| 9cab8cf | Philipp A | 07 June 2023, 13:46:06 UTC | Convert issue report templates to forms (#2503) Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> | 07 June 2023, 13:46:06 UTC |
| 8d9b772 | Philipp A | 07 June 2023, 13:36:49 UTC | update tutorials (#2502) | 07 June 2023, 13:36:49 UTC |
| f03c5b4 | Adam Gayoso | 08 May 2023, 11:53:31 UTC | api docs path (#2484) | 08 May 2023, 11:53:31 UTC |
| 6295596 | Gregor Sturm | 03 May 2023, 15:06:12 UTC | Test against pre-release dependencies (#2478) * Test against pre-release dependencies adapted from https://github.com/scverse/anndata/blob/main/.azure-pipelines.yml * fix pre-commit | 03 May 2023, 15:06:12 UTC |
| 08be4e9 | dshefter | 19 April 2023, 09:41:46 UTC | pheno_jaccard_ig to be a csr matrix (#2295) * pheno_jaccard fix * Simpler tocsr Co-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com> --------- Co-authored-by: Shefter <shefterd@lski2253.mskcc.org> Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> Co-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com> | 19 April 2023, 09:41:46 UTC |
| ab2177c | Govinda Kamath | 17 April 2023, 16:11:32 UTC | Spaceranger 2.1.0: Modify 10x reader to read probe barcode matrix (#2470) * make reader compatible with probe matrix * Update scanpy/readwrite.py Co-authored-by: Matt Cai <matthew.cai@10xgenomics.com> * Fix breaking test * Fix Shauns comments * Fix Shauns suggestion * fix shauns suggestions * add sample data and test for reader * Fix Zethson suggestion and update docstrings --------- Co-authored-by: Matt Cai <matthew.cai@10xgenomics.com> | 17 April 2023, 16:11:32 UTC |
| e79fcda | Philipp Weiler | 17 April 2023, 14:36:33 UTC | Pass delimiter to read_csv (#1969) To read from CSV files more flexibly, the delimiter can be passed to `read_csv`. Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> | 17 April 2023, 14:36:33 UTC |
| ff291d6 | Kalin Nonchev | 17 April 2023, 14:21:35 UTC | PCA fix random_state (#2469) * fix random_state * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 17 April 2023, 14:21:35 UTC |
| b863ce0 | Altana Namsaraeva | 12 April 2023, 13:28:11 UTC | Corrected method name (#2467) Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> | 12 April 2023, 13:28:11 UTC |
| aefac50 | Philipp A | 12 April 2023, 13:11:55 UTC | Fix CheckBuild job (#2468) Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> | 12 April 2023, 13:11:55 UTC |
| 554b226 | Philipp A | 12 April 2023, 12:46:02 UTC | Fix normalize_total for dask (#2466) | 12 April 2023, 12:46:02 UTC |
| 3e3427d | Lukas Heumos | 11 April 2023, 12:36:04 UTC | Fix Alex name | 11 April 2023, 12:36:04 UTC |
| a341e02 | Lukas Heumos | 11 April 2023, 12:31:59 UTC | Add scverse citation & restructure scanpy citation (#2463) * Add scverse citation * pre-commit Signed-off-by: zethson <lukas.heumos@posteo.net> --------- Signed-off-by: zethson <lukas.heumos@posteo.net> | 11 April 2023, 12:31:59 UTC |
| 7fc56a5 | LLehner | 02 April 2023, 20:21:21 UTC | updated read_visium() to read in spaceranger 2.0 files (#2424) Co-authored-by: Giovanni Palla <25887487+giovp@users.noreply.github.com> | 02 April 2023, 20:21:21 UTC |
| 9969734 | snigdhaAgarwal | 16 March 2023, 20:10:30 UTC | Issue-1673 (#2452) Co-authored-by: Snigdha Agarwal <sagarwal@bh-0261.lan> | 16 March 2023, 20:10:30 UTC |
| ada761b | Lukas Heumos | 15 March 2023, 15:58:27 UTC | Increase ubuntu version & python version for azure CI (#2447) * Increase ubuntu version & python version for azure CI Signed-off-by: zethson <lukas.heumos@posteo.net> * Set minimum Python version to 3.8 * Remove compatibility code Signed-off-by: zethson <lukas.heumos@posteo.net> * Replace Literal typings Signed-off-by: zethson <lukas.heumos@posteo.net> --------- Signed-off-by: zethson <lukas.heumos@posteo.net> | 15 March 2023, 15:58:27 UTC |
| 0692ef9 | Isaac Virshup | 02 March 2023, 00:11:46 UTC | Prepare for pandas 2.0 (#2434) * is_categorical -> is_categorical_dtype * cat.replace(to_remove, np.nan) -> cat.remove_categories(to_remove) * df1.append(df2) -> pd.concat([df1, df2]) * Series.iteritems -> Series.items * Fix indexing a pandas object with a set in score genes * Release notes | 02 March 2023, 00:11:46 UTC |
| 17e9aae | Martin Kim | 01 March 2023, 13:54:56 UTC | Update hashsolo docstring (#2429) * Update hashsolo docstring * Update scanpy/external/pp/_hashsolo.py | 01 March 2023, 13:54:56 UTC |
| 27493a4 | Isaac Virshup | 17 February 2023, 16:12:40 UTC | Update dev branch (#2421) * Fix anndata-dev install * Fix test_ingest by setting X dtype explicitly * Fix log1p test (implicit copy was no longer being made) * Fix test that relied on implicit dtype conversion * Fix dataset that now loaded in as float64 instead of float32 * Update visium default figure for matplotlib 3.7 * skip plotting test that changed on mpl 3.7 if mpl < 3.7 is installed * Update release notes | 17 February 2023, 16:12:40 UTC |
| d64282a | Isaac Virshup | 17 February 2023, 15:02:55 UTC | Revert "Stephen/spaceranger2.0 (#2296)" (#2422) This reverts commit 619bd7741c236902d0bebccf453c15cbb5859b02. | 17 February 2023, 15:02:55 UTC |
| 2dda1b6 | Isaac Virshup | 16 February 2023, 14:04:51 UTC | update anndata-dev tests to install anndata test deps (#2420) | 16 February 2023, 14:04:51 UTC |
| 00f8729 | Adam Gayoso | 15 February 2023, 19:04:33 UTC | update ecosystem page (#2417) | 15 February 2023, 19:04:33 UTC |
| 2b28b57 | Adam Gayoso | 15 February 2023, 17:24:47 UTC | Doc overhaul (#2220) * Update conf.py * add req * add override path * Create override.css * add pygments, remove scvi-tools colors * add myst extensions * remove github edit links * move css * add sphinx design, opengraph * move contributors out of index * show source * add submodule * add submodule * temp old tutorials rename * remove github links * remove github url from template * disable warning fail * disable warning fail * nbsphinx * fix headings * rtd use submodule * add viewcode * more headings fixes * tutorials index * add nbsphinx ext * remove sphinx pygments * fix colab link * add ipython as docs req * no signatures in tables * make ci happy * add sphinx design cards * break up api * fix icons * link to new api index in card * update colors * no latest release in index * release notes * colors * color typo * back to default colors * Update override.css * add module * move external * Make border color override work * grid * hoverxref and linkcode * fix grid * comment * grid spacing * intersphinx hoverxref * extlinks * extlinks * fix contributors * fix tutorials to use old page * hidden toc tree * toctree for tutorials hidden * clean up conf * fix extlinks * tutorial extlink * add leiden to docs build * buttons * small role * try rst badge * extlinks * fix image link * Update docs/conf.py * update submodule * remove hoverxref * warning code * add how to update submodule * remove unnecessary css * remove more scanpydoc * tutorials link * switch to sphinx book * pre commit' * update reqs * logo only * deps * linkcode * linkcode * exclude patterns * sidebar levels * remove external tools * fix external --------- Co-authored-by: Philipp A <flying-sheep@web.de> | 15 February 2023, 17:24:47 UTC |
| 619bd77 | Stephen Williams | 15 February 2023, 17:19:23 UTC | Stephen/spaceranger2.0 (#2296) * compatibility with spaceranger 2.0 * black formatting * check explicitly for tissue_positions file * correct header if else * Update readwrite.py * Fix header index --------- Co-authored-by: Giovanni Palla <25887487+giovp@users.noreply.github.com> Co-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com> | 15 February 2023, 17:19:23 UTC |
| 1313f7b | Isaac Virshup | 15 February 2023, 17:15:47 UTC | Remove usage of ABC (#2414) | 15 February 2023, 17:15:47 UTC |
| 0fec570 | Philipp A | 15 February 2023, 17:13:49 UTC | remove pre-commit workflow (#2206) | 15 February 2023, 17:13:49 UTC |
| dbfec2f | Adam Gayoso | 15 February 2023, 17:10:00 UTC | Revert "Update external page (#2400)" (#2415) This reverts commit de05de6ab3108948cfae4d72d4f74e194c88e3b8. | 15 February 2023, 17:10:00 UTC |
| ef715f1 | pre-commit-ci[bot] | 15 February 2023, 17:01:51 UTC | [pre-commit.ci] pre-commit autoupdate (#2373) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 22.10.0 → 23.1.0](https://github.com/psf/black/compare/22.10.0...23.1.0) - [github.com/PyCQA/flake8: 5.0.4 → 6.0.0](https://github.com/PyCQA/flake8/compare/5.0.4...6.0.0) - [github.com/pre-commit/mirrors-autopep8: v2.0.0 → v2.0.1](https://github.com/pre-commit/mirrors-autopep8/compare/v2.0.0...v2.0.1) - [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v4.4.0) * Fix flake8 * Style fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Philipp A <flying-sheep@web.de> | 15 February 2023, 17:01:51 UTC |
| d7dbbd5 | Wainberg | 15 February 2023, 17:01:25 UTC | Stop ignoring batch_size in sc.external.pp.scanorama_integrate (#2374) This was giving out-of-memory errors since scanorama's default is batch_size=None, and setting batch_size to another value wasn't doing anything | 15 February 2023, 17:01:25 UTC |
| b62891e | smautner | 15 February 2023, 17:00:07 UTC | Fixing mnn (#2407) * mnn fix n_jobs =1 is not enough to disable multiprocessing in mnn https://github.com/chriscainx/mnnpy/blob/2097dec30c193f036c5ed7e1c3d1e3a6270e102b/mnnpy/utils.py#L34 * Update _mnn_correct.py fix * Update _mnn_correct.py * whitespaces | 15 February 2023, 17:00:07 UTC |
| 316b90c | Adam Gayoso | 15 February 2023, 16:58:24 UTC | fix scrublet (#2395) | 15 February 2023, 16:58:24 UTC |
| c3d791a | Xiao Yuan | 15 February 2023, 16:55:31 UTC | Fix some typos (#2405) | 15 February 2023, 16:55:31 UTC |
| de05de6 | Isaac Virshup | 15 February 2023, 16:55:08 UTC | Update external page (#2400) * Update external page * Remove dev instructions for external | 15 February 2023, 16:55:08 UTC |
| b8277aa | Nikolay Markov | 15 February 2023, 16:48:12 UTC | Spell out flavors in HVG, add scikit-misc requirement to docs (#2379) * Spell out flavors in HVG, add scikit-misc requirement to docs * Remove trailing whitespace --------- Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> | 15 February 2023, 16:48:12 UTC |
| d26be44 | Clarence Mah | 17 January 2023, 11:22:21 UTC | Add bento to ecosystem (#2334) | 17 January 2023, 11:22:21 UTC |
| d7e1302 | pre-commit-ci[bot] | 03 November 2022, 13:52:21 UTC | [pre-commit.ci] pre-commit autoupdate (#2347) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 03 November 2022, 13:52:21 UTC |
| e5cdbbc | Isaac Virshup | 11 October 2022, 14:17:05 UTC | Pin matplotlib for doc builds (#2349) | 11 October 2022, 14:17:05 UTC |
| 3b2fd00 | Gökçen Eraslan | 10 October 2022, 21:49:28 UTC | Handle scalar datasets too (#2344) * Handle scalar datasets too After @ivirshup's pytables PR (#2064) we started having issues with loading h5 files with scalar datasets, such as those created by CellBender (https://github.com/broadinstitute/CellBender/issues/128). It is currently not an issue for the 10X h5 files for now since they don't have any scalars, however it'd be good to just handle scalars as well as arrays 1- to fix the cellbender file loading problem 2- to fix potential problems we might end up having if 10X h5 format includes scalar datasets. * Add a scalar to the multiple_genomes.h5 test file * Fixes #2203 | 10 October 2022, 21:49:28 UTC |
| ec54473 | Stephen Fleming | 29 September 2022, 23:39:38 UTC | Fix legacy 10x loader when more than one genome exists (#2248) * Fix bug with legacy 10x loader for multiple genomes * Add test and small test data h5 * black | 29 September 2022, 23:39:38 UTC |
| 11d0b8e | pre-commit-ci[bot] | 06 September 2022, 07:15:10 UTC | [pre-commit.ci] pre-commit autoupdate (#2320) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 06 September 2022, 07:15:10 UTC |
| 3d59704 | pre-commit-ci[bot] | 16 August 2022, 09:33:13 UTC | [pre-commit.ci] pre-commit autoupdate (#2307) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 16 August 2022, 09:33:13 UTC |
| 1844b91 | Luke Zappia | 12 August 2022, 09:35:06 UTC | Add check for number of normalized dispersions (#2231) * Add check for number of normalized dispersions In sc.pp.highly_variable_genes() when flavor='cell_ranger' and n_top_genes is set check that enough normalized dispersions have been calculated and if not raise a warning and set n_top_genes to the number of calculated dispersions. Fixes #2230 * Use .size instead of len() * Add test for n_top_genes warning * Add release note * Remove blank line Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 12 August 2022, 09:35:06 UTC |
| 4623bb7 | Dries Schaumont | 11 August 2022, 17:55:36 UTC | Fix using custom layer with highly_variable_genes (#2302) * Fix using custom layer with highly_variable_genes * Add tests * Add release note * Move release note to correct section | 11 August 2022, 17:55:36 UTC |
| ee39688 | pre-commit-ci[bot] | 08 August 2022, 19:15:04 UTC | [pre-commit.ci] pre-commit autoupdate (#2303) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 08 August 2022, 19:15:04 UTC |
| 41a7b83 | pre-commit-ci[bot] | 07 July 2022, 13:55:59 UTC | [pre-commit.ci] pre-commit autoupdate (#2289) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 07 July 2022, 13:55:59 UTC |
| 1c9e404 | pre-commit-ci[bot] | 15 June 2022, 22:06:53 UTC | [pre-commit.ci] pre-commit autoupdate (#2271) updates: - [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.2.0...v4.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 15 June 2022, 22:06:53 UTC |
| b938854 | michalk8 | 15 June 2022, 22:03:12 UTC | Update CellRank's metion in the ecosystem (#2269) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 15 June 2022, 22:03:12 UTC |
| d952682 | Lukas Heumos | 15 June 2022, 21:48:40 UTC | fix typo in log1p parameters (#2273) | 15 June 2022, 21:48:40 UTC |
| 8e5fedb | Lukas Heumos | 15 June 2022, 21:47:10 UTC | Fix error formatting (#2263) | 15 June 2022, 21:47:10 UTC |
| 394191f | Isaac Virshup | 15 June 2022, 21:23:42 UTC | Fix tests (#2274) * Fix reference image for visium test Reference image should just be black square since the image is black, and when an image is included the points default to transparent. * Update paga reference plots for igraph 0.9.11 igraph 0.9.11 seems to change the results for the "fr" layout significantly. * No longer check that random seed changes 32 bit pca computation It seems to have gotten more accurate, at least on CI platforms. * Unlink old reference * Bump down leiden resolution Some CI jobs were splitting a larger cluster * Unlink more old references * Bigger bandaid | 15 June 2022, 21:23:42 UTC |
| bd06cc3 | Lukas Heumos | 20 April 2022, 08:45:01 UTC | Add link to scverse Discourse for README badge (#2240) | 20 April 2022, 08:45:01 UTC |
| a38a22a | pre-commit-ci[bot] | 12 April 2022, 10:43:04 UTC | [pre-commit.ci] pre-commit autoupdate (#2232) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 12 April 2022, 10:43:04 UTC |
| 9018e16 | Philipp A | 06 April 2022, 11:23:12 UTC | Add CI job with minimal dependencies (#2222) Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 06 April 2022, 11:23:12 UTC |
| 87ae190 | Isaac Virshup | 05 April 2022, 16:11:43 UTC | Start 1.9.2 (#2223) | 05 April 2022, 16:11:43 UTC |
| 5f338ba | Isaac Virshup | 05 April 2022, 14:57:12 UTC | Finalize docs for 1.9.1 (#2219) | 05 April 2022, 14:57:12 UTC |
| 4592d52 | Isaac Virshup | 05 April 2022, 14:29:10 UTC | Fix contributor links (#2217) | 05 April 2022, 14:29:10 UTC |
| 86e2a35 | Isaac Virshup | 05 April 2022, 13:18:59 UTC | Bump matplotlib and pandas version deps (#2212) * Bump matplotlib and pandas version deps * release note | 05 April 2022, 13:18:59 UTC |
| 14d65b4 | Robrecht Cannoodt | 05 April 2022, 12:14:10 UTC | Fix isinstance arg 2 must be a type error (#2209) * Fix isinstance arg 2 must be a type error * fix markdown * Use dummy class Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 05 April 2022, 12:14:10 UTC |
| 05381a3 | Philipp A | 04 April 2022, 12:04:49 UTC | Fix pre commit (#2205) | 04 April 2022, 12:04:49 UTC |
| 771f43d | Isaac Virshup | 01 April 2022, 20:42:02 UTC | Make docs fast by removing elegant_typehints (#2199) | 01 April 2022, 20:42:02 UTC |
| 034ca28 | Isaac Virshup | 01 April 2022, 20:22:06 UTC | theislab -> scverse (#2200) | 01 April 2022, 20:22:06 UTC |
| 536ed15 | Isaac Virshup | 01 April 2022, 15:16:06 UTC | Release notes (#2197) | 01 April 2022, 15:16:06 UTC |
| 51ccbfd | Isaac Virshup | 01 April 2022, 14:27:03 UTC | Prep release notes (#2196) * Update release notes (including some old ones) * More updates to release notes * Tutorial links + zulip link * Tutorial links + zulip link * Fix up doc index page * Group release notes * Update news * Update ecosystem (+ add release notes) * Expand on 100 contributors * More rewording of contributor milestone * dammit | 01 April 2022, 14:27:03 UTC |
| 19d2ab2 | Anna Schaar | 31 March 2022, 16:18:34 UTC | remove colorbar if legend_loc=None for continuous colorbars (#1821) * remove colorbar im legend_loc is None for continuous colorbars * add show_colorbar argument to scatterplots * Rework arg, add test * Release note Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 31 March 2022, 16:18:34 UTC |
| b8c2cf5 | Benedikt Reiz | 30 March 2022, 14:48:50 UTC | Fix default `number_of_noise_barcodes` for hashsolo (#2190) * apply black * fix number of noise barcodes commit #8eeb3fc229d5daee8961c32756becae4b1504a36 broke correct calculation of `number_of_noise_barcodes` * fix precommit hook * Added more noise to test data With the given test data the signal was to clear for an acutal test case. | 30 March 2022, 14:48:50 UTC |
| 4322e82 | Yves33 | 29 March 2022, 17:44:24 UTC | Pca loadings n points patch (#2075) * pca_loadings n_points fix * Revert "pca_loadings n_points fix" This reverts commit ceb2d7844c0bb97eb9561573665e7ab990e8cb48. * pca_loadings n_points fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated docstring. added reference image * Updated docs and simplified logic * release note Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 29 March 2022, 17:44:24 UTC |
| 636316d | Jan Lause | 29 March 2022, 17:01:05 UTC | Normalization and gene selection by analytical Pearson residuals (#1715) * adding core functions and documentation for pearson residual normalization and hvg selection * adding Pearson residual+PCA bundles, minor bug fixes * some style cleanup, minor fixes * adapting _normalize_pearson_residuals() to cleaned-up _normalized_total() from #1667 * updating layer management as in #1667 for _highly_variable_pearson_residuals() as well * slight performance improvement for sparse input * style cleanup * fixing import issue, fixing docstring style, adding check_values param and warning as in #1642 * fixed small NameError, simplified clip argument * remove pd.categorical() * adding check_values to docstrings and remaining pearson residual functions * np.empty instead of np.nan * add references to docstrings, add HVG details to docstring * exposing pca keyword arguments to the user for the bundle/recipe functions * removed unneeded reversal in hvg, fix kwargs_pca bug, consistent defaults across files * fixing handling of `inplace` and `subset` arguments (see issue #1886), explicit typing of output, adding theta input check * renaming output fields for consistency, fixing minor bug * renaming output fields for consistency * adding function that prepares testdata (used for pearson residual tests) * adding tests for all pearson residual functions * fix precommit high_var_genes * try to get precommit to work * try to get precommit to work * fix recipes * fix normalization * remove relative imports * fix docstrings * retry to build docs * fix highvar docstring * more fixing docstrings * docs build locally ? :hammer: * minor cleanup test normalization * more minor cleanups * final cleanup normalization * fixes high var * init experimental module * fix column ordering for batch case * moving to experimental, minor fix for experimental version of hvg selection * linking tests to new experimental submodule, style cleanup * adapt input arguments and docstring for experimental version of hvg selection function * add recipes * fix docs * add correct module docs * fix recipe docstrings * try fix indentation * fix indentation * fix * new indentation * add space * fixing typo in docstring * renaming pca output fields * adapting tests to new output fieldname * fix docs :hammer: * update docs * fix test :hammer: * ensure argument and docstring consistency * update citation year * cleaning imports in `preprocessing` functions * making inputcheck tests specific to error/warning messages * making inputcheck tests specific to error/warning messages * resolve HVGs across batches more cleanly, fix dtype issue * renaming pca input arguments * renaming pca input arguments * _pca bundle: more efficient copy handling, added input check. both _pca and _recipe: varm field for PCs, adapted tests and docs * move repeated inputcheck code to helpers * merging tests *_values and *_general * condense code in pearson hvg selection test, smaller test data for speedup * condensing code in normalization tests * add asteriks for keyword * updating refs to Genome Biology publication * cleanup helpers.py * cleanup main files as requested by @ivirshup * revert unneeded settingWithCopy fix * cache data * use doc_params for doc * fix doc_params var * finalize docs * fix param doc * wrong var still * add cached datasets module and test on high_var_genes tests * use new cache dataset module for tests * fix precommit * fix docs * fix reference and add notebook to tutorials * add release note * add release note * fix release note * typo * remove duplicate reference * fixing black flake etc requirements * add _pca function to release note * last edits to docs * fix release and tutorial image * try fix pre-commit * minor docs * Remove accidentally included files from merge Co-authored-by: giovp <giov.pll@gmail.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 29 March 2022, 17:01:05 UTC |
| 0728d55 | Isaac Virshup | 29 March 2022, 14:42:34 UTC | Simplify embeddings a bit (#1538) * Remove dependency on execution order for scatter plot tests Previously `test_scatterplots[umap_with_edges]` would fail if it ran before `test_scatterplots[umap]`, since the `umap` case changed the color palette the anndata object used. Now the AnnData object is copied for each test that uses it. This is important because it means we don't have state spilling between the tests and can parallelize them. * Convert 'components' to 'dimensions' is sc.pl.embedding Mostly this was to get rid of `_get_data_points`, which was a bit of a horrible function. Now we get all values of the array, then for each plot index into it with the dimensions. This has removed a number of edge cases and special handling thoughout, making the dataflow a bit easier to follow. * Rearrange code in embedding to make a bit more sense * Fix paga plots * Implement broadcasting of dims and color * Add simple test for broadcasting of dimensions and color * Type dimensions * add test for components and dimensions being interoperable * Added docs for the dimension argument * Undo deprecation of components kwarg. I still want to eventually do that, but it shows up in many other parts of the codebase which I don't have time to replace at the moment. This includes, but is not limited to, the other pca plotting methods. * Release note * Fix type annotation for python 3.7 | 29 March 2022, 14:42:34 UTC |
| 3db321f | PGmajev | 29 March 2022, 13:32:43 UTC | n_pcs are no longer ignored for representations other than "X_pca" (#2179) * n_pcs are no longer ignored for non (scanpy-internal) X_pca reductions This change allows to only take the dimensions needed also for non X_pca representations. This can be useful when using harmony for example or storing different PCA embeddings in the same object. Then it is not needed to first store them as X_pca to be able to fully use the n_pcs parameter. It might make sense then to adapt the documentation as such as well. * Added error if n_pcs > dimensions in representation * Fixed typo in variable name * Fixed styling * using consistent quotation marks; all done from my side * first idea for test; check in detail tomorrow * Used wrong quotes before * shortened lines * Improved style * improved style in new function * trying to finish the test today after all * Removing wrong toarray() * Test changes as per pre-commit * Function changes as per pre-commit * Another try at implementing pre-commit changes * Added release note * Attempt to fix reference error Co-authored-by: pmajev <paul-georg.majev@mpi-muenster.mpg.de> | 29 March 2022, 13:32:43 UTC |
| 5e70a47 | Isaac Virshup | 29 March 2022, 12:39:41 UTC | slack -> zulip (#2192) | 29 March 2022, 12:39:41 UTC |
| 835c659 | Marco | 28 March 2022, 14:03:28 UTC | Add CIARA algorithm to ecosystem page (#2175) * Add CIARA algorithm to ecosystem page * Fixed title underline * Added description, changed to MD | 28 March 2022, 14:03:28 UTC |
| 4be01b7 | Jonathan Manning | 22 March 2022, 19:40:29 UTC | Make Scrublet batch-aware (#1965) * Make Scrublet batch-aware * Re-black * Correct param * Fix key * Fix key * misc fixes, make plotting do batch stuff automatically as required * Remove fossil batch help * Allow for Scrublet not detecting threshold * Revert "Allow for Scrublet not detecting threshold" This reverts commit 76ecb4e349ef226a7497a92a3670a8c45c4b3441. * Remove factored-out bugfixes * Blackify * Add test for batched scrublet * Add plot test for batched scrublet * Fix plotting errors * Replace scrublet plotting with @ivirshup suggestion * Add missing import * Batched Scrublet test improvement per @ivirshup suggestion * Blackify * poke for git * poke for git | 22 March 2022, 19:40:29 UTC |
| b7834c7 | Isaac Virshup | 22 March 2022, 10:38:50 UTC | Rst to myst (#2185) * rst to markdown * rst to markdown, configs * Fix names of files references in dev * Add myst-parser to doc deps * Go from ::: to ``` for notes Didn't really make sense to me for some blocks to use a different syntax. AFAICT, myst's intent in supporting that was just for a couple markdown editors. IDK. | 22 March 2022, 10:38:50 UTC |
| 087882b | Isaac Virshup | 21 March 2022, 18:24:59 UTC | Cast color vector back to categorical (#2187) | 21 March 2022, 18:24:59 UTC |
| 9cb915b | Genevieve Buckley | 21 March 2022, 17:43:39 UTC | Allow dask arrays to propagate through _normalize_data() (#1663) * First attempt at dask median for normalization * Allow dask arrays with _normalize_data, include tests * Clearer name ids for parameterized tests * Use isinstance pattern instead * Fix faking of dask array Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 21 March 2022, 17:43:39 UTC |
| 1be0a68 | Pau Badia i Mompel | 21 March 2022, 16:08:29 UTC | Change dorothea-py and progeny-py to decoupler (#2186) The packages dorothea-py and progeny-py are now deprecated, instead one should use decoupler (https://github.com/saezlab/decoupler-py). It contains both prior knowledge resources plus many more since it integrates the meta-resource OmniPath, and it also contains many footprint enrichment methods instead of a fixed one. | 21 March 2022, 16:08:29 UTC |
| a8bd4cf | Isaac Virshup | 18 March 2022, 22:53:55 UTC | Update release guide (#2184) | 18 March 2022, 22:53:55 UTC |
| 805bd63 | Philipp A | 18 March 2022, 14:56:04 UTC | Unpin scanpydoc (#2182) | 18 March 2022, 14:56:04 UTC |
| 495c905 | Philipp A | 15 March 2022, 21:59:43 UTC | Switch from sinfo to session_info (#2089) * Switch from sinfo to session_info * Utilize rich display * Fix use * oops * Import conditionally * Grammar * Remove update from old news file * Simplify, deprecate file argument * Added release note * Clean up unused imports Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 15 March 2022, 21:59:43 UTC |
| fdd602e | Isaac Virshup | 15 March 2022, 21:46:15 UTC | Point discourse links to scverse discourse (#2177) | 15 March 2022, 21:46:15 UTC |
| d805b41 | Lukas Heumos | 15 March 2022, 19:11:39 UTC | Merge pull request #2174 from theislab/fix/typo fix typo | 15 March 2022, 19:11:39 UTC |
| 680bae7 | Isaac Virshup | 15 March 2022, 18:58:54 UTC | Do link to release notes differently for some reason | 15 March 2022, 18:58:54 UTC |
| 67bb317 | Isaac Virshup | 15 March 2022, 17:37:13 UTC | pin scanpydoc | 15 March 2022, 17:37:13 UTC |
| fafcb90 | Lukas Heumos | 14 March 2022, 12:01:16 UTC | fix typo | 14 March 2022, 12:01:16 UTC |
| afc79b9 | Dinesh Reddy Palli | 08 March 2022, 10:41:01 UTC | modify test_read_visium_counts to test read_visium function (#2170) * modify test_read_visium_counts to test read_visium function * update variable name Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 08 March 2022, 10:41:01 UTC |
| 7b22b75 | Sergei Rybakov | 03 March 2022, 14:55:28 UTC | Use certifi if urlopen fails (#2119) * try using certifi if error * add warning | 03 March 2022, 14:55:28 UTC |
| edee93c | Isaac Virshup | 03 March 2022, 11:47:13 UTC | Update intersphinx links (#2166) | 03 March 2022, 11:47:13 UTC |
| 4373348 | Isaac Virshup | 28 February 2022, 14:39:56 UTC | Remove pytables dependency (#2064) * Remove pytables dependency * Bump h5py version, re-remove tables after merge * Add release note | 28 February 2022, 14:39:56 UTC |
| 92886db | Sergei Rybakov | 28 February 2022, 14:39:07 UTC | fix mappable error for older mpl (#2120) | 28 February 2022, 14:39:07 UTC |
| 0fde3f6 | pre-commit-ci[bot] | 25 February 2022, 17:32:18 UTC | [pre-commit.ci] pre-commit autoupdate (#2099) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 21.12b0 → 22.1.0](https://github.com/psf/black/compare/21.12b0...22.1.0) - [github.com/pre-commit/mirrors-autopep8: v1.5.7 → v1.6.0](https://github.com/pre-commit/mirrors-autopep8/compare/v1.5.7...v1.6.0) * apply black update Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 25 February 2022, 17:32:18 UTC |
| 3e1e94c | Lukas Heumos | 25 February 2022, 15:16:37 UTC | Merge pull request #2134 from theislab/tutorials-images Add tutorials images to static | 25 February 2022, 15:16:37 UTC |
| cacd57c | zethson | 24 February 2022, 10:59:40 UTC | Merge branch 'master' of https://github.com/theislab/scanpy into tutorials-images | 24 February 2022, 10:59:40 UTC |
| e1498c2 | Isaac Virshup | 23 February 2022, 19:11:44 UTC | Remove global state changes in plotting tests (#2150) | 23 February 2022, 19:11:44 UTC |
| aadb44f | Alex Wolf | 10 February 2022, 11:20:36 UTC | added tutorials images to static | 10 February 2022, 11:20:36 UTC |
| b69015e | Lukas Heumos | 06 January 2022, 19:53:33 UTC | Merge pull request #2103 from theislab/fix/scrublet_plots fix scrublet test tolerance | 06 January 2022, 19:53:33 UTC |
| 1005419 | zethson | 06 January 2022, 19:36:07 UTC | fix scrublet test tolerance Signed-off-by: zethson <lukas.heumos@posteo.net> | 06 January 2022, 19:36:07 UTC |
| 375a5fb | Lukas Heumos | 06 January 2022, 19:10:21 UTC | Merge pull request #2023 from ebi-gene-expression-group/scrublet_threshold_fix Bugfix for undefined threshold from Scrublet | 06 January 2022, 19:10:21 UTC |
| c2ae5b9 | Lukas Heumos | 06 January 2022, 17:04:32 UTC | Merge pull request #1828 from maximz/rapids-neighbors-metrics Bugfix in RAPIDS usage for neighbors(), and support for additional distance metrics | 06 January 2022, 17:04:32 UTC |
| b6bd872 | Maxim Zaslavsky | 03 May 2021, 20:56:43 UTC | Bugfix: RAPIDS cuML no longer returns squared Euclidean distance matrix | 06 January 2022, 16:23:58 UTC |
| 2c30784 | Maxim Zaslavsky | 03 May 2021, 20:55:33 UTC | Neighbors: Support additional RAPIDS cuML distance metrics | 06 January 2022, 16:23:58 UTC |
