Merge branch 'master' into fire

doc/utils/sphinx-config/conf.py

@@ -20,6 +20,7 @@ import os
 # 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.
 #sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
 
 # -- General configuration ------------------------------------------------
 
@@ -30,7 +31,10 @@ import os
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.mathjax', 'sphinx.ext.imgmath'
+    'sphinx.ext.mathjax',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.autodoc',
+    'table_from_list',
 ]
 # 2017-12-07: commented out, since this package is broken with Sphinx 16.x
 #             yet we can no longer use Sphinx 15.x, since that breaks with
@@ -323,3 +327,5 @@ import LAMMPSLexer
 from sphinx.highlighting import lexers
 
 lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
+
+sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))

doc/utils/sphinx-config/false_positives.txt

@@ -214,6 +214,7 @@ Berne
 Bertotti
 Bessarab
 Beutler
+Bext
 bgq
 Bh
 Biersack
@@ -1048,6 +1049,7 @@ Gunsteren
 Gunzenmuller
 Guo
 gw
+gyromagnetic
 gz
 gzipped
 Haak
@@ -1068,6 +1070,7 @@ Haswell
 Haugk
 Hayoun
 Hayre
+hbar
 hbcut
 hbn
 hbnewflag
@@ -1146,6 +1149,7 @@ ico
 icosahedral
 idealgas
 IDR
+idx
 ielement
 ieni
 ifdefs
@@ -1412,6 +1416,7 @@ Lammps
 LAMMPS
 lammpsplot
 Lamoureux
+Lande
 Landron
 langevin
 Langevin
@@ -1784,6 +1789,7 @@ mtk
 Mtotal
 muB
 Muccioli
+mui
 Mukherjee
 Mulders
 multi
@@ -2084,7 +2090,9 @@ Ouyang
 overlayed
 Ovito
 oxdna
+oxrna
 oxDNA
+oxRNA
 padua
 Padua
 palegoldenrod
@@ -2481,6 +2489,8 @@ Runge
 runtime
 Rutuparna
 rx
+ry
+rz
 Ryckaert
 Rycroft
 Rydbergs