netcdf: update to 4.9.3

macports · Feb 19, 2025 · b3e9f7e · b3e9f7e
1 parent e715cc9
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Showing 42 changed files with 129 additions and 81 deletions.
diff --git a/R/R-RNetCDF/Portfile b/R/R-RNetCDF/Portfile
@@ -4,7 +4,8 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 R.setup             github mjwoods RNetCDF 2.9-2 v
-revision            1
+revision            2
+extract.rename      yes
 maintainers         nomaintainer
 license             GPL-2+
 description         Interface to NetCDF file formats

diff --git a/R/R-easyNCDF/Portfile b/R/R-easyNCDF/Portfile
@@ -4,7 +4,7 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 R.setup             cran earth.bsc easyNCDF 0.1.2
-revision            1
+revision            2
 categories-append   math
 maintainers         nomaintainer
 license             GPL-3

diff --git a/R/R-ncdf4/Portfile b/R/R-ncdf4/Portfile
@@ -4,7 +4,7 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 R.setup             cran dpierce ncdf4 1.23
-revision            0
+revision            1
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3+
 description         Interface to unidata netCDF (v. 4 or earlier) data files

diff --git a/gis/gdal/Portfile b/gis/gdal/Portfile
@@ -9,7 +9,7 @@ PortGroup           muniversal 1.0
 
 name                gdal
 version             3.10.2
-revision            0
+revision            1
 
 checksums           rmd160  35e3e3a75959d0ab949f4e68dcb39b947508046d \
                     sha256  67b4e08acd1cc4b6bd67b97d580be5a8118b586ad6a426b09d5853898deeada5 \

diff --git a/math/petsc/Portfile b/math/petsc/Portfile
@@ -7,6 +7,7 @@ PortGroup                   muniversal 1.0
 
 name                        petsc
 version                     3.22.1
+revision                    1
 categories                  math science
 maintainers                 {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
 license                     BSD

diff --git a/octave/octave-netcdf/Portfile b/octave/octave-netcdf/Portfile
@@ -4,8 +4,7 @@ PortSystem          1.0
 PortGroup           octave 1.0
 
 octave.setup        sourceforge octave netcdf 1.0.18
-revision            0
-platforms           darwin
+revision            1
 license             GPL-3+
 maintainers         {mps @Schamschula} openmaintainer
 description         A MATLAB compatible NetCDF interface for Octave.

diff --git a/python/py-netcdf4/Portfile b/python/py-netcdf4/Portfile
@@ -7,7 +7,7 @@ PortGroup           mpi 1.0
 name                py-netcdf4
 python.rootname     netCDF4
 version             1.7.2
-revision            0
+revision            1
 
 categories-append   science
 license             MIT

diff --git a/python/py-nio/Portfile b/python/py-nio/Portfile
@@ -6,7 +6,7 @@ PortGroup compilers 1.0
 
 name                py-nio
 version             1.3.0b1
-revision            28
+revision            29
 categories-append   science
 license             PyNIO
 maintainers         {petr @petrrr} openmaintainer

diff --git a/python/py-scientific/Portfile b/python/py-scientific/Portfile
@@ -6,7 +6,7 @@ PortGroup           python 1.0
 PortGroup           mpi 1.0
 
 bitbucket.setup     khinsen scientificpython 2.9.4 rel
-revision            6
+revision            7
 checksums           rmd160  11d3cb9077cc17ea4dadac2f7887a9f76be300f3 \
                     sha256  ed5c2048a64a83cd56374d6a048c793066d0060e8589f0ec70d95caadbaaa5ed \
                     size    414165

diff --git a/science/cdo/Portfile b/science/cdo/Portfile
@@ -6,7 +6,7 @@ PortGroup                   legacysupport 1.0
 
 name                        cdo
 version                     2.5.0
-revision                    0
+revision                    1
 maintainers                 {takeshi @tenomoto} \
                             {me.com:remko.scharroo @remkos} \
                             openmaintainer

diff --git a/science/ecCodes/Portfile b/science/ecCodes/Portfile
@@ -6,7 +6,7 @@ PortGroup compilers 1.0
 
 name                ecCodes
 version             2.39.0
-revision            0
+revision            1
 maintainers         {takeshi @tenomoto} \
                     {me.com:remko.scharroo @remkos} \
                     openmaintainer

diff --git a/science/elmerfem/Portfile b/science/elmerfem/Portfile
@@ -15,7 +15,7 @@ legacysupport.newest_darwin_requires_legacy 10
 
 github.setup        ElmerCSC elmerfem 394d98700a395d5fbcc4bc47a8f186252f41c13f
 version             2024.11.29
-revision            0
+revision            1
 categories          science
 license             GPL-2
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer

diff --git a/science/esmf/Portfile b/science/esmf/Portfile
@@ -13,7 +13,7 @@ mpi.setup
 mpi.enforce_variant netcdf-fortran
 
 github.setup        esmf-org esmf 8.5.0 v
-revision            2
+revision            3
 checksums           rmd160  3d1edb514d5b09b46f1f60047e3f5cd3c0bf7b43 \
                     sha256  acd0b2641587007cc3ca318427f47b9cae5bfd2da8d2a16ea778f637107c29c4 \
                     size    14091400

diff --git a/science/gerris/Portfile b/science/gerris/Portfile
@@ -6,7 +6,7 @@ PortGroup             mpi 1.0
 name                  gerris
 set snapshot          131206
 version               0.9.2-20${snapshot}
-revision              5
+revision              6
 categories            science
 license               GPL-2+
 maintainers           {mcalhoun @MarcusCalhoun-Lopez} openmaintainer

diff --git a/science/gmt4/Portfile b/science/gmt4/Portfile
@@ -4,9 +4,8 @@ PortSystem          1.0
 
 name                gmt4
 version             4.5.18
-revision            20
+revision            21
 categories          science
-platforms           darwin
 maintainers         {takeshi @tenomoto} openmaintainer
 license             GPL-2
 description         The Generic Mapping Tools

diff --git a/science/gmt5/Portfile b/science/gmt5/Portfile
@@ -12,7 +12,7 @@ name                gmt5
 github.setup        GenericMappingTools gmt 5.4.5
 github.tarball_from releases
 distname            ${github.project}-${github.version}-src
-revision            20
+revision            21
 
 categories          science
 maintainers         {me.com:remko.scharroo @remkos} openmaintainer

diff --git a/science/gmt6/Portfile b/science/gmt6/Portfile
@@ -8,7 +8,7 @@ name                gmt6
 github.setup        GenericMappingTools gmt 6.5.0
 github.tarball_from releases
 distname            ${github.project}-${github.version}-src
-revision            2
+revision            3
 epoch               1
 
 categories          science

diff --git a/science/grads/Portfile b/science/grads/Portfile
@@ -4,7 +4,7 @@ PortSystem          1.0
 
 name                grads
 version             2.2.1
-revision            21
+revision            22
 set branch          [join [lrange [split ${version} .] 0 1] .]
 maintainers         {takeshi @tenomoto}
 license             GPL-2

diff --git a/science/libminc/Portfile b/science/libminc/Portfile
@@ -8,7 +8,7 @@ PortGroup           active_variants 1.1
 github.setup        BIC-MNI libminc 2.4.06 release-
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from tarball
-revision            2
+revision            3
 
 categories          science
 maintainers         nomaintainer

diff --git a/science/magicspp/Portfile b/science/magicspp/Portfile
@@ -9,7 +9,7 @@ if {[variant_isset qt5]} {
 
 name                magicspp
 version             4.5.1
-revision            14
+revision            15
 maintainers         {takeshi @tenomoto}
 license             Apache-2
 categories          science

diff --git a/science/mfem/Portfile b/science/mfem/Portfile
@@ -11,7 +11,7 @@ PortGroup           linear_algebra 1.0
 # PortGroup           mpi 1.0
 
 github.setup        mfem mfem 4.7 v
-revision            0
+revision            1
 categories          science
 license             BSD
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer

diff --git a/science/ncarg/Portfile b/science/ncarg/Portfile
@@ -11,7 +11,7 @@ compilers.allow_arguments_mismatch \
 
 name                        ncarg
 version                     6.6.2
-revision                    32
+revision                    33
 epoch                       1
 set version_no_dot [join [split ${version} "."] ""]
 categories                  science
@@ -90,6 +90,9 @@ patchfiles                  patch-Configure.diff \
                             patch-ni-src-lib-nfpfort-yMakefile.diff \
                             patch-ni-src-lib-hlu-Format.c.diff \
                             patch-ni-src-ncl-global-vars.diff \
+                            patch-ni-src-ncl-MakeNcl.diff \
+                            patch-ni-src-ncl-remove-nc-set-log.diff \
+                            patch-ni-src-ncl-yMakefile.diff \
                             patch-ncarg2d-src-libncarg_gks-bwi-argb2ci.f.diff
 if {$build_arch eq "x86_64" | $build_arch eq "arm64"} {
     patchfiles-append       patch-config-ymake.diff

diff --git a/science/ncarg/files/patch-ni-src-ncl-MakeNcl.diff b/science/ncarg/files/patch-ni-src-ncl-MakeNcl.diff
@@ -0,0 +1,15 @@
+Remove check for install lib directory $libpath, because it does not exist yet
+--- ni/src/ncl/MakeNcl.csh.orig	2019-02-28 00:44:39
++++ ni/src/ncl/MakeNcl.csh	2025-02-19 14:06:58
+@@ -28,11 +28,6 @@
+ set libmath       = "-lngmath"
+ set ncarg_libs    = "$libncl $libnfp $libhlu $libncarg $libgks $libncarg_c $libmath"
+
+-if (! -d "$libpath") then
+-  echo "Library directory <$libpath> does not exist."
+-  exit 1
+-endif
+-
+ set files      = ""
+ set extra_opts = ""
+
diff --git a/science/ncarg/files/patch-ni-src-ncl-remove-nc-set-log.diff b/science/ncarg/files/patch-ni-src-ncl-remove-nc-set-log.diff
@@ -0,0 +1,41 @@
+Remove nc_set_log_level() because it is not (no longer?) available in libnetcdf
+--- ni/src/ncl/NclNetCDF4.c.orig	2019-02-28 00:44:39
++++ ni/src/ncl/NclNetCDF4.c	2025-02-19 14:07:33
+@@ -409,7 +409,6 @@
+     }
+
+     /*nc_set_log_level(3);*/
+-    nc_set_log_level(3);
+
+     ChunkSizeHint = 2 * blksize;
+
+--- ni/src/ncl/NclNetCdf.c.orig	2019-02-28 00:44:39
++++ ni/src/ncl/NclNetCdf.c	2025-02-19 14:07:38
+@@ -614,7 +614,6 @@
+ 	}
+
+         /*nc_set_log_level(3);*/
+-        nc_set_log_level(3);
+
+ 	ChunkSizeHint = 64 * blksize;
+ 	therec = (NetCdfFileRecord*)NclCalloc(1, sizeof(NetCdfFileRecord));
+--- ni/src/ncl/NclNewHDF5.c.orig	2019-02-28 00:44:39
++++ ni/src/ncl/NclNewHDF5.c	2025-02-19 14:08:16
+@@ -3834,7 +3834,6 @@
+     }
+
+     /*nc_set_log_level(3);*/
+-    nc_set_log_level(3);
+
+     grpnode = (NclFileGrpNode *)NclCalloc(1, sizeof(NclFileGrpNode));
+     assert(grpnode);
+--- ni/src/ncl/NclNewHDFEOS5.c.orig	2019-02-28 00:44:39
++++ ni/src/ncl/NclNewHDFEOS5.c	2025-02-19 14:08:21
+@@ -530,7 +530,6 @@
+     }
+
+     /*nc_set_log_level(3);*/
+-    nc_set_log_level(3);
+
+     grpnode = (NclFileGrpNode *)NclCalloc(1, sizeof(NclFileGrpNode));
+     assert(grpnode);
diff --git a/science/ncarg/files/patch-ni-src-ncl-yMakefile.diff b/science/ncarg/files/patch-ni-src-ncl-yMakefile.diff
@@ -0,0 +1,22 @@
+Replace '+' with '|' in sed. With '+' it complains about wrong flag
+--- ni/src/ncl/yMakefile.orig	2019-02-28 00:44:39
++++ ni/src/ncl/yMakefile	2025-02-19 14:06:24
+@@ -655,12 +655,12 @@
+
+ MakeNcl: MakeNcl.csh Makefile
+ 	@sed \
+-	-e 's+SED_CC_LD+$(CC_LD)+' \
+-	-e 's+SED_CC_OPT+$(CCOPTIONS)+' \
+-	-e 's+SED_LDLIBS+$(LDLIBS)+' \
+-	-e 's+SED_EXTRA_LDLIBS+$(EXTRA_LDLIBS)+' \
+-	-e 's+SED_LIBPATH+$(LIBPATH)+' \
+-	-e 's+SED_INCPATH+$(INCPATH)+' \
++	-e 's|SED_CC_LD|$(CC_LD)|' \
++	-e 's|SED_CC_OPT|$(CCOPTIONS)|' \
++	-e 's|SED_LDLIBS|$(LDLIBS)|' \
++	-e 's|SED_EXTRA_LDLIBS|$(EXTRA_LDLIBS)|' \
++	-e 's|SED_LIBPATH|$(LIBPATH)|' \
++	-e 's|SED_INCPATH|$(INCPATH)|' \
+ 	<MakeNcl.csh > MakeNcl
+
+ #if defined(Darwin)
diff --git a/science/nccmp/Portfile b/science/nccmp/Portfile
@@ -7,7 +7,7 @@ PortGroup           gitlab 1.0
 #PortGroup          cmake 1.1
 
 gitlab.setup        remikz nccmp 1.9.1.0
-revision            0
+revision            1
 checksums           rmd160  d3eb0a8d2b55c93f42832e74dedab358f42fa243 \
                     sha256  44768ebdc5633207fbf1a7e087767782c6811f600c6a6c91b5829fb7787064ae \
                     size    312482

diff --git a/science/nco/Portfile b/science/nco/Portfile
@@ -7,7 +7,7 @@ PortGroup           github 1.0
 github.setup        nco nco 5.3.1
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from tarball
-revision            0
+revision            1
 maintainers         {takeshi @tenomoto} \
                     {me.com:remko.scharroo @remkos} \
                     openmaintainer

diff --git a/science/ncplot/Portfile b/science/ncplot/Portfile
@@ -6,7 +6,7 @@ PortGroup           github 1.0
 github.setup        ncar ncplot 4.11.0 v
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from tarball
-revision            2
+revision            3
 epoch               1
 
 categories          science

diff --git a/science/ncpp/Portfile b/science/ncpp/Portfile
@@ -6,7 +6,7 @@ PortGroup           github 1.0
 github.setup        NCAR ncpp 2.3.0 v
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from tarball
-revision            3
+revision            4
 
 categories          science
 license             permissive

diff --git a/science/ncview/Portfile b/science/ncview/Portfile
@@ -5,9 +5,8 @@ PortGroup               conflicts_build 1.0
 
 name                    ncview
 version                 2.1.11
-revision                0
+revision                1
 maintainers             {@thiagoveloso gmail.com:thiagoveloso} openmaintainer
-platforms               darwin
 categories              science
 license                 GPL-3
 

diff --git a/science/netcdf-cxx/Portfile b/science/netcdf-cxx/Portfile
@@ -5,10 +5,9 @@ PortGroup                   mpi 1.0
 
 name                        netcdf-cxx
 version                     4.2
-revision                    17
+revision                    18
 distname                    ${name}-${version}
 maintainers                 {takeshi @tenomoto} openmaintainer
-platforms                   darwin
 categories                  science
 license                     Permissive
 
@@ -24,9 +23,9 @@ master_sites                ftp://ftp.unidata.ucar.edu/pub/netcdf/ \
                             http://www.gfd-dennou.org/arch/netcdf/unidata-mirror/ \
                             ftp://www.gfd-dennou.org/arch/netcdf/unidata-mirror/
 
-checksums           md5     d32b20c00f144ae6565d9e98d9f6204c \
-                    sha1    bab9b2d873acdddbdbf07ab35481cd0267a3363b \
-                    rmd160  69e9348ced7da8b6ddf08dad4c3a92c4f18d0648
+checksums           rmd160  69e9348ced7da8b6ddf08dad4c3a92c4f18d0648 \
+                    sha256  95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1 \
+                    size    703482
 
 compilers.choose            cc cpp cxx
 mpi.setup

diff --git a/science/netcdf-cxx4/Portfile b/science/netcdf-cxx4/Portfile
@@ -9,7 +9,7 @@ PortGroup                   mpi 1.0
 github.setup                Unidata netcdf-cxx4 4.3.1 v
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from         tarball
-revision                    1
+revision                    2
 distname                    ${name}-${version}
 maintainers                 {takeshi @tenomoto} openmaintainer
 categories                  science

diff --git a/science/netcdf-fortran/Portfile b/science/netcdf-fortran/Portfile
@@ -24,7 +24,7 @@ mpi.enforce_variant         netcdf
 github.setup                Unidata netcdf-fortran 4.6.1 v
 # Change github.tarball_from to 'releases' or 'archive' next update
 github.tarball_from         tarball
-revision                    4
+revision                    5
 maintainers                 {takeshi @tenomoto} \
                             {@Dave-Allured noaa.gov:dave.allured} \
                             openmaintainer
@@ -99,3 +99,5 @@ if {[mpi_variant_isset]} {
         }
     }
 }
+
+github.livecheck.regex      {([^"rba]+)}