Fixing read the docs

deeptools · Feb 13, 2018 · a9e10df · a9e10df
1 parent 1949f08
commit a9e10df
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Showing 5 changed files with 19 additions and 10 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -16,7 +16,7 @@
 import os
 import warnings
 
-warnings.filterwarnings("ignore")
+warnings.filterwarnings("ignore", category=DeprecationWarning)
 
 # to allow readthedocs to compile without installing some dependencies
 import mock
@@ -69,7 +69,7 @@
 
 # General information about the project.
 project = u'HiCExplorer'
-copyright = u'2017, Fidel Ramírez, Bjoern Gruening, Vivek Bhardwaj, Joachim Wolff'
+copyright = u'2018, Fidel Ramírez, Bjoern Gruening, Vivek Bhardwaj, Joachim Wolff'
 author = u'Fidel Ramírez, Bjoern Gruening, Vivek Bhardwaj, Joachim Wolff'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -179,7 +179,7 @@ def get_version():
 # 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".
-html_static_path = ['_static']
+html_static_path = []
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

diff --git a/docs/content/example_usage.rst b/docs/content/example_usage.rst
@@ -215,7 +215,7 @@ The A / B compartments can be plotted with :ref:`hicPlotMatrix`.
 
    $ hicPlotMatrix -m pearson_all.h5 --outFileName pca1.png --perChr --pca pca1.bedgraph
 
-.. figure:: ../images/eigenvector1_lieberman.png
-    :scale: 90 %
-    :align: center
+//.. figure:: ../images/eigenvector1_lieberman.png
+//    :scale: 90 %
+//    :align: center
 
diff --git a/docs/content/list-of-tools.rst b/docs/content/list-of-tools.rst
@@ -51,4 +51,8 @@ HiCExplorer tools
    |:ref:`hicMergeTADbins`          | preprocessing    | one Hi-C matrix, one BED file     | one Hi-C matrix                             | Uses a BED file of domains or TAD boundaries to merge the                         |
    |                                |                  |                                   |                                             | bin counts of a Hi-C matrix.                                                      |
    +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
-
+
+.. toctree::
+    :glob:
+
+    tools/*
diff --git a/docs/index.rst b/docs/index.rst
@@ -53,12 +53,15 @@ Contents:
 
 .. toctree::
    :maxdepth: 2
-
+   
    content/installation
    content/list-of-tools
    content/example_usage
    content/News
 
+
+
+
 Citation
 ---------
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,7 @@
 mock
-sphinx_rtd_theme
+sphinx_rtd_theme==0.2.4
 sphinx-argparse==0.2.1
-sphinx>=1.2.0
+sphinx==1.5.0
 CommonMark>=0.5.6
+pillow>=5.0
+docutils==0.12