v 0.1.0

BioPandas · Nov 24, 2015 · dd3c07f · dd3c07f
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diff --git a/biopandas/pdb/tests/test_read_pdb.py b/biopandas/pdb/tests/test_read_pdb.py
@@ -64,9 +64,9 @@ def test__construct_df():
     exp = pd.Series(np.array(['ATOM', 1, '', 'N', '', 'SER', '', 'A', 2, '', '',
               2.527, 54.656, -1.667, 1.0, 52.73, '', '', 'N', None, 609]),
           index=['record_name', 'atom_number', 'blank_1',
-                 'atom_name', 'alt_loc', 'resi_name',
-                 'blank_2', 'chain_id', 'resi_number',
-                 'resi_insert_code', 'blank_3',
+                 'atom_name', 'alt_loc', 'residue_name',
+                 'blank_2', 'chain_id', 'residue_number',
+                 'insertion', 'blank_3',
                  'x_coord', 'y_coord', 'z_coord',
                  'occupancy', 'b_factor', 'blank_4',
                  'segment_id', 'element_symbol',

diff --git a/docs/make_api.py b/docs/make_api.py
@@ -251,9 +251,7 @@ def _generate_preamble(package, subpackages):
 
     yield "# `%s` API Documentation" % package
 
-    yield """<br><br>
-#### Table of Contents
-"""
+    yield """#### Table of Contents"""
     #yield _doc(_import_module(package))
 
     # Table of contents: list of modules.
@@ -289,7 +287,7 @@ def _generate_preamble(package, subpackages):
 
         yield ""
 
-    yield "<hr><br><br>"
+    yield "<hr>"
 
 
 def _generate_paragraphs(package, subpackages):
@@ -315,24 +313,20 @@ def _generate_paragraphs(package, subpackages):
             yield "## {}".format(_full_name(subpackage, klass))
             yield _doc(klass)
 
-            yield """<br>
-### Methods"""
+            yield """### Methods"""
             for method in _iter_methods(klass, package):
                 s = _doc_method(klass, method)
                 header = s.strip('`').split('(')[0]
-                yield """<br>
-####%s
+                yield """####%s
 
 %s
 """ % (header, s)
 #                yield """<br>
 ###### %s""" % _doc_method(klass, method)
 
-            yield """<br>
-### Properties"""
+            yield """### Properties"""
             for prop in _iter_properties(klass, package):
-                yield """<br>
-#### %s""" % _doc_property(klass, prop)
+                yield """#### %s""" % _doc_property(klass, prop)
 
 
 def _print_paragraph(paragraph):

diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -13,6 +13,7 @@ markdown_extensions:
   - extra
   - tables
   - fenced_code
+  - mathjax
 extra_javascript:
   - https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML
   - mathjaxhelper.js

diff --git a/docs/sources/CONTRIBUTING.md b/docs/sources/CONTRIBUTING.md
@@ -111,9 +111,3 @@ To deploy the documentation, execute
 ```bash
 ~/github/biopandas/docs$ mkdocs gh-deploy --clean
 ```
-
-and
-
-```bash
-~/github/biopandas/docs$ python setup.py upload_docs --upload-dir=site
-```
diff --git a/docs/sources/api/biopandas.pdb.md b/docs/sources/api/biopandas.pdb.md
@@ -1,9 +1,7 @@
 # `biopandas` API Documentation
 
-<br><br>
 #### Table of Contents
 
-
 <hr>
 **biopandas.pdb**
 
@@ -20,7 +18,7 @@ files in pandas DataFrames.<hr>
 * [PandasPDB.df](#pandaspdbdf)
 
 
-<hr><br><br>
+<hr>
 
 ## biopandas.pdb.PandasPDB
 
@@ -50,10 +48,8 @@ Object for working with Protein Databank structure files.
 
     PDB code
 
-<br>
 ### Methods
 
-<br>
 ####PandasPDB.fetch_pdb
 
 `PandasPDB.fetch_pdb(pdb_code)`
@@ -70,7 +66,6 @@ Fetches PDB file contents from the Protein Databank at rcsb.org.
 self
 
 
-<br>
 ####PandasPDB.get
 
 `PandasPDB.get(s, df=None, invert=False)`
@@ -102,7 +97,6 @@ Filter PDB DataFrames by properties
     Returns a DataFrame view on the filtered entries.
 
 
-<br>
 ####PandasPDB.read_pdb
 
 `PandasPDB.read_pdb(path)`
@@ -119,7 +113,6 @@ Read PDB files (unzipped or gzipped) from local drive
 self
 
 
-<br>
 ####PandasPDB.rmsd
 
 `PandasPDB.rmsd(df1, df2, s='main chain', invert=False)`
@@ -157,7 +150,6 @@ Compute the Root Mean Square Deviation between molecules.
     Root Mean Square Deviation between df1 and df2
 
 
-<br>
 ####PandasPDB.to_pdb
 
 `PandasPDB.to_pdb(path, records=None, gz=False, append_newline=True)`
@@ -188,10 +180,8 @@ Write record DataFrames to a PDB file or gzipped PDB file.
     Appends a new line at the end of the PDB file if True
 
 
-<br>
 ### Properties
 
-<br>
 #### PandasPDB.df
 
 Acccess dictionary of pandas DataFrames for PDB record sections.

diff --git a/docs/sources/extra.css b/docs/sources/extra.css
@@ -0,0 +1,14 @@
+h1, h2 {
+  margin-top:80px;
+  margin-bottom:30px;
+}
+
+ h3, h4 {
+   margin-top:50px;
+   margin-bottom:10px;
+ }
+
+h5, h6{
+   margin-top:30px;
+   margin-bottom:10px;
+ }