Docs 1.4.6 (scverse#1112)

* reorganized landing page and release notes * version 1.4.6 * added reference to sam docstring
tar-singh · Mar 17, 2020 · d47d373 · d47d373
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diff --git a/docs/conf.py b/docs/conf.py
@@ -145,5 +145,6 @@ def setup(app):
     # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
     ('py:class', 'seaborn.ClusterGrid'),
     # Won’t be documented
+    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
     ('py:class', 'scanpy._utils.Empty'),
 ]
diff --git a/docs/index.rst b/docs/index.rst
@@ -20,20 +20,22 @@
 .. _Genome Biology (2018): https://doi.org/10.1186/s13059-017-1382-0
 
 
-.. topic:: News - CZI grant :small:`2019-11-14`
+News - CZI grant :small:`2019-11-14`
+------------------------------------
 
-   Scanpy has been selected an `essential open source software for science`_ by
-   CZI among `32 projects`_, along with giants such as Scipy, Numpy, Pandas,
-   Matplotlib, scikit-learn, scikit-image/plotly, pip, jupyterhub/binder,
-   Bioconda, Seurat, Bioconductor, and others.
+Scanpy has been selected an `essential open source software for science`_ by
+CZI among `32 projects`_, along with giants such as Scipy, Numpy, Pandas,
+Matplotlib, scikit-learn, scikit-image/plotly, pip, jupyterhub/binder,
+Bioconda, Seurat, Bioconductor, and others.
 
 .. _essential open source software for science: https://chanzuckerberg.com/newsroom/chan-zuckerberg-initiative-awards-5-million-for-open-source-software-projects-essential-to-science/
 .. _32 projects: https://chanzuckerberg.com/eoss/proposals/
 
 
-.. topic:: Latest release - 1.4.5 :small:`2019-12-30`
+Latest release
+--------------
 
-   .. include:: release-latest.rst
+.. include:: release-latest.rst
 
 .. put references first so all references are resolved
 .. NO! there is a particular meaning to this sequence

diff --git a/docs/references.rst b/docs/references.rst
@@ -188,10 +188,14 @@ References
    *The emergent landscape of the mouse gut endoderm at single-cell resolution*
    `Nature <https://www.nature.com/articles/s41586-019-1127-1>`__.
 
-.. [Traag17] Traag (2017),
+.. [Traag17]  (2017),
    *Louvain*,
    `GitHub <https://doi.org/10.5281/zenodo.35117>`__.
 
+.. [Tarashansky19] Tarashansky (2019),
+   *Self-assembling manifolds in single-cell RNA sequencing data*,
+   `Elife <https://doi.org/10.7554/eLife.48994>`__.
+
 .. [Traag18] Traag *et al.* (2018),
    *From Louvain to Leiden: guaranteeing well-connected communities*
    `arXiv <https://arxiv.org/abs/1810.08473>`__.

diff --git a/docs/release-latest.rst b/docs/release-latest.rst
@@ -1,7 +1,29 @@
 .. role:: small
 .. role:: smaller
 
-Please install `scanpy==1.4.5.post1` instead of `scanpy==1.4.5`.
+1.4.6 :small:`2020-03-17`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. rubric:: Functionality in `external`
+
+- :func:`~scanpy.external.tl.sam` self-assembling manifolds [Tarashansky19]_ :pr:`903` :smaller:`A Tarashansky`
+- :func:`~scanpy.external.tl.harmony_timeseries` for trajectory inference on discrete time points :pr:`994` :smaller:`A Mousa`
+- :func:`~scanpy.external.tl.wishbone` for trajectory inference (bifurcations) :pr:`1063` :smaller:`A Mousa`
+
+.. rubric:: Code design
+
+- :mod:`~scanpy.pl.violin` now reads `.uns['colors_...']` :pr:`1029` :smaller:`michalk8`
+
+.. rubric:: Bug fixes
+
+- adapt :func:`~scanpy.tl.ingest` for UMAP 0.4 :pr:`1038` :pr:`1106` :smaller:`S Rybakov`
+- compat with matplotlib 3.1 and 3.2 :pr:`1090` :smaller:`I Virshup, P Angerer`
+- fix PAGA for new igraph :pr:`1037` :smaller:`P Angerer`
+- fix rapids compat of louvain :pr:`1079` :smaller:`LouisFaure`
+
+1.4.5 :small:`2019-12-30`
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Please install `scanpy==1.4.5.post3` instead of `scanpy==1.4.5`.
 
 .. rubric:: New functionality
 

diff --git a/docs/release-notes.rst b/docs/release-notes.rst
@@ -15,21 +15,6 @@ Release Notes
 Version 1.4
 -----------
 
-1.4.5.1 :small:`2020-02-13`
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. rubric:: New functionality
-
-- :func:`~scanpy.external.tl.harmony_timeseries` for trajectory detection and interpretation of scRNA-seq data measured at discrete time points :pr:`994`
-
-.. rubric:: Bug fixes
-
-- See the many PRs linked in the commits `1.4.5.post3...1.4.5.1`_.
-
-.. _1.4.5.post3...1.4.5.1: https://github.com/theislab/scanpy/compare/1.4.5.post3...1.4.5.1
-
-1.4.5 :small:`2019-12-30`
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
 .. include:: release-latest.rst
 
 1.4.4 :small:`2019-07-20`

diff --git a/scanpy/external/tl/_sam.py b/scanpy/external/tl/_sam.py
@@ -30,7 +30,7 @@ def sam(
     verbose: bool = True,
 ) -> Union[SAM, Tuple[SAM, AnnData]]:
     """\
-    Self-Assembling Manifolds single-cell RNA sequencing analysis tool.
+    Self-Assembling Manifolds single-cell RNA sequencing analysis tool [Tarashansky19]_.
 
     SAM iteratively rescales the input gene expression matrix to emphasize
     genes that are spatially variable along the intrinsic manifold of the data.