A set of tools used in climate modeling and numerical weather prediction. (#1317)

* Update grib-api: switched to cmake building system.

* Update harfbuzz: added pkg-config dependency.

* Update pango: added pkg-config dependency.

* Add libemos package.

* Add Magics (from ECMWF) package.

* Revert "Variant for building cdo without mpi (#1638)":
CDO does not use MPI.

This reverts commit 079d063c6d94be84974f1ddd6eb880e902c95b4a.

* Update CDO package: full featured implementation.

* Update magics: added python as build dependency.

* Update cdo: added disabling configuration options.

8 files changed, 367 insertions, 19 deletions

diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index 0a5ee60f7c..775dc31cf3 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -34,13 +34,84 @@ class Cdo(Package):
     version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
     version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2', url='https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz')
 
-    variant('mpi', default=True)
+    variant('szip', default=True, description='Enable szip compression for GRIB1')
+    variant('hdf5', default=False, description='Enable HDF5 support')
+    variant('netcdf', default=True, description='Enable NetCDF support')
+    variant('udunits2', default=True, description='Enable UDUNITS2 support')
+    variant('grib', default=True, description='Enable GRIB_API support')
+    variant('libxml2', default=True, description='Enable libxml2 support')
+    variant('proj', default=True, description='Enable PROJ library for cartographic projections')
+    variant('curl', default=True, description='Enable curl support')
+    variant('fftw', default=True, description='Enable support for fftw3')
+    variant('magics', default=True, description='Enable Magics library support')
 
-    depends_on('netcdf')
-    depends_on('netcdf+mpi', when='+mpi')
-    depends_on('netcdf~mpi', when='~mpi')
+    depends_on('szip', when='+szip')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('hdf5+threadsafe', when='+hdf5')
+    depends_on('udunits2', when='+udunits2')
+    depends_on('grib-api', when='+grib')
+    depends_on('libxml2', when='+libxml2')
+    depends_on('proj', when='+proj')
+    depends_on('curl', when='+curl')
+    depends_on('fftw', when='+fftw')
+    depends_on('magics', when='+magics') 
 
     def install(self, spec, prefix):
-        configure('--prefix={0}'.format(prefix))
+        config_args = ["--prefix=" + prefix,
+                       "--enable-shared",
+                       "--enable-static"]
+
+        if '+szip' in spec:
+            config_args.append('--with-szlib=' + spec['szip'].prefix)
+        else:
+            config_args.append('--without-szlib')
+
+        if '+hdf5' in spec:
+            config_args.append('--with-hdf5=' + spec['hdf5'].prefix)
+        else:
+            config_args.append('--without-hdf5')
+
+        if '+netcdf' in spec:
+            config_args.append('--with-netcdf=' + spec['netcdf'].prefix)
+        else:
+            config_args.append('--without-netcdf')
+
+        if '+udunits2' in spec:
+            config_args.append('--with-udunits2=' + spec['udunits2'].prefix)
+        else:
+            config_args.append('--without-udunits2')
+
+        if '+grib' in spec:
+            config_args.append('--with-grib_api=' + spec['grib-api'].prefix)
+        else:
+            config_args.append('--without-grib_api')
+
+        if '+libxml2' in spec:
+            config_args.append('--with-libxml2=' + spec['libxml2'].prefix)
+        else:
+            config_args.append('--without-libxml2')
+
+        if '+proj' in spec:
+            config_args.append('--with-proj=' + spec['proj'].prefix)
+        else:
+            config_args.append('--without-proj')
+
+        if '+curl' in spec:
+            config_args.append('--with-curl=' + spec['curl'].prefix)
+        else:
+            config_args.append('--without-curl')
+
+        if '+fftw' in spec:
+            config_args.append('--with-fftw3')
+        else:
+            config_args.append('--without-fftw3')
+
+        if '+magics' in spec:
+            config_args.append('--with-magics=' + spec['magics'].prefix)
+        else:
+            config_args.append('--without-magics')
+
+        configure(*config_args)
+
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
index 50164a6144..8b81e14a27 100644
--- a/var/spack/repos/builtin/packages/grib-api/package.py
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -26,25 +26,55 @@ from spack import *
 
 
 class GribApi(Package):
-    """The ECMWF GRIB API is an application program interface accessible from C,
-       FORTRAN and Python programs developed for encoding and decoding WMO
+    """The ECMWF GRIB API is an application program interface accessible from
+       C, FORTRAN and Python programs developed for encoding and decoding WMO
        FM-92 GRIB edition 1 and edition 2 messages."""
 
     homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz"
 
     version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
+    version('1.16.0', '8c7fdee03344e4379d400ae20976a460')
 
-    depends_on('netcdf')
-    depends_on('jasper')
+    variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library')
+    variant('jpeg', default=True, description='Enable jpeg 2000 for grib 2 decoding/encoding')
+    variant('png', default=False, description='Enable png for decoding/encoding')
+
+    depends_on('cmake', type='build')
+    depends_on('libpng', when='+png')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('jasper', when='+jpeg')
 
     def install(self, spec, prefix):
-        configure_options = [
-            '--prefix={0}'.format(prefix),
-            '--with-netcdf={0}'.format(spec['netcdf'].prefix),
-            '--with-jasper={0}'.format(spec['jasper'].prefix)
-        ]
-        configure(*configure_options)
-
-        make()
-        make('install')
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DBUILD_SHARED_LIBS=BOTH')
+
+        # We will add python support later.
+        options.append('-DENABLE_PYTHON=OFF')
+
+        # Disable FORTRAN interface if we don't have it.
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+jpeg' in spec:
+            options.append('-DENABLE_JPG=ON')
+            options.append('-DJASPER_PATH=%s' % spec['jasper'].prefix)
+        else:
+            options.append('-DENABLE_JPG=OFF')
+
+        if '+png' in spec:
+            options.append('-DENABLE_PNG=ON')
+        else:
+            options.append('-DENABLE_PNG=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index c8b4c7e645..7c98c2a96a 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -32,6 +32,7 @@ class Harfbuzz(Package):
 
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
+    depends_on("pkg-config", type="build")
     depends_on("glib")
     depends_on("icu4c")
     depends_on("freetype")
diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py
new file mode 100644
index 0000000000..0275c7ede9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libemos/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libemos(Package):
+    """The Interpolation library (EMOSLIB) includes Interpolation software and
+       BUFR & CREX encoding/decoding routines."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/EMOS/Emoslib"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz"
+
+    version('4.4.2', 'f15a9aff0f40861f3f046c9088197376')
+
+    depends_on('cmake', type='build')
+    depends_on('grib-api')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        options.append('-DGRIB_API_PATH=%s' % spec['grib_api'].prefix)
+
+        # To support long pathnames that spack generates
+        options.append('-DCMAKE_Fortran_FLAGS=-ffree-line-length-none')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
new file mode 100644
index 0000000000..e2e2a5d1ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch
@@ -0,0 +1,5 @@
+--- a/tools/xml2mv.py	2016-06-27 17:49:27.000000000 +0200
++++ a/tools/xml2mv.py	2016-09-13 16:25:17.246960456 +0200
+@@ -1 +1 @@
+-#!/usr/bin/python
++#!/usr/bin/env python
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
new file mode 100644
index 0000000000..cd793ae051
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -0,0 +1,115 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Magics(Package):
+    """Magics is the latest generation of the ECMWF's Meteorological plotting
+       software MAGICS. Although completely redesigned in C++, it is intended
+       to be as backwards-compatible as possible with the Fortran interface."""
+
+    homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
+    url      = "https://software.ecmwf.int/wiki/download/attachments/3473464/Magics-2.29.0-Source.tar.gz"
+
+    # Maintainers of Magics do not keep tarballs of minor releases. Once the
+    # next minor released is published the previous one becomes unavailable.
+    # That is why the preferred version is the latest stable one.
+    version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
+    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
+
+    # The patch changes the hardcoded path to python in shebang to enable the
+    # usage of the first python installation that appears in $PATH
+    patch('no_hardcoded_python.patch')
+
+    # The patch reorders includes and adds namespaces where necessary to
+    # resolve ambiguity of invocations of isnan and isinf functions. The
+    # patch is not needed since the version 2.29.1
+    patch('resolve_isnan_ambiguity.patch', when='@2.29.0')
+
+    variant('bufr', default=False, description='Enable BUFR support')
+    variant('netcdf', default=False, description='Enable NetCDF support')
+    variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
+    variant('metview', default=False, description='Enable metview support')
+    variant('qt', default=False, description='Enable metview support with qt')
+
+    depends_on('cmake', type='build')
+    depends_on('pkg-config', type='build')
+
+    # Currently python is only necessary to run
+    # building preprocessing scripts.
+    depends_on('python', type='build')
+    depends_on('grib-api')
+    depends_on('proj')
+    depends_on('boost')
+    depends_on('expat')
+    depends_on('pango', when='+cairo')
+    depends_on('netcdf-cxx', when='+netcdf')
+    depends_on('libemos', when='+bufr')
+    depends_on('qt', when='+metview+qt')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.append('-DENABLE_ODB=OFF')
+        options.append('-DENABLE_PYTHON=OFF')
+        options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix)
+        options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+        options.append('-DENABLE_TESTS=OFF')
+
+        if '+bufr' in spec:
+            options.append('-DENABLE_BUFR=ON')
+            options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
+        else:
+            options.append('-DENABLE_BUFR=OFF')
+
+        if '+netcdf' in spec:
+            options.append('-DENABLE_NETCDF=ON')
+            options.append('-DNETCDF_PATH=%s' % spec['netcdf-cxx'].prefix)
+        else:
+            options.append('-DENABLE_NETCDF=OFF')
+
+        if '+cairo' in spec:
+            options.append('-DENABLE_CAIRO=ON')
+        else:
+            options.append('-DENABLE_CAIRO=OFF')
+
+        if '+metview' in spec:
+            if '+qt' in spec:
+                options.append('-DENABLE_METVIEW=ON')
+                if spec['qt'].version.up_to(1) == '5':
+                    options.append('-DENABLE_QT5=ON')
+            else:
+                options.append('-DENABLE_METVIEW_NO_QT=ON')
+        else:
+            options.append('-DENABLE_METVIEW=OFF')
+
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            options.append('-DENABLE_FORTRAN=OFF')
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
new file mode 100644
index 0000000000..54b96ae88e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
@@ -0,0 +1,73 @@
+--- a/src/common/Polyline.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/common/Polyline.cc	2016-09-14 13:31:35.784617803 +0200
+@@ -31,2 +30,0 @@
+-#include "TeCoord2D.h"
+-#include "TeGeometryAlgorithms.h"
+--- a/src/decoders/GribRegularInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribRegularInterpretor.cc	2016-09-14 13:43:41.673614590 +0200
+@@ -2083,2 +2083,2 @@
+-                            if (isnan(val1)) {
+-                                if (isnan(val2)) {
++                            if (std::isnan(val1)) {
++                                if (std::isnan(val2)) {
+@@ -2090 +2090 @@
+-                                if (isnan(val2)) {
++                                if (std::isnan(val2)) {
+@@ -2101 +2101 @@
+-                            if (isnan(val) || isinf(val) || isinf(-val)) {
++                            if (std::isnan(val) || std::isinf(val) || std::isinf(-val)) {
+@@ -2105 +2105 @@
+-                        if (isnan(val))
++                        if (std::isnan(val))
+--- a/src/decoders/GribSatelliteInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/GribSatelliteInterpretor.cc	2016-09-14 13:48:55.243699910 +0200
+@@ -33,5 +32,0 @@
+-#include "TeProjection.h"
+-#include "TeDataTypes.h"
+-#include "TeRasterParams.h"
+-#include "TeDecoderMemory.h"
+-#include "TeRasterRemap.h"
+--- a/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfGeoMatrixInterpretor.cc	2016-09-14 13:52:37.481201085 +0200
+@@ -93 +93 @@
+-				if ( !isnan(*d) ) {
++				if ( !std::isnan(*d) ) {
+--- a/src/decoders/NetcdfOrcaInterpretor.cc	2016-04-28 14:38:09.000000000 +0200
++++ b/src/decoders/NetcdfOrcaInterpretor.cc	2016-09-14 13:51:16.248650570 +0200
+@@ -210,2 +210,2 @@
+-							if ( isnan(val1) ) {
+-								if ( isnan(val2) ) {
++							if ( std::isnan(val1) ) {
++								if ( std::isnan(val2) ) {
+@@ -218 +218 @@
+-								if ( isnan(val2) ) {
++								if ( std::isnan(val2) ) {
+@@ -226 +226 @@
+-							if (isnan(val) || isinf(val) || isinf(-val) ) {
++							if (std::isnan(val) || std::isinf(val) || std::isinf(-val) ) {
+@@ -230 +230 @@
+-						if (isnan(val) ) val = missing;
++						if (std::isnan(val) ) val = missing;
+@@ -296 +296 @@
+-           if (isnan(value) ) 
++           if (std::isnan(value) ) 
+--- a/src/terralib/kernel/TeCentroid.cpp	2016-04-28 14:38:09.000000000 +0200
++++ b/src/terralib/kernel/TeCentroid.cpp	2016-09-14 14:17:31.675996554 +0200
+@@ -23,0 +24,2 @@
++#include "TeGeometryAlgorithms.h"
++
+@@ -30 +31,0 @@
+-#include "TeGeometryAlgorithms.h"
+--- a/src/terralib/kernel/TeDatabase.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeDatabase.h	2016-09-14 14:20:01.041100590 +0200
+@@ -33,0 +34 @@
++#include "TeGeometry.h"
+@@ -38 +38,0 @@
+-#include "TeGeometry.h"
+--- a/src/terralib/kernel/TeOverlayUtils.h	2014-11-07 17:39:24.000000000 +0100
++++ b/src/terralib/kernel/TeOverlayUtils.h	2016-09-14 14:21:51.649920405 +0200
+@@ -37,0 +38,2 @@
++#include "TeGeometry.h"

++

+@@ -44 +45,0 @@
+-#include "TeGeometry.h"

diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 2da20e9dc2..75c4ac807d 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -38,6 +38,7 @@ class Pango(Package):
     version('1.36.8', '217a9a753006275215fa9fa127760ece')
     version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb')
 
+    depends_on("pkg-config", type="build")
     depends_on("harfbuzz")
     depends_on("cairo")