Merge branch 'master' into 2.0.1-bugfix

joachimwolff · web-flow · commit 57a1351392cc · 2018-03-05T19:40:18.000+01:00
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,3 @@
+* [ ] Flake8 passes (`flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712`)
+* [ ] Local tests pass (`py.test hicexplorer --doctest-modules`)
+
diff --git a/README.rst b/README.rst
@@ -27,9 +27,11 @@ any type of genomic scores), long range contacts and the visualization of viewpo
 Citation:
 ^^^^^^^^^
 
+
 Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke. 
 **"High-resolution TADs reveal DNA sequences underlying genome organization in flies". Nature Communications**, Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w
 
+
 .. image:: ./docs/images/hicex2.png
 
 Installation
diff --git a/docs/content/list-of-tools.rst b/docs/content/list-of-tools.rst
@@ -4,6 +4,7 @@ HiCExplorer tools
 .. contents::
     :local:
 
+
 +--------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 | tool                           | type             | input files                       | main output file(s)                         | application                                                                       |
 +================================+==================+===================================+=============================================+===================================================================================+
@@ -142,3 +143,4 @@ Miscellaneous
 
 :ref:`hicExport`
 """"""""""""""""
+
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
 ---------
 

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	+* [ ] Flake8 passes (`flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F403,E402,F999,F405,E712`)
	`2`	+* [ ] Local tests pass (`py.test hicexplorer --doctest-modules`)
	`3`	`+`