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* 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
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| ### 1.9.0 {small}`the future` | ||
| ### 1.9.0 {small}`2022-04-01` | ||
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| ```{rubric} Tutorials | ||
| ``` | ||
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| - New tutorial on the usage of Pearson Residuals: {tutorial}`tutorial_pearson_residuals` {smaller}`J Lause, G Palla` | ||
| - [Materials](https://github.com/theislab/scanpy-tutorials/tree/master/scanpy_workshop) and [recordings](https://www.youtube.com/playlist?list=PL4rcQcNPLZxWQQH7LlRBMkAo5NWuHX1e3) for Scanpy workshops by Maren Büttner | ||
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| ```{rubric} Experimental module | ||
| ``` | ||
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| - Added {mod}`scanpy.experimental` module! Currently contains functionality related to pearson residuals in {mod}`scanpy.experimental.pp` {pr}`1715` {smaller}`J Lause, G Palla, I Virshup`. This includes: | ||
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| - {func}`~scanpy.experimental.pp.normalize_pearson_residuals` for Pearson Residuals normalization | ||
| - {func}`~scanpy.experimental.pp.highly_variable_genes` for HVG selection with Pearson Residuals | ||
| - {func}`~scanpy.experimental.pp.normalize_pearson_residuals_pca` for Pearson Residuals normalization and dimensionality reduction with PCA | ||
| - {func}`~scanpy.experimental.pp.recipe_pearson_residuals` for Pearson Residuals normalization, HVG selection and dimensionality reduction with PCA | ||
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| ```{rubric} Features | ||
| ``` | ||
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| - {func}`~scanpy.tl.filter_rank_genes_groups` now allows to filter with absolute values of log fold change {pr}`1649` {smaller}`S Rybakov` | ||
| - {func}`~scanpy.pl.embedding_density` now allows more than 10 groups {pr}`1936` {smaller}`A Wolf` | ||
| - {func}`~scanpy.logging.print_versions` now uses `session_info` {pr}`2089` {smaller}`P Angerer` {smaller}`I Virshup` | ||
| - `_choose_representation` now subsets the provided representation to n_pcs, regardless of the name of the provided representation (should affect mostly {func}`~scanpy.pp.neighbors`) {pr}`2179` {smaller}`I Virshup` {smaller}`PG Majev` | ||
| - Embedding plots now have a `dimensions` argument, which lets users select which dimensions of their embedding to plot and uses the same broadcasting rules as other arguments {pr}`1538` {smaller}`I Virshup` | ||
| - {func}`scanpy.external.pp.scrublet` (and related functions) can now be used on `AnnData` objects containing multiple batches {pr}`1965` {smaller}`J Manning` | ||
| - Number of variables plotted with {func}`~scanpy.pl.pca_loadings` can now be controlled with `n_points` argument. Additionally, variables are no longer repeated if the anndata has less than 30 variables {pr}`2075` {smaller}`Yves33` | ||
| - Dask arrays now work with {func}`scanpy.pp.normalize_total` {pr}`1663` {smaller}`G Buckley, I Virshup` | ||
| - {func}`~scanpy.pl.embedding_density` now allows more than 10 groups {pr}`1936` {smaller}`A Wolf` | ||
| - Embedding plots can now pass `colorbar_loc` to specify the location of colorbar legend, or pass `None` to not show a colorbar {pr}`1821` {smaller}`A Schaar` {smaller}`I Virshup` | ||
| - Embedding plots now have a `dimensions` argument, which lets users select which dimensions of their embedding to plot and uses the same broadcasting rules as other arguments {pr}`1538` {smaller}`I Virshup` | ||
| - {func}`~scanpy.logging.print_versions` now uses `session_info` {pr}`2089` {smaller}`P Angerer` {smaller}`I Virshup` | ||
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| ```{rubric} Experimental module | ||
| ```{rubric} Ecosystem | ||
| ``` | ||
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| - Added {mod}`scanpy.experimental` module! | ||
| Multiple packages have been added to our ecosystem page, including: | ||
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| - [decoupler](https://github.com/saezlab/decoupler-py) a for footprint analysis and pathway enrichement {pr}`2186` {smaller}`PB Mompel` | ||
| - [dandelion](https://github.com/zktuong/dandelion) for B-cell receptor analysis {pr}`1953` {smaller}`Z Tuong` | ||
| - [CIARA](https://github.com/ScialdoneLab/CIARA_python) a feature selection tools for identifying rare cell types {pr}`2175` {smaller}`M Stock` | ||
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| ```{rubric} Bug fixes | ||
| ``` | ||
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| - Added {func}`scanpy.experimental.pp.normalize_pearson_residuals` for Pearson Residuals normalization {pr}`1715` {smaller}`J Lause, G Palla, I Virshup` | ||
| - Added {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca` for Pearson Residuals normalization and PCA {pr}`1715` {smaller}`J Lause, G Palla, I Virshup` | ||
| - Added {func}`scanpy.experimental.pp.highly_variable_genes` for HVG selection with Pearson Residuals {pr}`1715` {smaller}`J Lause, G Palla, I Virshup` | ||
| - Added {func}`scanpy.experimental.pp.normalize_pearson_residuals_pca` for Pearson Residuals normalization and dimensionality reduction with PCA {pr}`1715` {smaller}`J Lause, G Palla, I Virshup` | ||
| - Added {func}`scanpy.experimental.pp.recipe_pearson_residuals` for Pearson Residuals normalization, HVG selection and dimensionality reduction with PCA {pr}`1715` {smaller}`J Lause, G Palla, I Virshup` | ||
| - Fixed finding variables with `use_raw=True` and `basis=None` in {func}`scanpy.pl.scatter` {pr}`2027` {smaller}`E Rice` | ||
| - Fixed {func}`scanpy.external.pp.scrublet` to address {issue}`1957` {smaller}`FlMai` and ensure raw counts are used for simulation | ||
| - Functions in {mod}`scanpy.datasets` no longer throw `OldFormatWarnings` when using `anndata` `0.8` {pr}`2096` {smaller}`I Virshup` | ||
| - Fixed use of {func}`scanpy.pp.neighbors` with `method='rapids'`: RAPIDS cuML no longer returns a squared Euclidean distance matrix, so we should not square-root the kNN distance matrix. {pr}`1828` {smaller}`M Zaslavsky` | ||
| - Removed `pytables` dependency by implementing `read_10x_h5` with `h5py` due to installation errors on Windows {pr}`2064` | ||
| - Fixed bug in {func}`scanpy.external.pp.hashsolo` where default value was set improperly {pr}`2190` {smaller}`B Reiz` | ||
| - Fixed bug in {func}`scanpy.pl.embedding` functions where an error could be raised when there were missing values and large numbers of categories {pr}`2187` {smaller}`I Virshup` |
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