Updates for 6.2.14 Release (#46)

* Update to curl 7.83.1

* Update to HDF5 1.10.9

* Update to NCO 5.0.7

* Update to CDO 2.0.5

* Update VERSION

* Update GNUmakefile for HDF5 README name change

* Add xgboost v1.6.0

* Enable xgboost build

* Clean .python files

* Remove NAG HDF5 patch

* Fix Changelog

.gitmodules

@@ -58,3 +58,6 @@
 [submodule "antlr2"]
 	path = antlr2
 	url = https://github.com/nco/antlr2.git
+[submodule "xgboost"]
+	path = xgboost
+	url = https://github.com/dmlc/xgboost.git

CHANGELOG.md

@@ -8,7 +8,24 @@
 ### Removed
 ### Added
 
-## [6.2.13] - 2022-03-XX
+## [6.2.14] - 2022-06-03
+
+### Added
+
+* xgboost v1.6.0
+
+### Updates
+
+* curl 7.83.1
+* HDF5 1.10.9
+* NCO 5.0.7
+* CDO 2.0.5
+
+### Removed
+
+- Removed NAG HDF5 patch as 1.10.9 does not seem to need it anymore
+
+## [6.2.13] - 2022-03-09
 
 ### Updates
 

GNUmakefile

@@ -244,7 +244,7 @@ RELEASE_FILE = $(MKFILE_DIRNAME)-$(DATE)
 #                  --------------------------------
 
 ALLDIRS = antlr2 gsl jpeg zlib szlib curl hdf4 hdf5 netcdf netcdf-fortran netcdf-cxx4 \
-          udunits2 nco cdo nccmp esmf \
+          udunits2 nco cdo nccmp esmf xgboost \
           gFTL gFTL-shared fArgParse pFUnit yaFyaml pFlogger \
           FLAP hdfeos hdfeos5 SDPToolkit
 
@@ -268,7 +268,7 @@ endif
 
 GFE_DIRS = gFTL gFTL-shared fArgParse pFUnit yaFyaml pFlogger
 
-ESSENTIAL_DIRS = jpeg zlib szlib hdf4 hdf5 netcdf netcdf-fortran esmf \
+ESSENTIAL_DIRS = jpeg zlib szlib hdf4 hdf5 netcdf netcdf-fortran esmf xgboost \
                  $(GFE_DIRS) FLAP
 
 ifeq ($(MACH),aarch64)
@@ -445,7 +445,7 @@ clean:
 	  done
 
 distclean:
-	@/bin/rm -rf *.config *.install *.check
+	@/bin/rm -rf *.config *.install *.check *.python
 	@ t=$@; argv="$(SUBDIRS)" ;\
 	  for d in $$argv; do			      \
 	    ( $(MAKE) $$d.$$t ) \
@@ -499,13 +499,7 @@ hdf4.config: hdf4/README.txt jpeg.install zlib.install szlib.install
                       CFLAGS="$(CFLAGS) $(NO_IMPLICIT_FUNCTION_ERROR)" FFLAGS="$(NAG_FCFLAGS) $(NAG_DUSTY) $(ALLOW_ARGUMENT_MISMATCH)" CC=$(CC) FC=$(FC) CXX=$(CXX) )
 	touch $@
 
-ifeq ($(findstring nagfor,$(notdir $(FC))),nagfor)
-hdf5.config :: hdf5/README.txt
-	@echo Patching HDF5 for NAG
-	patch -f -p1 < ./patches/hdf5/nag.configure.patch
-endif
-
-hdf5.config :: hdf5/README.txt szlib.install zlib.install
+hdf5.config :: hdf5/README.md szlib.install zlib.install
 	echo Configuring hdf5
 	(cd hdf5; \
           export PATH="$(prefix)/bin:$(PATH)" ;\
@@ -520,12 +514,6 @@ hdf5.config :: hdf5/README.txt szlib.install zlib.install
                       CFLAGS="$(CFLAGS) $(HDF5_NCCS_MPT_CFLAG)" FCFLAGS="$(NAG_FCFLAGS)" CC=$(NC_CC) FC=$(NC_FC) CXX=$(NC_CXX) F77=$(NC_F77) )
 	touch $@
 
-ifeq ($(findstring nagfor,$(notdir $(FC))),nagfor)
-hdf5.config :: hdf5/README.txt
-	@echo Unpatching HDF5 for NAG
-	patch -f -p1 -R < ./patches/hdf5/nag.configure.patch
-endif
-
 ifneq ("$(wildcard $(prefix)/bin/curl-config)","")
 BUILD_DAP = --enable-dap
 LIB_CURL = $(shell $(prefix)/bin/curl-config --libs) $(DARWIN_ST_LIBS)
@@ -722,6 +710,13 @@ nccmp.config: nccmp/configure netcdf.install
                       FCFLAGS="$(NAG_FCFLAGS)" CC=$(NC_CC) FC=$(NC_FC) CXX=$(NC_CXX) F77=$(NC_F77) )
 	@touch $@
 
+xgboost.config:
+	@echo "Configuring xgboost"
+	@mkdir -p ./xgboost/build
+	@(cd ./xgboost/build; \
+		cmake -DCMAKE_INSTALL_PREFIX=$(prefix) .. )
+	@touch $@
+
 pFUnit.config: gFTL.install gFTL-shared.install fArgParse.install
 	@echo "Configuring pFUnit"
 	@mkdir -p ./pFUnit/build
@@ -931,6 +926,12 @@ nccmp.install: nccmp.config
           $(MAKE) install CC=$(NC_CC) FC=$(NC_FC) CXX=$(NC_CXX) F77=$(NC_F77))
 	@touch $@
 
+xgboost.install: xgboost.config
+	@echo "Installing xgboost"
+	@(cd ./xgboost/build; \
+		$(MAKE) install )
+	@touch $@
+
 pFUnit.install: pFUnit.config
 	@echo "Installing pFUnit"
 	@(cd ./pFUnit/build; \
@@ -1116,6 +1117,14 @@ netcdf-cxx4.distclean:
 	@echo "Cleaning netcdf-cxx4"
 	@rm -rf ./netcdf-cxx4/build
 
+xgboost.clean:
+	@echo "Cleaning xgboost"
+	@rm -rf ./xgboost/build
+
+xgboost.distclean:
+	@echo "Cleaning xgboost"
+	@rm -rf ./xgboost/build
+
 pFUnit.clean:
 	@echo "Cleaning pFUnit"
 	@rm -rf ./pFUnit/build
@@ -1200,6 +1209,9 @@ curl.check: curl.install
 	@echo "Checking curl"
 	@echo "We explicitly do not check cURL due to how long it takes"
 
+xgboost.check: xgboost.install
+	@echo "Not sure how to check xgboost"
+
 pFUnit.check: pFUnit.install
 	@echo "Checking pFUnit"
 	@(cd ./pFUnit/build; \

README.md

@@ -16,23 +16,24 @@ NASA/GSFC.
 | [netCDF](https://github.com/Unidata/netcdf-c)                           | 4.8.1        |
 | [netCDF Fortran](https://github.com/Unidata/netcdf-fortran)             | 4.5.4        |
 | [netCDF C++](https://github.com/Unidata/netcdf-cxx4)                    | 4.3.1        |
-| [HDF5](https://portal.hdfgroup.org/display/support)                     | 1.10.8       |
+| [HDF5](https://portal.hdfgroup.org/display/support)                     | 1.10.9       |
 | [HDF4](https://portal.hdfgroup.org/display/support)                     | 4.2.15       |
 | [pFUnit](https://github.com/Goddard-Fortran-Ecosystem/pFUnit)           | v4.2.2       |
 | [gFTL](https://github.com/Goddard-Fortran-Ecosystem/gFTL)               | v1.5.5       |
 | [gFTL-shared](https://github.com/Goddard-Fortran-Ecosystem/gFTL-shared) | v1.3.6       |
 | [fArgParse](https://github.com/Goddard-Fortran-Ecosystem/fArgParse)     | v1.1.2       |
 | [yaFyaml](https://github.com/Goddard-Fortran-Ecosystem/yaFyaml)         | v1.0-beta5   |
 | [pFlogger](https://github.com/Goddard-Fortran-Ecosystem/pFlogger)       | v1.6.1       |
+| [xgboost](https://github.com/dmlc/xgboost)                              | v1.6.0       |
 | [antlr2](https://www.antlr2.org/)                                       | 2.7.7        |
 | [GSL](https://www.gnu.org/software/gsl/)                                | 2.7          |
 | [jpeg](http://www.ijg.org/)                                             | 9e           |
 | [zlib](http://www.zlib.net/)                                            | 1.2.11       |
 | [szip](https://support.hdfgroup.org/doc_resource/SZIP/)                 | 2.1.1        |
-| [cURL](https://curl.haxx.se/)                                           | 7.80.0       |
+| [cURL](https://curl.haxx.se/)                                           | 7.83.1       |
 | [UDUNITS2](https://github.com/Unidata/UDUNITS-2)                        | 2.2.26       |
-| [NCO](http://nco.sourceforge.net/)                                      | 5.0.6        |
-| [CDO](https://code.mpimet.mpg.de/projects/cdo)                          | 2.0.4        |
+| [NCO](http://nco.sourceforge.net/)                                      | 5.0.7        |
+| [CDO](https://code.mpimet.mpg.de/projects/cdo)                          | 2.0.5        |
 | [nccmp](https://gitlab.com/remikz/nccmp)                                | 1.9.1.0      |
 | [FLAP](https://github.com/mathomp4/FLAP)                                | geos/v1.10.0 |
 | [HDF-EOS2](https://wiki.earthdata.nasa.gov/display/DAS)                 | 3.0          |

VERSION

@@ -1 +1 @@
-6.2.13
+6.2.14

scripts/cdo.sha512

@@ -1 +1 @@
-ad6a666eb99631a829139a07e0eda0e93ff09d9cdbc329ec4413af7fe234305e9565899f54424ed8871c5734d4d70264d2ea16e09686c9152ca50553d96c1975  cdo-2.0.4.tar.gz
+7aaa8b7c536085f4e4a328a6f49891e00a4662357cd2923cf331c4ae61bb7fb2691d8740dbd75384f1e2d41a3660f79a1122ff2983a7c0c373d6a63a3af9e2c8  cdo-2.0.5.tar.gz

scripts/download_cdo.bash

@@ -5,9 +5,9 @@
 # --------------
 
 package_name='cdo'
-tarball='cdo-2.0.4.tar.gz'
+tarball='cdo-2.0.5.tar.gz'
 # NOTE NOTE The last node of this URL changes with each new version
-base_url='https://code.mpimet.mpg.de/attachments/download/26761/'
+base_url='https://code.mpimet.mpg.de/attachments/download/26823/'
 
 export LMOD_SH_DBG_ON=0