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 |