Update main_v11.0-ref after #2761 upgraded seneca to Debian Bookworm (#…

…2770) Co-authored-by: MET Tools Test Account <[email protected]> Co-authored-by: Howard Soh <[email protected]> Co-authored-by: John Halley Gotway <[email protected]> Co-authored-by: jprestop <[email protected]> Co-authored-by: hsoh-u <[email protected]> Co-authored-by: George McCabe <[email protected]> Co-authored-by: lisagoodrich <[email protected]> Co-authored-by: Stephen Herbener <[email protected]> fix #2389 main_v11.0 flowchart (#2391) fix definitions of G172 and G220 based on comments in NOAA-EMC/NCEPLIBS-w3emc#157. (#2405) fix #2380 main_v11.0 override (#2381) fix #2408 main_v11.0 empty config (#2409) fix #2390 main_v11.0 fix compiling hdf5 with zlib and handle NetCDF-C zip (#2403) fix #2415 main_v11.0 modulefiles (#2416) fix #2412 main_v11.0 climo (#2420) fix #2426 main_v11.0 buoy (#2432) fix #2437 main_v11.0 convert (#2438) fix for main_v11.0, for #2437, forgot one reference to the search_parent for a dictionary lookup. fix 2428 python from env main v11.0 (#2443) fix 2428 python csv input (#2450) fix #2452 main_v11.0 airnow (#2453) fix #2402 main_v11.0 sonarqube (First PR) (#2447) fix #2449 main_v11.0 pdf (#2465) fix 2428 python csv input (#2467) fix #2514 main_v11.0 clang (#2556) fix #2575 main_v11.0 python_convert (#2577) fix 2596 main v11.0 rpath compilation (#2600) fix 2596 main v11.0 rpath compilation (#2613) fix #2644 main_v11.0 percentile (#2645)
dtcenter · Dec 18, 2023 · 2bf872c · 2bf872c
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diff --git a/docs/conf.py b/docs/conf.py
@@ -34,7 +34,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 # Adding 'sphinx_panels' to use drop-down menus in appendixA. 
-extensions = ['sphinx.ext.autodoc','sphinx.ext.intersphinx','sphinx_panels',]
+extensions = ['sphinx.ext.autodoc','sphinx.ext.intersphinx','sphinx_panels','sphinx_rtd_theme',]
 
 # settings for ReadTheDocs PDF creation
 latex_engine = 'pdflatex'

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,5 @@
-sphinx-gallery
-sphinxcontrib-bibtex
+sphinx-gallery==0.14.0
+sphinxcontrib-bibtex==2.6.1
+sphinx==5.3.0
 sphinx-panels
+sphinx_rtd_theme==1.3.0
diff --git a/internal/scripts/environment/development.seneca b/internal/scripts/environment/development.seneca
@@ -1,53 +1,59 @@
 # Define the development environment for NCAR project machine seneca
-# Based on settings in /usr/local/src/met/README.snat
+# Based on settings in /nrit/ral/src/met/README.ral-it
 
 # Top-level MET project directory
 MET_PROJ_DIR=/d1/projects/MET
 
 # Variables required to build MET
 export MET_DEVELOPMENT=true
-export MET_DST=/usr/local
-export MET_NETCDF=${MET_DST}/netcdf-4.7.0/gcc-8.3.0
-export MET_HDF5=${MET_DST}/hdf5-1.8.21
-export MET_HDFINC=${MET_DST}/hdf4-4.2.15/include/hdf
-export MET_HDFLIB=${MET_DST}/hdf4-4.2.15/lib
-export MET_HDFEOS=${MET_DST}/hdf-eos2-20v1
-export MET_BUFR=${MET_DST}
-export MET_GRIB2C=${MET_DST}
-export MET_GSL=${MET_PROJ_DIR}/MET_releases/external_libs/gnu_8.3.0
+export MET_DST=/nrit/ral
+export MET_PROJ=${MET_DST}/proj-9.2.1
+export MET_NETCDF=${MET_DST}/netcdf-4.9.2/gnu-12.2.0
+export MET_HDF5=${MET_DST}/hdf5-1.14.2
+export MET_HDFINC=${MET_DST}/hdf4-4.2.16-2/include/hdf
+export MET_HDFLIB=${MET_DST}/hdf4-4.2.16-2/lib
+export MET_HDFEOS=${MET_DST}/hdf-eos2-3.0
+export MET_BUFR=${MET_DST}/nceplibs-1.4.0/bufr-12.0.1
+export MET_GRIB2C=${MET_DST}/nceplibs-1.4.0/g2c-1.6.2
+export MET_GSLINC=/usr/include
+export MET_GSLLIB=/usr/lib/x86_64-linux-gnu
 export MET_CAIROINC=/usr/include/cairo
 export MET_CAIROLIB=/usr/lib/x86_64-linux-gnu
 export MET_FREETYPEINC=/usr/include/freetype2
 export MET_FREETYPELIB=/usr/lib/x86_64-linux-gnu
-export MET_JASPER=${MET_DST}/jasper-1.900.1
+export JASPER=${MET_DST}/jasper-1.900.1
 
 # For Python 3 in met-9.0
-export MET_PYTHON=/usr/local/met-python3
-export MET_PYTHON_CC="-I${MET_PYTHON}/include/python3.8"
-export MET_PYTHON_LD="-L${MET_PYTHON}/lib -lpython3.8 -lcrypt -lpthread -ldl -lutil -lm"
+export MET_PYTHON=${MET_DST}/met-python3
+export MET_PYTHON_BIN_EXE=${MET_PYTHON}/bin/python3.10
+export MET_PYTHON_CC="-I${MET_PYTHON}/include/python3.10"
+export MET_PYTHON_LD="-L${MET_PYTHON}/lib -lpython3.10 -lcrypt -lpthread -ldl -lutil -lm"
 
 # -D__64BIT__ is required because we've compiled libgrib2c.a with that flag
 export CFLAGS="-DUNDERSCORE -fPIC -D__64BIT__ -g"
 export CXXFLAGS=${CFLAGS}
 
 # Set LDFLAGS to include -rpath settings when compiling MET
 export LDFLAGS="-Wl,--disable-new-dtags"
-export LDFLAGS="${LDFLAGS} -Wl,-rpath,${MET_DST}/lib:${MET_HDFEOS}/lib:${MET_NETCDF}/lib:${MET_DST}/zlib-1.2.11/lib:${MET_DST}/szip-2.1.1/lib"
-export LDFLAGS="${LDFLAGS} -Wl,-rpath,${MET_HDFLIB}:${MET_HDF5}/lib:${MET_GSL}/lib:${MET_PYTHON}/lib:${MET_JASPER}/lib"
-export LDFLAGS="${LDFLAGS} -L${MET_JASPER}/lib"
+export LDFLAGS="${LDFLAGS} -Wl,-rpath,${MET_DST}/lib:${MET_HDFEOS}/lib:${MET_PROJ}/lib:${MET_NETCDF}/lib:${MET_DST}/zlib-1.2.11/lib:${MET_DST}/szip-2.1.1/lib"
+export LDFLAGS="${LDFLAGS} -Wl,-rpath,${MET_HDFLIB}:${MET_HDF5}/lib:${MET_GSL}/lib:${MET_PYTHON}/lib:${JASPER}/lib"
+export LDFLAGS="${LDFLAGS} -L${JASPER}/lib"
 
 # Variables required to run MET
 export MET_TEST_INPUT=${MET_PROJ_DIR}/MET_test_data/unit_test
 export MET_FONT_DIR=${MET_TEST_INPUT}/fonts
 
 # Define Rscript to use a version with the ncdf4 package 1.17 or later 
-export MET_TEST_RSCRIPT=/usr/local/R-4.1.2/bin/Rscript
+export MET_TEST_RSCRIPT=/nrit/ral/R-4.3.1/bin/Rscript
+
+# Define runtime Python version
+export MET_TEST_MET_PYTHON_EXE=${MET_PYTHON_BIN_EXE}
 
 # This is a cron script -- create the shell environment for this job
 # - NCO is for ncdiff
 # - NetCDF is for ncdump.
-export PATH="/usr/local/nco/bin:/usr/local/netcdf/bin:\
-             /usr/local/sbin:/usr/local/bin:/usr/sbin:\
+export PATH="/nrit/ral/nco/bin:/nrit/ral/netcdf4/bin:\
+             /nrit/ral/sbin:/nrit/ral/bin:/usr/sbin:\
              /usr/bin:/sbin:/bin:/usr/bin/X11:/opt/bin:$PATH"
 
 # SonarQube

diff --git a/internal/test_unit/R_test/test_util.R b/internal/test_unit/R_test/test_util.R
@@ -696,7 +696,7 @@ compareNc = function(nc1, nc2, verb, strict=0, delta=-1, comp_var=0){
 	}
 
 	# build and run the ncdiff command
-	strCmd = paste(strNcDiffExec, " -x -v time_bounds \\\n  ", nc1, " \\\n  ", nc2, " \\\n  ", strNcDiff, sep="");
+	strCmd = paste(strNcDiffExec, " -C -x -v time_bounds \\\n  ", nc1, " \\\n  ", nc2, " \\\n  ", strNcDiff, sep="");
 	if( 2 <= verb ){ cat("NCDIFF:", strCmd, "\n"); }
 	strCmdOut = system(paste(strCmd, "2>&1"), intern=T);