Collection of small structural changes

- Removes second topo_file entry in config.js
- Sets SP output off by default
- Removes whitespace in output_spec.csv
- Adds xarray and pypdf import for Docker container
- Adds Git SHA to restart and run_status files

config/config.js

@@ -17,12 +17,11 @@
     "fri_fire_file":      "demo-data/cru-ts40_ar5_rcp85_ncar-ccsm4_toolik_field_station_10x10/fri-fire.nc",
     "hist_exp_fire_file": "demo-data/cru-ts40_ar5_rcp85_ncar-ccsm4_toolik_field_station_10x10/historic-explicit-fire.nc",
     "proj_exp_fire_file": "demo-data/cru-ts40_ar5_rcp85_ncar-ccsm4_toolik_field_station_10x10/projected-explicit-fire.nc",
-    "topo_file":          "demo-data/cru-ts40_ar5_rcp85_ncar-ccsm4_toolik_field_station_10x10/topo.nc",
     "output_dir":         "output/",
     "output_spec_file":   "config/output_spec.csv",
     "output_monthly":     1, //JSON specific
     "output_nc_eq":       0,
-    "output_nc_sp":       1,
+    "output_nc_sp":       0,
     "output_nc_tr":       1,
     "output_nc_sc":       1, 
     "output_interval":    1 

config/output_spec.csv

@@ -4,7 +4,7 @@ AVLN,Total soil available N,g/m2,,,invalid,invalid,invalid,,double,
 BURNAIR2SOILN,Nitrogen deposit from fire emission,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 BURNSOIL2AIRC,Burned soil C,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 BURNSOIL2AIRN,Burned soil N,g/m2/time,,,invalid,invalid,invalid,invalid,double,
-BURNTHICK,Ground burn thickness ,m,,,invalid,invalid,invalid,invalid,double,
+BURNTHICK,Ground burn thickness,m,,,invalid,invalid,invalid,invalid,double,
 BURNVEG2AIRC,Burned vegetation C to atmosphere,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 BURNVEG2AIRN,Burned vegetation N to atmosphere,g/m2/time,,,invalid,invalid,invalid,invalid,double,
 BURNVEG2DEADC,Burned vegetation C to standing dead C,g/m2/time,,,invalid,invalid,invalid,invalid,double,

requirements_general_dev.txt

@@ -12,6 +12,8 @@ Sphinx==5.1.1
 sphinx-rtd-theme==1.1.0
 sphinx-toolbox==3.4.0
 sphinx-argparse==0.4.0
+xarray
+pypdf
 
 # for SA - maybe merits its own file??
 scikit-learn

src/RestartData.cpp

@@ -1280,7 +1280,8 @@ void RestartData::create_empty_file(const std::string& fname,
   temutil::nc( nc_def_var(ncid, "prvltrfcnA", NC_DOUBLE, 4, vartype4D_dimids, &prvltrfcnAV) );
   temutil::nc( nc_put_att_double(ncid, prvltrfcnAV, "_FillValue", NC_DOUBLE, 1, &MISSING_D) );
 
-  /* Create Attributes?? */
+  /* Global Attributes */
+  temutil::nc( nc_put_att_text(ncid, NC_GLOBAL, "Git_SHA", strlen(GIT_SHA), GIT_SHA ) );
 
   /* End Define Mode (not strictly necessary for netcdf 4) */
   BOOST_LOG_SEV(glg, debug) << "Leaving 'define mode'...";

src/TEM.cpp

@@ -929,6 +929,9 @@ void create_empty_run_status_file(const std::string& fname,
   std::string runtime_units = "seconds";
   temutil::nc( nc_put_att_text(ncid, total_runtimeV, "units", runtime_units.length(), runtime_units.c_str()) );
 
+  // Global attributes
+  temutil::nc( nc_put_att_text(ncid, NC_GLOBAL, "Git_SHA", strlen(GIT_SHA), GIT_SHA) );
+
   /* End Define Mode (not strictly necessary for netcdf 4) */
   BOOST_LOG_SEV(glg, debug) << "Leaving 'define mode' ["<<fname<<"]";
   temutil::nc( nc_enddef(ncid) );