gnu: ogs-serial: Update to 6.5.8

* gnu/packages/geo.scm (ogs-serial): Update to 6.5.8.
* gnu/packages/geo.scm (ogs-serial): Remove patch.
* gnu/packages/geo.scm (ogs-serial): Add xdmf input.
* packages/patches/ogs-6.5.7-netcdfconverter.patch: Removed.
* gnu/local.mk: Deregister patch.

Merges: guix/guix!8841
Change-Id: I9b4e502c37ca9470669296d6a038bb1b5e2de8b7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu/local.mk

@@ -2023,7 +2023,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ocaml-4.07-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-dynamically-allocate-signal-stack.patch	\
   %D%/packages/patches/ocaml-4.09-multiple-definitions.patch	\
-  %D%/packages/patches/ogs-6.5.7-netcdfconverter.patch \
   %D%/packages/patches/omake-fix-non-determinism.patch	\
   %D%/packages/patches/oneko-remove-nonfree-characters.patch	\
   %D%/packages/patches/onetbb-other-arches.patch	\

gnu/packages/geo.scm

@@ -807,7 +807,7 @@ OpenGeoSys")
 (define-public ogs-serial
   (package
     (name "ogs-serial")
-    (version "6.5.7")
+    (version "6.5.8")
     (source
      (origin
        (method git-fetch)
@@ -816,9 +816,7 @@ OpenGeoSys")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wflgkbcsa4sr8g63img0ld6h4jm1b7hjzsa2m4gsbzc6j7kd41w"))
-       ;; Remove patch on next release, likely 6.5.8
-       (patches (search-patches "ogs-6.5.7-netcdfconverter.patch"))))
+        (base32 "037il6jw2j1g7bvrwvbp20yf0cnz7c7f3wmszxfv5ay7l54sffqg"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -873,6 +871,7 @@ OpenGeoSys")
            tclap
            tfel
            vtk
+           xdmf
            xmlpatch
            zlib))
     (propagated-inputs

gnu/packages/patches/ogs-6.5.7-netcdfconverter.patch

@@ -1,23 +0,0 @@
-Upstream fix
-
-https://gitlab.opengeosys.org/ogs/ogs/-/commit/9a8399b0d3cff032e70fe79a85dc35c4e7c662f2
-
-diff --git a/Applications/Utils/FileConverter/NetCdfConverter.cpp b/Applications/Utils/FileConverter/NetCdfConverter.cpp
-index c6fb9f151d..622bd2cd54 100644
---- a/Applications/Utils/FileConverter/NetCdfConverter.cpp
-+++ b/Applications/Utils/FileConverter/NetCdfConverter.cpp
-@@ -232,11 +232,12 @@ static bool dimensionSelectionLoop(NcVar const& var,
-     if (n_dims > 1)
-     {
-         std::string temp_str("");
--        cout << "Is the parameter time-dependent?\n";
-+        std::cout << "Is the parameter time-dependent?\n";
-         while (dim_idx_map[0] == std::numeric_limits<std::size_t>::max() &&
-                is_time_dep == true)
-         {
--            cout << "Enter ID for temporal dimension or \"c\" to continue: ";
-+            std::cout
-+                << "Enter ID for temporal dimension or \"c\" to continue: ";
-             std::getline(std::cin, temp_str);
-             std::stringstream str_stream(temp_str);
-             if (str_stream.str() == "c" || str_stream.str() == "continue")