Reuse Sphinx environment again

Enabled the reuse of the sphinx environment again.
Fixed issue with build order for webpage and manual, and fixed minor
link error in user-guide.

Change-Id: I12c7fa1c2e93c3bcb92db85ba526c8cd65dd6339

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index e9742372813c54b8746bf16972bc9f0e0c0fe821..de8bd2e8aa6faf446284189adf93a5a0a68242b8 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -543,7 +543,7 @@ if (SPHINX_FOUND)
     add_custom_target(install-guide
         COMMAND
             ${SPHINX_EXECUTABLE}
-            -q -E -b text
+            -q -b text
             -w sphinx-install.log
             -d ${CMAKE_CURRENT_BINARY_DIR}/install-guide/_doctrees
             -c ${SPHINX_INPUT_DIR}
@@ -566,12 +566,13 @@ if (SPHINX_FOUND)
     add_custom_target(webpage-sphinx
         DEPENDS sphinx-programs
         DEPENDS sphinx-input
-        DEPENDS sphinx-image-conversion 
+        DEPENDS sphinx-image-conversion
+        DEPENDS manual 
         COMMAND
             ${CMAKE_COMMAND} -E make_directory ${SPHINX_INPUT_DIR}/_static
         COMMAND
             ${SPHINX_EXECUTABLE}
-            -q -E -b html
+            -q -b html
             -w sphinx-html.log
             -d "${SPHINX_CACHE_DIR}"
             "${SPHINX_INPUT_DIR}"
@@ -585,7 +586,7 @@ if (SPHINX_FOUND)
     add_custom_target(man
         COMMAND
             ${SPHINX_EXECUTABLE}
-            -q -E -b man
+            -q -b man
             -w sphinx-man.log
             -d ${SPHINX_CACHE_DIR}
             -t do_man

diff --git a/docs/manual/CMakeLists.txt b/docs/manual/CMakeLists.txt
index b0788a3cd2ab78cd346d15f180bb23324286de92..6bcecd540a8f6fb83412c4672d7244d7cb53ba17 100644 (file)
--- a/docs/manual/CMakeLists.txt
+++ b/docs/manual/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -38,7 +38,7 @@ if(MANUAL_BUILD_IS_POSSIBLE)
         DEPENDS sphinx-programs sphinx-input
         COMMAND
             ${SPHINX_EXECUTABLE}
-            -q -E -b latex
+            -q -b latex
             -w sphinx-latex.log
             -d "${SPHINX_CACHE_DIR}"
             "${SPHINX_INPUT_DIR}"

diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst
index ec0cb9f1310d031512a5fb1e753bbb684cce0532..ead69bfce4fe30c8c451563bd72ade01d1c9d66a 100644 (file)
--- a/docs/user-guide/mdp-options.rst
+++ b/docs/user-guide/mdp-options.rst
@@ -1075,7 +1075,7 @@ Temperature coupling
    integrators, the leap-frog :mdp-value:`integrator=md` integrator
    only supports 1. Data for the NH chain variables is not printed
    to the :ref:`edr` file by default, but can be turned on with the
-   :mdp:`print-nose-hoover-chains` option.
+   :mdp:`print-nose-hoover-chain-variables` option.
 
 .. mdp:: print-nose-hoover-chain-variables
 
@@ -3050,7 +3050,7 @@ Electric fields
    E(t) = E0 exp ( -(t-t0)\ :sup:`2`/(2 sigma\ :sup:`2`) ) cos(omega (t-t0))
 
    For example, the four parameters for direction x are set in the
-   three fields of :mdp:`electric-field-x` (and similar for y and z)
+   three fields of ``electric-field-x`` (and similar for y and z)
    like
 
    electric-field-x  = E0 omega t0 sigma