize for marker detection to preven division by zero errors * Remove extraneous line * Wire min_groupsize into interface, restore defaults, run black * Revert "Wire min_groupsize into interface, restore defaults, run black" This reverts commit 8df4767b38adee5daca54c7002845cd6baf15e8b. * Revert "Remove extraneous line" This reverts commit 5f9ac24132d0bb442b6abd842f2d520ced8a0590. * Revert "Require a minimum groupsize for marker detection to preven division by zero errors" This reverts commit cf61977c251ad8c6e5fdbc3a5c5616f0d2072f64. * Raise error when singlet groups are present for rank_genes_groups() * Add tests for singlets and empty categories * Apply singlets failure check modificiation Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Add new empty category test Co-authored-by: Isaac Virshup <ivirshup@gmail.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 17 December 2020, 04:36:08 UTC
f90803a Isaac Virshup 13 December 2020, 07:23:06 UTC Restrict umap to <0.5 13 December 2020, 09:20:12 UTC
974cca6 Isaac Virshup 13 December 2020, 07:09:34 UTC Update link for moignard15 (#1542) * Update link for moignard15 * Add release note 13 December 2020, 07:09:34 UTC
375a13c L Sikkema 11 December 2020, 12:32:08 UTC Heatmap colormatching (#1511) * harmonized coloring of column and row groups in heatmap * accounted for case where var labels is not subset of groupby groups 11 December 2020, 12:32:08 UTC
8d9eec4 Gökçen Eraslan 08 December 2020, 19:24:08 UTC Add pts and pts_rest to rank_genes_groups_df and allow multiple groups (#1388) * Add pts and pts_rest to rank_genes_groups_df * Add test for pts and pts_rest * Add pts * Allow multiple groups in rank_genes_groups_df * Fix pos arguments * Fix concat * remove group column for backward compat if len(group) == 1 * Update _utils.py * Preserve order * Rename pts and pts_rest to fraction_group and fraction_rest * Fix test * Update test_get.py * Fix ref * Make group parameter mandatory and reduce code duplication * Fix pts tests * Black * rename pts * Update scanpy/get.py Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Add var_names.name test Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 08 December 2020, 19:24:08 UTC
02fc946 Philipp A 04 December 2020, 13:17:57 UTC Use a VM that’s still supported 5 months from now (#1532) 04 December 2020, 13:17:57 UTC
d205474 Isaac Virshup 04 December 2020, 05:09:36 UTC more installation logs 04 December 2020, 05:22:11 UTC
b368a42 Isaac Virshup 04 December 2020, 04:46:02 UTC Add release note 04 December 2020, 05:22:11 UTC
da15970 Isaac Virshup 04 December 2020, 04:44:53 UTC Added test 04 December 2020, 05:22:11 UTC
00e058f Isaac Virshup 31 August 2020, 07:32:22 UTC Bugix for one gene being passed to score_genes 04 December 2020, 05:22:11 UTC
35519eb Isaac Virshup 03 December 2020, 05:51:40 UTC Add release note 04 December 2020, 04:12:53 UTC
f89d400 Fidel Ramírez 02 December 2020, 12:26:32 UTC small test change. 04 December 2020, 04:12:53 UTC
88993d6 Isaac Virshup 02 December 2020, 06:18:53 UTC Keep backed specific logic to backed This moves any backed specific logic to only apply to backed. 04 December 2020, 04:12:53 UTC
cc27d11 Fidel Ramírez 25 November 2020, 14:33:21 UTC instead of a boolean for slicing use indices 04 December 2020, 04:12:53 UTC
5a4260b Fidel Ramírez 25 November 2020, 16:46:40 UTC fix col names. Add test to check col names order and content 04 December 2020, 04:12:53 UTC
93ce4ae Fidel Ramírez 25 November 2020, 10:27:40 UTC use ordered indices to allow slicing in backed mode. Update backed tests. 04 December 2020, 04:12:53 UTC
27bab5f Fidel Ramírez 23 November 2020, 08:14:35 UTC remove parameter `use_raw` from `sc.get.var_df` 04 December 2020, 04:12:53 UTC
2bbca4b Fidel Ramírez 19 November 2020, 16:29:32 UTC fix indices for raw data. Update tests 04 December 2020, 04:12:53 UTC
83424d8 Fidel Ramírez 19 November 2020, 11:39:49 UTC fix issue with sparse matrices. Add sparse matrix to tests 04 December 2020, 04:12:53 UTC
8bf5eb6 Fidel Ramírez 19 November 2020, 11:25:41 UTC add test for backed mode vs memory. 04 December 2020, 04:12:53 UTC
b50f698 Fidel Ramírez 19 November 2020, 10:50:10 UTC add optimization to `sc.get.var_df` and add 'use_raw' to parameters. 04 December 2020, 04:12:53 UTC
fe2638b Fidel Ramírez 19 November 2020, 10:10:21 UTC use `df.join` instead of `pd.concat` 04 December 2020, 04:12:53 UTC
2bb76b8 Fidel Ramírez 19 November 2020, 09:44:45 UTC use pandas assert to compare data frames for `var_df` tests and add a couple of new tests. 04 December 2020, 04:12:53 UTC
081065b Fidel Ramírez 19 November 2020, 09:12:53 UTC use pandas assert to compare data frames. Fix issue with dtypes. 04 December 2020, 04:12:53 UTC
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