Per #3066, update usage statements in the docs and application code b…

…ased on PR feedback.

docs/Users_Guide/ensemble-stat.rst

@@ -89,7 +89,7 @@ The usage statement for the Ensemble Stat tool is shown below:
 .. code-block:: none
 
   Usage: ensemble_stat
-         n_ens ens_file_1 ... ens_file_n | ens_file_list
+         n_ens file_1 ... file_n | file_list
          config_file
          [-grid_obs file]
          [-point_obs file]
@@ -102,39 +102,37 @@ The usage statement for the Ensemble Stat tool is shown below:
          [-v level]
          [-compress level]
 
-ensemble_stat has three required arguments and accepts several optional ones.
+ensemble_stat has two required arguments and accepts several optional ones.
 
 Required Arguments ensemble_stat
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-1. The **n_ens ens_file_1 ... ens_file_n** is the number of ensemble members followed by a list of ensemble member file names. This argument is not required when ensemble files are specified in the **ens_file_list**, detailed below.
+1. The **n_ens file_1 ... file_n | file_list** specifies either the number of ensemble members followed by a list of ensemble member file names or an ASCII file list of the file names to be used, as described in :numref:`ascii_file_lists`.
 
-2. The **ens_file_list** is an ASCII file containing a list of ensemble member file names, as described in :numref:`ascii_file_lists`. This is not required when a file list is included on the command line, as described above.
-
-3. The **config_file** is an **EnsembleStatConfig** file containing the desired configuration settings.
+2. The **config_file** is an **EnsembleStatConfig** file containing the desired configuration settings.
 
 Optional Arguments for ensemble_stat
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-4. To produce ensemble statistics using gridded observations, use the **-grid_obs file** option to specify a gridded observation file. This option may be used multiple times if your observations are in several files.
+3. To produce ensemble statistics using gridded observations, use the **-grid_obs file** option to specify a gridded observation file. This option may be used multiple times if your observations are in several files.
 
-5. To produce ensemble statistics using point observations, use the **-point_obs file** option to specify a NetCDF point observation file. This option may be used multiple times if your observations are in several files. Python embedding for point observations is also supported, as described in :numref:`pyembed-point-obs-data`.
+4. To produce ensemble statistics using point observations, use the **-point_obs file** option to specify a NetCDF point observation file. This option may be used multiple times if your observations are in several files. Python embedding for point observations is also supported, as described in :numref:`pyembed-point-obs-data`.
 
-6. To override the simple ensemble mean value of the input ensemble members for the ECNT, SSVAR, and ORANK line types, the **-ens_mean file** option specifies an ensemble mean model data file. This option replaces the **-ssvar_mean file** option from earlier versions of MET.
+5. To override the simple ensemble mean value of the input ensemble members for the ECNT, SSVAR, and ORANK line types, the **-ens_mean file** option specifies an ensemble mean model data file. This option replaces the **-ssvar_mean file** option from earlier versions of MET.
 
-7. The **-ctrl file** option specifies an ensemble control member data file. The control member is included in the computation of the ensemble mean but excluded from the spread. The control file should not appear in the list of ensemble member files (unless processing a single file that contains all ensemble members).
+6. The **-ctrl file** option specifies an ensemble control member data file. The control member is included in the computation of the ensemble mean but excluded from the spread. The control file should not appear in the list of ensemble member files (unless processing a single file that contains all ensemble members).
 
-8. To filter point observations by time, use **-obs_valid_beg time** in YYYYMMDD[_HH[MMSS]] format to set the beginning of the matching observation time window.
+7. To filter point observations by time, use **-obs_valid_beg time** in YYYYMMDD[_HH[MMSS]] format to set the beginning of the matching observation time window.
 
-9. As above, use **-obs_valid_end time** in YYYYMMDD[_HH[MMSS]] format to set the end of the matching observation time window.
+8. As above, use **-obs_valid_end time** in YYYYMMDD[_HH[MMSS]] format to set the end of the matching observation time window.
 
-10. Specify the **-outdir path** option to override the default output directory (./).
+9. Specify the **-outdir path** option to override the default output directory (./).
 
-11. The **-log** file outputs log messages to the specified file.
+10. The **-log** file outputs log messages to the specified file.
 
-12. The **-v level** option indicates the desired level of verbosity. The value of "level" will override the default setting of 2. Setting the verbosity to 0 will make the tool run with no log messages, while increasing the verbosity will increase the amount of logging.
+11. The **-v level** option indicates the desired level of verbosity. The value of "level" will override the default setting of 2. Setting the verbosity to 0 will make the tool run with no log messages, while increasing the verbosity will increase the amount of logging.
 
-13. The **-compress level** option indicates the desired level of compression (deflate level) for NetCDF variables. The valid level is between 0 and 9. The value of "level" will override the default setting of 0 from the configuration file or the environment variable MET_NC_COMPRESS. Setting the compression level to 0 will make no compression for the NetCDF output. Lower number is for fast compression and higher number is for better compression.
+12. The **-compress level** option indicates the desired level of compression (deflate level) for NetCDF variables. The valid level is between 0 and 9. The value of "level" will override the default setting of 0 from the configuration file or the environment variable MET_NC_COMPRESS. Setting the compression level to 0 will make no compression for the NetCDF output. Lower number is for fast compression and higher number is for better compression.
 
 An example of the ensemble_stat calling sequence is shown below:
 

docs/Users_Guide/gen-ens-prod.rst

@@ -59,13 +59,11 @@ gen_ens_prod has three required arguments and accepts several optional ones.
 Required Arguments gen_ens_prod
 -------------------------------
 
-1. The **-ens file_1 ... file_n** option specifies the ensemble member file names. This argument is not required when ensemble files are specified in the **file_list**, detailed below.
+1. The **-ens file_1 ... file_n | file_list** option specifies the ensemble member files or ASCII file list of file names to be used, as described in :numref:`ascii_file_lists`.
 
-2. The **file_list** option is an ASCII file containing a list of ensemble member file names, as described in :numref:`ascii_file_lists`. This is not required when a file list is included on the command line, as described above.
+2. The **-out file** option specifies the NetCDF output file name to be written.
 
-3. The **-out file** option specifies the NetCDF output file name to be written.
-
-4. The **-config file** option is a **GenEnsProdConfig** file containing the desired configuration settings.
+3. The **-config file** option is a **GenEnsProdConfig** file containing the desired configuration settings.
 
 Optional Arguments for gen_ens_prod
 -----------------------------------

docs/Users_Guide/gsi-tools.rst

@@ -294,7 +294,7 @@ The usage statement for the GSIDENS2ORANK tool is shown below:
 .. code-block:: none
 
   Usage: gsidens2orank
-         ens_file_1 ... ens_file_n | ens_file_list
+         file_1 ... file_n | file_list
          -out path
          [-ens_mean path]
          [-swap]
@@ -304,35 +304,33 @@ The usage statement for the GSIDENS2ORANK tool is shown below:
          [-log file]
          [-v level]
 
-gsidens2orank has three required arguments and accepts several optional ones.
+gsidens2orank has two required arguments and accepts several optional ones.
 
 Required Arguments for gsidens2orank
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-1. The **ens_file_1 ... ens_file_n** argument is a list of ensemble binary GSI diagnostic files to be reformatted.
+1. The **file_1 ... file_n | file_list** argument specifies the ensemble binary GSI diagnostic files to be reformatted or ASCII file list of file names to be used, as described in :numref:`ascii_file_lists`.
 
-2. The **ens_file_list** argument is an ASCII file containing a list of ensemble GSI diagnostic files, as described in :numref:`ascii_file_lists`.
-
-3. The **-out path** argument specifies the name of the output **.stat** file.
+2. The **-out path** argument specifies the name of the output **.stat** file.
 
 Optional Arguments for gsidens2orank
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-4. The **-ens_mean path** option is the ensemble mean binary GSI diagnostic file.
+3. The **-ens_mean path** option is the ensemble mean binary GSI diagnostic file.
 
-5. The **-swap** option switches the endianness when reading the input binary files.
+4. The **-swap** option switches the endianness when reading the input binary files.
 
-6. The **-channel n** option overrides the default processing of all radiance channels with a comma-separated list.
+5. The **-channel n** option overrides the default processing of all radiance channels with a comma-separated list.
 
-7. The **-rng_name str** option overrides the default random number generator name (mt19937).
+6. The **-rng_name str** option overrides the default random number generator name (mt19937).
 
-8. The **-rng_seed str** option overrides the default random number generator seed.
+7. The **-rng_seed str** option overrides the default random number generator seed.
 
-9. The **-set_hdr col_name value** option specifies what should be written to the output header columns.
+8. The **-set_hdr col_name value** option specifies what should be written to the output header columns.
 
-10. The **-log file** option outputs log messages to the specified file.
+9. The **-log file** option outputs log messages to the specified file.
 
-11. The **-v level** option overrides the default level of logging (2).
+10. The **-v level** option overrides the default level of logging (2).
 
 An example of the gsidens2orank calling sequence is shown below:
 

docs/Users_Guide/mode-td.rst

@@ -197,7 +197,7 @@ The usage statement for the MODE-TD tool is listed below: The command line switc
   Usage: mtd
          -fcst    file_1 ... file_n | file_list
          -obs     file_1 ... file_n | file_list
-         -single  file_1 ... file_n | file_list
+         [-single  file_1 ... file_n | file_list]
          -config  config_file
          [-outdir path]
          [-log    file]

docs/Users_Guide/reformat_grid.rst

@@ -64,7 +64,7 @@ The add, subtract, and derive commands all require that the input files be expli
   INPUT_FILES:
          file_1 config_str_1 ... file_n config_str_n |
          file_1 ... file_n |
-         input_file_list
+         file_list
 
 Required Arguments for the pcp_combine
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -122,7 +122,7 @@ The input files for the add, subtract, and derive command can be specified in on
 
 2. Use **file_1 ... file_n** to specify the list of input files to be processed on the command line. Rather than specifying a separate configuration string for each input file, the "-field" command line option is required to specify the data to be processed.
 
-3. Use **input_file_list** to specify the name of an ASCII file which contains the paths for the gridded data files to be processed, as described in :numref:`ascii_file_lists`. As in the previous option, the "-field" command line option is required to specify the data to be processed.
+3. Use **file_list** to specify the name of an ASCII file which contains the paths for the gridded data files to be processed, as described in :numref:`ascii_file_lists`. As in the previous option, the "-field" command line option is required to specify the data to be processed.
 
 An example of the pcp_combine calling sequence is presented below:
 

docs/Users_Guide/rmw-analysis.rst

@@ -22,18 +22,18 @@ _______________________
 .. code-block:: none
 		
   Usage: rmw_analysis
-         -data file_1 ... file_n | data_file_list
+         -data file_1 ... file_n | file_list
          -config file
          -out file
          [-log file]
          [-v level]
 
-**rmw_analysis** has required arguments and can accept several optional arguments.
+**rmw_analysis** has three required arguments and can accept several optional arguments.
 
 Required Arguments for rmw_analysis
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-1. The **-data file_1 ... file_n | data_file_list** argument is the NetCDF output of TC-RMW to be processed or an ASCII file containing a list of files, as described in :numref:`ascii_file_lists`.
+1. The **-data file_1 ... file_n | file_list** option specifies the NetCDF TC-RMW output files or ASCII file list of file names to be processed, as described in :numref:`ascii_file_lists`.
 
 2. The **-config file** argument is the **RMWAnalysisConfig** to be used. The contents of the configuration file are discussed below.
 

docs/Users_Guide/tc-diag.rst

@@ -36,7 +36,7 @@ The following sections describe the usage statement, required arguments, and opt
 .. code-block:: none
 
   Usage: tc_diag
-         -data domain tech_id_list [ file_1 ... file_n | data_file_list ]
+         -data domain tech_id_list [ file_1 ... file_n | file_list ]
          -deck file
          -config file
          [-outdir path]
@@ -48,7 +48,7 @@ tc_diag has required arguments and can accept several optional arguments.
 Required Arguments for tc_diag
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-1. The **-data domain tech_id_list [ file_1 ... file_n | data_file_list ]** option specifies a domain name, a comma-separated list of ATCF tech ID's, and a list of gridded data files or an ASCII file containing a list of files to be used, as described in :numref:`ascii_file_lists`. Specify **-data** one for each gridded data source.
+1. The **-data domain tech_id_list [ file_1 ... file_n | file_list ]** option specifies a domain name, a comma-separated list of ATCF tech ID's, and a list of gridded data files or an ASCII file containing a list of files to be used, as described in :numref:`ascii_file_lists`. Specify **-data** once for each gridded data source.
 
 2. The **-deck source** option is the ATCF format track data source.
 

docs/Users_Guide/tc-rmw.rst

@@ -20,19 +20,19 @@ The following sections describe the usage statement, required arguments, and opt
 .. code-block:: none
 
   Usage: tc_rmw
-         -data file_1 ... file_n | data_file_list
+         -data file_1 ... file_n | file_list
          -deck file
          -config file
          -out file
          [-log file]
          [-v level]
 
-tc_rmw has required arguments and can accept several optional arguments.
+tc_rmw has four required arguments and can accept several optional arguments.
 
 Required Arguments for tc_rmw
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-1. The **-data file_1 ... file_n | data_file_list** options specify the gridded data files or an ASCII file containing a list of files to be used, as described in :numref:`ascii_file_lists`.
+1. The **-data file_1 ... file_n | file_list** option specifies the gridded data files or an ASCII file containing a list of files to be used, as described in :numref:`ascii_file_lists`.
 
 2. The **-deck source** argument is the ATCF format data source.
 

src/tools/core/ensemble_stat/ensemble_stat.cc

@@ -2844,7 +2844,7 @@ void usage() {
         << ") ***\n\n"
 
         << "Usage: " << program_name << "\n"
-        << "\tn_ens ens_file_1 ... ens_file_n | ens_file_list\n"
+        << "\tn_ens file_1 ... file_n | file_list\n"
         << "\tconfig_file\n"
         << "\t[-grid_obs file]\n"
         << "\t[-point_obs file]\n"
@@ -2857,11 +2857,11 @@ void usage() {
         << "\t[-v level]\n"
         << "\t[-compress level]\n\n"
 
-        << "\twhere\t\"n_ens ens_file_1 ... ens_file_n\" is the number "
+        << "\twhere\t\"n_ens file_1 ... file_n\" is the number "
         << "of ensemble members followed by a list of ensemble member "
         << "file names (required).\n"
 
-        << "\t\t\"ens_file_list\" is an ASCII file containing a list "
+        << "\t\t\"file_list\" is an ASCII file containing a list "
         << "of ensemble member file names (required).\n"
 
         << "\t\t\"config_file\" is an EnsembleStatConfig file "

src/tools/core/pcp_combine/pcp_combine.cc

@@ -1671,15 +1671,15 @@ void usage() {
         << "\tINPUT_FILES:\n"
         << "\t\tfile_1 config_str_1 ... file_n config_str_n | \n"
         << "\t\tfile_1 ... file_n |\n"
-        << "\t\tinput_file_list\n\n"
+        << "\t\tfile_list\n\n"
 
         << "\t\twhere\t\"file_i\" is the name of the i-th input "
         << "gridded data file.\n"
 
         << "\t\t\t\"config_str_i\" is the field to be extracted from "
         << "the i-th gridded data file.\n"
 
-        << "\t\t\t\"input_file_list\" is an ASCII file containing a list of "
+        << "\t\t\t\"file_list\" is an ASCII file containing a list of "
         << "gridded data files.\n\n"
 
         << "\t\tNote:\tFor \"-subtract\", exactly 2 input files must "

src/tools/core/series_analysis/series_analysis.cc

@@ -2624,9 +2624,9 @@ __attribute__((noreturn)) static void usage() {
         << ") ***\n\n"
 
         << "Usage: " << program_name << "\n"
-        << "\t-fcst  file_1 ... file_n | fcst_file_list\n"
-        << "\t-obs   file_1 ... file_n | obs_file_list\n"
-        << "\t[-both file_1 ... file_n | both_file_list]\n"
+        << "\t-fcst  file_1 ... file_n | file_list\n"
+        << "\t-obs   file_1 ... file_n | file_list\n"
+        << "\t[-both file_1 ... file_n | file_list]\n"
         << "\t[-aggr file]\n"
         << "\t[-paired]\n"
         << "\t-out file\n"
@@ -2636,15 +2636,15 @@ __attribute__((noreturn)) static void usage() {
         << "\t[-compress level]\n\n"
 
         << "\twhere\t"
-        << R"("-fcst file_1 ... file_n" are the gridded )"
+        << R"("-fcst file_1 ... file_n" is a list of gridded )"
         << "forecast files to be used (required).\n"
 
         << "\t\t"
-        << R"("-fcst fcst_file_list" is an ASCII file containing )"
+        << R"("-fcst file_list" is an ASCII file containing )"
         << "a list of gridded forecast files to be used (required).\n"
 
         << "\t\t"
-        << R"("-obs  file_1 ... file_n" are the gridded )"
+        << R"("-obs  file_1 ... file_n" is a list of gridded )"
         << "observation files to be used (required).\n"
 
         << "\t\t"

src/tools/other/gen_ens_prod/gen_ens_prod.cc

@@ -1262,17 +1262,17 @@ void usage() {
         << ") ***\n\n"
 
         << "Usage: " << program_name << "\n"
-        << "\t-ens file_1 ... file_n | ens_file_list\n"
+        << "\t-ens file_1 ... file_n | file_list\n"
         << "\t-out file\n"
         << "\t-config file\n"
         << "\t[-ctrl file]\n"
         << "\t[-log file]\n"
         << "\t[-v level]\n\n"
 
-        << "\twhere\t\"-ens file_1 ... file_n\" are the gridded ensemble "
-        << "data files to be used (required).\n"
+        << "\twhere\t\"-ens file_1 ... file_n\" is a list of ensemble "
+        << "member file names (required).\n"
 
-        << "\t\t\"ens_file_list\" is an ASCII file containing a list "
+        << "\t\t\"-ens ens_file_list\" is an ASCII file containing a list "
         << "of ensemble member file names (required).\n"
 
         << "\t\t\"-out file\" is the NetCDF output file for the derived "

src/tools/other/grid_diag/grid_diag.cc

@@ -813,14 +813,14 @@ void usage() {
         << ") ***\n\n"
 
         << "Usage: "<< program_name<< "\n"
-        << "\t-data  file_1 ... file_n | data_file_list\n"
+        << "\t-data  file_1 ... file_n | file_list\n"
         << "\t-out file\n"
         << "\t-config file\n"
         << "\t[-log file]\n"
         << "\t[-v level]\n"
         << "\t[-compress level]\n\n"
 
-        << "\twhere\t\"-data file_1 ... file_n\" are the gridded "
+        << "\twhere\t\"-data file_1 ... file_n\" is a list of gridded "
         << "data files to be used (required).\n"
 
         << "\t\t\"-data data_file_list\" is an ASCII file containing "