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https://github.com/scverse/scanpy
12 June 2023, 04:30:47 UTC
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Revision Author Date Message Commit Date
1693556 Isaac Virshup 22 March 2021, 09:40:56 UTC Update docs/release-notes/1.8.0.rst 22 March 2021, 09:40:56 UTC
257af22 giovp 22 March 2021, 08:48:31 UTC fix docs and link 22 March 2021, 08:48:31 UTC
a5a87c0 giovp 22 March 2021, 08:46:41 UTC Update scanpy/metrics/_morans_i.py Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 22 March 2021, 08:46:41 UTC
8dd0fb9 giovp 19 March 2021, 08:54:26 UTC add release note 19 March 2021, 08:54:26 UTC
90500bf Isaac Virshup 19 March 2021, 05:11:56 UTC Remove unused imports 19 March 2021, 05:11:56 UTC
e26399a Isaac Virshup 19 March 2021, 05:09:58 UTC Make argument order same as gearys_c 19 March 2021, 05:09:58 UTC
9c7495d Isaac Virshup 19 March 2021, 04:46:56 UTC Turn on cache-ing (oops, thought this was on by default now) 19 March 2021, 04:46:56 UTC
640939e Isaac Virshup 19 March 2021, 04:38:34 UTC Fix ups for morans_i * Work around numba parallelization issue: https://github.com/numba/numba/issues/6774#issuecomment-788789663 * Added test for sparse and dense arrays same result * Consistent ordering of arguments * Remove intermediate array in `_morans_i_vec_W`, sum directly to `inum` 19 March 2021, 04:38:34 UTC
33db5ce giovp 18 March 2021, 14:30:01 UTC update types for vals 18 March 2021, 14:30:01 UTC
23852e8 giovp 18 March 2021, 11:08:28 UTC address review 18 March 2021, 11:08:28 UTC
fc80233 giovp 16 March 2021, 21:38:03 UTC increase tol 16 March 2021, 21:38:03 UTC
d2a6dec giovp 16 March 2021, 20:24:58 UTC finish tests 16 March 2021, 20:24:58 UTC
8fd8e62 giovp 16 March 2021, 11:15:20 UTC update tests 16 March 2021, 11:15:20 UTC
4ba14fe giovp 15 March 2021, 21:13:58 UTC fix parallel for real 15 March 2021, 21:13:58 UTC
430b855 giovp 15 March 2021, 20:21:17 UTC fix sparsity 15 March 2021, 20:21:17 UTC
3847a70 giovp 15 March 2021, 15:23:05 UTC add docs 15 March 2021, 15:23:05 UTC
a97806b giovp 15 March 2021, 15:10:26 UTC refactor to match gearysc 15 March 2021, 15:10:26 UTC
2c90893 giovp 11 March 2021, 21:44:43 UTC minor fix docs 11 March 2021, 21:44:43 UTC
264016b giovp 11 March 2021, 21:36:36 UTC change nperms default 11 March 2021, 21:36:36 UTC
1391855 giovp 11 March 2021, 21:33:08 UTC fix permutation 11 March 2021, 21:33:08 UTC
9948b6f giovp 11 March 2021, 21:15:17 UTC clean up 11 March 2021, 21:15:17 UTC
35ac5c4 giovp 11 March 2021, 21:14:19 UTC init moran 11 March 2021, 21:14:19 UTC
af8f323 Gökçen Eraslan 11 March 2021, 15:35:15 UTC Preserve category order when groupby is a list (#1735) Preserve category order when groupby is a list 11 March 2021, 15:35:15 UTC
da66e15 Isaac Virshup 10 March 2021, 03:59:08 UTC Minor addition to contributing docs (#1726) 10 March 2021, 03:59:08 UTC
a085333 Alex M. Ascensión 09 March 2021, 08:39:54 UTC updated ecosystem.rst to add triku (#1722) 09 March 2021, 08:39:54 UTC
27761ef mjayasur 09 March 2021, 08:38:43 UTC deprecate scvi (#1703) * deprecate scvi * Update .azure-pipelines.yml Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * remove :func: links to scvi in release notes * remove tildes in front of scvi in release notes * Update docs/release-notes/1.5.0.rst Co-authored-by: Michael Jayasuriya <mjayasur@Michaels-MacBook-Air.local> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 09 March 2021, 08:38:43 UTC
976aa18 Isaac Virshup 05 March 2021, 04:18:21 UTC Cleanup normalize_total (#1667) * Cleanup normalize_total * Add modification tests and copy kwarg for normalize_total * Test that 'layers' argument is deprecated * Added more mutation checks for normalize_total * release note * Error message 05 March 2021, 04:18:21 UTC
b3eb354 Isaac Virshup 04 March 2021, 07:28:31 UTC Fix clipped images in docs (#1717) 04 March 2021, 07:28:31 UTC
b3a2a6d Isaac Virshup 04 March 2021, 06:18:33 UTC `sc.metrics` module (add confusion matrix & Geary's C methods) (#915) * Add `sc.metrics` with `gearys_c` Add a module for computing useful metrics. Started off with Geary's C since I'm using it and finding it useful. I've also got a fairly fast way to calculate it worked out. Unfortunatly my implementation runs into some issues with some global configs set by umap (see https://github.com/lmcinnes/umap/issues/306), so I'm going to see if that can be resolved before changing it. * Add sc.metrics.confusion_matrix * Better tests and output for confusion_matrix * Workaround umap<0.4 and increase numerical stability of gearys_c * Work around https://github.com/lmcinnes/umap/issues/306 by not calling out to kernel function. That code has been kept, but commented out. * Increase numerical stability by casting data to system width. Tests were failing due to instability. * Split up gearys_c tests * Improved unexpected error message * gearys_c working again. Sadly, a bit slower * One option for doc strings * Simplify implementation to use single dispatch * release notes 04 March 2021, 06:18:33 UTC
6569bd6 Philipp A 03 March 2021, 12:18:48 UTC Fix version on Travis (#1713) By default, Travis does `git clone --depth=50` which means the version can’t be detected from the git tag. 03 March 2021, 12:18:48 UTC
9fa0102 Jonathan Manning 03 March 2021, 10:09:08 UTC Add sparsificiation step before sparse-dependent Scrublet calls (#1707) * Add sparsificiation step before sparse-dependent Scrublet calls * Apply sparsification suggestion Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Fix imports Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 03 March 2021, 10:09:08 UTC
d69aa18 Isaac Virshup 03 March 2021, 09:29:48 UTC Use joblib for parallelism in regress_out (#1695) * Use joblib for parallism in regress_out * release note * fix link in release notes * Add todo for resource test 03 March 2021, 09:29:48 UTC
ae3f8b0 Isaac Virshup 02 March 2021, 23:47:22 UTC codecov comment (#1704) 02 March 2021, 23:47:22 UTC
7681458 Philipp A 02 March 2021, 11:03:15 UTC Go back to regular pip (#1702) * Go back to regular flit Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 02 March 2021, 11:03:15 UTC
0f7968c Philipp A 01 March 2021, 10:25:26 UTC Merge pull request #1527 from theislab/flit 01 March 2021, 10:25:26 UTC
f27ca71 Philipp A 01 March 2021, 09:18:39 UTC Fix paga_path (#1047) Fix paga_path Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 01 March 2021, 09:18:39 UTC
f653c3c Philipp A 11 February 2021, 10:27:18 UTC Circumvent new pip check (see pypa/pip#9628) 01 March 2021, 08:45:29 UTC
667de76 Philipp A 14 January 2021, 11:23:10 UTC Update install instructions 01 March 2021, 08:45:29 UTC
4bdebd6 Philipp A 15 January 2021, 14:51:45 UTC add setup.py while leaving it ignored 01 March 2021, 08:45:29 UTC
e8f4f4c Philipp A 03 December 2020, 10:04:35 UTC Switch to flit This reverts commit d6457902 01 March 2021, 08:45:29 UTC
3dc389e Isaac Virshup 25 February 2021, 08:00:34 UTC Attempt server-side search (#1672) 25 February 2021, 08:00:34 UTC
b6d5665 Isaac Virshup 25 February 2021, 07:59:11 UTC add codecov so we can have a badge to point to (#1693) 25 February 2021, 07:59:11 UTC
3b536fb Isaac Virshup 25 February 2021, 06:57:13 UTC Fix print_versions for python<3.8 (#1691) 25 February 2021, 06:57:13 UTC
c943b93 Sergei Rybakov 24 February 2021, 14:14:23 UTC rm call of black test (#1690) 24 February 2021, 14:14:23 UTC
f7279f6 giovp 24 February 2021, 12:57:42 UTC enables highly_variable_genes_seurat_v3 to accept pseudocounts (#1679) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 24 February 2021, 12:57:42 UTC
c4401b7 giovp 24 February 2021, 12:57:03 UTC address few docs issues (#1680) 24 February 2021, 12:57:03 UTC
5db49c2 Isaac Virshup 24 February 2021, 07:49:37 UTC Merge pull request #1684 from ivirshup/precommit Pre-commit 24 February 2021, 07:49:37 UTC
d654852 Isaac Virshup 24 February 2021, 07:05:00 UTC Fix some comment labelling in palettes 24 February 2021, 07:20:51 UTC
d040ce9 Isaac Virshup 11 February 2021, 06:17:25 UTC Add pre-commit, starting with `black` 24 February 2021, 07:20:51 UTC
99b1d03 Isaac Virshup 24 February 2021, 06:26:48 UTC Setup pre-commit * Add github action to run pre-commit * Remove black from azure pipelines * Remove blackdiff test case * Document pre-commit 24 February 2021, 07:19:52 UTC
1f1f6d5 Isaac Virshup 24 February 2021, 06:53:20 UTC Update release notes for 1.7.1 (#1683) 24 February 2021, 06:53:20 UTC
cf2e567 Marius van den Beek 23 February 2021, 19:03:44 UTC Drop passing of **kwds (#1655) This matches the else branch and fixes problem when figsize for instance is passed in. 23 February 2021, 19:03:44 UTC
d391398 giovp 22 February 2021, 16:58:40 UTC Revert "enable highly_variable_genes_seurat_v3 to work with pseudocounts" (#1678) This reverts commit 1043c6990098169d36077b76d8302f88d627c6ae. 22 February 2021, 16:58:40 UTC
1043c69 giovp 22 February 2021, 14:06:42 UTC enable highly_variable_genes_seurat_v3 to work with pseudocounts (#1642) 22 February 2021, 14:06:42 UTC
43eab07 Gökçen Eraslan 22 February 2021, 13:55:36 UTC More twitter handles (#1676) 22 February 2021, 13:55:36 UTC
de28381 Jonathan Manning 22 February 2021, 09:55:06 UTC Fix passing of arguments between scrublet routines (#1659) * Fix passing of arguments between scrublet routines * Sidestep annoy issue * Test with scrublet for differences in response to non-standard parameter settings * reduce test dataset size for scrublet 22 February 2021, 09:55:06 UTC
b9a7075 Isaac Virshup 21 February 2021, 07:23:13 UTC Close figures after all tests (#1671) 21 February 2021, 07:23:13 UTC
2183195 Marius van den Beek 19 February 2021, 05:21:02 UTC Fix timeseries plot traceback (#1654) * Add timeseries test * Pass generated img to plt.colorbar 19 February 2021, 05:21:02 UTC
6dcae7a Isaac Virshup 19 February 2021, 04:09:47 UTC Add release notes section for 1.8.0 (#1666) 19 February 2021, 04:09:47 UTC
bde96e2 Isaac Virshup 19 February 2021, 03:41:35 UTC Release notes reorganization (#1628) Move each versions release notes to its own file Also: * Stop using global paga link * Update dev-docs about release note processes 19 February 2021, 03:41:35 UTC
0c4ca5b Isaac Virshup 18 February 2021, 13:23:36 UTC Set-up for adding plot examples in documentation (#1632) 18 February 2021, 13:23:36 UTC
975ab54 Isaac Virshup 11 February 2021, 03:46:22 UTC Remove scanpy.api (#1640) * Remove scanpy.api Reviewed by: Philipp A <flying-sheep@web.de> 11 February 2021, 03:46:22 UTC
9f81f24 Isaac Virshup 10 February 2021, 09:11:28 UTC Fix failing CI for scanorama and python3.6 (#1638) Suggested by: https://github.com/brianhie/scanorama/issues/73#issuecomment-775647669 10 February 2021, 09:11:28 UTC
76e3c83 Isaac Virshup 10 February 2021, 09:04:32 UTC Fix sc.get.obs_df when keys not passed (#1637) 10 February 2021, 09:04:32 UTC
abfaef4 Fidel Ramirez 10 February 2021, 06:45:39 UTC fixes dendrogram issue #1228 (#1614) * addresses issue #1228 * update faling tests * black formatting * black code * add bug fix note * Move release note to 1.7.1 * apply black to code in `scanpy.get.__init__` that came from merging with master. Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 10 February 2021, 06:45:39 UTC
de0dd7f Isaac Virshup 03 February 2021, 05:25:44 UTC Release note for #1583 and update release date (#1623) * Release note for #1583 and update release date * Swap travis badge for azure 03 February 2021, 05:25:44 UTC
dd97d31 Isaac Virshup 02 February 2021, 10:30:15 UTC Merge pull request #1621 from ivirshup/get_cleanup 02 February 2021, 10:30:15 UTC
fbd2a01 Isaac Virshup 02 February 2021, 08:14:40 UTC Add tests for error messages 02 February 2021, 08:14:40 UTC
d5b2393 Isaac Virshup 02 February 2021, 05:13:41 UTC Add pip cache to CI (#1620) I'm assuming this worked, cause I don't think I can really check without merging it. 02 February 2021, 05:13:41 UTC
3c766f2 Isaac Virshup 02 February 2021, 05:08:55 UTC Cleanup sc.get namespace 02 February 2021, 05:08:55 UTC
b4226a3 Isaac Virshup 02 February 2021, 05:02:39 UTC Cleanup obs_df and var_df * Made common actions shared * Simplified gene aliasing and use_raw handling 02 February 2021, 05:06:03 UTC
81dbae9 Fidel Ramirez 02 February 2021, 02:14:27 UTC Allow plots to use adata.obs index as groupby (#1583) * Fix problem with pandas join when adata.obs index is not unique. Fix issue with duplicated key names. * simplify _prepare_dataframe by using sc.get.obs_df. Allow use of adata.obs index column as valid groupby category. * empty commit to triggir tests * use pd.concat instead of pd.join as this avoids the need to have a unique index. * remove modification to adata in _prepare_dataframe * add group by index test * change error for warning when too many categories will be plotted * black changes * address review comments * review changes * fix error when index is not category * changed df.join for pd.concat in `sc.get.var_df`. Added test for repeated keys * check that adata.obs.columns and adata.var.index are unique * added non unique var.index and non unique obs.columns tests * Trigger CI * Throw error if gene_symbol duplicated when accessed * Formatting for test_get Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 02 February 2021, 02:14:27 UTC
1baac54 Koncopd 01 February 2021, 14:18:21 UTC fix formatting 01 February 2021, 15:30:12 UTC
73876fd Koncopd 22 January 2021, 13:51:37 UTC add fix to release notes 01 February 2021, 12:50:28 UTC
6463cac Koncopd 20 January 2021, 00:08:25 UTC rm block on umap 0.5 01 February 2021, 12:50:28 UTC
e617d6a Koncopd 19 January 2021, 23:54:37 UTC fix ingest for umap 0.5 01 February 2021, 12:50:28 UTC
9e13ca9 Fidel Ramirez 27 January 2021, 10:49:40 UTC Address issues with heatmaps reported in #1591 (#1603) 27 January 2021, 10:49:40 UTC
3890300 Isaac Virshup 27 January 2021, 10:25:21 UTC Remove dependency on scvelo for doc builds (#1608) 27 January 2021, 10:25:21 UTC
a64a1e4 Lukas Heumos 25 January 2021, 01:49:27 UTC add twine check to azure CI + 3.8 matrix (#1602) Add twine check to azure CI + update latest python version tested. Co-authored-by: Isaac Virshup <ivirshup@gmail.com> 25 January 2021, 01:49:27 UTC
57ec8a7 Isaac Virshup 21 January 2021, 14:23:25 UTC Speedup plotting color performance (#1596) If values of color dict are not unique, `categorical.map(non_unique)` returns a string array, which caused `to_hex` to be called on each element, not just the categories. This was quite slow. 21 January 2021, 14:23:25 UTC
5fc12f4 Isaac Virshup 19 January 2021, 11:30:43 UTC Attach failing plots to CI results (#1587) * Attach failing plots via pytest-nunit * Document viewing plots through CI 19 January 2021, 11:30:43 UTC
47d4f0d Isaac Virshup 19 January 2021, 11:17:25 UTC fix sc.tl.umap for umap-0.5 (#1589) * fix sc.tl.umap for 0.5 * Hide tensorflow warnings on umap import https://github.com/lmcinnes/umap/issues/551#issuecomment-762548243 19 January 2021, 11:17:25 UTC
92da773 Isaac Virshup 19 January 2021, 02:43:22 UTC Update sam params (#1595) * updated default parameters * release note Co-authored-by: atarashansky <tarashan@stanford.edu> 19 January 2021, 02:43:22 UTC
e0c11ca Isaac Virshup 17 January 2021, 08:22:35 UTC release note 17 January 2021, 08:34:37 UTC
41e2474 Isaac Virshup 17 January 2021, 07:53:04 UTC Fix chunked pca 17 January 2021, 08:34:37 UTC
2a12306 Fidel Ramirez 14 January 2021, 07:00:09 UTC updated test that works with pandas 1.2 (#1584) 14 January 2021, 07:00:09 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
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