[med-svn] [pbseqlib] 01/05: Changes to support HDF5 1.10.1

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbseqlib.

commit 71793635bd5a19ed9e76256f251e8332a54ef652
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Nov 9 22:31:45 2017 -0500

    Changes to support HDF5 1.10.1
    
    Thanks: Gilles Filippini for the patches
    Closes: #880805
---
 debian/patches/hdf5-1.10.1-support.patch | 72 ++++++++++++++++++++++++++++++++
 debian/patches/series                    |  1 +
 debian/rules                             |  6 +++
 3 files changed, 79 insertions(+)

diff --git a/debian/patches/hdf5-1.10.1-support.patch b/debian/patches/hdf5-1.10.1-support.patch
new file mode 100644
index 0000000..1688874
--- /dev/null
+++ b/debian/patches/hdf5-1.10.1-support.patch
@@ -0,0 +1,72 @@
+Description: cope with HDF5 C++ API changes in release 1.10.1
+ From HDF5 upstream commits c78f1ec8829 and b1c4fd77d9c:
+ .
+ [svn-r30309] Purpose: Fix bug HDFFR-9920
+ Description:
+    Rearranged the classes to model the relationship of HDF5 objects more
+    accurately.  The changes included:
+    - moved CommonFG's methods to Group
+    - removed CommonFG from Group's base class list
+    - removed CommonFG from H5File's base class list and changed
+      "public H5Location" to "public Group" in the base class list
+    - CommonFG became unused
+    - result of the modified partial class diagram:
+ .
+                                IdComponent
+                                     |
+                                H5Location
+                                /
+                        H5Object
+                           |
+                        /  /  \
+                DadaType Group DataSet
+                          |
+                        H5File
+ .
+ [svn-r30311] Purpose: Fix bug HDFFR-9920 cont.
+ Description:
+    Continued rearranging the classes to model the relationship of HDF5
+    objects more accurately.  The changes included:
+    - in the baseclass list of Attribute, changed "public IdComponent" to
+      "public H5Location", because location sometime can be specified with
+      attribute
+    - moved H5A wrappers in H5Location to H5Object because H5A functions
+      can't be called on attribute id
+    - removed the stubs Attribute::iterateAttrs and Attribute::renameAttr
+    - removed Attribute::getFileName and Attribute::flush, because
+          H5Location has them
+    - result of the modified partial class diagram, regarding Attribute
+ .
+                                IdComponent
+                                     |
+                                H5Location   AbstractDs
+                                /       \   /
+                        H5Object     Attribute
+Author: Gilles Filippini <pini at debian.org>
+Index: pbseqlib/hdf/HDFConfig.hpp
+===================================================================
+--- pbseqlib.orig/hdf/HDFConfig.hpp
++++ pbseqlib/hdf/HDFConfig.hpp
+@@ -3,5 +3,10 @@
+ 
+ #define MAX_DIMS 10
+ 
++#ifdef HAVE_HDF5_1_10_1
++#define CommonFG Group
++#define H5Location H5Object
++#endif
++
+ 
+ #endif
+Index: pbseqlib/hdf/HDFAttributable.hpp
+===================================================================
+--- pbseqlib.orig/hdf/HDFAttributable.hpp
++++ pbseqlib/hdf/HDFAttributable.hpp
+@@ -5,6 +5,7 @@
+ #include <vector>
+ #include <H5Cpp.h>
+ #include <H5Location.h>
++#include "HDFConfig.hpp"
+ 
+ void CallStoreAttributeName(H5::H5Location &obj, std::string attrName, void *attrListPtr);
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7035c1d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+hdf5-1.10.1-support.patch
diff --git a/debian/rules b/debian/rules
index 503bf6f..bdaea56 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,6 +13,12 @@ export DEB_CXXFLAGS_MAINT_APPEND=-O3
 
 export LDLIBS += -lpbbam
 
+# Needed for patch hdf5-1.10.1-support.patch
+HDF5_VERSION := $(shell grep 'HDF5 Version' $(HDF5_LIB)/libhdf5.settings | awk '{print $$3}')
+ifeq (yes,$(shell dpkg --compare-versions $(HDF5_VERSION) '>=' 1.10.1 && echo yes))
+export DEB_CPPFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1
+endif
+
 %:
 	dh $@
 

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