Fix documentation issues [ci skip] (#929)

* Update `CONTRIBUTING.rst` [ci skip]

Update branch name convention.

* Update `docs/requirements.txt` [ci skip]

Pin `Jinja` version.

* Update `docs/source/conf.py` [ci skip]

Update `add_stylesheet` with `add_css_file`. The former is deprecated.

* Fix typo in `index.rst` [ci skip]

* Fix link to bone marrow dataset [ci skip]

* Fix `velocity_embedding` docs [ci skip]

CONTRIBUTING.rst

@@ -22,7 +22,7 @@ You can now clone your fork of scVelo and install the development mode
     git clone https://github.com/YOUR-USER-NAME/scvelo.git
     cd scvelo
     git checkout --track origin/develop
-    
+
 
 Unix Systems
 ^^^^^^^^^^^^
@@ -90,7 +90,7 @@ Submitting pull requests
 
 New features and bug fixes are added to the code base through a pull request (PR). To implement a feature or bug fix, create a branch from `develop`. For hotfixes use `master` as base. The existence of bugs suggests insufficient test coverage. As such, bug fixes should, ideally, include a unit test or extend an existing one. Please ensure that
 
-- branch names have the prefix `feat/`, `bug/` or `hotfix/`.
+- branch names have the prefix `feat/` or `fix/`.
 - your code follows the project conventions.
 - newly added functions are unit tested.
 - all tests pass locally.

docs/requirements.txt

@@ -6,8 +6,9 @@ typing_extensions
 importlib_metadata
 sphinx_rtd_theme>=0.3
 sphinx_autodoc_typehints<=1.6
+Jinja2<3.1
 
 # converting notebooks to html
 ipykernel
 sphinx>=1.7,<4.0
-nbsphinx>=0.7,<0.8.7
+nbsphinx>=0.7,<0.8.7

docs/source/conf.py

@@ -148,7 +148,7 @@
 
 
 def setup(app):
-    app.add_stylesheet("custom.css")
+    app.add_css_file("custom.css")
 
 
 # -- Options for other output ------------------------------------------

docs/source/index.rst

@@ -16,7 +16,7 @@ scVelo generalizes the concept of RNA velocity
 by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
 transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
 
-scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
+scVelo is compatible with Scanpy_ and hosts efficient implementations of all RNA velocity models.
 
 scVelo's key applications
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -104,7 +104,7 @@ For further information visit `scvelo.org <https://scvelo.org>`_.
 .. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=master
    :target: https://travis-ci.org/theislab/scvelo
 
-.. _scanpy: https://scanpy.readthedocs.io
+.. _Scanpy: https://scanpy.readthedocs.io
 
 .. _calendly: https://calendly.com/scvelo
 

scvelo/datasets/_datasets.py

@@ -20,7 +20,7 @@ def bonemarrow(
 ):
     """Human bone marrow.
 
-    Data from `Setty et al. (2019) <https://doi.org/10.1242/dev.173849>`__.
+    Data from `Setty et al. (2019) <https://doi.org/10.1038/s41587-019-0068-4>`__.
 
     The bone marrow is the primary site of new blood cell production or haematopoiesis.
     It is composed of hematopoietic cells, marrow adipose tissue, and supportive stromal

scvelo/tools/velocity_embedding.py

@@ -46,15 +46,17 @@ def velocity_embedding(
     """Projects the single cell velocities into any embedding.
 
     Given normalized difference of the embedding positions
-    :math:
-    `\\tilde \\delta_{ij} = \\frac{x_j-x_i}{\\left\\lVert x_j-x_i \\right\\rVert}`.
+
+    .. math::
+        \\tilde \\delta_{ij} = \\frac{x_j-x_i}{\\left\\lVert x_j-x_i \\right\\rVert},
+
     the projections are obtained as expected displacements with respect to the
     transition matrix :math:`\\tilde \\pi_{ij}` as
 
     .. math::
         \\tilde \\nu_i = E_{\\tilde \\pi_{i\\cdot}} [\\tilde \\delta_{i \\cdot}]
-        = \\sum_{j \\neq i} \\left( \\tilde \\pi_{ij} - \\frac1n \\right) \\tilde \\
-        delta_{ij}.
+        = \\sum_{j \\neq i} \\left( \\tilde \\pi_{ij} - \\frac1n \\right) \\tilde
+        \\delta_{ij}.
 
 
     Arguments