Add sphinxcontrib-bibtex

.pre-commit-config.yaml

@@ -4,10 +4,10 @@ default_language_version:
 default_stages:
 -   commit
 -   push
-minimum_pre_commit_version: 2.9.0
+minimum_pre_commit_version: 2.9.3
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.790
+    rev: v0.800
     hooks:
     -   id: mypy
         additional_dependencies: [numpy>=1.15.0, scipy>=1.5.0, pandas]
@@ -70,13 +70,13 @@ repos:
     -   id: script-must-have-extension
         name: Check executable files use .sh extension
         types: [shell, executable]
-    -   id: shellcheck
+# -   id: shellcheck  # TODO: The hook `shellcheck` specifies `additional_dependencies` but is using language `script` which does not install an environment.  Perhaps you meant to use a specific language?
 -   repo: https://github.com/myint/rstcheck
-    rev: master
+    rev: 3f92957478422df87bd730abde66f089cc1ee19b
     hooks:
     -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.9.1
+    rev: v1.9.2
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==20.8b1]

.rstcheck.cfg

@@ -1,3 +1,3 @@
 [rstcheck]
-ignore_messages=Unknown target name:.*|No (directive|role) entry for "(auto)?(class|method|property|function|func|mod|module)" in module "docutils\.parsers\.rst\.languages\.en"\.
+ignore_messages=Unknown target name:.*|No (directive|role) entry for "(auto)?(bibliography|class|method|property|function|func|mod|module)" in module "docutils\.parsers\.rst\.languages\.en"\.
 report=info

docs/requirements.txt

@@ -6,3 +6,4 @@ sphinx-autodoc-typehints>=1.10.3
 sphinx_gallery
 sphinx_last_updated_by_git
 sphinx_rtd_theme
+sphinxcontrib-bibtex>=2.1.0

docs/source/conf.py

@@ -49,6 +49,7 @@
     "sphinx.ext.autosummary",
     "sphinx_last_updated_by_git",
     "sphinx_gallery.load_style",
+    "sphinxcontrib.bibtex",
     "edit_on_github",
     "typed_returns",
 ]
@@ -63,7 +64,7 @@
     matplotlib=("https://matplotlib.org/", None),
     seaborn=("https://seaborn.pydata.org/", None),
     joblib=("https://joblib.readthedocs.io/en/latest/", None),
-    networkx=("https://networkx.github.io/documentation/stable/", None),
+    networkx=("https://networkx.org/documentation/stable", None),
     astropy=("https://docs.astropy.org/en/stable/", None),
     esda=("https://pysal.org/esda/", None),
     dask=("https://docs.dask.org/en/latest/", None),
@@ -109,6 +110,10 @@
 # 403 Client Error: Forbidden for url: https://www.jstor.org/stable/2332142?origin=crossref
 linkcheck_ignore = ["https://doi.org/10.2307/2332142"]
 
+bibtex_bibfiles = ["references.bib"]
+bibtex_reference_style = ["author_year"]
+bibtex_default_style = "alpha"
+
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

docs/source/index.rst

@@ -29,7 +29,6 @@ Squidpy
 
    auto_examples/index.rst
 
-
 .. |PyPI| image:: https://img.shields.io/pypi/v/squidpy.svg
     :target: https://img.shields.io/pypi/v/squidpy.svg
     :alt: PyPI

docs/source/references.bib

@@ -0,0 +1,51 @@
+@article {celloracle,
+	author = {Kamimoto, Kenji and Hoffmann, Christy M. and Morris, Samantha A.},
+	title = {CellOracle: Dissecting cell identity via network inference and in silico gene perturbation},
+	journal = {bioRxiv},
+	year = {2020},
+	publisher = {Cold Spring Harbor Laboratory},
+	doi = {10.1101/2020.02.17.947416}
+}
+
+@article{cellphonedb,
+  author={Efremova, Mirjana and Vento-Tormo, Miquel and Teichmann, Sarah A and Vento-Tormo, Roser},
+  title={CellPhoneDB: inferring cell--cell communication from combined expression of multi-subunit ligand--receptor complexes},
+  journal={Nature protocols},
+  year={2020},
+  volume={15},
+  number={4},
+  pages={1484--1506},
+  publisher={Nature Publishing Group},
+  doi = {10.1038/s41596-020-0292-x}
+}
+
+@incollection{pysal,
+  title={PySAL: A Python library of spatial analytical methods},
+  author={Rey, Sergio J and Anselin, Luc},
+  booktitle={Handbook of applied spatial analysis},
+  pages={175--193},
+  year={2010},
+  publisher={Springer},
+  doi = {10.1007/978-3-642-03647-7_11}
+}
+
+@article{omnipath,
+  title={OmniPath: guidelines and gateway for literature-curated signaling pathway resources},
+  author={T{\"u}rei, D{\'e}nes and Korcsm{\'a}ros, Tam{\'a}s and Saez-Rodriguez, Julio},
+  journal={Nature methods},
+  year={2016},
+  volume={13},
+  number={12},
+  pages={966--967},
+  publisher={Nature Publishing Group},
+  doi = {10.1038/nmeth.4077}
+}
+
+@techreport{networkx,
+  title={Exploring network structure, dynamics, and function using NetworkX},
+  author={Hagberg, Aric and Swart, Pieter and S Chult, Daniel},
+  year={2008},
+  place = {United States},
+  institution={Los Alamos National Lab.(LANL), Los Alamos, NM (United States)},
+  URL = {https://www.osti.gov/biblio/960616},
+}

docs/source/references.rst

@@ -1,32 +1,5 @@
-.. |br| raw:: html
-
-  <br/>
-
 References
-----------
-
-.. [CellOracle20]
-    Kamimoto, K., Hoffmann, C. M, Morris, S. A., |br|
-    *Dissecting cell identity via network inference and in silico gene perturbation*, |br|
-    `bioRxiv 2020.02.17.947416 <https://doi.org/10.1101/2020.02.17.947416>`__.
-
-.. [CellPhoneDB20] Efremova, M., Vento-Tormo, M., Teichmann, S. A. et al., |br|
-    *CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit
-    ligand–receptor complexes.*, |br|
-    `Nat Protoc 15, 1484–1506 (2020) <https://doi.org/10.1038/s41596-020-0292-x>`__.
-
-.. [Moran50] Rey, Sergio J. and Anselin, Luc, |br|
-    *PySAL: A Python Library of Spatial Analytical Methods*,  |br|
-    `The Review of Regional Studies, vol. 37, 1, 2007, pp. 17–23 <https://pysal.org/esda/index.html>`__.
-
-.. [OmniPath16] Türei, D., Korcsmáros, T., Saez-Rodriguez, J., |br|
-    *OmniPath: guidelines and gateway for literature-curated signaling pathway resources.*,  |br|
-    `Nat Methods 13, 966–967 (2016) <https://doi.org/10.1038/nmeth.4077>`__.
-
-.. [Visium] 10X Genomics |br|
-    `Visium <https://www.10xgenomics.com/products/spatial-gene-expression>`__.
+==========
 
-.. [NetworkX08]
-    Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, |br|
-    *Exploring Network Structure, Dynamics, and Function using NetworkX*, |br|
-    `SciPyProceedings_11 2008 <http://conference.scipy.org/proceedings/SciPy2008/paper_2/>`__.
+.. bibliography::
+   :cited:

squidpy/gr/_ligrec.py

@@ -231,8 +231,8 @@ def prepare(
         complex_policy
             Policy on how to handle complexes. Valid options are:
 
-                - `{cp.MIN.s!r}` - select gene with the minimum average expression.
-                  This is the same as in [CellPhoneDB20]_.
+                - `{cp.MIN.s!r}` - select gene with the minimum average expression. This is the same as in
+                  :cite:`cellphonedb`.
                 - `{cp.ALL.s!r}` - select all possible combinations between `{src!r}` and `{tgt!r}` complexes.
 
         Returns
@@ -320,7 +320,7 @@ def test(
         **kwargs: Any,
     ) -> Optional[LigrecResult]:
         """
-        Perform the permutation test as described in [CellPhoneDB20]_.
+        Perform the permutation test as described in :cite:`cellphonedb`.
 
         Parameters
         ----------
@@ -483,7 +483,7 @@ def _filter_interactions_complexes(self, complex_policy: ComplexPolicy) -> None:
             Policy on how to handle complexes. Valid options are:
 
                 - `{cp.MIN.s!r}` - select gene with the minimum average expression. This is the same as in
-                  [CellPhoneDB20]_.
+                  :cite:`cellphonedb`.
                 - `{cp.ALL.s!r}` - select all possible combinations between `{src!r}` and `{tgt!r}` complexes.
 
         Returns
@@ -571,7 +571,8 @@ def prepare(
         %(PT_prepare.parameters)s
         interactions_params
             Keyword arguments for :func:`omnipath.interactions.import_intercell_network` defining the interactions.
-            These datasets from [OmniPath16]_ are default: `omnipath`, `pathwayextra`, `kinaseextra`, `ligrecextra`.
+            These datasets from :cite:`omnipath` are used by default: `omnipath`, `pathwayextra`, `kinaseextra` and
+            `ligrecextra`.
         transmitter_params
             Keyword arguments for :func:`omnipath.interactions.import_intercell_network` defining the transmitter
             side of intercellular connections.
@@ -668,7 +669,7 @@ def _analysis(
     **kwargs: Any,
 ) -> TempResult:
     """
-    Run the analysis as described in [CellPhoneDB20]_.
+    Run the analysis as described in :cite:`cellphonedb`.
 
     This function runs the mean, percent and shuffled analysis.
 

squidpy/gr/build.py

@@ -38,13 +38,13 @@ def spatial_neighbors(
     coord_type
         Type of coordinate system. Can be one of the following:
 
-            - `{c.VISIUM!r}`: [Visium]_ coordinates.
+            - `{c.VISIUM!r}`: Visium coordinates.
             - `{c.GENERIC!r}`: generic coordinates.
 
         If `None`, use `{c.VISIUM!r}` if ``spatial_key`` is present in :attr:`anndata.AnnData.obsm`,
         otherwise use `{c.GENERIC!r}`.
     n_rings
-        Number of rings of neighbors for [Visium]_ data.
+        Number of rings of neighbors for Visium data.
     n_neigh
         Number of neighborhoods to consider for non-Visium data.
     radius

squidpy/gr/nhood.py

@@ -190,14 +190,14 @@ def centrality_scores(
     """
     Compute centrality scores per cluster or cell type.
 
-    Inspired by usage in  Gene Regulatory Networks (GRNs) in [CellOracle20]_.
+    Inspired by usage in  Gene Regulatory Networks (GRNs) in :cite:`celloracle`.
 
     Parameters
     ----------
     %(adata)s
     %(cluster_key)s
     score
-        Centrality measures as described in :class:`networkx.algorithms.centrality` [NetworkX08]_.
+        Centrality measures as described in :class:`networkx.algorithms.centrality` :cite:`networkx`.
         If `None`, use all the options below. Valid options are:
 
             - `{c.CLOSENESS.s!r}` - measure of how close the group is to other nodes.

squidpy/gr/ppatterns.py

@@ -159,10 +159,10 @@ def moran(
     %(conn_key)s
     genes
         List of gene names, as stored in :attr:`anndata.AnnData.var_names`, used to compute Moran's I statistics
-        [Moran50]_.
+        :cite:`pysal`.
 
-        If `None`, it's computed for `'highly_variable'` in :attr:`anndata.AnnData.var`, if present.
-        Otherwise, it's computed for all genes.
+        If `None`, it's computed :attr:`anndata.AnnData.var` ``['highly_variable']``, if present. Otherwise,
+        it's computed for all genes.
     transformation
         Transformation to be used, as reported in :class:`esda.Moran`. Default is `"B"`, binary.
     %(n_perms)s

squidpy/im/object.py

@@ -574,7 +574,7 @@ def interactive(
         Interactive view of this container. Screenshot of the canvas can be taken by
         :meth:`squidpy.pl.Interactive.screenshot`.
         """
-        from squidpy.pl import Interactive
+        from squidpy.pl import Interactive  # type: ignore[attr-defined]
 
         return Interactive(  # type: ignore[no-any-return]
             img=self,

squidpy/pl/_interactive/_controller.py

@@ -15,7 +15,7 @@
 
 from squidpy.im import ImageContainer  # type: ignore[attr-defined]
 from squidpy._docs import d
-from squidpy._utils import singledispatchmethod
+from squidpy._utils import singledispatchmethod  # type: ignore[attr-defined]
 from squidpy.pl._utils import _points_inside_triangles
 from squidpy.pl._interactive._view import ImageView
 from squidpy.pl._interactive._model import ImageModel

tox.ini

@@ -42,6 +42,7 @@ rst-roles =
     attr
     paramref
     ref
+    cite
 rst-directives =
     envvar
     exception
@@ -155,7 +156,7 @@ commands =
 [testenv:lint]
 description = Perform linting.
 basepython = python3.8
-deps = pre-commit>=2.9.0
+deps = pre-commit>=2.9.3
 skip_install = true
 commands = pre-commit run --all-files --show-diff-on-failure {posargs:}