Docu update.

NEWS

@@ -8,6 +8,8 @@ Version 1.8.0 (26 October 2016):
      * Changed default of option -f nc to netCDF2
      * masklonlatbox: added support for unstructured grids
    New operators:
+     * timcumsum: Cumulative sum over time.
+     * cmorlite: Apply variable_entry of cmor tables
    Changed operators:
    Fixed bugs:
      * ml2pl: interpolation failed for data on hybrid half levels [Bug #7225]

doc/tex/bib.tex

@@ -17,6 +17,14 @@
        {German Weather Service (Deutscher Wetterdienst, DWD)}
 
 
+\bibitem[CMOR]{CMOR} \ \\
+  \href{git://github.com/PCMDI/cmor.git}
+       {Climate Model Output Rewriter},
+  from the
+  \href{https://www-pcmdi.llnl.gov}
+       { Program For Climate Model Diagnosis and Intercomparison (PCMDI)}
+
+
 \bibitem[ECHAM]{ECHAM} \ \\
   \href{http://www.mpimet.mpg.de/wissenschaft/publikationen/reports.html}
        {The atmospheric general circulation model ECHAM5},

doc/tex/makedoc

@@ -1216,7 +1216,7 @@ sub print_description {
 	  $line =~ s/\@ref\{([^}]*)\}/{\\htmlref{\1}{\1}}/og;
 	  $line =~ s/\@env\{([^}]*)\}/\\texttt{\1}/og;
 	  $line =~ s/\@cite\{([^}]*)\}/\\cite{\1}/og;
-	  $line =~ s/\@boldtt\{([^}]*)\}/{\\ttfamily \\bfseries \1}/og;
+	  $line =~ s/\@boldtt\{([^}]*)\}/\\textbf{\\texttt{\1}}/og;
 	  $line =~ s/\@bold\{([^}]*)\}/\\textbf{\1}/og;
 	  $line =~ s/\@celsius/{\\textcelsius}/og;
 	  $line =~ s/</\$<\$/og;

doc/tex/mod/CMOR

@@ -14,12 +14,12 @@ Options is a comma separated list of "key=value" pairs with optional parameters.
 
 @BeginOperator_cmor
 @Title     = CMOR
-@Parameter = tab [options]
+@Parameter = table [options]
 @EndOperator
 
 
 @BeginParameter
-@Item = tab
+@Item = table
 STRING   Name of the CMOR table as specified from PCMDI
 @Item = var
 STRING   Comma separated list of variables

doc/tex/mod/CMORlite

@@ -7,20 +7,81 @@
 @Operators = cmorlite
 
 @BeginDescription
+The @cite{CMOR} (Climate Model Output Rewriter) library comprises a set of
+functions, that can be used to produce CF-compliant NetCDF files that 
+fulfill the requirements of many of the climate community's standard
+model experiments. These experiments are collectively referred to as
+MIP's. Much of the metadata written to the output files is defined in
+MIP-specific tables, typically made available from each MIP's web site.
+
+The CDO operator cmorlite process the header and variable section
+of such MIP tables and writes the result with the internal IO library @cite{CDI}.
+In addition to the CMOR 2 and 3 table format, the CDO parameter table format
+is also supported. The following parameter table entries are available:
+
+@BeginTable
+ @bold{Entry}           & @bold{Type}        & @bold{Description}      
+ @boldtt{name}            & WORD        & Name of the variable
+ @boldtt{out_name}        & WORD        & New name of the variable
+ @boldtt{type}            & WORD        & Data type (real or double)
+ @boldtt{standard_name}   & WORD        & As defined in the CF standard name table
+ @boldtt{long_name}       & STRING      & Describing the variable
+ @boldtt{units}           & STRING      & Specifying the units for the variable
+ @boldtt{comment}         & STRING      & Information concerning the variable
+ @boldtt{cell_methods}    & STRING      & Information concerning calculation of means or climatologies
+ @boldtt{cell_measures}   & STRING      & Indicates the names of the variables containing cell areas and volumes
+ @boldtt{missing_value}   & FLOAT       & Specifying how missing data will be identified
+ @boldtt{valid_min}       & FLOAT       & Minimum valid value
+ @boldtt{valid_max}       & FLOAT       & Maximum valid value
+ @boldtt{ok_min_mean_abs} & FLOAT       & Minimum absolute mean
+ @boldtt{ok_max_mean_abs} & FLOAT       & Maximum absolute mean
+ @boldtt{factor}          & FLOAT       & Scale factor
+ @boldtt{delete}          & INTEGER     & Set to 1 to delete variable
+ @boldtt{convert}         & INTEGER     & Set to 1 to convert the unit if necessary
+@EndTable
+
+Most of the above entries are stored as variables attributes, some of them are handled differently.
+The variable @boldtt{name} is used as a search key for the parameter table. @boldtt{valid_min}, @boldtt{valid_max},
+@boldtt{ok_min_mean_abs} and @boldtt{ok_max_mean_abs} are used to check the range of the data.
 @EndDescription
 @EndModule
 
 
 @BeginOperator_cmorlite
 @Title     = CMOR lite
-@Parameter = table
+@Parameter = table [convert]
 @EndOperator
 
 
 @BeginParameter
 @Item = table
 STRING   Name of the CMOR table as specified from PCMDI
+@Item = convert
+STRING   Converts the units if necessary
 @EndParameter
 
+
 @BeginExample
+Here is an example of a parameter table for one variable:
+@BeginVerbatim
+prompt> cat mypartab
+&parameter
+  name            = t
+  out_name        = ta
+  standard_name   = air_temperature
+  units           = "K"
+  missing_value   = 1e+20
+  valid_min       = 157.1
+  valid_max       = 336.3
+/
+@EndVerbatim
+
+To apply this parameter table to a dataset use:
+@BeginVerbatim
+cdo -f nc cmorlite,mypartab,convert  ifile  ofile
+@EndVerbatim
+This command renames the variable @boldtt{t} to @boldtt{ta}. The standard name of this variable is set to @boldtt{air_temperature} and 
+the unit is set to [@boldtt{K}] (converts the unit if necessary). The missing value will be set to @boldtt{1e+20}. 
+In addition it will be checked whether the values of the variable are in the range of @bold{157.1} to @boldtt{336.3}.
+The result will be stored in NetCDF.
 @EndExample

doc/tex/mod/Gradsdes

@@ -13,7 +13,7 @@
 @Parameter = [mapversion]
 
 @BeginDescription
-Creates a @ref{GrADS} data descriptor file. Supported file formats are GRIB1, NetCDF, SERVICE, 
+Creates a @cite{GrADS} data descriptor file. Supported file formats are GRIB1, NetCDF, SERVICE, 
 EXTRA and IEG. For GRIB1 files the GrADS map file is also generated. For SERVICE and EXTRA
 files the grid have to be specified with the CDO option '-g <grid>'. This module takes @file{ifile}
 in order to create filenames for the descriptor (@file{ifile.ctl}) and the map (@file{ifile.gmp}) file.

doc/tex/mod/Mastrfu

@@ -12,7 +12,7 @@
 
 @BeginDescription
 This is a special operator for the post processing of the atmospheric general circulation
-model @ref{ECHAM}. It computes the mass stream function (code=272). The input dataset have 
+model @cite{ECHAM}. It computes the mass stream function (code=272). The input dataset have 
 to be a zonal mean of v-velocity [m/s] (code=132) on pressure levels.
 @EndDescription
 @EndOperator

doc/tex/mod/Remap

@@ -22,7 +22,7 @@ These interpolation weights can be reused for every remapping process with the o
 This operator remaps all input fields to a new horizontal grid. The remap type and 
 the interpolation weights of one input grid are read from a NetCDF file. More weights 
 are computed if the input fields are on different grids. The NetCDF file with the 
-weights should follow the @ref{SCRIP} convention. Normally these weights come from a previous
+weights should follow the @cite{SCRIP} convention. Normally these weights come from a previous
 call to one of the genXXX operators (e.g. @mod{genbil}) or were created by the original SCRIP package.
 @EndDescription
 @EndOperator

doc/tex/mod/Rhopot

@@ -12,7 +12,7 @@
 @Parameter = [pressure]
 
 @BeginDescription
-This is a special operator for the post processing of the ocean and sea ice model @ref{MPIOM}.
+This is a special operator for the post processing of the ocean and sea ice model @cite{MPIOM}.
 It calculates the sea water potential density (name=rhopoto; code=18). Required input fields 
 are sea water in-situ temperature (name=to; code=20) and sea water salinity (name=sao; code=5).
 Pressure is calculated from the level information or can be specified by the optional parameter.

doc/tex/mod/Setpartab

@@ -79,7 +79,6 @@ prompt> cat mypartab
   name            = t
   out_name        = ta
   standard_name   = air_temperature
-  convert         = 1
   units           = "K"
   missing_value   = 1e+20
   valid_min       = 157.1

src/modules.c

@@ -583,7 +583,7 @@ static modules_t Modules[] =
   { Change_e5slm,   NULL,              Change_e5slmOperators,  0,   CDI_REAL,  1,  1 },
   { Cloudlayer,     NULL,              CloudlayerOperators,    1,   CDI_REAL,  1,  1 },
   { CMOR,           CMORHelp,          CMOROperators,          1,   CDI_REAL,  1,  0 },
-  { CMOR_lite,      NULL,              CMORliteOperators,      1,   CDI_REAL,  1,  1 },
+  { CMOR_lite,      CMORliteHelp,      CMORliteOperators,      1,   CDI_REAL,  1,  1 },
   { CMOR_table,     NULL,              CMORtableOperators,     1,   CDI_REAL,  0,  0 },
   { Collgrid,       CollgridHelp,      CollgridOperators,      1,   CDI_REAL, -1,  1 },
   { Command,        NULL,              CommandOperators,       0,   CDI_REAL,  1,  0 },

src/operator_help.h

@@ -4997,12 +4997,47 @@ static const char *CMORliteHelp[] = {
     "    cmorlite - CMOR lite",
     "",
     "SYNOPSIS",
-    "    cmorlite,table  ifile ofile",
+    "    cmorlite,table[,convert]  ifile ofile",
     "",
     "DESCRIPTION",
+    "    The CMOR (Climate Model Output Rewriter) library comprises a set of",
+    "    functions, that can be used to produce CF-compliant NetCDF files that ",
+    "    fulfill the requirements of many of the climate community's standard",
+    "    model experiments. These experiments are collectively referred to as",
+    "    MIP's. Much of the metadata written to the output files is defined in",
+    "    MIP-specific tables, typically made available from each MIP's web site.",
+    "    ",
+    "    The CDO operator cmorlite process the header and variable section",
+    "    of such MIP tables and writes the result with the internal IO library CDI.",
+    "    In addition to the CMOR 2 and 3 table format, the CDO parameter table format",
+    "    is also supported. The following parameter table entries are available:",
+    "    ",
+    "     Entry           & Type        & Description      ",
+    "     name            & WORD        & Name of the variable",
+    "     out_name        & WORD        & New name of the variable",
+    "     type            & WORD        & Data type (real or double)",
+    "     standard_name   & WORD        & As defined in the CF standard name table",
+    "     long_name       & STRING      & Describing the variable",
+    "     units           & STRING      & Specifying the units for the variable",
+    "     comment         & STRING      & Information concerning the variable",
+    "     cell_methods    & STRING      & Information concerning calculation of means or climatologies",
+    "     cell_measures   & STRING      & Indicates the names of the variables containing cell areas and volumes",
+    "     missing_value   & FLOAT       & Specifying how missing data will be identified",
+    "     valid_min       & FLOAT       & Minimum valid value",
+    "     valid_max       & FLOAT       & Maximum valid value",
+    "     ok_min_mean_abs & FLOAT       & Minimum absolute mean",
+    "     ok_max_mean_abs & FLOAT       & Maximum absolute mean",
+    "     factor          & FLOAT       & Scale factor",
+    "     delete          & INTEGER     & Set to 1 to delete variable",
+    "     convert         & INTEGER     & Set to 1 to convert the unit if necessary",
+    "    ",
+    "    Most of the above entries are stored as variables attributes, some of them are handled differently.",
+    "    The variable name is used as a search key for the parameter table. valid_min, valid_max,",
+    "    ok_min_mean_abs and ok_max_mean_abs are used to check the range of the data.",
     "",
     "PARAMETER",
-    "    table  STRING   Name of the CMOR table as specified from PCMDI",
+    "    table    STRING   Name of the CMOR table as specified from PCMDI",
+    "    convert  STRING   Converts the units if necessary",
     NULL
 };
 
@@ -5011,13 +5046,13 @@ static const char *CMORHelp[] = {
     "    cmor - CMOR",
     "",
     "SYNOPSIS",
-    "    cmor,tab[,options]  ifile",
+    "    cmor,table[,options]  ifile",
     "",
     "DESCRIPTION",
     "    Options is a comma separated list of \"key=value\" pairs with optional parameters.",
     "",
     "PARAMETER",
-    "    tab       STRING   Name of the CMOR table as specified from PCMDI",
+    "    table     STRING   Name of the CMOR table as specified from PCMDI",
     "    var       STRING   Comma separated list of variables",
     "    expinfo   STRING   Experiment specific parameter file",
     "    modinfo   STRING   Model specific parameter file",