Merge branch 'ghasemi1_nco_cdo' into '2020'

Ghasemi1 nco cdo

See merge request hps-public/easybuild-repository!341

Golden_Repo/c/CDO/CDO-1.9.8-gpsmpi-2020.eb

+easyblock = 'ConfigureMake'
+
+name = 'CDO'
+version = '1.9.8'
+
+homepage = 'https://code.zmaw.de/projects/cdo'
+description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data."""
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+# stick to lowopt (-O1) to avoid internal compiler error when building on Intel Skylake
+toolchainopts = {'pic': True, 'usempi': True, 'lowopt': True}
+
+source_urls = ['https://code.mpimet.mpg.de/attachments/download/20826/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f2660ac6f8bf3fa071cf2a3a196b3ec75ad007deb3a782455e80f28680c5252a']
+
+dependencies = [
+    ('HDF5', '1.10.6'),
+    ('netCDF', '4.7.4'),
+    ('YAXT', '0.9.0'),
+    ('ecCodes', '2.18.0'),
+]
+
+
+configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES --with-szlib=yes"
+
+# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5
+# prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && "
+preconfigopts = 'export CFLAGS="$CFLAGS -lhdf5" && '
+sanity_check_paths = {
+    'files': ['bin/cdo'],
+    'dirs': [],
+}
+
+moduleclass = 'data'

Golden_Repo/n/NCO/NCO-4.9.5-gpsmpi-2020.eb

+easyblock = 'ConfigureMake'
+
+name = 'NCO'
+version = '4.9.5'
+
+homepage = 'http://nco.sourceforge.net'
+description = """NCO manipulates data stored in netCDF-accessible formats,
+ including HDF4 and HDF5. It also exploits the geophysical expressivity of many
+ CF (Climate & Forecast) metadata conventions, the flexible description of
+ physical dimensions translated by UDUnits, the network transparency of OPeNDAP,
+ the storage features (e.g., compression, chunking, groups) of HDF (the
+ Hierarchical Data Format), and many powerful mathematical and statistical
+ algorithms of GSL (the GNU Scientific Library).
+"""
+
+site_contacts = 'a.ghasemi@fz-juelich.de'
+
+toolchain = {'name': 'gpsmpi', 'version': '2020'}
+toolchainopts = {'opt': True, 'pic': True}
+
+configopts = '--enable-optimize-custom --enable-debug-custom '
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://nco.sourceforge.net/src/']
+
+patches = ['nco_4.9.5_yyget_gcc9.patch']
+
+builddependencies = [
+    ('Bison', '3.6.4'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('cURL', '7.71.1'),
+    ('netCDF', '4.7.4'),
+    ('UDUNITS', '2.2.26'),
+    ('GSL', '2.6'),
+    ('expat', '2.2.9'),
+    # ANTLR 3.X doesn't have C++ support and therefore is not usable
+    # ANTLR 4.X has C++ support, but right now is not compatible with NCO
+    # See https://sourceforge.net/p/nco/discussion/9831/thread/1a424aac/
+    ('ANTLR', '2.7.7', '-Python-3.8.5'),
+    ('libdap', '3.20.6'),
+]
+
+sanity_check_paths = {
+    'files': ["bin/ncks", "bin/ncrename"],
+    'dirs': [],
+}
+
+moduleclass = 'data'

Golden_Repo/n/NCO/nco_4.9.5_yyget_gcc9.patch

+diff -ruN nco-4.9.5.orig/src/nco/ncap_lex.l nco-4.9.5/src/nco/ncap_lex.l
+--- nco-4.9.5.orig/src/nco/ncap_lex.l	2018-09-21 17:23:39.000000000 +0200
++++ nco-4.9.5/src/nco/ncap_lex.l	2018-11-09 16:43:31.201995148 +0100
+@@ -107,7 +107,7 @@
+      Once all platforms upgrade to Flex >= 2.6.4 we can deprecate yy_size_t code
+      However, MacOSX may never upgrade to newer Flex
+      CZ's decision is to keep current behavior until breakage cannot be ignored and then sacrifice buildability on older Flex */
+-  yy_size_t yyget_leng(void); /* fixes: warning: no previous prototype for `yyget_leng' */
++  int yyget_leng(void); /* fixes: warning: no previous prototype for `yyget_leng' */
+   int yyget_lineno(void); /* fixes: warning: no previous prototype for `yyget_lineno' */
+   int yylex_destroy(void); /* fixes: warning: no previous prototype for `yylex_destroy' */
+   void yyset_debug(int bdebug); /* fixes: warning: no previous prototype for `yyset_debug' */