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Merge pull request #2356 from WardF/gh2343.wif

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#2343 with updated Github Actions
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Ward Fisher 2022-05-24 11:34:00 -06:00 committed by GitHub
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16 changed files with 119 additions and 59 deletions
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1
RELEASE_NOTES.md
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@ -8,6 +8,7 @@ This file contains a high-level description of this package's evolution. Release
## 4.8.2 - TBD
* [Bug Fix] Get "make distcheck" to work See [Github #/2343](https://github.com/Unidata/netcdf-c/pull/2343).
* [Enhancement] Allow the read/write of JSON-valued Zarr attributes to allow
for domain specific info such as used by GDAL/Zarr. See [Github #????](https://github.com/Unidata/netcdf-c/pull/????).
* [Enhancement] Turn on the XArray convention for NCZarr files by default. WARNING, this means that the mode should explicitly specify nczarr" or "zarr" even if "xarray" or "noxarray" is specified. See [Github #2257](https://github.com/Unidata/netcdf-c/pull/2257).

3
configure.ac
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@ -1991,12 +1991,13 @@ AC_CONFIG_FILES(test_common.sh:test_common.in)
AC_CONFIG_FILES(nc_test4/findplugin.sh:nc_test4/findplugin.in)
AC_CONFIG_FILES(nczarr_test/findplugin.sh:nc_test4/findplugin.in)
AC_CONFIG_FILES(plugins/findplugin.sh:nc_test4/findplugin.in)
AC_CONFIG_FILES(plugins/stdinstall.sh:plugins/stdinstall.in)
AC_CONFIG_FILES(examples/C/findplugin.sh:nc_test4/findplugin.in)
AC_CONFIG_FILES(ncdap_test/findtestserver.c:ncdap_test/findtestserver.c.in)
AC_CONFIG_FILES([nc_test/run_pnetcdf_tests.sh:nc_test/run_pnetcdf_tests.sh.in],[chmod ugo+x nc_test/run_pnetcdf_tests.sh])
AC_CONFIG_FILES(dap4_test/findtestserver4.c:ncdap_test/findtestserver.c.in)
AC_CONFIG_FILES(dap4_test/pingurl4.c:ncdap_test/pingurl.c)
AC_CONFIG_FILES([h5_test/run_par_tests.sh], [chmod ugo+x h5_test/run_par_tests.sh])
AC_CONFIG_FILES([nc_test/run_pnetcdf_tests.sh], [chmod ugo+x nc_test/run_pnetcdf_tests.sh])
AC_CONFIG_FILES([nc_test4/run_par_test.sh], [chmod ugo+x nc_test4/run_par_test.sh])
AC_CONFIG_FILES([nc_perf/run_par_bm_test.sh], [chmod ugo+x nc_perf/run_par_bm_test.sh])
AC_CONFIG_FILES([nc_perf/run_gfs_test.sh], [chmod ugo+x nc_perf/run_gfs_test.sh])

2
dap4_test/Makefile.am
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@ -19,7 +19,7 @@ LDADD = ${top_builddir}/liblib/libnetcdf.la
AM_CPPFLAGS += -I$(top_srcdir)/liblib
AM_CPPFLAGS += -I$(top_srcdir)/libdap4
AM_CPPFLAGS += -DTOPSRCDIR=${abs_top_srcdir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_bindir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_builddir}
# Set up the tests; do the .sh first, then .c
check_PROGRAMS =

12
nc_test/Makefile.am
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@ -7,16 +7,16 @@
# Ed Hartnett, Dennis Heimbigner, Ward Fisher
# Un comment to use a more verbose test driver
#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#TESTS_ENVIRONMENT = export SETX=1;
SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
TESTS_ENVIRONMENT = export SETX=1;
# Put together AM_CPPFLAGS and AM_LDFLAGS.
include $(top_srcdir)/lib_flags.am
AM_CPPFLAGS += -I$(top_srcdir)/libsrc
AM_CPPFLAGS += -DTOPSRCDIR=${abs_top_srcdir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_bindir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_builddir}
LDADD = ${top_builddir}/liblib/libnetcdf.la
AM_CPPFLAGS += -I$(top_builddir)/liblib -I$(top_builddir)/include -I$(top_srcdir)/libsrc
@ -107,7 +107,7 @@ endif
# The .c files that are generated with m4 are already distributed, but
# we also include the original m4 files, plus test scripts data.
EXTRA_DIST = test_get.m4 test_put.m4 run_diskless.sh run_diskless2.sh \
run_diskless5.sh run_mmap.sh run_pnetcdf_test.sh test_read.m4 \
run_diskless5.sh run_mmap.sh test_read.m4 \
test_write.m4 ref_tst_diskless2.cdl tst_diskless5.cdl \
ref_tst_diskless3_create.cdl ref_tst_diskless3_open.cdl \
run_inmemory.sh run_mmap.sh f03tst_open_mem.nc test_byterange.sh \

2
nc_test/run_pnetcdf_tests.sh.in
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@ -2,7 +2,9 @@
# This script runs some PnetCDF I/O tests
set -x
set -e
echo
echo "Testing file created with PnetCDF is modifiable with netCDF..."
./tst_pnetcdf

5
nc_test4/Makefile.am
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@ -110,7 +110,7 @@ ref_ncgenF.cdl ref_nccopyF.cdl \
ref_filter_repeat.txt ref_fillonly.cdl test_fillonly.sh \
ref_filter_order_create.txt ref_filter_order_read.txt \
ref_any.cdl tst_specific_filters.sh \
tst_virtual_datasets.c
tst_virtual_datasets.c noop1.cdl
# The tst_filterinstall test can only be run after an install
# occurred with --with-plugin-dir enabled. So there is no point
@ -128,7 +128,8 @@ perftest.txt bigmeta.nc bigvars.nc *.gz MSGCPP_*.nc \
floats*.nc floats*.cdl shorts*.nc shorts*.cdl ints*.nc ints*.cdl \
testfilter_reg.nc filterrepeat.txt tmp_fillonly.nc \
testfilter_order.nc crfilterorder.txt rdfilterorder.txt 1 \
tmp_*.txt tmp_*.nc tmp*.dump tmp*.cdl tmp*.txt tmp*.tmp tmp_bzip2.c bzip2.nc
tmp_*.txt tmp_*.nc tmp*.dump tmp*.cdl tmp*.txt tmp*.tmp \
tmp_bzip2.c bzip2.nc noop.nc
DISTCLEANFILES = findplugin.sh run_par_test.sh

83
nc_test4/noop1.cdl Normal file
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@ -0,0 +1,83 @@
netcdf bzip2 {
dimensions:
dim0 = 4 ;
dim1 = 4 ;
dim2 = 4 ;
dim3 = 4 ;
variables:
float var(dim0, dim1, dim2, dim3) ;
var:_Storage = "chunked" ;
var:_ChunkSizes = 4, 4, 4, 4 ;
var:_Filter = "40001,17" ;
var:_NoFill = "true" ;
// global attributes:
:_Format = "netCDF-4" ;
data:
var =
0, 1, 2, 3,
4, 5, 6, 7,
8, 9, 10, 11,
12, 13, 14, 15,
16, 17, 18, 19,
20, 21, 22, 23,
24, 25, 26, 27,
28, 29, 30, 31,
32, 33, 34, 35,
36, 37, 38, 39,
40, 41, 42, 43,
44, 45, 46, 47,
48, 49, 50, 51,
52, 53, 54, 55,
56, 57, 58, 59,
60, 61, 62, 63,
64, 65, 66, 67,
68, 69, 70, 71,
72, 73, 74, 75,
76, 77, 78, 79,
80, 81, 82, 83,
84, 85, 86, 87,
88, 89, 90, 91,
92, 93, 94, 95,
96, 97, 98, 99,
100, 101, 102, 103,
104, 105, 106, 107,
108, 109, 110, 111,
112, 113, 114, 115,
116, 117, 118, 119,
120, 121, 122, 123,
124, 125, 126, 127,
128, 129, 130, 131,
132, 133, 134, 135,
136, 137, 138, 139,
140, 141, 142, 143,
144, 145, 146, 147,
148, 149, 150, 151,
152, 153, 154, 155,
156, 157, 158, 159,
160, 161, 162, 163,
164, 165, 166, 167,
168, 169, 170, 171,
172, 173, 174, 175,
176, 177, 178, 179,
180, 181, 182, 183,
184, 185, 186, 187,
188, 189, 190, 191,
192, 193, 194, 195,
196, 197, 198, 199,
200, 201, 202, 203,
204, 205, 206, 207,
208, 209, 210, 211,
212, 213, 214, 215,
216, 217, 218, 219,
220, 221, 222, 223,
224, 225, 226, 227,
228, 229, 230, 231,
232, 233, 234, 235,
236, 237, 238, 239,
240, 241, 242, 243,
244, 245, 246, 247,
248, 249, 250, 251,
252, 253, 254, 255 ;
}

3
ncdap_test/Makefile.am
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@ -18,7 +18,7 @@ TEST_EXTENSIONS = .sh
LDADD = ${top_builddir}/liblib/libnetcdf.la
AM_CPPFLAGS += -I$(top_srcdir)/liblib
AM_CPPFLAGS += -DTOPSRCDIR=${abs_top_srcdir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_bindir}
AM_CPPFLAGS += -DTOPBINDIR=${abs_top_builddir}
# Set up the tests; do the .sh first, then .c
check_PROGRAMS =
@ -52,6 +52,7 @@ TESTS += test_partvar
if ENABLE_DAP_LONG_TESTS
TESTS += tst_longremote3.sh
tst_longremote3.log: tst_remote3.log
test_manyurls_SOURCES = test_manyurls.c manyurls.h
check_PROGRAMS += test_manyurls
TESTS += test_manyurls
test_manyurls.log: tst_longremote3.log

2
ncdump/Makefile.am
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@ -245,7 +245,7 @@ tst_roman_szip_unlim.cdl tst_perdimpspecs.nc tmppds.* \
keyword1.nc keyword2.nc keyword3.nc keyword4.nc \
tmp_keyword1.cdl tmp_keyword2.cdl tmp_keyword3.cdl tmp_keyword4.cdl \
type_*.nc copy_type_*.cdl \
scope_*.nc copy_scope_*.cdl
scope_*.nc copy_scope_*.cdl keyword5.nc
# Remove directories
clean-local:

1
ncdump/test_scope.sh
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@ -31,7 +31,6 @@ diff -wB ${srcdir}/$1.cdl ${execdir}/copy_$1.cdl
}
typescope() {
echo ">>>"
ls -l ${execdir}/printfqn* ${execdir}/$1.nc ${execdir}/$1_copy.nc
REFT=`${execdir}/printfqn -f ${execdir}/$1.nc -v test_variable -t`
COPYT=`${execdir}/printfqn -f ${execdir}/$1_copy.nc -v test_variable -t`

1
ncdump/tst_output.sh
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@ -4,6 +4,7 @@ if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh
# This shell script tests the output from several previous tests.
set -e
echo ""

24
nczarr_test/Makefile.am
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@ -10,10 +10,10 @@ TESTS_ENVIRONMENT =
#TEST_EXTENSIONS = .sh
#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#TESTS_ENVIRONMENT += export SETX=1;
SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
TESTS_ENVIRONMENT += export SETX=1;
AM_CPPFLAGS += -I${top_srcdir} -I${top_srcdir}/libnczarr
AM_LDFLAGS += ${top_builddir}/liblib/libnetcdf.la
@ -128,7 +128,9 @@ run_ut_map.sh run_ut_mapapi.sh run_ut_misc.sh run_ut_chunk.sh run_ncgen4.sh \
run_nccopyz.sh run_fillonlyz.sh run_chunkcases.sh test_nczarr.sh run_perf_chunks1.sh run_s3_cleanup.sh \
run_purezarr.sh run_interop.sh run_misc.sh \
run_filter.sh run_specific_filters.sh \
run_newformat.sh run_nczarr_fill.sh run_quantize.sh run_jsonconvention.sh
run_newformat.sh run_nczarr_fill.sh run_quantize.sh run_jsonconvention.sh \
run_nczfilter.sh
EXTRA_DIST += \
ref_ut_map_create.cdl ref_ut_map_writedata.cdl ref_ut_map_writemeta2.cdl ref_ut_map_writemeta.cdl \
@ -146,14 +148,13 @@ ref_avail1.cdl ref_avail1.dmp ref_avail1.txt \
ref_xarray.cdl ref_purezarr.cdl ref_purezarr_base.cdl ref_nczarr2zarr.cdl \
ref_bzip2.cdl ref_filtered.cdl ref_multi.cdl \
ref_any.cdl ref_oldformat.cdl ref_oldformat.zip ref_newformatpure.cdl \
ref_quotes.zip ref_quotes.cdl \
ref_groups.h5 ref_byte.zarr.zip ref_byte_fill_value_null.zarr.zip \
ref_groups_regular.cdl ref_byte.cdl ref_byte_fill_value_null.cdl ref_jsonconvention.cdl
# Interoperability files
EXTRA_DIST += ref_power_901_constants.zip ref_power_901_constants.cdl ref_quotes.zip ref_quotes.cdl
EXTRA_DIST += ref_power_901_constants_orig.zip ref_power_901_constants.cdl ref_quotes_orig.zip ref_quotes.cdl
CLEANFILES = ut_*.txt ut*.cdl tmp*.nc tmp*.cdl tmp*.txt tmp*.dmp tmp*.zip tmp*.nc tmp*.dump tmp*.tmp tmp_ngc.c ref_zarr_test_data.cdl
CLEANFILES = ut_*.txt ut*.cdl tmp*.nc tmp*.cdl tmp*.txt tmp*.dmp tmp*.zip tmp*.nc tmp*.dump tmp*.tmp tmp_ngc.c ref_zarr_test_data.cdl tst_*.nc.zip ref_quotes.zip ref_power_901_constants.zip
BUILT_SOURCES = test_quantize.c test_filter_avail.c run_specific_filters.sh run_filterinstall.sh
test_quantize.c: $(top_srcdir)/nc_test4/tst_quantize.c
@ -186,10 +187,11 @@ run_filterinstall.sh: $(top_srcdir)/nc_test4/tst_filterinstall.sh
# Remove directories
clean-local:
rm -fr tmp*.file results.file results.s3 results.zip
rm -fr rcmiscdir
rm -fr tmp_*.nc tmp_*.zarr tst_quantize*.zarr tmp*.file results.file results.s3 results.zip
rm -fr rcmiscdir ref_power_901_constants.file
DISTCLEANFILES = findplugin.sh test_quantize.c run_specific_filters.sh
DISTCLEANFILES = findplugin.sh test_quantize.c run_specific_filters.sh run_filterinstall.sh
# If valgrind is present, add valgrind targets.
@VALGRIND_CHECK_RULES@

0
nczarr_test/ref_power_901_constants.zip → nczarr_test/ref_power_901_constants_orig.zip
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0
nczarr_test/ref_quotes.zip → nczarr_test/ref_quotes_orig.zip
View File

29
nczarr_test/run_filter.sh
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@ -12,7 +12,6 @@ testset() {
testapi $1
testng $1
testncp $1
testunk $1
testngc $1
testmisc $1
testmulti $1
@ -53,11 +52,6 @@ sed -e 's/[ ]*\([^ ].*\)/\1/' <$1 >$2
findplugin h5misc
MISCDIR="${HDF5_PLUGIN_DIR}/${HDF5_PLUGIN_LIB}"
# Find noop and capture
findplugin h5noop
NOOPLIB="${HDF5_PLUGIN_LIB}"
NOOPDIR="${HDF5_PLUGIN_DIR}/${NOOPLIB}"
# Find bzip2 and capture
findplugin h5bzip2
BZIP2LIB="${HDF5_PLUGIN_LIB}"
@ -132,29 +126,6 @@ diff -b -w ${srcdir}/ref_filtered.cdl ./tmp_ncp_$zext.dump
echo " *** Pass: nccopy simple filter for map $zext"
}
testunk() {
zext=$1
echo "*** Testing access to filter info when filter implementation is not available for map $zext"
fileargs tmp_known
deletemap $zext $file
# build noop.nc
${NCGEN} -lb -4 -o $fileurl ${srcdir}/../nc_test4/noop.cdl
# dump and clean noop.nc header when filter is avail
${NCDUMP} -hs $fileurl > ./tmp_known_$zext.txt
# Remove irrelevant -s output
sclean ./tmp_known_$zext.txt tmp_known_$zext.dump
# Now hide the filter code
mv ${NOOPDIR} ./${NOOPLIB}.save
# dump and clean noop.nc header when filter is not avail
${NCDUMP} -hs $fileurl > ./tmp_unk_$zext.txt
# Restore the filter code
mv ./${NOOPLIB}.save ${NOOPDIR}
# Verify that the filter is no longer defined
UNK=`sed -e '/var:_Filter/p' -e d ./tmp_unk_$zext.txt`
test "x$UNK" = x
echo "*** Pass: ncgen dynamic filter for map $zext"
}
testngc() {
zext=$1
echo "*** Testing dynamic filters using ncgen with -lc for map $zext"

8
nczarr_test/run_interop.sh
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@ -54,16 +54,14 @@ case "$zext" in
file)
# need to unpack
rm -fr ref_power_901_constants ref_power_901_constants.file
unzip ${srcdir}/ref_power_901_constants.zip > /dev/null
unzip ${srcdir}/ref_power_901_constants_orig.zip > /dev/null
mv ref_power_901_constants ref_power_901_constants.file
testcasefile ref_power_901_constants zarr metaonly; # test xarray as default
;;
zip)
# Move into position
if test "x$srcdir" != "x$execdir" ; then
cp ${srcdir}/ref_power_901_constants.zip ${execdir}
cp ${srcdir}/ref_quotes.zip ${execdir}
fi
cp ${srcdir}/ref_power_901_constants_orig.zip ${execdir}/ref_power_901_constants.zip
cp ${srcdir}/ref_quotes_orig.zip ${execdir}/ref_quotes.zip
testcasezip ref_power_901_constants xarray metaonly
# Test large constant interoperability
testcasezip ref_quotes zarr metaonly