| 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 |
| 60353cc | Lukas Heumos | 06 January 2022, 14:52:29 UTC | Merge pull request #2102 from theislab/update-scanpydoc Update scanpydoc to fix builds | 06 January 2022, 14:52:29 UTC |
| 393715c | Philipp A | 06 January 2022, 14:36:38 UTC | Update scanpydoc to fix builds | 06 January 2022, 14:36:38 UTC |
| 0dfd353 | Philipp A | 29 December 2021, 08:36:21 UTC | Add extra descriptions (#2087) | 29 December 2021, 08:36:21 UTC |
| 33aa35d | pre-commit-ci[bot] | 29 December 2021, 08:17:21 UTC | [pre-commit.ci] pre-commit autoupdate (#2094) updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.0.1...v4.1.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 29 December 2021, 08:17:21 UTC |
| 849e6b9 | Isaac Virshup | 29 December 2021, 08:02:04 UTC | Fix dataset warnings (#2096) * Filter OldFormatWarnings from sc.datasets functions * Fix numpy deprecation warning from ebi_expression_atlas * Filter OldFormatWarnings from test_backed_vs_memory * Release note | 29 December 2021, 08:02:04 UTC |
| 83f9014 | Philipp A | 18 December 2021, 11:59:54 UTC | Fix RAPIDS PR link in changelog (#2086) | 18 December 2021, 11:59:54 UTC |
| 60bb5be | Lukas Heumos | 14 December 2021, 08:57:22 UTC | Merge pull request #2081 from theislab/feature/contributors Add myself to key contributors | 14 December 2021, 08:57:22 UTC |
| cdfbeb1 | Lukas Heumos | 13 December 2021, 22:31:59 UTC | Add myself to key contributors | 13 December 2021, 22:31:59 UTC |
| a739cad | Lukas Heumos | 12 December 2021, 14:54:45 UTC | Merge pull request #1805 from avantikalal/rapids-resolution Allowing resolution parameter to be used with RAPIDS Louvain clustering | 12 December 2021, 14:54:45 UTC |
| 58f4904 | Isaac Virshup | 09 December 2021, 13:44:21 UTC | Turn off pre-commit auto commit for PRs (#2076) | 09 December 2021, 13:44:21 UTC |
| 96dafa3 | Isaac Virshup | 07 December 2021, 12:38:57 UTC | Remove top level import from test_scrublet.py (#2071) | 07 December 2021, 12:38:57 UTC |
| 750689f | Jonathan Manning | 07 December 2021, 11:53:45 UTC | Misc scrublet buxfixes (#2025) * Fix for https://github.com/theislab/scanpy/issues/1957 * Raw counts should be used for simulation in Scrublet * Fix object names * Add check that provision of simulated data produces same results as auto-simulation * remove unused variable * Add a release note | 07 December 2021, 11:53:45 UTC |
| 4ada9ab | pre-commit-ci[bot] | 06 December 2021, 19:39:58 UTC | [pre-commit.ci] pre-commit autoupdate (#2069) updates: - [github.com/psf/black: 21.11b1 → 21.12b0](https://github.com/psf/black/compare/21.11b1...21.12b0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 06 December 2021, 19:39:58 UTC |
| 50f015b | Isaac Virshup | 06 December 2021, 13:01:24 UTC | pep-621 pyproject.toml (#2042) * Initial pep-621 commit * Add content-type to readme * Update metadata retrieval * Update `__author__` field usage in docs It was getting pretty unwieldy and out of date anyways. * Require flit>=3.4 to allow editable installs * Update phil’s maintainer email * update install instructions * Clean up for install instructions * Remove setup.py * Syntax highlighting Co-authored-by: Philipp A <flying-sheep@web.de> | 06 December 2021, 13:01:24 UTC |
| 16e62d1 | pre-commit-ci[bot] | 01 December 2021, 18:05:02 UTC | [pre-commit.ci] pre-commit autoupdate (#2056) updates: - [github.com/psf/black: 21.10b0 → 21.11b1](https://github.com/psf/black/compare/21.10b0...21.11b1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 01 December 2021, 18:05:02 UTC |
| 4cb8a61 | Isaac Virshup | 01 December 2021, 17:03:30 UTC | Make louvain optional for tests (#2063) * Make louvain dep optional for CI * Make clustering tests relying on louvain optional * Make louvain optional in test_neighbors_key_added.py * Make logreg rank_genes_groups tests not require louvain * Skip paul15 paga tests if louvain not installed * Replace louvain with leiden in pbmc3k test * Fix doc builds by updating mpl.colorbar.ColorBarBase to mpl.colorbar.ColorBar | 01 December 2021, 17:03:30 UTC |
| 48cc7b3 | Edward S. Rice | 15 November 2021, 14:35:15 UTC | Fix finding variables with sc.pl.scatter(..., use_raw=True) (#2027) * Fixes #1097 sc.pl.scatter() is a wrapper for _scatter_obs(). It checks to make sure the variable names the caller is requesting to plot exist in var and/or obs, but does not take into account whether it should look in raw based on the use_raw flag, as _scatter_obs() does. This leads to errors when a user asks to plot variables that are in the raw but not the filtered matrix of adata. This commit fixes that bug. * Only use adata.raw.var for index, not keys If `use_raw in [None, True]`, we want to look up gene names in adata.raw.var, but we still want to look up var columns in adata.var. Thus, this reverts the part of ec6ae95e084f37eaa4146645920ee61bf4dc9d34 that mistakenly tries to look up var_names in adata.raw.var.keys(). * Added tests for sc.pl.scatter(..., basis=None) * Blacked * Remove accidentally included test image * Different tests for scatter successes and failures As requested in code review, divide tests of `sc.pl.scatter()` with `basis=None` into those in which the function should successfully make a plot and those in which the function should raise a `ValueError`. * Add test for scatterplots of raw with no basis * Break scatter tests into per-var and per-obs * Fix path typo Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Plot all three first, then check This allows having all the files for debugging in case the first comparison fails. Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Use tmpdir instead of FIGS Co-authored-by: Isaac Virshup <ivirshup@gmail.com> * Blacked * Add release note * Fix release note formatting * Name change to release note Co-authored-by: Isaac Virshup <ivirshup@gmail.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 15 November 2021, 14:35:15 UTC |
| 417845d | Jonathan Manning | 08 November 2021, 14:44:08 UTC | Remove unused variable | 08 November 2021, 14:44:08 UTC |
| cf9b17f | Jonathan Manning | 08 November 2021, 14:40:47 UTC | Add plotting test | 08 November 2021, 14:40:47 UTC |
| 7fddd21 | Jonathan Manning | 08 November 2021, 10:57:30 UTC | Use get() for threshold Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 08 November 2021, 10:57:30 UTC |
| cab9f78 | Alex Wolf | 04 November 2021, 18:42:31 UTC | embedding_density: remove limitation <10 categories (#1936) * embedding_density: remove <10 categories * consistency in docstring * clarified docstring with warning on few cells * fixed white space * release note Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 04 November 2021, 18:42:31 UTC |
| 8277774 | Isaac Virshup | 03 November 2021, 19:30:54 UTC | Start 1.8.3 (#2039) | 03 November 2021, 19:30:54 UTC |
| 5cb6343 | Isaac Virshup | 03 November 2021, 17:02:39 UTC | Finalize release notes (#2037) | 03 November 2021, 17:02:39 UTC |
| 023bb9f | pre-commit-ci[bot] | 03 November 2021, 15:28:51 UTC | [pre-commit.ci] pre-commit autoupdate (#2031) updates: - [github.com/psf/black: 21.9b0 → 21.10b0](https://github.com/psf/black/compare/21.9b0...21.10b0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 03 November 2021, 15:28:51 UTC |
| d02fc4d | Isaac Virshup | 03 November 2021, 14:20:49 UTC | Fix paga exact reproducibility (#1922) * Fix paga exact reproducibility * Update test figures * release note * Fix refs in release notes * Add test * Update release notes | 03 November 2021, 14:20:49 UTC |
| cfcc5b0 | Leland McInnes | 03 November 2021, 13:50:00 UTC | Update for cope with issue introduced in umap-learn 0.5.2 (#2028) * Update for cope with issue introduced in umap-learn 0.5.2 As of umap-learn 0.5.2 an ``n_epochs`` value of 0 is now a valid value and None is used instead to indicate a value should be generated. To maintain forward compatability and backward compatibility with older umap-learn versions we instead make use of the epch setting criterion internal to umap-learn here directly. This should resolve issue #2026 and lmcinnes/umap#798 * Extra param that is needed before internal validate parameters call * ... on the umap object * Add release note Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 03 November 2021, 13:50:00 UTC |
| 6694fa2 | Jonathan Manning | 28 October 2021, 08:37:36 UTC | Blackify | 28 October 2021, 08:37:36 UTC |
| 37c280d | Jonathan Manning | 28 October 2021, 08:36:24 UTC | Fix for undefined Scrublet threshold | 28 October 2021, 08:36:24 UTC |
| 8c07642 | michalk8 | 27 October 2021, 16:13:20 UTC | Fix use_raw=None in scanpy.tl.score_genes (#1999) * Fix use_raw=None in scanpy.tl.score_genes * Fix type of use_raw * Add release notes #1999 * [ci skip] Improve release notes #1999 Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 27 October 2021, 16:13:20 UTC |
| 1b74015 | Lukas Heumos | 27 October 2021, 15:36:07 UTC | Merge pull request #1974 from theislab/feature/conda_forge add conda-forge installation instructions | 27 October 2021, 15:36:07 UTC |
| 985f680 | Isaac Virshup | 27 October 2021, 15:21:32 UTC | Merge branch 'master' into feature/conda_forge | 27 October 2021, 15:21:32 UTC |
| b13cf8e | pre-commit-ci[bot] | 27 October 2021, 14:33:31 UTC | [pre-commit.ci] pre-commit autoupdate (#1994) * [pre-commit.ci] pre-commit autoupdate updates: - https://github.com/python/black → https://github.com/psf/black - [github.com/psf/black: 20.8b1 → 21.9b0](https://github.com/psf/black/compare/20.8b1...21.9b0) - https://gitlab.com/pycqa/flake8 → https://github.com/PyCQA/flake8 - [github.com/PyCQA/flake8: 3.8.4 → 4.0.1](https://github.com/PyCQA/flake8/compare/3.8.4...4.0.1) - [github.com/pre-commit/mirrors-autopep8: v1.5.5 → v1.5.7](https://github.com/pre-commit/mirrors-autopep8/compare/v1.5.5...v1.5.7) * [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> Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 27 October 2021, 14:33:31 UTC |
| 5acf8cb | Isaac Virshup | 26 October 2021, 18:13:53 UTC | CI bugfixes (#2019) * pin sphinx<4.2 * update violin plots | 26 October 2021, 18:13:53 UTC |
| a6e031d | zethson | 17 August 2021, 11:47:00 UTC | Merge branch 'master' of https://github.com/theislab/scanpy into feature/conda_forge | 17 August 2021, 11:47:00 UTC |
| d6ad9f0 | zethson | 17 August 2021, 11:32:10 UTC | [EMPTY] Trigger CI | 17 August 2021, 11:32:10 UTC |
| 63b42e4 | Lukas Heumos | 17 August 2021, 11:26:50 UTC | Merge pull request #1979 from theislab/fix/typo_#1973 fix typo #1973 | 17 August 2021, 11:26:50 UTC |
| b715319 | Lukas Heumos | 13 August 2021, 13:34:26 UTC | fix typo | 13 August 2021, 13:34:26 UTC |
| 3c1270c | zethson | 02 August 2021, 13:40:55 UTC | add conda-forge installation instructions Signed-off-by: zethson <lukas.heumos@posteo.net> | 02 August 2021, 13:40:55 UTC |
| 4e4e6ab | Lukas Heumos | 28 July 2021, 17:26:53 UTC | Merge pull request #1953 from zktuong/master Add dandelion, scBCR-seq package to scanpy ecosystem | 28 July 2021, 17:26:53 UTC |
| 91af268 | Max Land | 27 July 2021, 08:55:34 UTC | Add PASTE to Scanpy ecosystem. (#1950) * Add PASTE to Scanpy ecosystem Co-authored-by: Isaac Virshup <ivirshup@gmail.com> | 27 July 2021, 08:55:34 UTC |
| 3402af1 | Kelvin | 27 July 2021, 08:48:25 UTC | Merge branch 'theislab:master' into master | 27 July 2021, 08:48:25 UTC |
| d7dc745 | Isaac Virshup | 27 July 2021, 08:32:29 UTC | Fix plotting tests for networkx >= 2.6.2 (#1960) * Update PAGA plots * Update umap edges plot | 27 July 2021, 08:32:29 UTC |
| e9d892f | Kelvin | 27 July 2021, 08:13:57 UTC | Update ecosystem.rst | 27 July 2021, 08:13:57 UTC |
| eb06ffb | Kelvin | 26 July 2021, 08:04:07 UTC | Update ecosystem.rst | 26 July 2021, 08:04:07 UTC |
| 6bb9143 | Kelvin | 19 July 2021, 15:50:47 UTC | Update ecosystem.rst | 19 July 2021, 15:50:47 UTC |
| ecd2845 | Sergei Rybakov | 19 July 2021, 09:43:32 UTC | Fix _rank_genes_groups_plot for filtered genes (#1942) * fix _rank_genes_groups_plot for filtered * add to release notes * move notes * test plots filter_rank_genes_groups * temp dir, no args * manual filtering | 19 July 2021, 09:43:32 UTC |
| b34c45c | Philipp A | 16 July 2021, 20:46:32 UTC | Sphinx 4.1 fixes (#1948) | 16 July 2021, 20:46:32 UTC |
| e1bfb46 | Sergei Rybakov | 12 July 2021, 13:27:16 UTC | compare_abs argument in filter_rank_genes_groups (#1649) * compare_abs * test compare_abs * add to release notes | 12 July 2021, 13:27:16 UTC |
| 8460225 | Isaac Virshup | 12 July 2021, 09:12:14 UTC | Start 1.8.2 release notes file (#1945) * Add 1.8.2 release notes file * Pin sphinx (#1946) | 12 July 2021, 09:12:14 UTC |
