gnu: Add xdmf.

* gnu/packages/math.scm (xdmf): New variable.
* gnu/packages/patches/xdmf-3.0.0-hdf5.patch: Patch for xdmf.
* gnu/local.mk: Register patch.

Relates-to: guix/guix!8841
Change-Id: I0606eaf8f6524f3efe71b442405438e4df070ff7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

2 files changed, 77 insertions, 0 deletions

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1cb54b1d7b6..875e6209be3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -11732,3 +11732,35 @@ use the library and researchers to make new capabilities available under a
 common interface.
 ")
     (license license:bsd-3)))
+
+(define-public xdmf
+  (package
+    (name "xdmf")
+    ;; Project does not publish releases / tags
+    (properties '((commit . "04a84bab0eb1568e0f1a27c8fb60c6931efda003")
+                  (revision . "0")))
+    (version (git-version "3.0.0"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://gitlab.kitware.com/xdmf/xdmf")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (patches
+        (search-patches "xdmf-3.0.0-hdf5.patch"))
+       (sha256
+        (base32 "06k4vibkvgxlzkn06x470aq5q18p7yhql8awrpdz3czys3z8i288"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f)) ;has no tests
+    (inputs
+     (list boost hdf5 libxml2))
+    (home-page "https://www.xdmf.org/index.html")
+    (synopsis "XDMF library")
+    (description
+     "This package provides the eXtensible Data Model and Format (XDMF) C++
+library.")
+    (license license:bsd-4)))
diff --git a/gnu/packages/patches/xdmf-3.0.0-hdf5.patch b/gnu/packages/patches/xdmf-3.0.0-hdf5.patch
new file mode 100644
index 00000000000..98138f250bb
--- /dev/null
+++ b/gnu/packages/patches/xdmf-3.0.0-hdf5.patch
@@ -0,0 +1,45 @@
+From 92a851f1acb87ad5367eb62f9b97785bedb700bb Mon Sep 17 00:00:00 2001
+From: Dmitri Naumov <github@naumov.de>
+Date: Thu, 28 Oct 2021 22:34:00 +0200
+Subject: [PATCH] Detect if hid_t is defined in new versions of HDF5
+
+In HDF5 development the header file guards were changed,
+namely the leading underscore was removed. This lead to
+a redefinition of the hid_t type, which is int64_t.
+
+The change happened in commit
+https://github.com/HDFGroup/hdf5/commit/c17b4b93d680340af2b3f2c026f2c03c3baeb33ahttps://github.com/HDFGroup/hdf5/commit/c17b4b93d680340af2b3f2c026f2c03c3baeb33a
+and is published in HDF5 version hdf5-1_13_0-rc6.
+---
+ core/XdmfHDF5Controller.hpp | 2 +-
+ core/XdmfHDF5Writer.hpp     | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/core/XdmfHDF5Controller.hpp b/core/XdmfHDF5Controller.hpp
+index c5c15d0a..b52bab3f 100644
+--- a/core/XdmfHDF5Controller.hpp
++++ b/core/XdmfHDF5Controller.hpp
+@@ -30,7 +30,7 @@
+ 
+ // So that hdf5 does not need to be included in the header files
+ // It would add a dependancy to programs that use Xdmf
+-#ifndef _H5Ipublic_H
++#if !defined(_H5Ipublic_H) && !defined(H5Ipublic_H)
+   #ifndef XDMF_HID_T
+   #define XDMF_HID_T
+     typedef int hid_t;
+diff --git a/core/XdmfHDF5Writer.hpp b/core/XdmfHDF5Writer.hpp
+index cfbec6f4..6f8cfd4f 100644
+--- a/core/XdmfHDF5Writer.hpp
++++ b/core/XdmfHDF5Writer.hpp
+@@ -31,7 +31,7 @@
+ 
+ // So that hdf5 does not need to be included in the header files
+ // It would add a dependancy to programs that use Xdmf
+-#ifndef _H5Ipublic_H
++#if !defined(_H5Ipublic_H) && !defined(H5Ipublic_H)
+   #ifndef XDMF_HID_T
+   #define XDMF_HID_T
+     typedef int hid_t;
+-- 
+GitLab