From 405eb63a5133b8772927a207b108100083ac638d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 21 Jan 2020 11:39:29 -0500
Subject: [PATCH] update sphinx extension to automatically pad lists to fill
 tables and avoid errors processing the documentation

---
 doc/src/Commands_all.rst        | 12 +++++-------
 doc/src/Commands_bond.rst       |  5 -----
 doc/src/Commands_compute.rst    |  4 +---
 doc/src/Commands_fix.rst        |  4 ----
 doc/src/Commands_kspace.rst     |  1 -
 doc/src/Commands_pair.rst       |  1 -
 doc/src/_ext/table_from_list.py |  8 ++++++--
 7 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index 1576b23714..6e87ffbad6 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -132,10 +132,8 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`units <units>`
    * :doc:`variable <variable>`
    * :doc:`velocity <velocity>`
-   * :doc:`write\_coeff <write_coeff>`
-   * :doc:`write\_data <write_data>`
-   * :doc:`write\_dump <write_dump>`
-   * :doc:`write\_restart <write_restart>`
-   *
-   *
-   *
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`
+
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index 27ff2d19da..5412675ee4 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -47,7 +47,6 @@ OPT.
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
    * :doc:`table (o) <bond_table>`
-   *
 
 .. _angle:
 
@@ -89,7 +88,6 @@ OPT.
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`sdk (o) <angle_sdk>`
    * :doc:`table (o) <angle_table>`
-   *
 
 .. _dihedral:
 
@@ -127,8 +125,6 @@ OPT.
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
    * :doc:`table/cut <dihedral_table_cut>`
-   *
-   *
 
 .. _improper:
 
@@ -162,4 +158,3 @@ OPT.
    * :doc:`ring (o) <improper_ring>`
    * :doc:`sqdistharm <improper_sqdistharm>`
    * :doc:`umbrella (o) <improper_umbrella>`
-   *
diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
index 01943ac803..79f0e8d83f 100644
--- a/doc/src/Commands_compute.rst
+++ b/doc/src/Commands_compute.rst
@@ -163,6 +163,4 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`
-   *
-   *
-   *
+
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index c1c97b6e59..0b6b892b9d 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -240,7 +240,3 @@ OPT.
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
-   *
-   *
-   *
-   *
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index 3a23520171..be953c5277 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -37,4 +37,3 @@ OPT.
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
-   *
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index 1d4f832015..28f50bfd8e 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -257,4 +257,3 @@ OPT.
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`
-   *
diff --git a/doc/src/_ext/table_from_list.py b/doc/src/_ext/table_from_list.py
index 715a3c2488..da82069d87 100644
--- a/doc/src/_ext/table_from_list.py
+++ b/doc/src/_ext/table_from_list.py
@@ -1,6 +1,6 @@
 from docutils import nodes
 from sphinx.util.docutils import SphinxDirective
-from docutils.nodes import Element, Node
+from docutils.nodes import Element, Node, list_item
 from typing import Any, Dict, List
 from sphinx import addnodes
 from sphinx.util import logging
@@ -26,8 +26,12 @@ class TableFromList(SphinxDirective):
             raise SphinxError('table_from_list content is not a list')
         fulllist = node.children[0]
 
+        # fill list with empty items to have a number of entries
+        # that is divisible by ncolumns
         if (len(fulllist) % ncolumns) != 0:
-            raise SphinxError('number of list elements not a multiple of column number')
+            missing = int(ncolumns - (len(fulllist) % ncolumns))
+            for i in range(0,missing):
+                fulllist += list_item()
 
         table = nodes.table()
         tgroup = nodes.tgroup(cols=ncolumns)