Include doi strings from zenodo during release

Add functionality to include doi strings
gathered from Zenodo into the release build
source code and manual. Actual registration
of the DOI has to be handled somewhere else.

Change-Id: I1ce4c913c313e56e77e031e742367420e25da36d

diff --git a/cmake/gmxVersionInfo.cmake b/cmake/gmxVersionInfo.cmake
index 5c28f3553abe408317604ff3d4df940de4370cb7..c39d4bc21c6db3597e3e86c5d5c84e4573ce5aae 100644 (file)
--- a/cmake/gmxVersionInfo.cmake
+++ b/cmake/gmxVersionInfo.cmake
@@ -76,6 +76,13 @@
 #   REGRESSIONTEST_MD5SUM
 #       The MD5 checksum of the regressiontest tarball. Only used when building
 #       from a source package.
+#   GMX_SOURCE_DOI_ID
+#       ID collected from Zenodo connected to the doi for a released version
+#       used to identify the source when building an official released version.
+#       This ID is used for the source code tarball.
+#   GMX_MANUAL_DOI_ID
+#       Same as above, but for the reference manual.
+# Setting and retrieving of those variables is handled in gmxCheckReleaseDOI.cmake
 # They are collected into a single section below.
 # The following variables are set based on these:
 #   GMX_VERSION            String composed from GMX_VERSION_* numeric variables
@@ -101,6 +108,8 @@
 # tree is a git, but can be disabled with
 #   GMX_GIT_VERSION_INFO           Advanced CMake variable to disable git
 #                                  version info generation.
+# If the version generation is disabled, then the source and manual doi
+# will be based on the stored values for the ID.
 # The main interface to this machinery is the gmx_configure_version_file()
 # CMake function.  The signature is
 #   gmx_configure_version_file(<input> <output>
@@ -245,6 +254,13 @@ if (CMAKE_SCRIPT_MODE_FILE)
     return()
 endif()
 
+# Set those values only in release versions, after getting the identifiers
+# from Zenodo for the manual and source code
+# Has to be done by hand before every final release
+# Use force to override anything given as a cmake command line input
+set(GMX_MANUAL_DOI "" CACHE INTERNAL "reserved doi for GROMACS manual" FORCE)
+set(GMX_SOURCE_DOI "" CACHE INTERNAL "reserved doi for GROMACS source code" FORCE)
+
 #####################################################################
 # git version info management
 

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 6a773d85e106a077ebbc609bba1972ab6ae2a95c..644b5c3ec65fe7cc6931e53c1609519b6033c82c 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -375,6 +375,31 @@ if (SPHINX_FOUND)
     include(SphinxMacros.cmake)
     gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
 
+    # set temporary variables for doi inclusion
+    # into the manual, plain string + some wrapping
+    # for release builds, and dummy string for non-release
+    # builds
+    if("${GMX_MANUAL_DOI}" STREQUAL "")
+      # empty string means no doi, set dummy text
+      set(GMX_MANUAL_DOI_STRING "This is not a release build of GROMACS, so please reference")
+      set(GMX_MANUAL_DOI_STRING "${GMX_MANUAL_DOI_STRING} one of the GROMACS papers and the base release of the manual.")
+    else()
+      # release version, set plain old boring string
+      set(GMX_MANUAL_DOI_STRING "Please reference this documentation as https://doi.org/${GMX_MANUAL_DOI}.")
+    endif()
+    # same for source doi, but modify the text
+    if("${GMX_SOURCE_DOI}" STREQUAL "")
+      # empty string means no release build
+      set(GMX_SOURCE_DOI_STRING "This is not a release build of GROMACS. Please reference one of the")
+      set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} GROMACS papers, as well as the base release that this version is built from.")
+      set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} Also, please state what modifcations have been performed or where the version")
+      set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} was sourced from.")
+    else()
+      # release version, give them a doi url string
+      set(GMX_SOURCE_DOI_STRING "To cite the source code for this release, please cite")
+      set(GMX_SOURCE_DOI_STRING "${GMX_SOURCE_DOI_STRING} https://doi.org/${GMX_SOURCE_DOI}.")
+    endif()
+
     set(SPHINX_CONFIG_VARS_FILE ${SPHINX_INPUT_DIR}/conf-vars.py)
     gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
         EXTRA_VARS
@@ -387,6 +412,8 @@ if (SPHINX_FOUND)
             SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
             GMX_TNG_MINIMUM_REQUIRED_VERSION
             GMX_LMFIT_REQUIRED_VERSION
+            GMX_MANUAL_DOI_STRING
+            GMX_SOURCE_DOI_STRING
         COMMENT "Configuring Sphinx configuration file")
     gmx_add_sphinx_input_file(${SPHINX_CONFIG_VARS_FILE})
     gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})

diff --git a/docs/conf-vars.py.cmakein b/docs/conf-vars.py.cmakein
index 038014a7398cf78d9593f43623a7220107e2a042..e1c8b531c8c4fa6d5fd8c07c581c02e8dad89304 100644 (file)
--- a/docs/conf-vars.py.cmakein
+++ b/docs/conf-vars.py.cmakein
@@ -48,5 +48,7 @@ variables = [
         ('SOURCE_MD5SUM', '@SOURCE_MD5SUM@'),
         ('REGRESSIONTEST_MD5SUM', '@REGRESSIONTEST_MD5SUM_STRING@'),
         ('GMX_TNG_MINIMUM_REQUIRED_VERSION', '@GMX_TNG_MINIMUM_REQUIRED_VERSION@'),
-        ('GMX_LMFIT_REQUIRED_VERSION', '@GMX_LMFIT_REQUIRED_VERSION@')
+        ('GMX_LMFIT_REQUIRED_VERSION', '@GMX_LMFIT_REQUIRED_VERSION@'),
+        ('GMX_MANUAL_DOI_STRING', '@GMX_MANUAL_DOI_STRING@'),
+        ('GMX_SOURCE_DOI_STRING', '@GMX_SOURCE_DOI_STRING@')
     ]

diff --git a/docs/download.rst b/docs/download.rst
index c77ef35aa36670d6b0ed16a7688969004845cc27..8586bd89fc2b33e68da2956f5d2d94ce557006cb 100644 (file)
--- a/docs/download.rst
+++ b/docs/download.rst
@@ -3,6 +3,10 @@
 Downloads
 =========
 
+|GMX_MANUAL_DOI_STRING|
+
+|GMX_SOURCE_DOI_STRING|
+
 Source code
 -----------
 * |gmx-source-package-ftp|

diff --git a/docs/user-guide-old/index.rst b/docs/user-guide-old/index.rst
index 636c85f7c0f2dd07b3d70b9e679d47c7476f3f16..0890011729baaf7232931f30671c65cd059e6604 100644 (file)
--- a/docs/user-guide-old/index.rst
+++ b/docs/user-guide-old/index.rst
@@ -16,6 +16,10 @@ For getting, building and installing |Gromacs|, see the
 For background on algorithms and implementations, see the
 `reference manual`_.
 
+|GMX_MANUAL_DOI_STRING|
+
+|GMX_SOURCE_DOI_STRING|
+
 .. _reference manual: gmx-manual-parent-dir_
 
 .. toctree::

diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst
index 3c7ae2186549b20203a1fdd7f565b225e909ae81..036a5aecf4bdefb395392ee659505e65fad2d994 100644 (file)
--- a/docs/user-guide/index.rst
+++ b/docs/user-guide/index.rst
@@ -16,6 +16,10 @@ For getting, building and installing |Gromacs|, see the
 For background on algorithms and implementations, see the
 :ref:`reference manual part <gmx-reference-manual-rst>` of the documentation.
 
+|GMX_MANUAL_DOI_STRING|
+
+|GMX_SOURCE_DOI_STRING|
+
 .. TODO This is going to require more organization now that
    we are getting more content available.
 

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index b305b92326bf45e85b5baac028c4ba3d9d0080a9..5f9ad79b925affacb6c4ef1088d64e985382bf55 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -171,7 +171,10 @@ gmx_install_headers(
 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
 gmx_configure_version_file(
     utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
-    REMOTE_HASH)
+    REMOTE_HASH
+    EXTRA_VARS
+        GMX_SOURCE_DOI
+    )
 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
      $<TARGET_OBJECTS:libgromacs_external>
      $<TARGET_OBJECTS:libgromacs_generated>)

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 8b9d48d79571ebbea4729ce8369a8b7560ee5a67..1e8c85149a16fa63e59775fe6b9cdf9a952c2b28 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -525,6 +525,7 @@ int Mdrunner::mdrunner()
         please_cite(fplog, "Spoel2005a");
         please_cite(fplog, "Lindahl2001a");
         please_cite(fplog, "Berendsen95a");
+        writeSourceDoi(fplog);
     }
 
     std::unique_ptr<t_state> globalState;

diff --git a/src/gromacs/utility/baseversion-gen.cpp.cmakein b/src/gromacs/utility/baseversion-gen.cpp.cmakein
index b4c80730e3ae2c6ce6a4da819f8672426b30343f..441cefebd35f1d642c95773446a2ee9255eefc12 100644 (file)
--- a/src/gromacs/utility/baseversion-gen.cpp.cmakein
+++ b/src/gromacs/utility/baseversion-gen.cpp.cmakein
@@ -37,3 +37,4 @@
 const char _gmx_ver_string[] = "@GMX_VERSION_STRING_FULL@";
 const char _gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@";
 const char _gmx_central_base_hash[] = "@GMX_VERSION_CENTRAL_BASE_HASH@";
+const char gmxSourceDoiString[] = "@GMX_SOURCE_DOI@";

diff --git a/src/gromacs/utility/baseversion-gen.h b/src/gromacs/utility/baseversion-gen.h
index d7a0392731aeb7da44c0ef1d56ff0bedabb5bcef..1efca7a64e7c1eb7bb22b83219378f9f14c8b585 100644 (file)
--- a/src/gromacs/utility/baseversion-gen.h
+++ b/src/gromacs/utility/baseversion-gen.h
@@ -52,6 +52,15 @@ extern const char _gmx_ver_string[];
 extern const char _gmx_full_git_hash[];
 //! Full git hash of the latest commit in a central \Gromacs repository.
 extern const char _gmx_central_base_hash[];
+/*! \brief
+ *  DOI string for the \Gromacs source code populated by CMake.
+ *
+ *  The variable is populated with the generated DOI string
+ *  by CMake when the build of a release version is
+ *  requested by Jenkins. Allows identification and
+ *  referencing of different \Gromacs releases.
+ */
+extern const char gmxSourceDoiString[];
 
 //! \}
 //! \endcond

diff --git a/src/gromacs/utility/baseversion.cpp b/src/gromacs/utility/baseversion.cpp
index 05d1c18f82cbafdd1954129b8cc699589ab77603..1cf7cc0652fe6b7d4b5daa472ef3d6e65e5b8e14 100644 (file)
--- a/src/gromacs/utility/baseversion.cpp
+++ b/src/gromacs/utility/baseversion.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018, 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.
@@ -55,6 +55,11 @@ const char *gmx_version_git_central_base_hash()
     return _gmx_central_base_hash;
 }
 
+const char *gmxDOI()
+{
+    return gmxSourceDoiString;
+}
+
 #if GMX_DOUBLE
 void gmx_is_double_precision()
 {

diff --git a/src/gromacs/utility/baseversion.h b/src/gromacs/utility/baseversion.h
index 545517186828cdaf643cb14bd6482bc1777a76cb..b4e7fc4a74219f1e0a4c1ca5d33361b5873a95cc 100644 (file)
--- a/src/gromacs/utility/baseversion.h
+++ b/src/gromacs/utility/baseversion.h
@@ -96,4 +96,9 @@ void gmx_is_single_precision();
 /*! \brief Return a string describing what kind of GPU suport was configured in the build. */
 const char *getGpuImplementationString();
 
+/*! \brief
+ * DOI string, or empty when not a release build.
+ */
+const char *gmxDOI();
+
 #endif

diff --git a/src/gromacs/utility/pleasecite.cpp b/src/gromacs/utility/pleasecite.cpp
index f3664822f9a00f698efccbb13369d7d3955c5b7f..261d733b5b7b0abde00fbef2e4417b62f9886808 100644 (file)
--- a/src/gromacs/utility/pleasecite.cpp
+++ b/src/gromacs/utility/pleasecite.cpp
@@ -41,6 +41,7 @@
 #include <cstring>
 
 #include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/baseversion.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 
@@ -419,3 +420,28 @@ void please_cite(FILE *fp, const char *key)
     fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
     fflush(fp);
 }
+
+void
+writeSourceDoi(FILE *fp)
+{
+    /* Check if we are in release mode or not.
+     * TODO The check should properly target something else than
+     * the string being empty
+     */
+    if (strlen(gmxDOI()) == 0)
+    {
+        /* Not a release build, return without printing anything */
+        return;
+    }
+
+    const char *doiString = wrap_lines(gmxDOI(), LINE_WIDTH, 0, FALSE);
+
+    if (fp == nullptr)
+    {
+        return;
+    }
+    fprintf(fp, "\n++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++\n");
+    fprintf(fp, "%s%s\n", "https://doi.org/", doiString);
+    fprintf(fp, "-------- -------- --- Thank You --- -------- --------\n\n");
+    fflush(fp);
+}

diff --git a/src/gromacs/utility/pleasecite.h b/src/gromacs/utility/pleasecite.h
index 1ae9e7fdb3fc219dd38189de34598eb101a8c8a5..3257f03dd0932a80a419db7255ac065f34223306 100644 (file)
--- a/src/gromacs/utility/pleasecite.h
+++ b/src/gromacs/utility/pleasecite.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2018, 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.
@@ -37,6 +37,7 @@
 /*! \libinternal \file
  * \brief
  * Declares please_cite() for printing out literature references.
+ * Declares writeSourceDoi for printing of source code DOI.
  *
  * \inlibraryapi
  * \ingroup module_utility
@@ -50,4 +51,8 @@
 void
 please_cite(FILE *fp, const char *key);
 
+//! Write a message to \c fp to request citation also of the source-code DOI.
+void
+writeSourceDoi(FILE *fp);
+
 #endif