Merge remote-tracking branch 'origin/master'

multipaths · Mar 12, 2020 · 6d308d5 · 6d308d5
2 parents 156fba0 + b23d4cc
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diff --git a/README.rst b/README.rst
@@ -41,16 +41,18 @@ Generates the regularised Laplian kernel of a given graph.
 
 References
 ----------
-.. [1] Picart-Armada, S., *et al.* (2017). `Null diffusion-based enrichment for metabolomics data <https://doi.org/10.1371/journal.pone.0189012>`_. *PloS one* 12.12.
+.. [1] Picart-Armada, S., *et al.* (2017). `Null diffusion-based enrichment for metabolomics data
+   <https://doi.org/10.1371/journal.pone.0189012>`_. *PloS one* 12.12.
 
 Disclaimer
 ----------
-DiffuPy is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.
+DiffuPy is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or
+guarantee of maintenance, support, or back-up of data.
 
 .. |build| image:: https://travis-ci.com/multipaths/diffupy.svg?branch=master
     :target: https://travis-ci.com/multipaths/diffupy
     :alt: Build Status
-    
+
 .. |docs| image:: http://readthedocs.org/projects/diffupy/badge/?version=latest
     :target: https://diffupy.readthedocs.io/en/latest/
     :alt: Documentation Status

diff --git a/docs/source/diffusion.rst b/docs/source/diffusion.rst
@@ -76,8 +76,20 @@ Summary table of methods with statistical normalization
 +-------------+----------+----------+----------+---------------+----------------+----------------+---------------------+
 
 
-.. automodule:: diffupy.diffusion
+.. automodule:: diffupy.diffuse
    :members:
 
-.. automodule:: diffupy.diffusion_raw
+.. automodule:: diffupy.diffuse_raw
    :members:
+
+References
+----------
+1. Bersanelli, M. et al. (2016). Network diffusion-based analysis of high-throughput data for the detection of
+differentially enriched modules. Scientific Reports. (6), 34841.
+2. Harchaoui, Z., et al. (2013). Kernel-based methods for hypothesis testing: a unified view. IEEE Signal Processing
+Magazine. (30), 87–97.
+3. Mostafavi, S., et al. (2008). Genemania: a real-time multiple association network integration algorithm for
+predicting gene function.Genome Biology. (9), S4.
+4. Tsuda, K., et al. (2005).  Fast  protein  classification  with  multiple  networks. Bioinformatics, (21), 59–65.
+5. Vandin, F., et al. (2010). Algorithms for detecting significantly mutated pathways in cancer. Lecture Notes in
+Computer Science. 6044, 506–521.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,7 +1,7 @@
 DiffuPy |release| Documentation
 ===============================
 DiffuPy is a generalizable Python implementation of the numerous label propagation algorithms inspired by the diffuStats
-R package [1]. DiffuPy supports generic graph formats such as JSON, CSV, GraphML, or GML.
+R package [1]_. DiffuPy supports generic graph formats such as JSON, CSV, GraphML, or GML.
 
 Installation is as easy as getting the code from `PyPI <https://pypi.python.org/pypi/diffupy>`_ with
 :code:`python3 -m pip install diffupy`. See the :doc:`installation <installation>` documentation.
@@ -21,15 +21,15 @@ Installation is as easy as getting the code from `PyPI <https://pypi.python.org/
 
    installation
    cli
-   kernel
+   kernels
    diffusion
    constants
    matrix
 
 References
 ----------
 .. [1] Picart-Armada, S., *et al.* (2017). `Null diffusion-based enrichment for metabolomics data
-<https://doi.org/10.1371/journal.pone.0189012>`_. *PloS one* 12.12.
+   <https://doi.org/10.1371/journal.pone.0189012>`_. *PloS one* 12.12.
 
 Disclaimer
 ----------

diff --git a/docs/source/kernel.rst → docs/source/kernels.rst b/docs/source/kernel.rst → docs/source/kernels.rst
@@ -2,5 +2,5 @@ Kernel
 ======
 Pool of kernels available at DiffuPy.
 
-.. automodule:: diffupy.kernel
+.. automodule:: diffupy.kernels
    :members:
diff --git a/setup.cfg b/setup.cfg
@@ -51,7 +51,6 @@ install_requires =
     numpy
     scipy
     pybel==0.13.2
-    pybel_tools
 
 # Random options
 zip_safe = false

diff --git a/src/diffupy/utils.py b/src/diffupy/utils.py
@@ -37,7 +37,7 @@ def set_diagonal_matrix(matrix, d):
     return matrix
 
 
-def get_label_node(node: nx.Graph.node) -> str:
+def get_label_node(node: pybel.dsl.BaseAbundance) -> str:
     """Get label node."""
     if hasattr(node, 'name') and node.name is not None:
         if node.name.lower() == "":
@@ -144,7 +144,7 @@ def print_dict_dimensions(entities_db, title):
     print(f'Total: {total} ')
 
 
-def get_simplegraph_from_multigraph(multigraph):
+def get_simple_graph_from_multigraph(multigraph):
     """Convert undirected graph from multigraph."""
     graph = nx.Graph()
     for u, v, data in multigraph.edges(data=True):