fix code style issues

Author: CunliangGeng

README.md

@@ -3,19 +3,19 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3232888.svg)](https://doi.org/10.5281/zenodo.3232888)
 [![Travis](https://secure.travis-ci.org/DeepRank/pdb2sql.svg?branch=master)](https://travis-ci.org/DeepRank/pdb2sql)
 [![Coverage Status](https://coveralls.io/repos/github/DeepRank/pdb2sql/badge.svg)](https://coveralls.io/github/DeepRank/pdb2sql)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/7cce335b21cc49d6bb3ff9878d6ac904)](https://www.codacy.com/manual/CunliangGeng/pdb2sql?utm_source=github.com&utm_medium=referral&utm_content=DeepRank/pdb2sql&utm_campaign=Badge_Grade)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/7cce335b21cc49d6bb3ff9878d6ac904)](https://www.codacy.com/manual/CunliangGeng/pdb2sql?utm_source=github.com&utm_medium=referral&utm_content=DeepRank/pdb2sql&utm_campaign=Badge_Grade)
 [![Documentation Status](https://readthedocs.org/projects/pdb2sql/badge/?version=latest)](https://pdb2sql.readthedocs.io/en/latest/?badge=latest)
 
-
 PDB2SQL is a Python package that allows to use SQL queries to handle PDB files.
 This project grew out of the developement of DeepRank.
 
-- Source code: https://github.com/DeepRank/pdb2sql
-- Documentation: https://pdb2sql.readthedocs.io
+-   Source code: <https://github.com/DeepRank/pdb2sql>
+-   Documentation: <https://pdb2sql.readthedocs.io>
 
 It provides:
-- a powerful `pdb2sql` object to manipulate PDB data in SQL database
-- strcuture transformation functions (rotations, translations...)
-- useful capablities to
-  - calculate structure interface (contact atoms and residues)
-  - calculate structure similarity (iRMSD, lRMSD, FNAT, DockQ...)
+
+-   a powerful `pdb2sql` object to manipulate PDB data in SQL database
+-   strcuture transformation functions (rotations, translations...)
+-   useful capablities to
+    -   calculate structure interface (contact atoms and residues)
+    -   calculate structure similarity (iRMSD, lRMSD, FNAT, DockQ...)

docs/source/backup.py

@@ -10,6 +10,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import pdb2sql
 import os
 import sys
 
@@ -27,7 +28,6 @@
 copyright = '2019, Netherlands eScience Center'
 author = 'Nicolas Renaud'
 
-import pdb2sql
 # The full version, including alpha/beta/rc tags
 release = pdb2sql.__version__
 
@@ -100,14 +100,14 @@
     'numpy': ('http://docs.scipy.org/doc/numpy/', None)
 }
 
-## autosummary
+# autosummary
 # Make _autosummary files and include them
 autosummary_generate = True
 # autosummary_imported_members = True
 
 
-## ipython
+# ipython
 ipython_warning_is_error = False
 ipython_execlines = [
     "import numpy as np",
-]
+]