Finalize release notes (#1905)

* update release notes * Update release-latest * Add Development processes section to 1.8 release notes * Fix warnings from matrixplot * Update docs/release-notes/1.8.0.rst Co-authored-by: Giovanni Palla <[email protected]>
scverse · Jun 29, 2021 · f732706 · f732706
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diff --git a/docs/release-notes/1.7.3.rst b/docs/release-notes/1.7.3.rst
diff --git a/docs/release-notes/1.8.0.rst b/docs/release-notes/1.8.0.rst
@@ -1,33 +1,41 @@
-1.8.0 :small:`the future`
+1.8.0 :small:`2021-06-28`
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. rubric:: Features
-
-- Switched to flit_ for building and deploying the package,
-  a simple tool with an easy to understand command line interface and metadata.
-- Added `layer` and `copy` kwargs to :func:`~scanpy.pp.normalize_total` :pr:`1667` :smaller:`I Virshup`
-- Added `vcenter` and `norm` arguments to the plotting functions :pr:`1551` :smaller:`G Eraslan`
-- Standardized and expanded available arguments to the `sc.pl.rank_genes_groups*` family of functions. :pr:`1529` :smaller:`F Ramirez` :smaller:`I Virshup`
-  - See examples sections of :func:`~scanpy.pl.rank_genes_groups_dotplot` and :func:`~scanpy.pl.rank_genes_groups_matrixplot` for demonstrations.
-- :func:`scanpy.tl.tsne` now supports the metric argument and records the passed parameters :pr:`1854` :smaller:`I Virshup`
-
-.. _flit: https://flit.readthedocs.io/en/latest/
-
 .. rubric:: Metrics module
 
 - Added :mod:`scanpy.metrics` module!
 
-    - Added :func:`scanpy.metrics.confusion_matrix` for comparing labellings :pr:`915` :smaller:`I Virshup`
     - Added :func:`scanpy.metrics.gearys_c` for spatial autocorrelation :pr:`915` :smaller:`I Virshup`
     - Added :func:`scanpy.metrics.morans_i` for global spatial autocorrelation :pr:`1740` :smaller:`I Virshup, G Palla`
+    - Added :func:`scanpy.metrics.confusion_matrix` for comparing labellings :pr:`915` :smaller:`I Virshup`
 
-.. rubric:: External tools
+.. rubric:: Features
+
+- Added `layer` and `copy` kwargs to :func:`~scanpy.pp.normalize_total` :pr:`1667` :smaller:`I Virshup`
+- Added `vcenter` and `norm` arguments to the plotting functions :pr:`1551` :smaller:`G Eraslan`
+- Standardized and expanded available arguments to the `sc.pl.rank_genes_groups*` family of functions. :pr:`1529` :smaller:`F Ramirez` :smaller:`I Virshup`
+  - See examples sections of :func:`~scanpy.pl.rank_genes_groups_dotplot` and :func:`~scanpy.pl.rank_genes_groups_matrixplot` for demonstrations.
+- :func:`scanpy.tl.tsne` now supports the metric argument and records the passed parameters :pr:`1854` :smaller:`I Virshup`
 
 .. rubric:: Ecosystem
 
 - Added `Cubé <https://github.com/connerlambden/Cube>`_ to ecosystem page :pr:`1878` :smaller:`C Lambden`
+- Added `triku` a feature selection method to the ecosystem page :pr:`1722` :smaller:`AM Ascensión`
+- Added `dorothea` and `progeny` to the ecosystem page :pr:`1767` :smaller:`P Badia-i-Mompel`
+
+.. rubric:: Documentation
+
+- Added :doc:`/community` page to docs :pr:`1856` :smaller:`I Virshup`
+- Added rendered examples to many plotting functions :issue:`1664` :smaller:`A Schaar` :smaller:`L Zappia` :smaller:`bio-la` :smaller:`L Hetzel` :smaller:`L Dony` :smaller:`M Buttner` :smaller:`K Hrovatin` :smaller:`F Ramirez` :smaller:`I Virshup` :smaller:`LouisK92` :smaller:`mayarali`
+- Integrated DocSearch_, a find-as-you-type documentation index search. :pr:`1754` :smaller:`P Angerer`
+- - Reorganized reference docs :pr:`1753` :smaller:`I Virshup`
+- Clarified docs issues for :func:`~scanpy.pp.neighbors`,
+  :func:`~scanpy.tl.diffmap`, :func:`~scanpy.pp.calculate_qc_metrics` :pr:`1680` :smaller:`G Palla`
+- Fixed typos in grouped plot doc-strings :pr:`1877` :smaller:`C Rands`
+- Extended examples for differential expression plotting. :pr:`1529` :smaller:`F Ramirez`
+  - See :func:`~scanpy.pl.rank_genes_groups_dotplot` or :func:`~scanpy.pl.rank_genes_groups_matrixplot` for examples.
 
-.. rubric:: Performance enhancements
+.. _docsearch: https://docsearch.algolia.com/
 
 .. rubric:: Bug fixes
 
@@ -37,22 +45,17 @@
 - Fixed errors and warnings from embedding plots with small numbers of categories after `sns.set_palette` was called :pr:`1886` :smaller:`I Virshup`
 - Fixed handling of `gene_symbols` argument in a number of `sc.pl.rank_genes_groups*` functions :pr:`1529` :smaller:`F Ramirez` :smaller:`I Virshup`
 - Fixed handling of `use_raw` for `sc.tl.rank_genes_groups` when no `.raw` is present :pr:`1895` :smaller:`I Virshup`
+- :func:`scanpy.pl.rank_genes_groups_violin` now works for `raw=False` :pr:`1669` :smaller:`M van den Beek`
+
+.. rubric:: Development processes
+
+- Switched to flit_ for building and deploying the package, a simple tool with an easy to understand command line interface and metadata :pr:`1527` :smaller:`P Angerer`
+- Use `pre-commit <https://pre-commit.com>`_ for style checks :pr:`1684` :pr:`1848` :smaller:`L Heumos` :smaller:`I Virshup`
+
+.. _flit: https://flit.readthedocs.io/en/latest/
 
 .. rubric:: Deprecations
 
 - Dropped support for Python 3.6. `More details here <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_. :pr:`1897` :smaller:`I Virshup`
 - Deprecated `layers` and `layers_norm` kwargs to :func:`~scanpy.pp.normalize_total` :pr:`1667` :smaller:`I Virshup`
 - Deprecated `MulticoreTSNE` backend for :func:`scanpy.tl.tsne` :pr:`1854` :smaller:`I Virshup`
-
-.. rubric:: Documentation
-
-- Added :doc:`/community` page to docs :pr:`1856` :smaller:`I Virshup`
-- Clarified docs issues for :func:`~scanpy.pp.neighbors`,
-  :func:`~scanpy.tl.diffmap`, :func:`~scanpy.pp.calculate_qc_metrics` :pr:`1680` :smaller:`G Palla`
-- Integrated DocSearch_, a find-as-you-type documentation index search. :pr:`1754` :smaller:`P Angerer`
-- Fixed typos in grouped plot doc-strings :pr:`1877` :smaller:`C Rands`
-- Extended examples for differential expression plotting. :pr:`1529` :smaller:`F Ramirez`
-  - See :func:`~scanpy.pl.rank_genes_groups_dotplot` or :func:`~scanpy.pl.rank_genes_groups_matrixplot` for examples.
-- Reorganized reference docs :pr:`1753` :smaller:`I Virshup`
-
-.. _docsearch: https://docsearch.algolia.com/
diff --git a/docs/release-notes/index.rst b/docs/release-notes/index.rst
@@ -3,6 +3,13 @@ Release notes
 
 .. include:: release-latest.rst
 
+Version 1.7
+-----------
+
+.. include:: /release-notes/1.7.2.rst
+.. include:: /release-notes/1.7.1.rst
+.. include:: /release-notes/1.7.0.rst
+
 Version 1.6
 -----------
 

diff --git a/docs/release-notes/release-latest.rst b/docs/release-notes/release-latest.rst
@@ -2,11 +2,3 @@ Version 1.8
 -----------
 
 .. include:: /release-notes/1.8.0.rst
-
-Version 1.7
------------
-
-.. include:: /release-notes/1.7.3.rst
-.. include:: /release-notes/1.7.2.rst
-.. include:: /release-notes/1.7.1.rst
-.. include:: /release-notes/1.7.0.rst
diff --git a/scanpy/plotting/_matrixplot.py b/scanpy/plotting/_matrixplot.py
@@ -188,6 +188,8 @@ def style(
         .. plot::
             :context: close-figs
 
+            import scanpy as sc
+
             adata = sc.datasets.pbmc68k_reduced()
             markers = ['C1QA', 'PSAP', 'CD79A', 'CD79B', 'CST3', 'LYZ']
 
@@ -197,7 +199,11 @@ def style(
         .. plot::
             :context: close-figs
 
-            sc.pl.MatrixPlot(adata, markers, groupby='bulk_labels').style(cmap='Blues', edge_color='none').show()
+            (
+                sc.pl.MatrixPlot(adata, markers, groupby='bulk_labels')
+                .style(cmap='Blues', edge_color='none')
+                .show()
+            )
 
         """