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 |