01/09: gnu: gromacs: Update to 2022.4.

[guix-commits]

civodul pushed a commit to branch master
in repository guix.

commit 7934e9c55669ebabce3791a9f532188c4ec9eb48
Author: Ludovic Courtès <ludovic.courtes@inria.fr>
AuthorDate: Tue Jan 10 10:34:51 2023 +0100

    gnu: gromacs: Update to 2022.4.
    
    * gnu/packages/chemistry.scm (gromacs): Update to 2022.4.
    * gnu/packages/patches/gromacs-tinyxml2.patch: Adjust accordingly.
---
 gnu/packages/chemistry.scm                  |  4 +--
 gnu/packages/patches/gromacs-tinyxml2.patch | 40 ++++++++++++++---------------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 6549da3453..33c15dbacc 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -357,14 +357,14 @@ stored with user-specified precision.")
 (define-public gromacs
   (package
     (name "gromacs")
-    (version "2020.2")
+    (version "2022.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-";
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
+                "15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
               ;; Our version of tinyxml2 is far newer than the bundled one and
               ;; require fixing `testutils' code. See patch header for more 
info
               (patches (search-patches "gromacs-tinyxml2.patch"))))
diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch 
b/gnu/packages/patches/gromacs-tinyxml2.patch
index cc7d7459a8..6f11e174df 100644
--- a/gnu/packages/patches/gromacs-tinyxml2.patch
+++ b/gnu/packages/patches/gromacs-tinyxml2.patch
@@ -1,10 +1,7 @@
 Unbundling tinyxml2 from gromacs and using our own, which is newer, broke 
gromacs
 build.
 
-This patch fixes three issues:
-
-- cmake now errors out if using multiple target_link_libraries with mixed 
styles
-  of signatures.
+This patch fixes this issue:
 
 - Error handling API changed, fix the testutils/refdata_xml.cpp code by using 
the
   new API: document.ErrorStr() & tinyxml2::XML_SUCCESS.
@@ -15,22 +12,25 @@ there as long as they still keep the old version bundled.
 First hunk has already been requested for merging. Third is in discussion. 
Second
 will only be sent if third is OK'ed.
 
-diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt 
gromacs-2020.2-fixed/src/testutils/CMakeLists.txt
---- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 
+0200
-+++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt   2020-05-01 
22:52:16.356000000 +0200
-@@ -73,7 +73,7 @@
- 
- if(HAVE_TINYXML2)
-     include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
--    target_link_libraries(testutils ${TinyXML2_LIBRARIES})
-+    target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
- else()
-     include_directories(BEFORE SYSTEM "../external/tinyxml2")
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index cd748c9..1e90c95 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -539,9 +539,6 @@ if(GMX_EXTERNAL_TINYXML2)
+     if(NOT HAVE_TINYXML2)
+         message(FATAL_ERROR "External TinyXML-2 could not be found, please 
adjust your search paths")
+     endif()
+-    if (TinyXML2_FOUND AND TinyXML2_VERSION VERSION_GREATER "6")
+-        message(FATAL_ERROR "External TinyXML-2 is later than the highest 
supported version 6. Please adjust your search paths to include a supported 
version")
+-    endif()
  endif()
-diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp 
gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp
---- gromacs-2020.2/src/testutils/refdata_xml.cpp        2020-04-30 
18:33:44.000000000 +0200
-+++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp  2020-05-01 
23:17:09.556000000 +0200
-@@ -206,21 +206,12 @@
+ 
+ option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
+diff --git a/src/testutils/refdata_xml.cpp b/src/testutils/refdata_xml.cpp
+index 0eb2209..57cebff 100644
+--- a/src/testutils/refdata_xml.cpp
++++ b/src/testutils/refdata_xml.cpp
+@@ -206,21 +206,12 @@ ReferenceDataEntry::EntryPointer 
readReferenceDataFile(const std::string& path)
      document.LoadFile(path.c_str());
      if (document.Error())
      {
@@ -56,7 +56,7 @@ diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp 
gromacs-2020.2-fixed/src/
          GMX_THROW(TestException("Reference data not parsed successfully: " + 
path + "\n."
                                  + errorString + "\n"));
      }
-@@ -371,7 +362,7 @@
+@@ -371,7 +362,7 @@ void writeReferenceDataFile(const std::string& path, const 
ReferenceDataEntry& r
      XMLElementPtr rootElement = createRootElement(&document);
      createChildElements(rootElement, rootEntry);