Fix some issues reported by 'make depcheck doccheck'

Fix some minor documentation issues and make swapcoords.h not installed,
since that is internal mdrun functionality.

There is a dependency issue in update.h including a non-installed
random/random.h, but this is planned to go away when the stateful RNG is
replaced in mdrun, so left it there for now.  User code probably doesn't
have much use for including update.h, anyways.

Change-Id: I491697f8528d9dd5da299f366ccccf7eecb46f8a

diff --git a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
index 8d02c5c82f85f97a88378cc9ddd589b5bfd1106b..4fb136f52c2624f62cfc127c6648f3682a2ae793 100644 (file)
--- a/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
+++ b/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
@@ -37,7 +37,7 @@
  * Tests for gmx::CommandLineProgramContext.
  *
  * \author Teemu Murtola <teemu.murtola@gmail.com>
- * \ingroup module_utility
+ * \ingroup module_commandline
  */
 #include <string>
 #include <vector>

diff --git a/src/gromacs/legacyheaders/physics.h b/src/gromacs/legacyheaders/physics.h
index 31d49a3747e4fe619816517ff0d56bca173184d0..6134f954b5d0faa87c8338356343e59ef7cfe2f5 100644 (file)
--- a/src/gromacs/legacyheaders/physics.h
+++ b/src/gromacs/legacyheaders/physics.h
@@ -44,7 +44,7 @@
  * be anywhere else in the code.
  */
 
-#include "gromacs/math/utilities.h"
+#include "../math/utilities.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/groupcoord.h b/src/gromacs/mdlib/groupcoord.h
index de7946b15d0404bf9e4b51ec8090780964ebf365..a664e343208793810299882c119c793aacee9bf9 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.h
+++ b/src/gromacs/mdlib/groupcoord.h
@@ -35,9 +35,8 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-/*! \file groupcoord.h
- *
- *  @brief Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
+/*! \libinternal \file
+ * \brief Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
  *
  *  This file contains functions to assemble the positions of a subset of the
  *  atoms and to do operations on it like determining the center of mass, or

diff --git a/src/gromacs/swap/CMakeLists.txt b/src/gromacs/swap/CMakeLists.txt
index 547143bddf45df1aa51a7ca283effb7f9bf42201..093d6e74eeb2df0c341974bd35e3ee3d9b86a06e 100644 (file)
--- a/src/gromacs/swap/CMakeLists.txt
+++ b/src/gromacs/swap/CMakeLists.txt
@@ -34,7 +34,3 @@
 
 file(GLOB SWAP_SOURCES *.cpp *.c)
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SWAP_SOURCES} PARENT_SCOPE)
-
-set(SWAP_PUBLIC_HEADERS
-    swapcoords.h)
-gmx_install_headers(timing ${SWAP_PUBLIC_HEADERS})

diff --git a/src/gromacs/swap/swapcoords.h b/src/gromacs/swap/swapcoords.h
index bf30894f8aa2f3ad0489c0321b8e5f0af27ae9de..ea4c9915e95728302abe86b738c097cf8d5c99fc 100644 (file)
--- a/src/gromacs/swap/swapcoords.h
+++ b/src/gromacs/swap/swapcoords.h
@@ -33,7 +33,6 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
 /*! \defgroup module_swap "Computational Electrophysiology" position swapping (swap)
  * \ingroup group_mdrun
  * \brief
@@ -41,13 +40,14 @@
  *
  * \author Carsten Kutzner <ckutzne@gwdg.de>
  */
-/*! \file
+/*! \libinternal \file
  * \brief
  * The "Computational Electrophysiology" protocol for ion/water position swapping.
  *
- * \ingroup group_mdrun
+ * \author Carsten Kutzner <ckutzne@gwdg.de>
+ * \inlibraryapi
+ * \ingroup module_swap
  */
-
 #ifndef GMX_SWAP_SWAPCOORDS_H
 #define GMX_SWAP_SWAPCOORDS_H