From 889187a464d83475715a124805c99fb57ee99c31 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Tue, 12 Apr 2016 10:04:01 -0500
Subject: [PATCH] gnu: Add NetCDF.

* gnu/packages/maths.scm (netcdf, netcdf-parallel-openmpi): New variables.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/maths.scm                        | 51 +++++++++++++++++++
 gnu/packages/patches/netcdf-config-date.patch | 47 +++++++++++++++++
 3 files changed, 99 insertions(+)
 create mode 100644 gnu/packages/patches/netcdf-config-date.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 0582d9ea8c..e7001ec455 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -643,6 +643,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/mupen64plus-ui-console-notice.patch	\
   gnu/packages/patches/mutt-store-references.patch		\
   gnu/packages/patches/net-tools-bitrot.patch			\
+  gnu/packages/patches/netcdf-config-date.patch			\
   gnu/packages/patches/ngircd-handle-zombies.patch		\
   gnu/packages/patches/ngircd-no-dns-in-tests.patch		\
   gnu/packages/patches/ninja-tests.patch			\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 57d27a11d7..10b1e9be45 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -55,6 +55,7 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
   #:use-module (gnu packages ghostscript)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages less)
@@ -489,6 +490,56 @@ extremely large and complex data collections.")
 HDF5 file is encoded according to the HDF File Format Specification.")
     (license (license:x11-style "file://COPYING"))))
 
+(define-public netcdf
+  (package
+    (name "netcdf")
+    (version "4.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
+                           "netcdf-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d"))
+       (patches (list (search-patch "netcdf-config-date.patch")))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("m4" ,m4)
+       ("doxygen" ,doxygen)
+       ("graphviz" ,graphviz)))
+    (inputs
+     `(("hdf5" ,hdf5)
+       ("zlib" ,zlib)))
+    (arguments
+     `(#:configure-flags '("--enable-doxygen" "--enable-dot")
+       #:parallel-tests? #f))           ;various race conditions
+    (home-page "http://www.unidata.ucar.edu/software/netcdf/")
+    (synopsis "Library for scientific data")
+    (description "NetCDF is an interface for scientific data access and a
+software library that provides an implementation of the interface.  The netCDF
+library defines a machine-independent format for representing scientific data.
+Together, the interface, library, and format support the creation, access, and
+sharing of scientific data.")
+    (license (license:x11-style "file://COPYRIGHT"))))
+
+(define-public netcdf-parallel-openmpi
+  (package (inherit netcdf)
+    (name "netcdf-parallel-openmpi")
+    (inputs
+     `(("mpi" ,openmpi)
+       ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
+                        (package-inputs netcdf))))
+    ;; TODO: Replace pkg-config references in nc-config with absolute references
+    (arguments
+     (substitute-keyword-arguments (package-arguments netcdf)
+       ((#:configure-flags flags)
+        `(cons* "CC=mpicc" "CXX=mpicxx"
+                "--enable-parallel-tests"
+                ;; Shared libraries not supported with parallel IO.
+                "--disable-shared" "--with-pic"
+                ,flags))))))
+
 (define-public nlopt
   (package
     (name "nlopt")
diff --git a/gnu/packages/patches/netcdf-config-date.patch b/gnu/packages/patches/netcdf-config-date.patch
new file mode 100644
index 0000000000..5054612e95
--- /dev/null
+++ b/gnu/packages/patches/netcdf-config-date.patch
@@ -0,0 +1,47 @@
+Honor SOURCE_DATE_EPOCH when exporting configuration date.
+Autoconf-level patch submitted upstream on Fri Apr 15 23:07:42 UTC 2016
+
+--- a/configure
++++ b/configure
+@@ -2866,7 +2866,17 @@
+ 
+ 
+ # Configuration Date
+- CONFIG_DATE="`date`"
++ CONFIG_DATE="`date -u`"
++if test -n "$SOURCE_DATE_EPOCH"; then
++  CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \
++               || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null`
++  if test -z "$CONFIG_DATE"; then
++    as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5
++  fi
++fi
++cat >>confdefs.h <<_ACEOF
++#define CONFIG_DATE "$CONFIG_DATE"
++_ACEOF
+ 
+ # Find out about the host we're building on.
+ ac_aux_dir=
+--- a/libdispatch/derror.c
++++ b/libdispatch/derror.c
+@@ -13,7 +13,7 @@
+ #endif
+ 
+ /* Tell the user the version of netCDF. */
+-static const char nc_libvers[] = PACKAGE_VERSION " of "__DATE__" "__TIME__" $";
++static const char nc_libvers[] = PACKAGE_VERSION " of "CONFIG_DATE" $";
+ 
+ /**
+ \defgroup lib_version Library Version
+--- a/config.h.in
++++ b/config.h.in
+@@ -393,6 +393,9 @@
+ /* Define to the version of this package. */
+ #undef PACKAGE_VERSION
+ 
++/* Define to the configuration date */
++#undef CONFIG_DATE
++
+ /* The size of `double', as computed by sizeof. */
+ #undef SIZEOF_DOUBLE
+