From 3c74be44bdd9555d3829df9c4089f8c0a57d7940 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 8 Aug 2023 14:48:51 -0600
Subject: [PATCH 01/55] added helper function to clean up logic to add new
 dictionaries that contain time and file information to a list

---
 metplus/wrappers/runtime_freq_wrapper.py | 38 ++++++++++--------------
 1 file changed, 15 insertions(+), 23 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 15de1d1ed..66c6596cd 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -250,14 +250,8 @@ def run_at_time(self, input_dict):
 
             # since run_all_times was not called (LOOP_BY=times) then
             # get files for current run time
-            file_dict = self.get_files_from_time(time_info)
             all_files = []
-            if file_dict:
-                if isinstance(file_dict, list):
-                    all_files = file_dict
-                else:
-                    all_files = [file_dict]
-
+            self._update_list_with_new_files(time_info, all_files)
             self.c_dict['ALL_FILES'] = all_files
 
             # Run for given init/valid time and forecast lead combination
@@ -318,12 +312,7 @@ def get_all_files_from_leads(self, time_input):
             if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
                 continue
 
-            file_dict = self.get_files_from_time(time_info)
-            if file_dict:
-                if isinstance(file_dict, list):
-                    lead_files.extend(file_dict)
-                else:
-                    lead_files.append(file_dict)
+            self._update_list_with_new_files(time_info, lead_files)
 
         return lead_files
 
@@ -346,12 +335,8 @@ def get_all_files_for_lead(self, time_input):
             time_info = time_util.ti_calculate(current_time_input)
             if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
                 continue
-            file_dict = self.get_files_from_time(time_info)
-            if file_dict:
-                if isinstance(file_dict, list):
-                    new_files.extend(file_dict)
-                else:
-                    new_files.append(file_dict)
+
+            self._update_list_with_new_files(time_info, new_files)
 
         return new_files
 
@@ -360,12 +345,19 @@ def get_files_from_time(time_info):
         """! Create dictionary containing time information (key time_info) and
              any relevant files for that runtime.
              @param time_info dictionary containing time information
-             @returns dictionary containing time_info dict and any relevant
+             @returns list of dict containing time_info dict and any relevant
              files with a key representing a description of that file
         """
-        file_dict = {}
-        file_dict['time_info'] = time_info.copy()
-        return file_dict
+        return {'time_info': time_info.copy()}
+
+    def _update_list_with_new_files(self, time_info, list_to_update):
+        new_files = self.get_files_from_time(time_info)
+        if not new_files:
+            return
+        if isinstance(new_files, list):
+            list_to_update.extend(new_files)
+        else:
+            list_to_update.append(file_dict)
 
     @staticmethod
     def compare_time_info(runtime, filetime):

From 60662e482fd9b2ca9fe3d61dd822f8fbc40038c8 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 8 Aug 2023 14:50:16 -0600
Subject: [PATCH 02/55] fix incorrect variable name

---
 metplus/wrappers/runtime_freq_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 66c6596cd..9870e8ede 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -357,7 +357,7 @@ def _update_list_with_new_files(self, time_info, list_to_update):
         if isinstance(new_files, list):
             list_to_update.extend(new_files)
         else:
-            list_to_update.append(file_dict)
+            list_to_update.append(new_files)
 
     @staticmethod
     def compare_time_info(runtime, filetime):

From 927d63153ce88c8039e37f0ae0bfd921cc860491 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 8 Aug 2023 17:05:22 -0600
Subject: [PATCH 03/55] log error if wrapper was not loaded properly to help
 debug issue

---
 metplus/util/run_util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/metplus/util/run_util.py b/metplus/util/run_util.py
index efe2ecd57..9bd1ab6a6 100644
--- a/metplus/util/run_util.py
+++ b/metplus/util/run_util.py
@@ -153,8 +153,8 @@ def _get_wrapper_instance(config, process, instance=None):
         metplus_wrapper = (
             getattr(module, f"{process}Wrapper")(config, instance=instance)
         )
-    except AttributeError:
-        config.logger.error(f"There was a problem loading {process} wrapper.")
+    except AttributeError as err:
+        config.logger.error(f"There was a problem loading {process} wrapper: {err}")
         return None
     except ModuleNotFoundError:
         config.logger.error(f"Could not load {process} wrapper. "

From ffe1f23b50f9330a2997aee9437c175c28e599f9 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 8 Aug 2023 17:07:26 -0600
Subject: [PATCH 04/55] improve logging to print input dir/template once at
 beginning to avoid cluttering log output, make wrapper a LoopTimes wrapper to
 remove run_at_time function and reduce redundancy, log if example file path
 is found to make wrapper more useful

---
 metplus/wrappers/example_wrapper.py | 76 ++++++++---------------------
 1 file changed, 20 insertions(+), 56 deletions(-)

diff --git a/metplus/wrappers/example_wrapper.py b/metplus/wrappers/example_wrapper.py
index 04f8ddcd0..c2dfcb332 100755
--- a/metplus/wrappers/example_wrapper.py
+++ b/metplus/wrappers/example_wrapper.py
@@ -14,9 +14,10 @@
 
 from ..util import do_string_sub, ti_calculate, get_lead_sequence
 from ..util import skip_time
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
-class ExampleWrapper(CommandBuilder):
+
+class ExampleWrapper(LoopTimesWrapper):
     """!Wrapper can be used as a base to develop a new wrapper"""
     def __init__(self, config, instance=None):
         self.app_name = 'example'
@@ -25,7 +26,7 @@ def __init__(self, config, instance=None):
     def create_c_dict(self):
         c_dict = super().create_c_dict()
         # get values from config object and set them to be accessed by wrapper
-        c_dict['INPUT_TEMPLATE'] = self.config.getraw('filename_templates',
+        c_dict['INPUT_TEMPLATE'] = self.config.getraw('config',
                                                       'EXAMPLE_INPUT_TEMPLATE')
         c_dict['INPUT_DIR'] = self.config.getdir('EXAMPLE_INPUT_DIR', '')
 
@@ -38,64 +39,27 @@ def create_c_dict(self):
         if not c_dict['INPUT_DIR']:
             self.logger.debug('EXAMPLE_INPUT_DIR was not set')
 
+        full_path = os.path.join(c_dict['INPUT_DIR'], c_dict['INPUT_TEMPLATE'])
+        self.logger.info(f"Input directory is {c_dict['INPUT_DIR']}")
+        self.logger.info(f"Input template is {c_dict['INPUT_TEMPLATE']}")
+        self.logger.info(f"Full input template path is {full_path}")
+
         return c_dict
 
-    def run_at_time(self, input_dict):
+    def run_at_time_once(self, time_info):
         """! Do some processing for the current run time (init or valid)
 
-            @param input_dict dictionary with time information of current run
+            @param time_info dictionary with time information of current run
         """
-        # fill in time info dictionary
-        time_info = ti_calculate(input_dict)
-
-        # check if looping by valid or init and log time for run
-        loop_by = time_info['loop_by']
-        current_time = time_info[loop_by + '_fmt']
-        self.logger.info('Running ExampleWrapper at '
-                         f'{loop_by} time {current_time}')
-
         # read input directory and template from config dictionary
-        input_dir = self.c_dict['INPUT_DIR']
-        input_template = self.c_dict['INPUT_TEMPLATE']
-        self.logger.info(f'Input directory is {input_dir}')
-        self.logger.info(f'Input template is {input_template}')
-
-        # get forecast leads to loop over
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-
-            # set forecast lead time in hours
-            time_info['lead'] = lead
-
-            # recalculate time info items
-            time_info = ti_calculate(time_info)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(
-                        f"Processing custom string: {custom_string}"
-                    )
-
-                time_info['custom'] = custom_string
-
-                # log init/valid/forecast lead times for current loop iteration
-                self.logger.info(
-                    'Processing forecast lead '
-                    f'{time_info["lead_string"]} initialized at '
-                    f'{time_info["init"].strftime("%Y-%m-%d %HZ")} '
-                    'and valid at '
-                    f'{time_info["valid"].strftime("%Y-%m-%d %HZ")}'
-                )
-
-                # perform string substitution to find filename based on
-                # template and current run time
-                filename = do_string_sub(input_template,
-                                         **time_info)
-                self.logger.info('Looking in input directory '
-                                 f'for file: {filename}')
+        full_template = os.path.join(self.c_dict['INPUT_DIR'],
+                                     self.c_dict['INPUT_TEMPLATE'])
+
+        # perform string substitution to find filename based on
+        # template and current run time
+        filename = do_string_sub(full_template, **time_info)
+        self.logger.info(f'Looking for file: {filename}')
+        if os.path.exists(filename):
+            self.logger.info(f'FOUND FILE: {filename}')
 
         return True

From fee61a2cb48a9331fcae5595366721e30c8fa50e Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 8 Aug 2023 17:08:45 -0600
Subject: [PATCH 05/55] make wrappers LoopTimes (RuntimeFreq using run all
 times) to remove redundant run_at_time functions in each wrapper,
 ci-run-all-diff

---
 metplus/wrappers/ascii2nc_wrapper.py        | 57 +--------------------
 metplus/wrappers/compare_gridded_wrapper.py |  5 +-
 metplus/wrappers/cyclone_plotter_wrapper.py |  7 ---
 metplus/wrappers/ensemble_stat_wrapper.py   |  1 +
 metplus/wrappers/extract_tiles_wrapper.py   | 44 ++--------------
 metplus/wrappers/gempak_to_cf_wrapper.py    | 30 +----------
 metplus/wrappers/gen_ens_prod_wrapper.py    |  1 +
 metplus/wrappers/gen_vx_mask_wrapper.py     | 33 ++----------
 metplus/wrappers/grid_stat_wrapper.py       |  7 +++
 metplus/wrappers/ioda2nc_wrapper.py         | 24 ---------
 metplus/wrappers/mode_wrapper.py            |  1 +
 metplus/wrappers/mtd_wrapper.py             | 27 ++--------
 metplus/wrappers/pb2nc_wrapper.py           | 29 ++---------
 metplus/wrappers/runtime_freq_wrapper.py    | 27 ++++++++++
 14 files changed, 60 insertions(+), 233 deletions(-)

diff --git a/metplus/wrappers/ascii2nc_wrapper.py b/metplus/wrappers/ascii2nc_wrapper.py
index 482ce6b9b..b29cbf95c 100755
--- a/metplus/wrappers/ascii2nc_wrapper.py
+++ b/metplus/wrappers/ascii2nc_wrapper.py
@@ -13,7 +13,7 @@
 import os
 
 from ..util import time_util
-from . import CommandBuilder
+from . import LoopTimesWrapper
 from ..util import do_string_sub, skip_time, get_lead_sequence
 
 '''!@namespace ASCII2NCWrapper
@@ -22,7 +22,7 @@
 '''
 
 
-class ASCII2NCWrapper(CommandBuilder):
+class ASCII2NCWrapper(LoopTimesWrapper):
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_TIME_SUMMARY_DICT',
@@ -234,59 +234,6 @@ def get_command(self):
         cmd += ' -v ' + self.c_dict['VERBOSITY']
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the application for
-              each.
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-
-            time_info = time_util.ti_calculate(input_dict)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing custom string: {custom_string}")
-
-                time_info['custom'] = custom_string
-
-                self.run_at_time_once(time_info)
-
-    def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run ascii2nc
-             Args:
-                @param time_info dictionary containing timing information
-        """
-        # get input files
-        if self.find_input_files(time_info) is None:
-            return
-
-        # get output path
-        if not self.find_and_check_output_file(time_info):
-            return
-
-        # get other configurations for command
-        self.set_command_line_arguments(time_info)
-
-        # set environment variables if using config file
-        self.set_environment_variables(time_info)
-
-        # build command and run
-        cmd = self.get_command()
-        if cmd is None:
-            self.log_error("Could not generate command")
-            return
-
-        self.build()
-
     def find_input_files(self, time_info):
         # if using python embedding input, don't check if file exists,
         # just substitute time info and add to input file list
diff --git a/metplus/wrappers/compare_gridded_wrapper.py b/metplus/wrappers/compare_gridded_wrapper.py
index 4d242d3ba..728e099cb 100755
--- a/metplus/wrappers/compare_gridded_wrapper.py
+++ b/metplus/wrappers/compare_gridded_wrapper.py
@@ -16,7 +16,7 @@
 from ..util import parse_var_list
 from ..util import get_lead_sequence, skip_time, sub_var_list
 from ..util import field_read_prob_info, add_field_info_to_time_info
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
 '''!@namespace CompareGriddedWrapper
 @brief Common functionality to wrap similar MET applications
@@ -27,7 +27,8 @@
 @endcode
 '''
 
-class CompareGriddedWrapper(CommandBuilder):
+
+class CompareGriddedWrapper(LoopTimesWrapper):
     """!Common functionality to wrap similar MET applications
 that reformat gridded data
     """
diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
index 0e0de9009..8b7ceb53a 100644
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -166,7 +166,6 @@ def __init__(self, config, instance=None):
         self.extent_region = [self.west_lon, self.east_lon, self.south_lat, self.north_lat]
         self.logger.debug(f"extent region: {self.extent_region}")
 
-
     def run_all_times(self):
         """! Calls the defs needed to create the cyclone plots
              run_all_times() is required by CommandBuilder.
@@ -177,7 +176,6 @@ def run_all_times(self):
             return None
         self.create_plot()
 
-
     def retrieve_data(self):
         """! Retrieve data from track files.
             Returns:
@@ -358,7 +356,6 @@ def retrieve_data(self):
 
         return final_sorted_df
 
-
     def create_plot(self):
         """
          Create the plot, using Cartopy
@@ -514,7 +511,6 @@ def create_plot(self):
             # use Matplotlib's default if no resolution is set in config file
             plt.savefig(plot_filename)
 
-
     def get_plot_points(self):
         """
            Get the lon and lat points to be plotted, along with any other plotting-relevant
@@ -552,7 +548,6 @@ def get_plot_points(self):
 
         return points_list
 
-
     def get_points_by_track(self):
         """
             Get all the lats and lons for each storm track. Used to generate the line
@@ -583,7 +578,6 @@ def get_points_by_track(self):
 
         return track_dict
 
-
     def subset_by_region(self, sanitized_df):
         """
             Args:
@@ -618,7 +612,6 @@ def subset_by_region(self, sanitized_df):
 
         return masked
 
-
     @staticmethod
     def sanitize_lonlist(lon_list):
         """
diff --git a/metplus/wrappers/ensemble_stat_wrapper.py b/metplus/wrappers/ensemble_stat_wrapper.py
index 5e621792a..cadfab36c 100755
--- a/metplus/wrappers/ensemble_stat_wrapper.py
+++ b/metplus/wrappers/ensemble_stat_wrapper.py
@@ -22,6 +22,7 @@
 @endcode
 """
 
+
 class EnsembleStatWrapper(CompareGriddedWrapper):
     """!Wraps the MET tool ensemble_stat to compare ensemble datasets
     """
diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index ed11b3835..5b404cec4 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -17,9 +17,10 @@
 from ..util import get_lead_sequence, sub_var_list
 from ..util import parse_var_list, round_0p5, get_storms, prune_empty
 from .regrid_data_plane_wrapper import RegridDataPlaneWrapper
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
-class ExtractTilesWrapper(CommandBuilder):
+
+class ExtractTilesWrapper(LoopTimesWrapper):
     """! Takes tc-pairs data and regrids paired data to an n x m grid as
          specified in the config file.
     """
@@ -163,8 +164,7 @@ def regrid_data_plane_init(self):
         """
         rdp = 'REGRID_DATA_PLANE'
 
-        overrides = {}
-        overrides[f'{rdp}_METHOD'] = 'NEAREST'
+        overrides = {f'{rdp}_METHOD': 'NEAREST'}
         for data_type in ['FCST', 'OBS']:
             overrides[f'{data_type}_{rdp}_RUN'] = True
 
@@ -198,41 +198,7 @@ def regrid_data_plane_init(self):
         rdp_wrapper.c_dict['SHOW_WARNINGS'] = False
         return rdp_wrapper
 
-    def run_at_time(self, input_dict):
-        """!Loops over loop strings and calls run_at_time_loop_string() to
-            process data
-
-            @param input_dict dictionary containing initialization time
-        """
-
-        # loop of forecast leads and process each
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            input_dict['lead'] = lead
-
-            # set current lead time config and environment variables
-            time_info = ti_calculate(input_dict)
-
-            self.logger.info(
-                f"Processing forecast lead {time_info['lead_string']}"
-            )
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            # loop over custom loop list. If not defined,
-            # it will run once with an empty string as the custom string
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(
-                        f"Processing custom string: {custom_string}"
-                    )
-
-                time_info['custom'] = custom_string
-                self.run_at_time_loop_string(time_info)
-
-    def run_at_time_loop_string(self, time_info):
+    def run_at_time_once(self, time_info):
         """!Read TCPairs track data into TCStat to filter the data. Using the
             resulting track data, run RegridDataPlane on the model data to
             create tiles centered on the storm.
diff --git a/metplus/wrappers/gempak_to_cf_wrapper.py b/metplus/wrappers/gempak_to_cf_wrapper.py
index 53a5a5cb7..f54eb22b0 100755
--- a/metplus/wrappers/gempak_to_cf_wrapper.py
+++ b/metplus/wrappers/gempak_to_cf_wrapper.py
@@ -14,7 +14,7 @@
 
 from ..util import do_string_sub, skip_time, get_lead_sequence
 from ..util import time_util
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
 '''!@namespace GempakToCFWrapper
 @brief Wraps the GempakToCF tool to reformat Gempak format to NetCDF Format
@@ -22,7 +22,7 @@
 '''
 
 
-class GempakToCFWrapper(CommandBuilder):
+class GempakToCFWrapper(LoopTimesWrapper):
     def __init__(self, config, instance=None):
         self.app_name = "GempakToCF"
         self.app_path = config.getstr('exe', 'GEMPAKTOCF_JAR', '')
@@ -66,32 +66,6 @@ def get_command(self):
         cmd += " " + self.get_output_path()
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. Processing forecast
-              or observation data is determined by conf variables. This function
-              loops over the list of forecast leads and runs the application for
-              each.
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing custom string: {custom_string}")
-
-                input_dict['custom'] = custom_string
-
-                time_info = time_util.ti_calculate(input_dict)
-
-                if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                    self.logger.debug('Skipping run time')
-                    continue
-
-                self.run_at_time_once(time_info)
-
     def run_at_time_once(self, time_info):
         """! Runs the MET application for a given time and forecast lead combination
              Args:
diff --git a/metplus/wrappers/gen_ens_prod_wrapper.py b/metplus/wrappers/gen_ens_prod_wrapper.py
index 74c87ffcc..27d79d0d8 100755
--- a/metplus/wrappers/gen_ens_prod_wrapper.py
+++ b/metplus/wrappers/gen_ens_prod_wrapper.py
@@ -10,6 +10,7 @@
 
 from . import LoopTimesWrapper
 
+
 class GenEnsProdWrapper(LoopTimesWrapper):
     """! Wrapper for gen_ens_prod MET application """
 
diff --git a/metplus/wrappers/gen_vx_mask_wrapper.py b/metplus/wrappers/gen_vx_mask_wrapper.py
index b6aa36abe..6338c9ec6 100755
--- a/metplus/wrappers/gen_vx_mask_wrapper.py
+++ b/metplus/wrappers/gen_vx_mask_wrapper.py
@@ -13,7 +13,7 @@
 import os
 
 from ..util import getlist, get_lead_sequence, skip_time, ti_calculate, mkdir_p
-from . import CommandBuilder
+from . import LoopTimesWrapper
 from ..util import do_string_sub
 
 '''!@namespace GenVxMaskWrapper
@@ -22,7 +22,7 @@
 '''
 
 
-class GenVxMaskWrapper(CommandBuilder):
+class GenVxMaskWrapper(LoopTimesWrapper):
 
     def __init__(self, config, instance=None):
         self.app_name = "gen_vx_mask"
@@ -122,34 +122,7 @@ def get_command(self):
         cmd += ' -v ' + self.c_dict['VERBOSITY']
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the application for
-              each.
-              Args:
-                @param input_dict dictionary containing timing information
-                @returns None
-        """
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-
-            time_info = ti_calculate(input_dict)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing custom string: {custom_string}")
-
-                time_info['custom'] = custom_string
-
-                self.run_at_time_all(time_info)
-
-    def run_at_time_all(self, time_info):
+    def run_at_time_once(self, time_info):
         """!Loop over list of mask templates and call GenVxMask for each, adding the
             corresponding command line arguments for each call
             Args:
diff --git a/metplus/wrappers/grid_stat_wrapper.py b/metplus/wrappers/grid_stat_wrapper.py
index 666a148e6..c087cfc76 100755
--- a/metplus/wrappers/grid_stat_wrapper.py
+++ b/metplus/wrappers/grid_stat_wrapper.py
@@ -113,6 +113,13 @@ def create_c_dict(self):
                                                  'LOG_GRID_STAT_VERBOSITY',
                                                  c_dict['VERBOSITY'])
 
+        if c_dict['RUNTIME_FREQ'] != 'RUN_ONCE_FOR_EACH':
+            self.logger.warning(
+                f"GRID_STAT_RUNTIME_FREQ={c_dict['RUNTIME_FREQ']} not "
+                "supported. Using RUN_ONCE_FOR_EACH"
+            )
+            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
+
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('GridStatConfig_wrapped')
 
diff --git a/metplus/wrappers/ioda2nc_wrapper.py b/metplus/wrappers/ioda2nc_wrapper.py
index dfc75b4c7..d8354144d 100755
--- a/metplus/wrappers/ioda2nc_wrapper.py
+++ b/metplus/wrappers/ioda2nc_wrapper.py
@@ -109,30 +109,6 @@ def get_command(self):
                 f" {self.infiles[0]} {self.get_output_path()}"
                 f" {' '.join(self.args)}")
 
-    def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run ioda2nc
-
-        @param time_info dictionary containing timing information
-        @returns True if command was built/run successfully or
-         False if something went wrong
-        """
-        # get input files
-        if not self.find_input_files(time_info):
-            return False
-
-        # get output path
-        if not self.find_and_check_output_file(time_info):
-            return False
-
-        # get other configurations for command
-        self.set_command_line_arguments(time_info)
-
-        # set environment variables if using config file
-        self.set_environment_variables(time_info)
-
-        # build command and run
-        return self.build()
-
     def find_input_files(self, time_info):
         """! Get all input files for ioda2nc. Sets self.infiles list.
 
diff --git a/metplus/wrappers/mode_wrapper.py b/metplus/wrappers/mode_wrapper.py
index 57518403d..fc0d5bbaf 100755
--- a/metplus/wrappers/mode_wrapper.py
+++ b/metplus/wrappers/mode_wrapper.py
@@ -15,6 +15,7 @@
 from . import CompareGriddedWrapper
 from ..util import do_string_sub
 
+
 class MODEWrapper(CompareGriddedWrapper):
     """!Wrapper for the mode MET tool"""
 
diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index 432f7f375..efeafc52a 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -18,6 +18,7 @@
 from ..util import parse_var_list, add_field_info_to_time_info
 from . import CompareGriddedWrapper
 
+
 class MTDWrapper(CompareGriddedWrapper):
 
     WRAPPER_ENV_VAR_KEYS = [
@@ -54,6 +55,9 @@ def create_c_dict(self):
         #  a time window. Does not refer to time series of files
         c_dict['ALLOW_MULTIPLE_FILES'] = False
 
+        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
+        c_dict['FIND_FILES'] = False
+
         c_dict['OUTPUT_DIR'] = self.config.getdir('MTD_OUTPUT_DIR',
                                            self.config.getdir('OUTPUT_BASE'))
         c_dict['OUTPUT_TEMPLATE'] = (
@@ -172,26 +176,7 @@ def read_field_values(self, c_dict, read_type, write_type):
         if c_dict['SINGLE_RUN']:
             c_dict['OBS_CONV_THRESH'] = conf_value
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function loops
-              over the list of user-defined strings and runs the application
-               for each. Overrides run_at_time in compare_gridded_wrapper.py
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-
-        if skip_time(input_dict, self.c_dict.get('SKIP_TIMES', {})):
-            self.logger.debug('Skipping run time')
-            return
-
-        for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            input_dict['custom'] = custom_string
-            self.run_at_time_loop_string(input_dict)
-
-    def run_at_time_loop_string(self, input_dict):
+    def run_at_time_once(self, input_dict):
         """! Runs the MET application for a given run time. This function loops
              over the list of forecast leads and runs the application for each.
               Overrides run_at_time in compare_gridded_wrapper.py
@@ -306,7 +291,6 @@ def run_at_time_loop_string(self, input_dict):
 
             self.process_fields_one_thresh(time_info, var_info, **arg_dict)
 
-
     def run_single_mode(self, input_dict, var_info):
         single_list = []
 
@@ -446,7 +430,6 @@ def process_fields_one_thresh(self, time_info, var_info, model_path,
             # the lists are the same length
             obs_field_list = fcst_field_list
 
-
         # loop through fields and call MTD
         for fcst_field, obs_field in zip(fcst_field_list, obs_field_list):
             self.format_field('FCST',
diff --git a/metplus/wrappers/pb2nc_wrapper.py b/metplus/wrappers/pb2nc_wrapper.py
index 6d3848ca4..1de898ffd 100755
--- a/metplus/wrappers/pb2nc_wrapper.py
+++ b/metplus/wrappers/pb2nc_wrapper.py
@@ -16,9 +16,10 @@
 from ..util import getlistint, skip_time, get_lead_sequence
 from ..util import ti_calculate
 from ..util import do_string_sub
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
-class PB2NCWrapper(CommandBuilder):
+
+class PB2NCWrapper(LoopTimesWrapper):
     """! Wrapper to the MET tool pb2nc which converts prepbufr files
          to NetCDF for MET's point_stat tool can recognize.
     """
@@ -252,30 +253,6 @@ def set_valid_window_variables(self, time_info):
                 do_string_sub(end_template,
                               **time_info)
 
-
-    def run_at_time(self, input_dict):
-        """! Loop over each forecast lead and build pb2nc command """
-         # loop of forecast leads and process each
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            input_dict['lead'] = lead
-
-            lead_string = ti_calculate(input_dict)['lead_string']
-            self.logger.info("Processing forecast lead {}".format(lead_string))
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(
-                        f"Processing custom string: {custom_string}"
-                    )
-
-                input_dict['custom'] = custom_string
-
-                # Run for given init/valid time and forecast lead combination
-                self.clear()
-                self.run_at_time_once(input_dict)
-
-
     def run_at_time_once(self, input_dict):
         """!Find files needed to run pb2nc and run if found"""
         # look for input files to process
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 9870e8ede..57a0df0ef 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -261,6 +261,33 @@ def run_at_time(self, input_dict):
 
         return success
 
+    def run_at_time_once(self, time_info):
+        """! Process runtime and try to build command to run. Most wrappers
+        should be able to call this function to perform all of the actions
+        needed to build the commands using this template. This function can
+        be overridden if necessary.
+
+        @param time_info dictionary containing timing information
+        @returns True if command was built/run successfully or
+         False if something went wrong
+        """
+        # get input files
+        if not self.find_input_files(time_info):
+            return False
+
+        # get output path
+        if not self.find_and_check_output_file(time_info):
+            return False
+
+        # get other configurations for command
+        self.set_command_line_arguments(time_info)
+
+        # set environment variables if using config file
+        self.set_environment_variables(time_info)
+
+        # build command and run
+        return self.build()
+
     def get_all_files(self, custom=None):
         """! Get all files that can be processed with the app.
         @returns A dictionary where the key is the type of data that was found,

From 89a34d83bedb7980806f15b0b95a7de54534a6d5 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 08:44:49 -0600
Subject: [PATCH 06/55] fix function name in test, ci-run-all-diff

---
 .../tests/pytests/wrappers/gen_vx_mask/test_gen_vx_mask.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/internal/tests/pytests/wrappers/gen_vx_mask/test_gen_vx_mask.py b/internal/tests/pytests/wrappers/gen_vx_mask/test_gen_vx_mask.py
index fa1d660f9..d92a79c8e 100644
--- a/internal/tests/pytests/wrappers/gen_vx_mask/test_gen_vx_mask.py
+++ b/internal/tests/pytests/wrappers/gen_vx_mask/test_gen_vx_mask.py
@@ -37,7 +37,7 @@ def test_run_gen_vx_mask_once(metplus_config):
 #    wrap.c_dict['MASK_INPUT_TEMPLATES'] = ['LAT', 'LON']
 #    wrap.c_dict['COMMAND_OPTIONS'] = ["-type lat -thresh 'ge30&&le50'", "-type lon -thresh 'le-70&&ge-130' -intersection"]
 
-    wrap.run_at_time_all(time_info)
+    wrap.run_at_time_once(time_info)
 
     expected_cmd = f"{wrap.app_path} 2018020100_ZENITH LAT {wrap.config.getdir('OUTPUT_BASE')}/GenVxMask_test/2018020100_ZENITH_LAT_MASK.nc -type lat -thresh 'ge30&&le50' -v 2"
 
@@ -62,7 +62,7 @@ def test_run_gen_vx_mask_twice(metplus_config):
     cmd_args = ["-type lat -thresh 'ge30&&le50'", "-type lon -thresh 'le-70&&ge-130' -intersection -name lat_lon_mask"]
     wrap.c_dict['COMMAND_OPTIONS'] = cmd_args
 
-    wrap.run_at_time_all(time_info)
+    wrap.run_at_time_once(time_info)
 
     expected_cmds = [f"{wrap.app_path} 2018020100_ZENITH LAT {wrap.config.getdir('OUTPUT_BASE')}/stage/gen_vx_mask/temp_0.nc {cmd_args[0]} -v 2",
                      f"{wrap.app_path} {wrap.config.getdir('OUTPUT_BASE')}/stage/gen_vx_mask/temp_0.nc LON {wrap.config.getdir('OUTPUT_BASE')}/GenVxMask_test/2018020100_ZENITH_LAT_LON_MASK.nc {cmd_args[1]} -v 2"]

From a3f6c70425665bf94da0fcd7d7f6773f4c224889 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 12:43:35 -0600
Subject: [PATCH 07/55] set self.app_name if unset for all wrappers to prevent
 errors when creating unit tests

---
 metplus/wrappers/command_builder.py         | 5 +++++
 metplus/wrappers/compare_gridded_wrapper.py | 4 ----
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index 893562d06..b52539981 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -65,6 +65,11 @@ def __init__(self, config, instance=None):
         self.param = ""
         self.all_commands = []
 
+        # set app name to empty string if not set by wrapper
+        # needed to create instance of parent wrapper for unit tests
+        if not hasattr(self, 'app_name'):
+            self.app_name = ''
+
         # store values to set in environment variables for each command
         self.env_var_dict = {}
 
diff --git a/metplus/wrappers/compare_gridded_wrapper.py b/metplus/wrappers/compare_gridded_wrapper.py
index 728e099cb..81fff520b 100755
--- a/metplus/wrappers/compare_gridded_wrapper.py
+++ b/metplus/wrappers/compare_gridded_wrapper.py
@@ -34,10 +34,6 @@ class CompareGriddedWrapper(LoopTimesWrapper):
     """
 
     def __init__(self, config, instance=None):
-        # set app_name if not set by child class for unit tests
-        if not hasattr(self, 'app_name'):
-            self.app_name = 'compare_gridded'
-
         super().__init__(config, instance=instance)
 
     def create_c_dict(self):

From 5673a615a4a32ca5c6484b96b6a8cecc73806f5b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 12:43:55 -0600
Subject: [PATCH 08/55] set self.app_name if unset for all wrappers to prevent
 errors when creating unit tests

---
 metplus/wrappers/loop_times_wrapper.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/metplus/wrappers/loop_times_wrapper.py b/metplus/wrappers/loop_times_wrapper.py
index 9b7b4fae9..09570364c 100755
--- a/metplus/wrappers/loop_times_wrapper.py
+++ b/metplus/wrappers/loop_times_wrapper.py
@@ -16,10 +16,6 @@
 class LoopTimesWrapper(RuntimeFreqWrapper):
 
     def __init__(self, config, instance=None):
-        # set app_name if not set by child class to allow tests to run
-        if not hasattr(self, 'app_name'):
-            self.app_name = 'loop_times'
-
         super().__init__(config, instance=instance)
 
     def create_c_dict(self):

From d82c5e8707e706ab89e5bf35172f0bd98319ace9 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 12:45:37 -0600
Subject: [PATCH 09/55] change all CompareGridded (GridStat, PointStat,
 EnsembleStat, MODE, MTD) and ReformatGridded (PCPCombine, RegridDataPlane)
 wrappers to be LoopTimes wrappers so they use the same run_at_time method

---
 .../compare_gridded/test_compare_gridded.py   |  1 +
 .../pcp_combine/test_pcp_combine_wrapper.py   | 10 ++--
 .../test_regrid_data_plane.py                 |  9 ++--
 metplus/wrappers/compare_gridded_wrapper.py   | 32 ------------
 metplus/wrappers/pcp_combine_wrapper.py       | 32 ++++++++----
 metplus/wrappers/reformat_gridded_wrapper.py  | 50 +++----------------
 metplus/wrappers/regrid_data_plane_wrapper.py | 12 ++---
 7 files changed, 46 insertions(+), 100 deletions(-)

diff --git a/internal/tests/pytests/wrappers/compare_gridded/test_compare_gridded.py b/internal/tests/pytests/wrappers/compare_gridded/test_compare_gridded.py
index 0eaf8d5ab..d00857ca9 100644
--- a/internal/tests/pytests/wrappers/compare_gridded/test_compare_gridded.py
+++ b/internal/tests/pytests/wrappers/compare_gridded/test_compare_gridded.py
@@ -7,6 +7,7 @@
 
 from metplus.wrappers.compare_gridded_wrapper import CompareGriddedWrapper
 
+
 def compare_gridded_wrapper(metplus_config):
     """! Returns a default GridStatWrapper with /path/to entries in the
          metplus_system.conf and metplus_runtime.conf configuration
diff --git a/internal/tests/pytests/wrappers/pcp_combine/test_pcp_combine_wrapper.py b/internal/tests/pytests/wrappers/pcp_combine/test_pcp_combine_wrapper.py
index 3cfe0e676..5b4ed1131 100644
--- a/internal/tests/pytests/wrappers/pcp_combine/test_pcp_combine_wrapper.py
+++ b/internal/tests/pytests/wrappers/pcp_combine/test_pcp_combine_wrapper.py
@@ -114,7 +114,7 @@ def test_get_lowest_forecast_file_dated_subdir(metplus_config):
     valid_time = datetime.strptime("201802012100", '%Y%m%d%H%M')
     pcw.c_dict[f'{data_src}_INPUT_DIR'] = input_dir
     pcw._build_input_accum_list(data_src, {'valid': valid_time})
-    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src)
+    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src, custom='')
     assert(out_file == input_dir+"/20180201/file.2018020118f003.nc" and
            fcst == 10800)
 
@@ -128,7 +128,7 @@ def test_forecast_constant_init(metplus_config):
     init_time = datetime.strptime("2018020112", '%Y%m%d%H')
     valid_time = datetime.strptime("2018020121", '%Y%m%d%H')
     pcw.c_dict[f'{data_src}_INPUT_DIR'] = input_dir
-    out_file, fcst = pcw.find_input_file(init_time, valid_time, 0, data_src)
+    out_file, fcst = pcw.find_input_file(init_time, valid_time, 0, data_src, custom='')
     assert(out_file == input_dir+"/20180201/file.2018020112f009.nc" and
            fcst == 32400)
 
@@ -143,7 +143,7 @@ def test_forecast_not_constant_init(metplus_config):
     valid_time = datetime.strptime("2018020121", '%Y%m%d%H')
     pcw.c_dict[f'{data_src}_INPUT_DIR'] = input_dir
     pcw._build_input_accum_list(data_src, {'valid': valid_time})
-    out_file, fcst = pcw.find_input_file(init_time, valid_time, 0, data_src)
+    out_file, fcst = pcw.find_input_file(init_time, valid_time, 0, data_src, custom='')
     assert(out_file == input_dir+"/20180201/file.2018020118f003.nc" and
            fcst == 10800)
 
@@ -158,7 +158,7 @@ def test_get_lowest_forecast_file_no_subdir(metplus_config):
     pcw.c_dict[f'{data_src}_INPUT_TEMPLATE'] = template
     pcw.c_dict[f'{data_src}_INPUT_DIR'] = input_dir
     pcw._build_input_accum_list(data_src, {'valid': valid_time})
-    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src)
+    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src, custom='')
     assert(out_file == input_dir+"/file.2018020118f003.nc" and fcst == 10800)
 
 
@@ -172,7 +172,7 @@ def test_get_lowest_forecast_file_yesterday(metplus_config):
     pcw.c_dict[f'{data_src}_INPUT_TEMPLATE'] = template
     pcw.c_dict[f'{data_src}_INPUT_DIR'] = input_dir
     pcw._build_input_accum_list(data_src, {'valid': valid_time})
-    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src)
+    out_file, fcst = pcw.get_lowest_fcst_file(valid_time, data_src, custom='')
     assert(out_file == input_dir+"/file.2018013118f012.nc" and fcst == 43200)
 
 
diff --git a/internal/tests/pytests/wrappers/regrid_data_plane/test_regrid_data_plane.py b/internal/tests/pytests/wrappers/regrid_data_plane/test_regrid_data_plane.py
index bce689fb2..0ec4edbfb 100644
--- a/internal/tests/pytests/wrappers/regrid_data_plane/test_regrid_data_plane.py
+++ b/internal/tests/pytests/wrappers/regrid_data_plane/test_regrid_data_plane.py
@@ -156,7 +156,9 @@ def test_run_rdp_once_per_field(metplus_config):
     wrap.c_dict['FCST_OUTPUT_DIR'] = os.path.join(wrap.config.getdir('OUTPUT_BASE'),
                                                   'RDP_test')
 
-    wrap.run_at_time_once(time_info, var_list, data_type)
+    wrap.c_dict['VAR_LIST'] = var_list
+    wrap.c_dict['DATA_SRC'] = data_type
+    wrap.run_at_time_once(time_info)
 
     expected_cmds = [f"{wrap.app_path} -v 2 -method BUDGET -width 2 -field 'name=\"FNAME1\"; "
                      "level=\"A06\";' -name FNAME1 2018020100_ZENITH \"VERIF_GRID\" "
@@ -205,8 +207,9 @@ def test_run_rdp_all_fields(metplus_config):
     wrap.c_dict['VERIFICATION_GRID'] = 'VERIF_GRID'
     wrap.c_dict['FCST_OUTPUT_DIR'] = os.path.join(wrap.config.getdir('OUTPUT_BASE'),
                                                   'RDP_test')
-
-    wrap.run_at_time_once(time_info, var_list, data_type)
+    wrap.c_dict['VAR_LIST'] = var_list
+    wrap.c_dict['DATA_SRC'] = data_type
+    wrap.run_at_time_once(time_info)
 
     expected_cmds = [f"{wrap.app_path} -v 2 -method BUDGET -width 2 -field 'name=\"FNAME1\"; "
                      "level=\"A06\";' -field 'name=\"FNAME2\"; level=\"A03\";' "
diff --git a/metplus/wrappers/compare_gridded_wrapper.py b/metplus/wrappers/compare_gridded_wrapper.py
index 81fff520b..f45eb85da 100755
--- a/metplus/wrappers/compare_gridded_wrapper.py
+++ b/metplus/wrappers/compare_gridded_wrapper.py
@@ -106,38 +106,6 @@ def set_environment_variables(self, time_info):
 
         super().set_environment_variables(time_info)
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function loops
-             over the list of forecast leads and runs the application for each.
-
-             @param input_dict dictionary containing time information
-        """
-
-        # loop of forecast leads and process each
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            input_dict['lead'] = lead
-
-            # set current lead time config and environment variables
-            time_info = ti_calculate(input_dict)
-
-            self.logger.info("Processing forecast lead "
-                             f"{time_info['lead_string']}")
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info("Processing custom string: "
-                                     f"{custom_string}")
-
-                time_info['custom'] = custom_string
-
-                # Run for given init/valid time and forecast lead combination
-                self.run_at_time_once(time_info)
-
     def run_at_time_once(self, time_info):
         """! Build MET command for a given init/valid time and
          forecast lead combination.
diff --git a/metplus/wrappers/pcp_combine_wrapper.py b/metplus/wrappers/pcp_combine_wrapper.py
index a02cacb7d..b702e74a6 100755
--- a/metplus/wrappers/pcp_combine_wrapper.py
+++ b/metplus/wrappers/pcp_combine_wrapper.py
@@ -12,13 +12,15 @@
 from ..util import get_relativedelta, ti_get_seconds_from_relativedelta
 from ..util import time_string_to_met_time, seconds_to_met_time
 from ..util import parse_var_list, template_to_regex, split_level
-from ..util import add_field_info_to_time_info
+from ..util import add_field_info_to_time_info, sub_var_list
 from . import ReformatGriddedWrapper
 
 '''!@namespace PCPCombineWrapper
 @brief Wraps the MET tool pcp_combine to combine/divide
 precipitation accumulations or derive additional fields
 '''
+
+
 class PCPCombineWrapper(ReformatGriddedWrapper):
     """! Wraps the MET tool pcp_combine to combine or divide
          precipitation accumulations """
@@ -226,7 +228,9 @@ def set_fcst_or_obs_dict_items(self, d_type, c_dict):
 
         return c_dict
 
-    def run_at_time_once(self, time_info, var_list, data_src):
+    def run_at_time_once(self, time_info):
+        var_list = sub_var_list(self.c_dict['VAR_LIST'], time_info)
+        data_src = self.c_dict['DATA_SRC']
 
         if not var_list:
             var_list = [None]
@@ -635,6 +639,7 @@ def get_accumulation(self, time_info, accum, data_src,
           @return True if full set of files to build accumulation is found
         """
         search_time = time_info['valid']
+        custom = time_info.get('custom', '')
         # last time to search is the output accumulation subtracted from the
         # valid time, then add back the smallest accumulation that is available
         # in the input. This is done because data contains an accumulation from
@@ -687,7 +692,8 @@ def get_accumulation(self, time_info, accum, data_src,
                 search_file, lead = self.find_input_file(time_info['init'],
                                                          search_time,
                                                          accum_dict['amount'],
-                                                         data_src)
+                                                         data_src,
+                                                         custom)
 
                 if not search_file:
                     continue
@@ -699,7 +705,8 @@ def get_accumulation(self, time_info, accum, data_src,
                     accum_amount = self.get_template_accum(accum_dict,
                                                            search_time,
                                                            lead,
-                                                           data_src)
+                                                           data_src,
+                                                           custom)
                     if accum_amount > total_accum:
                         self.logger.debug("Accumulation amount is bigger "
                                           "than remaining accumulation.")
@@ -746,11 +753,12 @@ def get_accumulation(self, time_info, accum, data_src,
 
         return files_found
 
-    def get_lowest_fcst_file(self, valid_time, data_src):
+    def get_lowest_fcst_file(self, valid_time, data_src, custom):
         """! Find the lowest forecast hour that corresponds to the valid time
 
           @param valid_time valid time to search
           @param data_src data type (FCST or OBS) to get filename template
+          @param custom string from custom loop list to use in template sub
           @rtype string
           @return Path to file with the lowest forecast hour
     """
@@ -786,7 +794,7 @@ def get_lowest_fcst_file(self, valid_time, data_src):
                 'lead_seconds': forecast_lead
             }
             time_info = ti_calculate(input_dict)
-            time_info['custom'] = self.c_dict.get('CUSTOM_STRING', '')
+            time_info['custom'] = custom
             search_file = os.path.join(self.c_dict[f'{data_src}_INPUT_DIR'],
                                        self.c_dict[data_src+'_INPUT_TEMPLATE'])
             search_file = do_string_sub(search_file, **time_info)
@@ -821,7 +829,8 @@ def get_field_string(self, time_info=None, search_accum=0, name=None,
             field_info = do_string_sub(field_info, **time_info)
         return field_info
 
-    def find_input_file(self, init_time, valid_time, search_accum, data_src):
+    def find_input_file(self, init_time, valid_time, search_accum, data_src,
+                        custom):
         lead = 0
 
         in_template = self.c_dict[data_src+'_INPUT_TEMPLATE']
@@ -829,7 +838,7 @@ def find_input_file(self, init_time, valid_time, search_accum, data_src):
         if ('{lead?' in in_template or
                 ('{init?' in in_template and '{valid?' in in_template)):
             if not self.c_dict[f'{data_src}_CONSTANT_INIT']:
-                return self.get_lowest_fcst_file(valid_time, data_src)
+                return self.get_lowest_fcst_file(valid_time, data_src, custom)
 
             # set init time and lead in time dict if init should be constant
             # ti_calculate cannot currently handle both init and valid
@@ -842,7 +851,7 @@ def find_input_file(self, init_time, valid_time, search_accum, data_src):
                 input_dict = {'valid': valid_time}
 
         time_info = ti_calculate(input_dict)
-        time_info['custom'] = self.c_dict.get('CUSTOM_STRING', '')
+        time_info['custom'] = custom
         time_info['level'] = int(search_accum)
         input_path = os.path.join(self.c_dict[f'{data_src}_INPUT_DIR'],
                                   in_template)
@@ -852,11 +861,12 @@ def find_input_file(self, init_time, valid_time, search_accum, data_src):
                                self.c_dict[f'{data_src}_INPUT_DATATYPE'],
                                self.config), lead
 
-    def get_template_accum(self, accum_dict, search_time, lead, data_src):
+    def get_template_accum(self, accum_dict, search_time, lead, data_src,
+                           custom):
         # apply string substitution to accum amount
         search_time_dict = {'valid': search_time, 'lead_seconds': lead}
         search_time_info = ti_calculate(search_time_dict)
-        search_time_info['custom'] = self.c_dict.get('CUSTOM_STRING', '')
+        search_time_info['custom'] = custom
         amount = do_string_sub(accum_dict['template'],
                                **search_time_info)
         amount = get_seconds_from_string(amount, default_unit='S',
diff --git a/metplus/wrappers/reformat_gridded_wrapper.py b/metplus/wrappers/reformat_gridded_wrapper.py
index fc0dd5078..92aa3ce16 100755
--- a/metplus/wrappers/reformat_gridded_wrapper.py
+++ b/metplus/wrappers/reformat_gridded_wrapper.py
@@ -12,9 +12,9 @@
 
 import os
 
-from ..util import get_lead_sequence, sub_var_list
+from ..util import get_lead_sequence
 from ..util import time_util, skip_time
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
 # pylint:disable=pointless-string-statement
 '''!@namespace ReformatGriddedWrapper
@@ -27,20 +27,13 @@
 '''
 
 
-class ReformatGriddedWrapper(CommandBuilder):
+class ReformatGriddedWrapper(LoopTimesWrapper):
     """! Common functionality to wrap similar MET applications
          that reformat gridded data
     """
     def __init__(self, config, instance=None):
         super().__init__(config, instance=instance)
 
-    # this class should not be called directly
-    # pylint:disable=unused-argument
-    def run_at_time_once(self, time_info, var_list, data_type):
-        """!To be implemented by child class"""
-        self.log_error('ReformatGridded wrapper cannot be called directly.'
-                       ' Please use child wrapper')
-
     def run_at_time(self, input_dict):
         """! Runs the MET application for a given run time. Processing forecast
              or observation data is determined by conf variables.
@@ -50,9 +43,6 @@ def run_at_time(self, input_dict):
             @param input_dict dictionary containing init or valid time info
         """
         app_name_caps = self.app_name.upper()
-        class_name = self.__class__.__name__[0: -7]
-        lead_seq = get_lead_sequence(self.config, input_dict)
-
         run_list = []
         if self.config.getbool('config', 'FCST_'+app_name_caps+'_RUN', False):
             run_list.append("FCST")
@@ -60,6 +50,7 @@ def run_at_time(self, input_dict):
             run_list.append("OBS")
 
         if not run_list:
+            class_name = self.__class__.__name__[0: -7]
             self.log_error(f"{class_name} specified in process_list, but "
                            f"FCST_{app_name_caps}_RUN and "
                            f"OBS_{app_name_caps}_RUN  are both False. "
@@ -69,33 +60,6 @@ def run_at_time(self, input_dict):
 
         for to_run in run_list:
             self.logger.info("Processing {} data".format(to_run))
-            for lead in lead_seq:
-                input_dict['lead'] = lead
-
-                time_info = time_util.ti_calculate(input_dict)
-
-                self.logger.info("Processing forecast lead "
-                                 f"{time_info['lead_string']}")
-
-                if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
-                    self.logger.debug('Skipping run time')
-                    continue
-
-                # loop over custom string list and set
-                # custom in the time_info dictionary
-                for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                    if custom_string:
-                        self.logger.info("Processing custom string: "
-                                         f"{custom_string}")
-
-                    time_info['custom'] = custom_string
-                    self.c_dict['CUSTOM_STRING'] = custom_string
-                    var_list_name = f'VAR_LIST_{to_run}'
-                    var_list = (
-                        sub_var_list(self.c_dict.get(var_list_name, ''),
-                                     time_info)
-                    )
-                    if not var_list:
-                        var_list = None
-
-                    self.run_at_time_once(time_info, var_list, to_run)
+            self.c_dict['VAR_LIST'] = self.c_dict.get(f'VAR_LIST_{to_run}')
+            self.c_dict['DATA_SRC'] = to_run
+            super().run_at_time(input_dict)
diff --git a/metplus/wrappers/regrid_data_plane_wrapper.py b/metplus/wrappers/regrid_data_plane_wrapper.py
index 0211af427..3f9776807 100755
--- a/metplus/wrappers/regrid_data_plane_wrapper.py
+++ b/metplus/wrappers/regrid_data_plane_wrapper.py
@@ -14,7 +14,7 @@
 
 from ..util import get_seconds_from_string, do_string_sub
 from ..util import parse_var_list, get_process_list
-from ..util import add_field_info_to_time_info
+from ..util import add_field_info_to_time_info, sub_var_list
 from ..util import remove_quotes, split_level, format_level
 from . import ReformatGriddedWrapper
 
@@ -292,14 +292,14 @@ def run_once_for_all_fields(self, time_info, var_list, data_type):
         # build and run commands
         return self.build()
 
-    def run_at_time_once(self, time_info, var_list, data_type):
+    def run_at_time_once(self, time_info):
         """!Build command or commands to run at the given run time
-            Args:
-                @param time_info time dictionary used for string substitution
-                @param var_list list of field dictionaries to process
-                @param data_type type of data to process, i.e. FCST or OBS
+
+            @param time_info time dictionary used for string substitution
         """
         self.clear()
+        var_list = sub_var_list(self.c_dict['VAR_LIST'], time_info)
+        data_type = self.c_dict['DATA_SRC']
 
         # set output dir and template to current data type's values
         self.c_dict['OUTPUT_DIR'] = self.c_dict.get(f'{data_type}_OUTPUT_DIR')

From 39e858231735d7fd0cc301c009dc370ff8205634 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 12:50:51 -0600
Subject: [PATCH 10/55] add test for usage wrapper, ci-run-all-diff

---
 .../tests/pytests/wrappers/usage/test_usage.py    | 15 +++++++++++++++
 metplus/wrappers/usage_wrapper.py                 |  1 +
 2 files changed, 16 insertions(+)
 create mode 100644 internal/tests/pytests/wrappers/usage/test_usage.py

diff --git a/internal/tests/pytests/wrappers/usage/test_usage.py b/internal/tests/pytests/wrappers/usage/test_usage.py
new file mode 100644
index 000000000..4489f8491
--- /dev/null
+++ b/internal/tests/pytests/wrappers/usage/test_usage.py
@@ -0,0 +1,15 @@
+#!/usr/bin/env python3
+
+import pytest
+
+from metplus.wrappers.usage_wrapper import UsageWrapper
+
+
+@pytest.mark.wrapper
+def test_usage_wrapper_run(metplus_config):
+    config = metplus_config
+    wrapper = UsageWrapper(config)
+    assert wrapper.isOK
+
+    all_commands = wrapper.run_all_times()
+    assert not all_commands
diff --git a/metplus/wrappers/usage_wrapper.py b/metplus/wrappers/usage_wrapper.py
index 77c26b575..f37151a80 100644
--- a/metplus/wrappers/usage_wrapper.py
+++ b/metplus/wrappers/usage_wrapper.py
@@ -6,6 +6,7 @@
 from . import CommandBuilder
 from ..util import LOWER_TO_WRAPPER_NAME
 
+
 class UsageWrapper(CommandBuilder):
     """! A default process, prints out usage when nothing is defined in
          the PROCESS_LIST

From 6dbc6aafdd74d8f3dd080ad5521ddeb33be63d4f Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 13:42:25 -0600
Subject: [PATCH 11/55] fix call to RegridDataPlane from ExtractTiles wrapper

---
 metplus/wrappers/extract_tiles_wrapper.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index 5b404cec4..8f8de6b97 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -350,6 +350,7 @@ def get_object_indices(object_cats):
     def call_regrid_data_plane(self, time_info, track_data, input_type):
         # set var list from config using time info
         var_list = sub_var_list(self.c_dict['VAR_LIST_TEMP'], time_info)
+        self.regrid_data_plane.c_dict['VAR_LIST'] = var_list
 
         for data_type in ['FCST', 'OBS']:
             grid = self.get_grid(data_type, track_data[data_type],
@@ -358,9 +359,8 @@ def call_regrid_data_plane(self, time_info, track_data, input_type):
             self.regrid_data_plane.c_dict['VERIFICATION_GRID'] = grid
 
             # run RegridDataPlane wrapper
-            ret = self.regrid_data_plane.run_at_time_once(time_info,
-                                                          var_list,
-                                                          data_type=data_type)
+            self.regrid_data_plane.c_dict['DATA_SRC'] = data_type
+            ret = self.regrid_data_plane.run_at_time_once(time_info)
             self.all_commands.extend(self.regrid_data_plane.all_commands)
             self.regrid_data_plane.all_commands.clear()
             if not ret:

From 82f04e4ec6fe3c5e9df01ea80a14405644d86ade Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 13:46:42 -0600
Subject: [PATCH 12/55] changed more wrappers to use consistent time looping,
 ci-run-all-cases

---
 metplus/wrappers/plot_data_plane_wrapper.py | 31 ++----------------
 metplus/wrappers/point2grid_wrapper.py      | 25 ++------------
 metplus/wrappers/py_embed_ingest_wrapper.py | 36 +++------------------
 3 files changed, 9 insertions(+), 83 deletions(-)

diff --git a/metplus/wrappers/plot_data_plane_wrapper.py b/metplus/wrappers/plot_data_plane_wrapper.py
index 26f844772..7e8c09ef2 100755
--- a/metplus/wrappers/plot_data_plane_wrapper.py
+++ b/metplus/wrappers/plot_data_plane_wrapper.py
@@ -13,8 +13,8 @@
 import os
 
 from ..util import time_util
-from . import CommandBuilder
 from ..util import do_string_sub, remove_quotes, skip_time, get_lead_sequence
+from . import LoopTimesWrapper
 
 '''!@namespace PlotDataPlaneWrapper
 @brief Wraps the PlotDataPlane tool to plot data
@@ -22,7 +22,7 @@
 '''
 
 
-class PlotDataPlaneWrapper(CommandBuilder):
+class PlotDataPlaneWrapper(LoopTimesWrapper):
     def __init__(self, config, instance=None):
         self.app_name = "plot_data_plane"
         self.app_path = os.path.join(config.getdir('MET_BIN_DIR', ''),
@@ -107,33 +107,6 @@ def get_command(self):
         cmd += f" -v {self.c_dict['VERBOSITY']}"
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the application for
-              each.
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-
-            time_info = time_util.ti_calculate(input_dict)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info("Processing custom string: "
-                                     f"{custom_string}")
-
-                time_info['custom'] = custom_string
-
-                self.run_at_time_once(time_info)
-
     def run_at_time_once(self, time_info):
         """! Process runtime and try to build command to run ascii2nc
              Args:
diff --git a/metplus/wrappers/point2grid_wrapper.py b/metplus/wrappers/point2grid_wrapper.py
index e502554e7..6443bcf18 100755
--- a/metplus/wrappers/point2grid_wrapper.py
+++ b/metplus/wrappers/point2grid_wrapper.py
@@ -16,7 +16,7 @@
 from ..util import ti_calculate
 from ..util import do_string_sub
 from ..util import remove_quotes
-from . import CommandBuilder
+from . import LoopTimesWrapper
 
 '''!@namespace Point2GridWrapper
 @brief Wraps the Point2Grid tool to reformat ascii format to NetCDF
@@ -24,7 +24,7 @@
 '''
 
 
-class Point2GridWrapper(CommandBuilder):
+class Point2GridWrapper(LoopTimesWrapper):
 
     def __init__(self, config, instance=None):
         self.app_name = "point2grid"
@@ -145,27 +145,6 @@ def get_command(self):
         cmd += ' -v ' + self.c_dict['VERBOSITY']
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the application for
-              each.
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-
-            time_info = ti_calculate(input_dict)
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing custom string: {custom_string}")
-
-                time_info['custom'] = custom_string
-
-                self.run_at_time_once(time_info)
-
     def run_at_time_once(self, time_info):
         """! Process runtime and try to build command to run point2grid
              Args:
diff --git a/metplus/wrappers/py_embed_ingest_wrapper.py b/metplus/wrappers/py_embed_ingest_wrapper.py
index 22732f473..1d4fe7845 100755
--- a/metplus/wrappers/py_embed_ingest_wrapper.py
+++ b/metplus/wrappers/py_embed_ingest_wrapper.py
@@ -14,13 +14,14 @@
 import re
 
 from ..util import time_util
-from . import CommandBuilder
-from . import RegridDataPlaneWrapper
 from ..util import do_string_sub, get_lead_sequence
+from . import LoopTimesWrapper
+from . import RegridDataPlaneWrapper
 
 VALID_PYTHON_EMBED_TYPES = ['NUMPY', 'XARRAY', 'PANDAS']
 
-class PyEmbedIngestWrapper(CommandBuilder):
+
+class PyEmbedIngestWrapper(LoopTimesWrapper):
     """!Wrapper to utilize Python Embedding in the MET tools to read in
     data using a python script"""
     def __init__(self, config, instance=None):
@@ -123,34 +124,7 @@ def get_ingest_items(self, item_type, index, ingest_script_addons):
 
         return ingest_items
 
-    def run_at_time(self, input_dict):
-        """! Do some processing for the current run time (init or valid)
-              Args:
-                @param input_dict dictionary containing time information of current run
-                        generally contains 'now' (current) time and 'init' or 'valid' time
-        """
-        # get forecast leads to loop over
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-
-            # set forecast lead time in hours
-            input_dict['lead'] = lead
-
-            # recalculate time info items
-            time_info = time_util.ti_calculate(input_dict)
-
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing loop string: {custom_string}")
-
-                time_info['custom'] = custom_string
-
-                if not self.run_at_time_lead(time_info):
-                    return False
-
-        return True
-
-    def run_at_time_lead(self, time_info):
+    def run_at_time_once(self, time_info):
         rdp = self.c_dict['regrid_data_plane']
 
         # run each ingester specified

From 469bbe5fc1624458f007c216f88d6b4f7683d2b4 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 14:28:05 -0600
Subject: [PATCH 13/55] formatting

---
 metplus/wrappers/regrid_data_plane_wrapper.py | 1 -
 metplus/wrappers/tc_gen_wrapper.py            | 9 ++-------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/metplus/wrappers/regrid_data_plane_wrapper.py b/metplus/wrappers/regrid_data_plane_wrapper.py
index 3f9776807..c4f93f0a5 100755
--- a/metplus/wrappers/regrid_data_plane_wrapper.py
+++ b/metplus/wrappers/regrid_data_plane_wrapper.py
@@ -111,7 +111,6 @@ def create_c_dict(self):
                 met_tool=self.app_name
             )
 
-
         if self.config.getbool('config', 'OBS_REGRID_DATA_PLANE_RUN', False):
             window_types.append('OBS')
             c_dict['OBS_INPUT_DIR'] = \
diff --git a/metplus/wrappers/tc_gen_wrapper.py b/metplus/wrappers/tc_gen_wrapper.py
index db77f7cc5..aae6c991c 100755
--- a/metplus/wrappers/tc_gen_wrapper.py
+++ b/metplus/wrappers/tc_gen_wrapper.py
@@ -24,6 +24,7 @@
 @endcode
 '''
 
+
 class TCGenWrapper(CommandBuilder):
 
     WRAPPER_ENV_VAR_KEYS = [
@@ -92,7 +93,6 @@ class TCGenWrapper(CommandBuilder):
         'best_fn_oy',
     ]
 
-
     def __init__(self, config, instance=None):
         self.app_name = "tc_gen"
         self.app_path = os.path.join(config.getdir('MET_BIN_DIR'),
@@ -327,12 +327,7 @@ def get_command(self):
         return cmd
 
     def run_all_times(self):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the
-               application for each.
-
-             @param input_dict dictionary containing timing information
-        """
+        """!Runs tc_gen for the first run time"""
         # run using input time dictionary
         self.run_at_time(self.c_dict['INPUT_TIME_DICT'])
         return self.all_commands

From 83e0286a027cfd20cd296c63656cc04081b6e535 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 14:47:48 -0600
Subject: [PATCH 14/55] more formatting

---
 metplus/wrappers/tcrmw_wrapper.py       | 2 --
 metplus/wrappers/user_script_wrapper.py | 1 +
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/metplus/wrappers/tcrmw_wrapper.py b/metplus/wrappers/tcrmw_wrapper.py
index 4784c18bf..3cb78ff2a 100755
--- a/metplus/wrappers/tcrmw_wrapper.py
+++ b/metplus/wrappers/tcrmw_wrapper.py
@@ -342,8 +342,6 @@ def find_input_files(self, time_info):
         return self.infiles
 
     def set_command_line_arguments(self, time_info):
-
-        # add config file - passing through do_string_sub to get custom string if set
         if self.c_dict['CONFIG_FILE']:
             config_file = do_string_sub(self.c_dict['CONFIG_FILE'],
                                         **time_info)
diff --git a/metplus/wrappers/user_script_wrapper.py b/metplus/wrappers/user_script_wrapper.py
index 32e50ac38..71274997a 100755
--- a/metplus/wrappers/user_script_wrapper.py
+++ b/metplus/wrappers/user_script_wrapper.py
@@ -22,6 +22,7 @@
 @endcode
 '''
 
+
 class UserScriptWrapper(RuntimeFreqWrapper):
     def __init__(self, config, instance=None):
         self.app_name = "user_script"

From 9cb8b7ef76563af5dd68257c263c32ab57c6477a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 15:08:33 -0600
Subject: [PATCH 15/55] remove unnessary check for skip times because it is
 called upstream, remove command check that is done inside build function

---
 metplus/wrappers/pb2nc_wrapper.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/metplus/wrappers/pb2nc_wrapper.py b/metplus/wrappers/pb2nc_wrapper.py
index 1de898ffd..42aad03a0 100755
--- a/metplus/wrappers/pb2nc_wrapper.py
+++ b/metplus/wrappers/pb2nc_wrapper.py
@@ -262,10 +262,6 @@ def run_at_time_once(self, input_dict):
         if time_info is None:
             return
 
-        if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-            self.logger.debug('Skipping run time')
-            return
-
         # look for output file path and skip running pb2nc if necessary
         if not self.find_and_check_output_file(time_info):
             return
@@ -279,11 +275,7 @@ def run_at_time_once(self, input_dict):
         self.c_dict['CONFIG_FILE'] = do_string_sub(self.c_dict['CONFIG_FILE'],
                                                    **time_info)
 
-        # build command and run if successful
-        cmd = self.get_command()
-        if cmd is None:
-            self.log_error("Could not generate command")
-            return
+        # build and run command
         self.build()
 
     def get_command(self):

From da19788a5f0cb1ae2c6cf411e4e25e71e3a35c36 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 9 Aug 2023 15:39:53 -0600
Subject: [PATCH 16/55] add SKIP_LEAD_SEQ check to RuntimeFreq run_at_time and
 change TCPairs, TCStat, and TCRMW to be RuntimeFreq wrappers -- testing if
 any issues arise because there may be an assumption that init==valid for
 these tools, but RuntimeFreq RUN_ONCE_PER_INIT_OR_VALID uses wildcard for
 forecast lead and does not compute the opposite of init/valid,
 ci-run-all-diff

---
 metplus/wrappers/runtime_freq_wrapper.py |  7 ++++-
 metplus/wrappers/tc_pairs_wrapper.py     | 36 +++---------------------
 metplus/wrappers/tc_stat_wrapper.py      |  8 ++++--
 metplus/wrappers/tcrmw_wrapper.py        |  6 ++--
 4 files changed, 19 insertions(+), 38 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 57a0df0ef..aa40d8d3f 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -232,8 +232,13 @@ def run_once_for_each(self, custom):
 
     def run_at_time(self, input_dict):
         success = True
+
         # loop of forecast leads and process each
-        lead_seq = get_lead_sequence(self.config, input_dict)
+        if self.c_dict.get('SKIP_LEAD_SEQ', False):
+            lead_seq = [0]
+        else:
+            lead_seq = get_lead_sequence(self.config, input_dict)
+
         for lead in lead_seq:
             input_dict['lead'] = lead
 
diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index 78377e431..5f7c67914 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -26,7 +26,7 @@
 from ..util import get_tags, find_indices_in_config_section
 from ..util.met_config import add_met_config_dict_list
 from ..util import time_generator, log_runtime_banner, add_to_time_input
-from . import CommandBuilder
+from . import RuntimeFreqWrapper
 
 '''!@namespace TCPairsWrapper
 @brief Wraps the MET tool tc_pairs to parse ADeck and BDeck ATCF_by_pairs
@@ -37,7 +37,8 @@
 @endcode
 '''
 
-class TCPairsWrapper(CommandBuilder):
+
+class TCPairsWrapper(RuntimeFreqWrapper):
     """!Wraps the MET tool, tc_pairs to parse and match ATCF_by_pairs adeck and
        bdeck files.  Pre-processes extra tropical cyclone data.
     """
@@ -339,36 +340,7 @@ def run_all_times(self):
         self.run_at_time(input_dict)
         return self.all_commands
 
-    def run_at_time(self, input_dict):
-        """! Create the arguments to run MET tc_pairs
-             Args:
-                 input_dict dictionary containing init or valid time
-             Returns:
-        """
-        input_dict['instance'] = self.instance if self.instance else ''
-        for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            input_dict['custom'] = custom_string
-
-            # if skipping lead sequence, only run once per init/valid time
-            if self.c_dict['SKIP_LEAD_SEQ']:
-                lead_seq = [0]
-            else:
-                lead_seq = get_lead_sequence(self.config, input_dict)
-
-            for lead in lead_seq:
-                input_dict['lead'] = lead
-                time_info = ti_calculate(input_dict)
-
-                if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                    self.logger.debug('Skipping run time')
-                    continue
-
-                self.run_at_time_loop_string(time_info)
-
-    def run_at_time_loop_string(self, time_info):
+    def run_at_time_once(self, time_info):
         """! Create the arguments to run MET tc_pairs
 
          @param time_info dictionary containing time information
diff --git a/metplus/wrappers/tc_stat_wrapper.py b/metplus/wrappers/tc_stat_wrapper.py
index 9c7b6722b..027637cd9 100755
--- a/metplus/wrappers/tc_stat_wrapper.py
+++ b/metplus/wrappers/tc_stat_wrapper.py
@@ -17,7 +17,7 @@
 from datetime import datetime
 
 from ..util import getlist, mkdir_p, do_string_sub, ti_calculate
-from . import CommandBuilder
+from . import RuntimeFreqWrapper
 
 ## @namespace TCStatWrapper
 #  @brief Wrapper to the MET tool tc_stat, which is used for filtering tropical
@@ -29,7 +29,7 @@
 # attribute data.
 
 
-class TCStatWrapper(CommandBuilder):
+class TCStatWrapper(RuntimeFreqWrapper):
     """! Wrapper for the MET tool, tc_stat, which is used to filter tropical
          cyclone pair data.
     """
@@ -111,6 +111,8 @@ def create_c_dict(self):
                                                  'LOG_TC_STAT_VERBOSITY',
                                                  c_dict['VERBOSITY'])
 
+        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
+
         c_dict['LOOKIN_DIR'] = self.config.getdir('TC_STAT_LOOKIN_DIR', '')
 
         # support LOOKIN_DIR and INPUT_DIR
@@ -245,7 +247,7 @@ def set_met_config_for_environment_variables(self):
                                              'TC_STAT_INIT_STR_EXCLUDE_VAL',
                                              ])
 
-    def run_at_time(self, input_dict=None):
+    def run_at_time_once(self, input_dict=None):
         """! Builds the call to the MET tool TC-STAT for all requested
              initialization times (init or valid).  Called from run_metplus
         """
diff --git a/metplus/wrappers/tcrmw_wrapper.py b/metplus/wrappers/tcrmw_wrapper.py
index 3cb78ff2a..990e93f22 100755
--- a/metplus/wrappers/tcrmw_wrapper.py
+++ b/metplus/wrappers/tcrmw_wrapper.py
@@ -13,7 +13,7 @@
 import os
 
 from ..util import time_util
-from . import CommandBuilder
+from . import RuntimeFreqWrapper
 from ..util import do_string_sub, skip_time, get_lead_sequence
 from ..util import parse_var_list, sub_var_list
 
@@ -23,7 +23,7 @@
 '''
 
 
-class TCRMWWrapper(CommandBuilder):
+class TCRMWWrapper(RuntimeFreqWrapper):
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
@@ -60,6 +60,8 @@ def create_c_dict(self):
                                                  c_dict['VERBOSITY'])
         c_dict['ALLOW_MULTIPLE_FILES'] = True
 
+        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
+
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('TCRMWConfig_wrapped')
 

From f19aaf55f28e4f1cc7fbaff731d8fcba671e78a3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Thu, 10 Aug 2023 10:21:40 -0600
Subject: [PATCH 17/55] run each time input through ti_calculate before passing
 it to run_at_time_once to compute missing time values, ci-run-all-diff

---
 .../pytests/util/time_util/test_time_util.py  | 19 +++++++++---
 metplus/util/time_util.py                     | 30 ++++++++++++-------
 metplus/wrappers/runtime_freq_wrapper.py      | 15 ++++++----
 3 files changed, 45 insertions(+), 19 deletions(-)

diff --git a/internal/tests/pytests/util/time_util/test_time_util.py b/internal/tests/pytests/util/time_util/test_time_util.py
index cddf3470b..c7a887c0f 100644
--- a/internal/tests/pytests/util/time_util/test_time_util.py
+++ b/internal/tests/pytests/util/time_util/test_time_util.py
@@ -130,18 +130,29 @@ def test_time_string_to_met_time(time_string, default_unit, met_time):
     'input_dict, expected_time_info', [
         ({'init': datetime(2014, 10, 31, 12),
           'lead': relativedelta(hours=3)},
-          {'init': datetime(2014, 10, 31, 12),
-           'lead': 10800,
-           'valid':  datetime(2014, 10, 31, 15)}
-         ),
+         {'init': datetime(2014, 10, 31, 12), 'lead': 10800,
+          'valid':  datetime(2014, 10, 31, 15)}),
+        # RUN_ONCE: init/valid/lead all wildcards
+        ({'init': '*', 'valid': '*', 'lead': '*'},
+         {'init': '*', 'valid': '*', 'lead': '*', 'date': '*'}),
+        # RUN_ONCE_PER_INIT_OR_VALID: init/valid is time, wildcard lead/opposite
+        ({'init': datetime(2014, 10, 31, 12), 'valid': '*', 'lead': '*'},
+         {'init': datetime(2014, 10, 31, 12), 'valid': '*', 'lead': '*', 'date': datetime(2014, 10, 31, 12)}),
+        ({'init': '*', 'valid': datetime(2014, 10, 31, 12), 'lead': '*'},
+         {'init': '*', 'valid': datetime(2014, 10, 31, 12), 'lead': '*', 'date': '*'}),
+        # RUN_ONCE_PER_LEAD: lead is time interval, init/valid are wildcards
+        #({'init': '*', 'valid': '*', 'lead': relativedelta(hours=3)},
+        # {'init': '*', 'valid': '*', 'lead': 10800, 'date': '*'}),
         ]
 )
 @pytest.mark.util
 def test_ti_calculate(input_dict, expected_time_info):
+    # pass input_dict into ti_calculate and check that expected values are set
     time_info = time_util.ti_calculate(input_dict)
     for key, value in expected_time_info.items():
         assert time_info[key] == value
 
+    # pass output of ti_calculate back into ti_calculate and check values
     time_info2 = time_util.ti_calculate(time_info)
     for key, value in expected_time_info.items():
         assert time_info[key] == value
diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 10f53f47f..54cc7a058 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -345,11 +345,10 @@ def ti_calculate(input_dict_preserve):
     # look for forecast lead information in input
     # set forecast lead to 0 if not specified
     if 'lead' in input_dict.keys():
-        # if lead is relativedelta, pass it through
-        # if lead is not, treat it as seconds
-        if isinstance(input_dict['lead'], relativedelta):
-            out_dict['lead'] = input_dict['lead']
-        elif input_dict['lead'] == '*':
+        # if lead is relativedelta or wildcard, pass it through
+        # if not, treat it as seconds
+        if (isinstance(input_dict['lead'], relativedelta) or
+                input_dict['lead'] == '*'):
             out_dict['lead'] = input_dict['lead']
         else:
             out_dict['lead'] = relativedelta(seconds=input_dict['lead'])
@@ -377,13 +376,20 @@ def ti_calculate(input_dict_preserve):
     if 'offset_hours' in input_dict.keys():
         out_dict['offset'] = datetime.timedelta(hours=input_dict['offset_hours'])
     elif 'offset' in input_dict.keys():
-        out_dict['offset'] = datetime.timedelta(seconds=input_dict['offset'])
+        if not isinstance(input_dict['offset'], datetime.timedelta):
+            out_dict['offset'] = datetime.timedelta(seconds=input_dict['offset'])
     else:
         out_dict['offset'] = datetime.timedelta(seconds=0)
 
+    if input_dict.get('valid') == '*' or input_dict.get('init') == '*' or input_dict.get('lead') == '*':
+        if 'date' not in out_dict:
+            out_dict['date'] = out_dict['init']
+        return out_dict
+
     # if init and valid are set, check which was set first via loop_by
     # remove the other to recalculate
     if 'init' in input_dict.keys() and 'valid' in input_dict.keys():
+
         if 'loop_by' in input_dict.keys():
             if input_dict['loop_by'] == 'init':
                 del input_dict['valid']
@@ -394,11 +400,13 @@ def ti_calculate(input_dict_preserve):
         out_dict['init'] = input_dict['init']
 
         if 'valid' in input_dict.keys():
-            print("ERROR: Cannot specify both valid and init to time utility")
+            #if input_dict['valid'] != '*' and input_dict['init'] != '*':
+            print("ERROR: Cannot specify both valid and init "
+                  f"non-wildcard to time utility: {input_dict}")
             return None
 
         # compute valid from init and lead if lead is not wildcard
-        if out_dict['lead'] == '*':
+        elif out_dict['lead'] == '*':
             out_dict['valid'] = '*'
         else:
             out_dict['valid'] = out_dict['init'] + out_dict['lead']
@@ -424,7 +432,8 @@ def ti_calculate(input_dict_preserve):
         out_dict['da_init'] = input_dict['da_init']
 
         if 'valid' in input_dict.keys():
-            print("ERROR: Cannot specify both valid and da_init to time utility")
+            print("ERROR: Cannot specify both valid and da_init "
+                  f"to time utility: {input_dict}")
             return None
 
         # compute valid from da_init and offset
@@ -436,7 +445,8 @@ def ti_calculate(input_dict_preserve):
         else:
             out_dict['init'] = out_dict['valid'] - out_dict['lead']
     else:
-        print("ERROR: Need to specify valid, init, or da_init to time utility")
+        print("ERROR: Need to specify valid, init, or da_init "
+              f"to time utility: {input_dict}")
         return None
 
     # calculate da_init from valid and offset
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index aa40d8d3f..17a94157d 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -146,11 +146,13 @@ def run_once(self, custom):
         time_input['valid'] = '*'
         time_input['lead'] = '*'
 
+        time_info = time_util.ti_calculate(time_input)
+
         if not self.get_all_files(custom):
             self.log_error("A problem occurred trying to obtain input files")
             return None
 
-        return self.run_at_time_once(time_input)
+        return self.run_at_time_once(time_info)
 
     def run_once_per_init_or_valid(self, custom):
         self.logger.debug(f"Running once for each init/valid time")
@@ -172,11 +174,12 @@ def run_once_per_init_or_valid(self, custom):
                 time_input['init'] = '*'
 
             time_input['lead'] = '*'
+            time_info = time_util.ti_calculate(time_input)
 
-            self.c_dict['ALL_FILES'] = self.get_all_files_from_leads(time_input)
+            self.c_dict['ALL_FILES'] = self.get_all_files_from_leads(time_info)
 
             self.clear()
-            if not self.run_at_time_once(time_input):
+            if not self.run_at_time_once(time_info):
                 success = False
 
         return success
@@ -202,10 +205,12 @@ def run_once_per_lead(self, custom):
             time_input['init'] = '*'
             time_input['valid'] = '*'
 
-            self.c_dict['ALL_FILES'] = self.get_all_files_for_lead(time_input)
+            time_info = time_util.ti_calculate(time_input)
+
+            self.c_dict['ALL_FILES'] = self.get_all_files_for_lead(time_info)
 
             self.clear()
-            if not self.run_at_time_once(time_input):
+            if not self.run_at_time_once(time_info):
                 success = False
 
         return success

From e0a68d2ceb3acceeb0a914ac80bf6156a37ebd29 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 11 Aug 2023 17:08:44 -0600
Subject: [PATCH 18/55] move runtime log banner

---
 metplus/wrappers/tc_pairs_wrapper.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index 5f7c67914..10ee11343 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -324,9 +324,7 @@ def run_all_times(self):
         if not input_dict:
             return self.all_commands
 
-        add_to_time_input(input_dict,
-                          instance=self.instance)
-        log_runtime_banner(self.config, input_dict, self)
+        add_to_time_input(input_dict, instance=self.instance)
 
         # if running in READ_ALL_FILES mode, call tc_pairs once and exit
         if self.c_dict['READ_ALL_FILES']:
@@ -337,6 +335,7 @@ def run_all_times(self):
 
         self.logger.debug('Only processing first run time. Set '
                           'TC_PAIRS_RUN_ONCE=False to process all run times.')
+        log_runtime_banner(self.config, input_dict, self)
         self.run_at_time(input_dict)
         return self.all_commands
 

From 21f8f273cf927f5e09d829cec999cad97e834509 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 11 Aug 2023 17:10:30 -0600
Subject: [PATCH 19/55] rename function to avoid confusion with other
 find_input_files functions

---
 metplus/wrappers/grid_diag_wrapper.py    | 2 +-
 metplus/wrappers/runtime_freq_wrapper.py | 2 +-
 metplus/wrappers/user_script_wrapper.py  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/metplus/wrappers/grid_diag_wrapper.py b/metplus/wrappers/grid_diag_wrapper.py
index eb1c5e98b..bcdb52eb2 100755
--- a/metplus/wrappers/grid_diag_wrapper.py
+++ b/metplus/wrappers/grid_diag_wrapper.py
@@ -231,7 +231,7 @@ def get_files_from_time(self, time_info):
              files with a key representing a description of that file
         """
         file_dict = super().get_files_from_time(time_info)
-        input_files = self.find_input_files(time_info)
+        input_files = self.get_input_files(time_info)
         if input_files is None:
             return None
 
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 17a94157d..7aa7f846f 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -429,7 +429,7 @@ def compare_time_info(runtime, filetime):
 
         return runtime_lead == filetime_lead
 
-    def find_input_files(self, time_info, fill_missing=False):
+    def get_input_files(self, time_info, fill_missing=False):
         """! Loop over list of input templates and find files for each
 
              @param time_info time dictionary to use for string substitution
diff --git a/metplus/wrappers/user_script_wrapper.py b/metplus/wrappers/user_script_wrapper.py
index 71274997a..aba672b69 100755
--- a/metplus/wrappers/user_script_wrapper.py
+++ b/metplus/wrappers/user_script_wrapper.py
@@ -96,7 +96,7 @@ def get_files_from_time(self, time_info):
         """
         file_dict = super().get_files_from_time(time_info)
 
-        input_files = self.find_input_files(time_info, fill_missing=True)
+        input_files = self.get_input_files(time_info, fill_missing=True)
         if input_files is None:
             return file_dict
 

From ba819873e5437d5572411d253c08d96a91fb70b3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 11:37:28 -0600
Subject: [PATCH 20/55] refactored logic in ti_calculate and added unit tests
 for common inputs to function

---
 .../pytests/util/time_util/test_time_util.py  |  22 +-
 metplus/util/time_util.py                     | 250 +++++++++---------
 2 files changed, 136 insertions(+), 136 deletions(-)

diff --git a/internal/tests/pytests/util/time_util/test_time_util.py b/internal/tests/pytests/util/time_util/test_time_util.py
index c7a887c0f..74d40d16d 100644
--- a/internal/tests/pytests/util/time_util/test_time_util.py
+++ b/internal/tests/pytests/util/time_util/test_time_util.py
@@ -128,10 +128,18 @@ def test_time_string_to_met_time(time_string, default_unit, met_time):
 
 @pytest.mark.parametrize(
     'input_dict, expected_time_info', [
-        ({'init': datetime(2014, 10, 31, 12),
-          'lead': relativedelta(hours=3)},
-         {'init': datetime(2014, 10, 31, 12), 'lead': 10800,
-          'valid':  datetime(2014, 10, 31, 15)}),
+        # init and lead input
+        ({'init': datetime(2014, 10, 31, 12), 'lead': relativedelta(hours=3)},
+         {'init': datetime(2014, 10, 31, 12), 'lead': 10800, 'valid':  datetime(2014, 10, 31, 15)}),
+        # valid and lead input
+        ({'valid': datetime(2014, 10, 31, 12), 'lead': relativedelta(hours=3)},
+         {'valid': datetime(2014, 10, 31, 12), 'lead': 10800, 'init':  datetime(2014, 10, 31, 9)}),
+        # init/valid/lead input, loop_by init
+        ({'init': datetime(2014, 10, 31, 12), 'lead': relativedelta(hours=6), 'valid': datetime(2014, 10, 31, 15), 'loop_by': 'init'},
+         {'init': datetime(2014, 10, 31, 12), 'lead': 21600, 'valid':  datetime(2014, 10, 31, 18)}),
+        # init/valid/lead input, loop_by valid
+        ({'valid': datetime(2014, 10, 31, 12), 'lead': relativedelta(hours=6), 'init':  datetime(2014, 10, 31, 9), 'loop_by': 'valid'},
+         {'valid': datetime(2014, 10, 31, 12), 'lead': 21600, 'init':  datetime(2014, 10, 31, 6)}),
         # RUN_ONCE: init/valid/lead all wildcards
         ({'init': '*', 'valid': '*', 'lead': '*'},
          {'init': '*', 'valid': '*', 'lead': '*', 'date': '*'}),
@@ -139,10 +147,10 @@ def test_time_string_to_met_time(time_string, default_unit, met_time):
         ({'init': datetime(2014, 10, 31, 12), 'valid': '*', 'lead': '*'},
          {'init': datetime(2014, 10, 31, 12), 'valid': '*', 'lead': '*', 'date': datetime(2014, 10, 31, 12)}),
         ({'init': '*', 'valid': datetime(2014, 10, 31, 12), 'lead': '*'},
-         {'init': '*', 'valid': datetime(2014, 10, 31, 12), 'lead': '*', 'date': '*'}),
+         {'init': '*', 'valid': datetime(2014, 10, 31, 12), 'lead': '*', 'date': datetime(2014, 10, 31, 12)}),
         # RUN_ONCE_PER_LEAD: lead is time interval, init/valid are wildcards
-        #({'init': '*', 'valid': '*', 'lead': relativedelta(hours=3)},
-        # {'init': '*', 'valid': '*', 'lead': 10800, 'date': '*'}),
+        ({'init': '*', 'valid': '*', 'lead': relativedelta(hours=3)},
+         {'init': '*', 'valid': '*', 'lead': relativedelta(hours=3), 'date': '*'}),
         ]
 )
 @pytest.mark.util
diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 54cc7a058..f16342694 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -333,139 +333,35 @@ def _format_time_list(string_value, get_met_format, sort_list=True):
     return out_list
 
 
-def ti_calculate(input_dict_preserve):
-    # copy input dictionary so valid or init can be removed to recalculate it
-    # without modifying the input to the function
-    input_dict = input_dict_preserve.copy()
-    out_dict = input_dict
+def ti_calculate(input_dict):
+    """!Read in input dictionary items and compute missing items. Output from
+    this function can be passed back into it to re-compute items that have
+    changed.
+    Required inputs: init, valid
+
+    @param input_dict dictionary containing time info to use in computations
+    @returns dictionary with updated items/values
+    """
+    # copy input dictionary to prevent modifying input dictionary
+    out_dict = input_dict.copy()
 
-    # read in input dictionary items and compute missing items
-    # valid inputs: valid, init, lead, offset
+    _set_loop_by(out_dict)
 
     # look for forecast lead information in input
     # set forecast lead to 0 if not specified
-    if 'lead' in input_dict.keys():
-        # if lead is relativedelta or wildcard, pass it through
-        # if not, treat it as seconds
-        if (isinstance(input_dict['lead'], relativedelta) or
-                input_dict['lead'] == '*'):
-            out_dict['lead'] = input_dict['lead']
-        else:
-            out_dict['lead'] = relativedelta(seconds=input_dict['lead'])
-
-    elif 'lead_seconds' in input_dict.keys():
-        out_dict['lead'] = relativedelta(seconds=input_dict['lead_seconds'])
-
-    elif 'lead_minutes' in input_dict.keys():
-        out_dict['lead'] = relativedelta(minutes=input_dict['lead_minutes'])
-
-    elif 'lead_hours' in input_dict.keys():
-        lead_hours = int(input_dict['lead_hours'])
-        lead_days = 0
-        # if hours is more than a day, pull out days and relative hours
-        if lead_hours > 23:
-            lead_days = lead_hours // 24
-            lead_hours = lead_hours % 24
-
-        out_dict['lead'] = relativedelta(hours=lead_hours, days=lead_days)
-
-    else:
-        out_dict['lead'] = relativedelta(seconds=0)
+    _set_lead(out_dict)
 
     # set offset to 0 if not specified
-    if 'offset_hours' in input_dict.keys():
-        out_dict['offset'] = datetime.timedelta(hours=input_dict['offset_hours'])
-    elif 'offset' in input_dict.keys():
-        if not isinstance(input_dict['offset'], datetime.timedelta):
-            out_dict['offset'] = datetime.timedelta(seconds=input_dict['offset'])
-    else:
-        out_dict['offset'] = datetime.timedelta(seconds=0)
-
-    if input_dict.get('valid') == '*' or input_dict.get('init') == '*' or input_dict.get('lead') == '*':
-        if 'date' not in out_dict:
-            out_dict['date'] = out_dict['init']
-        return out_dict
-
-    # if init and valid are set, check which was set first via loop_by
-    # remove the other to recalculate
-    if 'init' in input_dict.keys() and 'valid' in input_dict.keys():
+    _set_offset(out_dict)
 
-        if 'loop_by' in input_dict.keys():
-            if input_dict['loop_by'] == 'init':
-                del input_dict['valid']
-            elif input_dict['loop_by'] == 'valid':
-                del input_dict['init']
-
-    if 'init' in input_dict.keys():
-        out_dict['init'] = input_dict['init']
-
-        if 'valid' in input_dict.keys():
-            #if input_dict['valid'] != '*' and input_dict['init'] != '*':
-            print("ERROR: Cannot specify both valid and init "
-                  f"non-wildcard to time utility: {input_dict}")
-            return None
-
-        # compute valid from init and lead if lead is not wildcard
-        elif out_dict['lead'] == '*':
-            out_dict['valid'] = '*'
-        else:
-            out_dict['valid'] = out_dict['init'] + out_dict['lead']
-
-        # set loop_by to init or valid to be able to see what was set first
-        out_dict['loop_by'] = 'init'
-
-    # if valid is provided, compute init and da_init
-    elif 'valid' in input_dict:
-        out_dict['valid'] = input_dict['valid']
-
-        # compute init from valid and lead if lead is not wildcard
-        if out_dict['lead'] == '*':
-            out_dict['init'] = '*'
-        else:
-            out_dict['init'] = out_dict['valid'] - out_dict['lead']
-
-        # set loop_by to init or valid to be able to see what was set first
-        out_dict['loop_by'] = 'valid'
-
-    # if da_init is provided, compute init and valid
-    elif 'da_init' in input_dict.keys():
-        out_dict['da_init'] = input_dict['da_init']
-
-        if 'valid' in input_dict.keys():
-            print("ERROR: Cannot specify both valid and da_init "
-                  f"to time utility: {input_dict}")
-            return None
-
-        # compute valid from da_init and offset
-        out_dict['valid'] = out_dict['da_init'] - out_dict['offset']
-
-        # compute init from valid and lead if lead is not wildcard
-        if out_dict['lead'] == '*':
-            out_dict['init'] = '*'
-        else:
-            out_dict['init'] = out_dict['valid'] - out_dict['lead']
-    else:
-        print("ERROR: Need to specify valid, init, or da_init "
-              f"to time utility: {input_dict}")
-        return None
+    _set_init_valid_lead(out_dict)
 
     # calculate da_init from valid and offset
     if out_dict['valid'] != '*':
         out_dict['da_init'] = out_dict['valid'] + out_dict['offset']
-
-        # add common formatted items
         out_dict['da_init_fmt'] = out_dict['da_init'].strftime('%Y%m%d%H%M%S')
-        out_dict['valid_fmt'] = out_dict['valid'].strftime('%Y%m%d%H%M%S')
-
-    if out_dict['init'] != '*':
-        out_dict['init_fmt'] = out_dict['init'].strftime('%Y%m%d%H%M%S')
-
-    # get string representation of forecast lead
-    if out_dict['lead'] == '*':
-        out_dict['lead_string'] = 'ALL'
-    else:
-        out_dict['lead_string'] = ti_get_lead_string(out_dict['lead'])
 
+    # convert offset to seconds and compute offset hours
     out_dict['offset'] = int(out_dict['offset'].total_seconds())
     out_dict['offset_hours'] = int(out_dict['offset'] // 3600)
 
@@ -476,8 +372,8 @@ def ti_calculate(input_dict_preserve):
     else:
         out_dict['date'] = out_dict['init']
 
-    # if lead is wildcard, skip updating other lead values
-    if out_dict['lead'] == '*':
+    # if any init/valid/lead are wildcard, skip updating other lead values
+    if out_dict['lead'] == '*' or out_dict['valid'] == '*' or out_dict['init'] == '*':
         return out_dict
 
     # get difference between valid and init to get total seconds since relativedelta
@@ -488,17 +384,113 @@ def ti_calculate(input_dict_preserve):
     # if they are, keep lead as a relativedelta object to be handled differently
     if out_dict['lead'].months == 0 and out_dict['lead'].years == 0:
         out_dict['lead'] = total_seconds
-
-    # add common uses for relative times
-    # Specifying integer division // Python 3,
-    # assuming that was the intent in Python 2.
-    out_dict['lead_hours'] = int(total_seconds // 3600)
-    out_dict['lead_minutes'] = int(total_seconds // 60)
-    out_dict['lead_seconds'] = total_seconds
+        out_dict['lead_hours'] = int(total_seconds // 3600)
+        out_dict['lead_minutes'] = int(total_seconds // 60)
+        out_dict['lead_seconds'] = total_seconds
 
     return out_dict
 
 
+def _set_lead(the_dict):
+    if 'lead' in the_dict.keys():
+        # if lead is relativedelta or wildcard, pass it through
+        # if not, treat it as seconds
+        if (not isinstance(the_dict['lead'], relativedelta) and
+                the_dict['lead'] != '*'):
+            the_dict['lead'] = relativedelta(seconds=the_dict['lead'])
+
+    elif 'lead_seconds' in the_dict.keys():
+        the_dict['lead'] = relativedelta(seconds=the_dict['lead_seconds'])
+
+    elif 'lead_minutes' in the_dict.keys():
+        the_dict['lead'] = relativedelta(minutes=the_dict['lead_minutes'])
+
+    elif 'lead_hours' in the_dict.keys():
+        lead_hours = int(the_dict['lead_hours'])
+        lead_days = 0
+        # if hours is more than a day, pull out days and relative hours
+        if lead_hours > 23:
+            lead_days = lead_hours // 24
+            lead_hours = lead_hours % 24
+
+        the_dict['lead'] = relativedelta(hours=lead_hours, days=lead_days)
+    else:
+        # set lead to 0 if it was no specified
+        the_dict['lead'] = relativedelta(seconds=0)
+
+    # get string representation of forecast lead
+    if the_dict['lead'] == '*':
+        the_dict['lead_string'] = 'ALL'
+    else:
+        the_dict['lead_string'] = ti_get_lead_string(the_dict['lead'])
+
+
+def _set_offset(the_dict):
+    if 'offset_hours' in the_dict.keys():
+        the_dict['offset'] = datetime.timedelta(hours=the_dict['offset_hours'])
+        return
+
+    if 'offset' in the_dict.keys():
+        if not isinstance(the_dict['offset'], datetime.timedelta):
+            the_dict['offset'] = datetime.timedelta(seconds=the_dict['offset'])
+        return
+
+    the_dict['offset'] = datetime.timedelta(seconds=0)
+
+
+def _set_loop_by(the_dict):
+    # loop_by is already set
+    if the_dict.get('loop_by'):
+        return
+
+    init = the_dict.get('init')
+    valid = the_dict.get('valid')
+    # if init and valid are both set, don't set loop_by
+    if init and valid:
+        return
+
+    # set loop_by to which init or valid is set
+    if init:
+        the_dict['loop_by'] = 'init'
+    elif valid:
+        the_dict['loop_by'] = 'valid'
+
+
+def _set_init_valid_lead(the_dict):
+    wildcard_items = [item for item in ('init', 'lead', 'valid')
+                      if the_dict.get(item) == '*']
+    # if 2 or more are wildcards, cannot compute init/valid/lead, so return
+    if len(wildcard_items) >= 2:
+        return
+
+    # assumed that 1 or fewer items are wildcard or unset
+    init = the_dict.get('init')
+    valid = the_dict.get('valid')
+    lead = the_dict.get('lead')
+    loop_by = the_dict.get('loop_by')
+
+    # if init and valid are both set and not wildcard, compute based on loop_by
+    if init and valid and init != '*' and valid != '*':
+        if loop_by == 'init':
+            the_dict['valid'] = init + lead
+        elif loop_by == 'valid':
+            the_dict['init'] = valid - lead
+    elif init and init != '*':
+        the_dict['valid'] = init + lead
+        if not loop_by:
+            the_dict['loop_by'] = 'init'
+    elif valid and valid != '*':
+        the_dict['init'] = valid - lead
+        if not loop_by:
+            the_dict['loop_by'] = 'valid'
+
+    # set valid_fmt and init_fmt if they are not wildcard
+    if the_dict['valid'] != '*':
+        the_dict['valid_fmt'] = the_dict['valid'].strftime('%Y%m%d%H%M%S')
+
+    if the_dict['init'] != '*':
+        the_dict['init_fmt'] = the_dict['init'].strftime('%Y%m%d%H%M%S')
+
 def add_to_time_input(time_input, clock_time=None, instance=None, custom=None):
     if clock_time:
         clock_dt = datetime.datetime.strptime(clock_time, '%Y%m%d%H%M%S')

From 3bc665ad237166b3f3e631fadd758869c941caa5 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 11:39:38 -0600
Subject: [PATCH 21/55] formatting cleanup

---
 metplus/wrappers/mtd_wrapper.py | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index efeafc52a..5385c06bb 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -58,32 +58,29 @@ def create_c_dict(self):
         c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
         c_dict['FIND_FILES'] = False
 
-        c_dict['OUTPUT_DIR'] = self.config.getdir('MTD_OUTPUT_DIR',
-                                           self.config.getdir('OUTPUT_BASE'))
+        c_dict['OUTPUT_DIR'] = (
+            self.config.getdir('MTD_OUTPUT_DIR',
+                               self.config.getdir('OUTPUT_BASE'))
+        )
         c_dict['OUTPUT_TEMPLATE'] = (
-            self.config.getraw('config',
-                               'MTD_OUTPUT_TEMPLATE')
+            self.config.getraw('config', 'MTD_OUTPUT_TEMPLATE')
         )
 
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('MTDConfig_wrapped')
 
         # new method of reading/setting MET config values
-        self.add_met_config(name='min_volume',
-                            data_type='int')
+        self.add_met_config(name='min_volume', data_type='int')
 
         # old approach to reading/setting MET config values
-        c_dict['MIN_VOLUME'] = self.config.getstr('config',
-                                                  'MTD_MIN_VOLUME', '2000')
+        c_dict['MIN_VOLUME'] = self.config.getstr('config', 'MTD_MIN_VOLUME', '2000')
 
-        c_dict['SINGLE_RUN'] = self.config.getbool('config',
-                                                   'MTD_SINGLE_RUN',
-                                                   False)
+        c_dict['SINGLE_RUN'] = (
+            self.config.getbool('config', 'MTD_SINGLE_RUN', False)
+        )
         if c_dict['SINGLE_RUN']:
             c_dict['SINGLE_DATA_SRC'] = (
-                self.config.getstr('config',
-                                   'MTD_SINGLE_DATA_SRC',
-                                   '')
+                self.config.getstr('config', 'MTD_SINGLE_DATA_SRC', '')
             )
             if not c_dict['SINGLE_DATA_SRC']:
                 self.log_error('Must set MTD_SINGLE_DATA_SRC if '
@@ -378,7 +375,7 @@ def process_fields_one_thresh(self, time_info, var_info, model_path,
             if not fcst_thresh_list:
                 fcst_thresh_list = [""]
 
-           # loop over thresholds and build field list with one thresh per item
+            # loop over thresholds and build field list with one thresh per item
             for fcst_thresh in fcst_thresh_list:
                 fcst_field = (
                     self.get_field_info(v_name=var_info['fcst_name'],

From 92d5d260166faa5e825412b98116a99654145648 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:17:26 -0600
Subject: [PATCH 22/55] moved logic to compute formatted init or valid so it is
 still run even if init/valid are not computed

---
 metplus/util/time_util.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index f16342694..67423d1ce 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -356,6 +356,13 @@ def ti_calculate(input_dict):
 
     _set_init_valid_lead(out_dict)
 
+    # set valid_fmt and init_fmt if they are not wildcard
+    if out_dict['valid'] != '*':
+        out_dict['valid_fmt'] = out_dict['valid'].strftime('%Y%m%d%H%M%S')
+
+    if out_dict['init'] != '*':
+        out_dict['init_fmt'] = out_dict['init'].strftime('%Y%m%d%H%M%S')
+
     # calculate da_init from valid and offset
     if out_dict['valid'] != '*':
         out_dict['da_init'] = out_dict['valid'] + out_dict['offset']
@@ -484,12 +491,6 @@ def _set_init_valid_lead(the_dict):
         if not loop_by:
             the_dict['loop_by'] = 'valid'
 
-    # set valid_fmt and init_fmt if they are not wildcard
-    if the_dict['valid'] != '*':
-        the_dict['valid_fmt'] = the_dict['valid'].strftime('%Y%m%d%H%M%S')
-
-    if the_dict['init'] != '*':
-        the_dict['init_fmt'] = the_dict['init'].strftime('%Y%m%d%H%M%S')
 
 def add_to_time_input(time_input, clock_time=None, instance=None, custom=None):
     if clock_time:

From 2c60cd47ee562579f0e434046c22bfc428daccf8 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:23:40 -0600
Subject: [PATCH 23/55] pass data type to find_data and change template c_dict
 key if data type is FCST or OBS

---
 metplus/wrappers/runtime_freq_wrapper.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 7aa7f846f..7f3831ecb 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -443,10 +443,16 @@ def get_input_files(self, time_info, fill_missing=False):
             return None
 
         for label, input_template in self.c_dict['TEMPLATE_DICT'].items():
-            self.c_dict['INPUT_TEMPLATE'] = input_template
+            data_type = ''
+            template_key = 'INPUT_TEMPLATE'
+            if label in ('FCST', 'OBS'):
+                data_type = label
+                template_key = f'{label}_{template_key}'
+
+            self.c_dict[template_key] = input_template
             # if fill missing is true, data is not mandatory to find
             mandatory = not fill_missing
-            input_files = self.find_data(time_info,
+            input_files = self.find_data(time_info, data_type=data_type,
                                          return_list=True,
                                          mandatory=mandatory)
             if not input_files:

From 77987c240c111c53a3a5fb591109215d9955e566 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:25:56 -0600
Subject: [PATCH 24/55] refactor MTD wrapper to use RuntimeFreq methods to find
 files to process, update unit tests to match changes to calls to wrapper and
 naming of file list files

---
 .../pytests/wrappers/mtd/test_mtd_wrapper.py  | 208 ++++++-----
 metplus/wrappers/mtd_wrapper.py               | 322 +++++++-----------
 2 files changed, 242 insertions(+), 288 deletions(-)

diff --git a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
index 2101ccfef..6c53d3bfb 100644
--- a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
+++ b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
@@ -21,12 +21,14 @@
            f'level="{obs_level_no_quotes}"; cat_thresh=[ gt12.7 ]; }};')
 
 
-def get_test_data_dir(config, subdir):
-    return os.path.join(config.getdir('METPLUS_BASE'),
-                        'internal', 'tests', 'data', subdir)
+def get_test_data_dir(subdir):
+    internal_tests_dir = os.path.abspath(
+        os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir)
+    )
+    return os.path.join(internal_tests_dir, 'data', subdir)
 
 
-def mtd_wrapper(metplus_config, lead_seq=None):
+def mtd_wrapper(metplus_config, config_overrides):
     """! Returns a default MTDWrapper with /path/to entries in the
          metplus_system.conf and metplus_runtime.conf configuration
          files.  Subsequent tests can customize the final METplus configuration
@@ -39,8 +41,8 @@ def mtd_wrapper(metplus_config, lead_seq=None):
     config.set('config', 'LOOP_BY', 'VALID')
     config.set('config', 'MTD_CONV_THRESH', '>=10')
     config.set('config', 'MTD_CONV_RADIUS', '15')
-    if lead_seq:
-        config.set('config', 'LEAD_SEQ', lead_seq)
+    for key, value in config_overrides.items():
+        config.set('config', key, value)
 
     return MTDWrapper(config)
 
@@ -69,7 +71,7 @@ def set_minimum_config_settings(config):
                '{valid?fmt=%Y%m%d%H}/obs_file')
     config.set('config', 'MTD_OUTPUT_DIR',
                '{OUTPUT_BASE}/MTD/output')
-    config.set('config', 'MTD_OUTPUT_TEMPLATE', '{valid?fmt=%Y%m%d%H}')
+    config.set('config', 'MTD_OUTPUT_TEMPLATE', '{init?fmt=%Y%m%d%H}')
 
     config.set('config', 'FCST_VAR1_NAME', fcst_name)
     config.set('config', 'FCST_VAR1_LEVELS', fcst_level)
@@ -173,11 +175,11 @@ def test_mode_single_field(metplus_config, config_overrides, env_var_values):
     out_dir = wrapper.c_dict.get('OUTPUT_DIR')
     expected_cmds = [(f"{app_path} {verbosity} "
                       f"-fcst {file_list_dir}/"
-                      f"20050807060000_mtd_fcst_{fcst_name}.txt "
+                      f"init20050807000000_mtd_fcst_{fcst_name}.txt "
                       f"-obs {file_list_dir}/"
-                      f"20050807060000_mtd_obs_{obs_name}.txt "
+                      f"init20050807000000_mtd_obs_{obs_name}.txt "
                       f"-config {config_file} "
-                      f"-outdir {out_dir}/2005080706"),
+                      f"-outdir {out_dir}/2005080700"),
                      ]
 
     all_cmds = wrapper.run_all_times()
@@ -208,18 +210,22 @@ def test_mode_single_field(metplus_config, config_overrides, env_var_values):
 
 @pytest.mark.wrapper
 def test_mtd_by_init_all_found(metplus_config):
-    mw = mtd_wrapper(metplus_config, '1,2,3')
-    obs_dir = get_test_data_dir(mw.config, 'obs')
-    fcst_dir = get_test_data_dir(mw.config, 'fcst')
-    mw.c_dict['OBS_INPUT_DIR'] = obs_dir
-    mw.c_dict['FCST_INPUT_DIR'] = fcst_dir
-    mw.c_dict['OBS_INPUT_TEMPLATE'] = "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc"
-    mw.c_dict['FCST_INPUT_TEMPLATE'] = "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2"
-    input_dict = {'init': datetime.datetime.strptime("201705100300", '%Y%m%d%H%M')}
-    
-    mw.run_at_time(input_dict)
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_obs_APCP.txt')
+    obs_data_dir = get_test_data_dir('obs')
+    fcst_data_dir = get_test_data_dir('fcst')
+    overrides = {
+        'LEAD_SEQ': '1,2,3',
+        'FCST_MTD_INPUT_DIR': fcst_data_dir,
+        'OBS_MTD_INPUT_DIR': obs_data_dir,
+        'FCST_MTD_INPUT_TEMPLATE': "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2",
+        'OBS_MTD_INPUT_TEMPLATE': "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc",
+        'LOOP_BY': 'INIT',
+        'INIT_TIME_FMT': '%Y%m%d%H%M',
+        'INIT_BEG': '201705100300'
+    }
+    mw = mtd_wrapper(metplus_config, overrides)
+    mw.run_all_times()
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -231,29 +237,33 @@ def test_mtd_by_init_all_found(metplus_config):
     fcst_list = fcst_list[1:]
     obs_list = obs_list[1:]
 
-    assert(fcst_list[0] == os.path.join(fcst_dir,'20170510', '20170510_i03_f001_HRRRTLE_PHPT.grb2') and
-           fcst_list[1] == os.path.join(fcst_dir,'20170510', '20170510_i03_f002_HRRRTLE_PHPT.grb2') and
-           fcst_list[2] == os.path.join(fcst_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2') and
-           obs_list[0] == os.path.join(obs_dir,'20170510', 'qpe_2017051004_A06.nc') and
-           obs_list[1] == os.path.join(obs_dir,'20170510', 'qpe_2017051005_A06.nc') and
-           obs_list[2] == os.path.join(obs_dir,'20170510', 'qpe_2017051006_A06.nc')
+    assert(fcst_list[0] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f001_HRRRTLE_PHPT.grb2') and
+           fcst_list[1] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f002_HRRRTLE_PHPT.grb2') and
+           fcst_list[2] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2') and
+           obs_list[0] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051004_A06.nc') and
+           obs_list[1] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051005_A06.nc') and
+           obs_list[2] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051006_A06.nc')
            )
 
 
 @pytest.mark.wrapper
 def test_mtd_by_valid_all_found(metplus_config):
-    mw = mtd_wrapper(metplus_config, '1, 2, 3')
-    obs_dir = get_test_data_dir(mw.config, 'obs')
-    fcst_dir = get_test_data_dir(mw.config, 'fcst')
-    mw.c_dict['OBS_INPUT_DIR'] = obs_dir
-    mw.c_dict['FCST_INPUT_DIR'] = fcst_dir
-    mw.c_dict['OBS_INPUT_TEMPLATE'] = "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc"
-    mw.c_dict['FCST_INPUT_TEMPLATE'] = "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2"
-    input_dict = {'valid' : datetime.datetime.strptime("201705100300", '%Y%m%d%H%M') }
-    
-    mw.run_at_time(input_dict)
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510030000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510030000_mtd_obs_APCP.txt')
+    obs_data_dir = get_test_data_dir('obs')
+    fcst_data_dir = get_test_data_dir('fcst')
+    overrides = {
+        'LEAD_SEQ': '1, 2, 3',
+        'FCST_MTD_INPUT_DIR': fcst_data_dir,
+        'OBS_MTD_INPUT_DIR': obs_data_dir,
+        'FCST_MTD_INPUT_TEMPLATE': "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2",
+        'OBS_MTD_INPUT_TEMPLATE': "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc",
+        'LOOP_BY': 'VALID',
+        'VALID_TIME_FMT': '%Y%m%d%H%M',
+        'VALID_BEG': '201705100300'
+    }
+    mw = mtd_wrapper(metplus_config, overrides)
+    mw.run_all_times()
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'valid20170510030000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'valid20170510030000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -265,29 +275,33 @@ def test_mtd_by_valid_all_found(metplus_config):
     fcst_list = fcst_list[1:]
     obs_list = obs_list[1:]
 
-    assert(fcst_list[0] == os.path.join(fcst_dir,'20170510', '20170510_i02_f001_HRRRTLE_PHPT.grb2') and
-           fcst_list[1] == os.path.join(fcst_dir,'20170510', '20170510_i01_f002_HRRRTLE_PHPT.grb2') and
-           fcst_list[2] == os.path.join(fcst_dir,'20170510', '20170510_i00_f003_HRRRTLE_PHPT.grb2') and
-           obs_list[0] == os.path.join(obs_dir,'20170510', 'qpe_2017051003_A06.nc') and
-           obs_list[1] == os.path.join(obs_dir,'20170510', 'qpe_2017051003_A06.nc') and
-           obs_list[2] == os.path.join(obs_dir,'20170510', 'qpe_2017051003_A06.nc')
+    assert(fcst_list[0] == os.path.join(fcst_data_dir,'20170510', '20170510_i02_f001_HRRRTLE_PHPT.grb2') and
+           fcst_list[1] == os.path.join(fcst_data_dir,'20170510', '20170510_i01_f002_HRRRTLE_PHPT.grb2') and
+           fcst_list[2] == os.path.join(fcst_data_dir,'20170510', '20170510_i00_f003_HRRRTLE_PHPT.grb2') and
+           obs_list[0] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051003_A06.nc') and
+           obs_list[1] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051003_A06.nc') and
+           obs_list[2] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051003_A06.nc')
            )
 
 
 @pytest.mark.wrapper
 def test_mtd_by_init_miss_fcst(metplus_config):
-    mw = mtd_wrapper(metplus_config, '3, 6, 9, 12')
-    obs_dir = get_test_data_dir(mw.config, 'obs')
-    fcst_dir = get_test_data_dir(mw.config, 'fcst')
-    mw.c_dict['OBS_INPUT_DIR'] = obs_dir
-    mw.c_dict['FCST_INPUT_DIR'] = fcst_dir
-    mw.c_dict['OBS_INPUT_TEMPLATE'] = "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc"
-    mw.c_dict['FCST_INPUT_TEMPLATE'] = "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2"
-    input_dict = {'init' : datetime.datetime.strptime("201705100300", '%Y%m%d%H%M') }
-    
-    mw.run_at_time(input_dict)
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510060000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510060000_mtd_obs_APCP.txt')
+    obs_data_dir = get_test_data_dir('obs')
+    fcst_data_dir = get_test_data_dir('fcst')
+    overrides = {
+        'LEAD_SEQ': '3, 6, 9, 12',
+        'FCST_MTD_INPUT_DIR': fcst_data_dir,
+        'OBS_MTD_INPUT_DIR': obs_data_dir,
+        'FCST_MTD_INPUT_TEMPLATE': "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2",
+        'OBS_MTD_INPUT_TEMPLATE': "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc",
+        'LOOP_BY': 'INIT',
+        'INIT_TIME_FMT': '%Y%m%d%H%M',
+        'INIT_BEG': '201705100300'
+    }
+    mw = mtd_wrapper(metplus_config, overrides)
+    mw.run_all_times()
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -299,29 +313,33 @@ def test_mtd_by_init_miss_fcst(metplus_config):
     fcst_list = fcst_list[1:]
     obs_list = obs_list[1:]
 
-    assert(fcst_list[0] == os.path.join(fcst_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2') and
-           fcst_list[1] == os.path.join(fcst_dir,'20170510', '20170510_i03_f006_HRRRTLE_PHPT.grb2') and
-           fcst_list[2] == os.path.join(fcst_dir,'20170510', '20170510_i03_f012_HRRRTLE_PHPT.grb2') and
-           obs_list[0] == os.path.join(obs_dir,'20170510', 'qpe_2017051006_A06.nc') and
-           obs_list[1] == os.path.join(obs_dir,'20170510', 'qpe_2017051009_A06.nc') and
-           obs_list[2] == os.path.join(obs_dir,'20170510', 'qpe_2017051015_A06.nc')
+    assert(fcst_list[0] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2') and
+           fcst_list[1] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f006_HRRRTLE_PHPT.grb2') and
+           fcst_list[2] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f012_HRRRTLE_PHPT.grb2') and
+           obs_list[0] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051006_A06.nc') and
+           obs_list[1] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051009_A06.nc') and
+           obs_list[2] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051015_A06.nc')
            )
 
 
 @pytest.mark.wrapper
 def test_mtd_by_init_miss_both(metplus_config):
-    mw = mtd_wrapper(metplus_config, '6, 12, 18')
-    obs_dir = get_test_data_dir(mw.config, 'obs')
-    fcst_dir = get_test_data_dir(mw.config, 'fcst')
-    mw.c_dict['OBS_INPUT_DIR'] = obs_dir
-    mw.c_dict['FCST_INPUT_DIR'] = fcst_dir
-    mw.c_dict['OBS_INPUT_TEMPLATE'] = "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc"
-    mw.c_dict['FCST_INPUT_TEMPLATE'] = "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2"
-    input_dict = {'init' : datetime.datetime.strptime("201705100300", '%Y%m%d%H%M') }
-    
-    mw.run_at_time(input_dict)
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510090000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510090000_mtd_obs_APCP.txt')
+    obs_data_dir = get_test_data_dir('obs')
+    fcst_data_dir = get_test_data_dir('fcst')
+    overrides = {
+        'LEAD_SEQ': '6, 12, 18',
+        'FCST_MTD_INPUT_DIR': fcst_data_dir,
+        'OBS_MTD_INPUT_DIR': obs_data_dir,
+        'FCST_MTD_INPUT_TEMPLATE': "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2",
+        'OBS_MTD_INPUT_TEMPLATE': "{valid?fmt=%Y%m%d}/qpe_{valid?fmt=%Y%m%d%H}_A{level?fmt=%.2H}.nc",
+        'LOOP_BY': 'INIT',
+        'INIT_TIME_FMT': '%Y%m%d%H%M',
+        'INIT_BEG': '201705100300'
+    }
+    mw = mtd_wrapper(metplus_config, overrides)
+    mw.run_all_times()
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -333,25 +351,29 @@ def test_mtd_by_init_miss_both(metplus_config):
     fcst_list = fcst_list[1:]
     obs_list = obs_list[1:]
 
-    assert(fcst_list[0] == os.path.join(fcst_dir,'20170510', '20170510_i03_f006_HRRRTLE_PHPT.grb2') and
-           fcst_list[1] == os.path.join(fcst_dir,'20170510', '20170510_i03_f012_HRRRTLE_PHPT.grb2') and
-           obs_list[0] == os.path.join(obs_dir,'20170510', 'qpe_2017051009_A06.nc') and
-           obs_list[1] == os.path.join(obs_dir,'20170510', 'qpe_2017051015_A06.nc')
+    assert(fcst_list[0] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f006_HRRRTLE_PHPT.grb2') and
+           fcst_list[1] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f012_HRRRTLE_PHPT.grb2') and
+           obs_list[0] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051009_A06.nc') and
+           obs_list[1] == os.path.join(obs_data_dir,'20170510', 'qpe_2017051015_A06.nc')
            )
 
 
 @pytest.mark.wrapper
 def test_mtd_single(metplus_config):
-    mw = mtd_wrapper(metplus_config, '1, 2, 3')
-    fcst_dir = get_test_data_dir(mw.config, 'fcst')
-    mw.c_dict['SINGLE_RUN'] = True
-    mw.c_dict['SINGLE_DATA_SRC'] = 'FCST'
-    mw.c_dict['FCST_INPUT_DIR'] = fcst_dir
-    mw.c_dict['FCST_INPUT_TEMPLATE'] = "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2"
-    input_dict = {'init': datetime.datetime.strptime("201705100300", '%Y%m%d%H%M') }
-
-    mw.run_at_time(input_dict)
-    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_single_APCP.txt')
+    fcst_data_dir = get_test_data_dir('fcst')
+    overrides = {
+        'LEAD_SEQ': '1, 2, 3',
+        'MTD_SINGLE_RUN': True,
+        'MTD_SINGLE_DATA_SRC': 'FCST',
+        'FCST_MTD_INPUT_DIR': fcst_data_dir,
+        'FCST_MTD_INPUT_TEMPLATE': "{init?fmt=%Y%m%d}/{init?fmt=%Y%m%d}_i{init?fmt=%H}_f{lead?fmt=%.3H}_HRRRTLE_PHPT.grb2",
+        'LOOP_BY': 'INIT',
+        'INIT_TIME_FMT': '%Y%m%d%H%M',
+        'INIT_BEG': '201705100300'
+    }
+    mw = mtd_wrapper(metplus_config, overrides)
+    mw.run_all_times()
+    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
     with open(single_list_file) as f:
         single_list = f.readlines()
     single_list = [x.strip() for x in single_list]
@@ -359,9 +381,9 @@ def test_mtd_single(metplus_config):
     # remove file_list line from lists
     single_list = single_list[1:]
 
-    assert(single_list[0] == os.path.join(fcst_dir,'20170510', '20170510_i03_f001_HRRRTLE_PHPT.grb2') and
-           single_list[1] == os.path.join(fcst_dir,'20170510', '20170510_i03_f002_HRRRTLE_PHPT.grb2') and
-           single_list[2] == os.path.join(fcst_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2')
+    assert(single_list[0] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f001_HRRRTLE_PHPT.grb2') and
+           single_list[1] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f002_HRRRTLE_PHPT.grb2') and
+           single_list[2] == os.path.join(fcst_data_dir,'20170510', '20170510_i03_f003_HRRRTLE_PHPT.grb2')
            )
 
 
diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index 5385c06bb..eeb4809dc 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -13,7 +13,7 @@
 import os
 
 from ..util import get_lead_sequence, sub_var_list
-from ..util import ti_calculate
+from ..util import ti_calculate, getlist
 from ..util import do_string_sub, skip_time
 from ..util import parse_var_list, add_field_info_to_time_info
 from . import CompareGriddedWrapper
@@ -56,7 +56,7 @@ def create_c_dict(self):
         c_dict['ALLOW_MULTIPLE_FILES'] = False
 
         c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
-        c_dict['FIND_FILES'] = False
+        c_dict['ONCE_PER_FIELD'] = True
 
         c_dict['OUTPUT_DIR'] = (
             self.config.getdir('MTD_OUTPUT_DIR',
@@ -86,31 +86,7 @@ def create_c_dict(self):
                 self.log_error('Must set MTD_SINGLE_DATA_SRC if '
                                'MTD_SINGLE_RUN is True')
 
-        c_dict['FCST_INPUT_DIR'] = (
-            self.config.getdir('FCST_MTD_INPUT_DIR', '')
-        )
-        c_dict['FCST_INPUT_TEMPLATE'] = (
-            self.config.getraw('filename_templates',
-                               'FCST_MTD_INPUT_TEMPLATE')
-        )
-        c_dict['OBS_INPUT_DIR'] = (
-            self.config.getdir('OBS_MTD_INPUT_DIR', '')
-        )
-        c_dict['OBS_INPUT_TEMPLATE'] = (
-            self.config.getraw('filename_templates',
-                               'OBS_MTD_INPUT_TEMPLATE')
-        )
-
-        c_dict['FCST_FILE_LIST'] = (
-            self.config.getraw('config',
-                               'FCST_MTD_INPUT_FILE_LIST')
-        )
-        c_dict['OBS_FILE_LIST'] = (
-            self.config.getraw('config',
-                               'OBS_MTD_INPUT_FILE_LIST')
-        )
-        if c_dict['FCST_FILE_LIST'] or c_dict['OBS_FILE_LIST']:
-            c_dict['EXPLICIT_FILE_LIST'] = True
+        self.get_input_templates(c_dict)
 
         # if single run for OBS, read OBS values into FCST keys
         read_type = 'FCST'
@@ -128,6 +104,9 @@ def create_c_dict(self):
                            data_type=c_dict.get('SINGLE_DATA_SRC'),
                            met_tool=self.app_name)
         )
+        if not c_dict['VAR_LIST_TEMP']:
+            self.log_error('No input fields were specified.'
+                           'Must set [FCST/OBS]_VAR<n>_[NAME/LEVELS].')
 
         return c_dict
 
@@ -173,182 +152,50 @@ def read_field_values(self, c_dict, read_type, write_type):
         if c_dict['SINGLE_RUN']:
             c_dict['OBS_CONV_THRESH'] = conf_value
 
-    def run_at_time_once(self, input_dict):
-        """! Runs the MET application for a given run time. This function loops
-             over the list of forecast leads and runs the application for each.
-              Overrides run_at_time in compare_gridded_wrapper.py
-              Args:
-                @param input_dict dictionary containing timing information
-        """        
-        var_list = sub_var_list(self.c_dict['VAR_LIST_TEMP'], input_dict)
-
-        # if only processing a single data set (FCST or OBS) then only read
-        # that var list and process
-        if self.c_dict['SINGLE_RUN']:
-            for var_info in var_list:
-                self.run_single_mode(input_dict, var_info)
-
-            return
-
-        # if comparing FCST and OBS data, get var list from
-        # FCST/OBS or BOTH variables
-        # report error and exit if field info is not set
-        if not var_list:
-            self.log_error('No input fields were specified to MTD. You must '
-                           'set [FCST/OBS]_VAR<n>_[NAME/LEVELS].')
-            return None
-
-        for var_info in var_list:
-
-            if self.c_dict.get('EXPLICIT_FILE_LIST', False):
-                time_info = ti_calculate(input_dict)
-                add_field_info_to_time_info(time_info, var_info)
-                model_list_path = do_string_sub(self.c_dict['FCST_FILE_LIST'],
-                                                **time_info)
-                self.logger.debug(f"Explicit FCST file: {model_list_path}")
-                if not os.path.exists(model_list_path):
-                    self.log_error('FCST file list file does not exist: '
-                                   f'{model_list_path}')
-                    return None
-
-                obs_list_path = do_string_sub(self.c_dict['OBS_FILE_LIST'],
-                                              **time_info)
-                self.logger.debug(f"Explicit OBS file: {obs_list_path}")
-                if not os.path.exists(obs_list_path):
-                    self.log_error('OBS file list file does not exist: '
-                                   f'{obs_list_path}')
-                    return None
-
-                arg_dict = {'obs_path': obs_list_path,
-                            'model_path': model_list_path}
-
-                self.process_fields_one_thresh(time_info, var_info, **arg_dict)
-                continue
-
-            model_list = []
-            obs_list = []
-
-            # find files for each forecast lead time
-            lead_seq = get_lead_sequence(self.config, input_dict)
-
-            tasks = []
-            for lead in lead_seq:
-                input_dict['lead'] = lead
-
-                time_info = ti_calculate(input_dict)
-                add_field_info_to_time_info(time_info, var_info)
-                tasks.append(time_info)
-
-            for current_task in tasks:
-                # call find_model/obs as needed
-                model_file = self.find_model(current_task, mandatory=False)
-                obs_file = self.find_obs(current_task, mandatory=False)
-                if model_file is None and obs_file is None:
+    def run_at_time_once(self, time_info):
+        # get formatted time to use to name file list files
+        if 'valid_fmt' in time_info:
+            time_fmt = f"valid{time_info['valid_fmt']}"
+        elif 'init_fmt' in time_info:
+            time_fmt = f"init{time_info['init_fmt']}"
+        else:
+            time_fmt = 'all'
+
+        # loop through the files found for each field (var_info)
+        for file_dict in self.c_dict['ALL_FILES']:
+            var_info = file_dict['var_info']
+            inputs = {}
+            for data_type in ('FCST', 'OBS'):
+                file_list = file_dict.get(data_type)
+                if not file_list:
                     continue
-
-                if model_file is None:
+                if len(file_list) == 1:
+                    if not os.path.exists(file_list[0]):
+                        self.log_error(f'{data_type} file does not exist: '
+                                       f'{file_list[0]}')
+                        continue
+                    inputs[data_type] = file_list[0]
                     continue
 
-                if obs_file is None:
+                file_ext = self.check_for_python_embedding(data_type, var_info)
+                if not file_ext:
                     continue
 
-                self.logger.debug(f"Adding forecast file: {model_file}")
-                self.logger.debug(f"Adding observation file: {obs_file}")
-                model_list.append(model_file)
-                obs_list.append(obs_file)
-
-            # only check model list because obs list should have same size
-            if not model_list:
-                self.log_error('Could not find any files to process')
-                return
-
-            # write ascii file with list of files to process
-            input_dict['lead'] = lead_seq[0]
-            time_info = ti_calculate(input_dict)
-
-            # if var name is a python embedding script, check type of python
-            # input and name file list file accordingly
-            fcst_file_ext = self.check_for_python_embedding('FCST', var_info)
-            obs_file_ext = self.check_for_python_embedding('OBS', var_info)
-            # if check_for_python_embedding returns None, an error occurred
-            if not fcst_file_ext or not obs_file_ext:
-                return
-
-            model_outfile = (
-                f"{time_info['valid_fmt']}_mtd_fcst_{fcst_file_ext}.txt"
-            )
-            obs_outfile = (
-                    f"{time_info['valid_fmt']}_mtd_obs_{obs_file_ext}.txt"
-            )
-            model_list_path = self.write_list_file(model_outfile, model_list)
-            obs_list_path = self.write_list_file(obs_outfile, obs_list)
-
-            arg_dict = {'obs_path': obs_list_path,
-                        'model_path': model_list_path}
+                outfile = f"{time_fmt}_mtd_{data_type.lower()}_{file_ext}.txt"
+                inputs[data_type] = self.write_list_file(outfile, file_list)
 
+            if not inputs:
+                self.log_error('Input files not found')
+                continue
+            if len(inputs) < 2 and not self.c_dict['SINGLE_RUN']:
+                self.log_error('Could not find all required inputs files')
+                continue
+            arg_dict = {
+                'obs_path': inputs.get('OBS'),
+                'model_path': inputs.get('FCST'),
+            }
             self.process_fields_one_thresh(time_info, var_info, **arg_dict)
 
-    def run_single_mode(self, input_dict, var_info):
-        single_list = []
-
-        data_src = self.c_dict.get('SINGLE_DATA_SRC')
-
-        if self.c_dict.get('EXPLICIT_FILE_LIST', False):
-            time_info = ti_calculate(input_dict)
-            add_field_info_to_time_info(time_info, var_info)
-            single_list_path = do_string_sub(
-                self.c_dict[f'{data_src}_FILE_LIST'],
-                **time_info
-            )
-            self.logger.debug(f"Explicit file list: {single_list_path}")
-            if not os.path.exists(single_list_path):
-                self.log_error(f'{data_src} file list file does not exist: '
-                               f'{single_list_path}')
-                return None
-
-        else:
-            if data_src == 'OBS':
-                find_method = self.find_obs
-            else:
-                find_method = self.find_model
-
-            lead_seq = get_lead_sequence(self.config, input_dict)
-            for lead in lead_seq:
-                input_dict['lead'] = lead
-                current_task = ti_calculate(input_dict)
-
-                single_file = find_method(current_task)
-                if single_file is None:
-                    continue
-
-                single_list.append(single_file)
-
-            if len(single_list) == 0:
-                return
-
-            # write ascii file with list of files to process
-            input_dict['lead'] = lead_seq[0]
-            time_info = ti_calculate(input_dict)
-            file_ext = self.check_for_python_embedding(data_src, var_info)
-            if not file_ext:
-                return
-
-            single_outfile = (
-                    f"{time_info['valid_fmt']}_mtd_single_{file_ext}.txt"
-            )
-            single_list_path = self.write_list_file(single_outfile,
-                                                    single_list)
-
-        arg_dict = {}
-        if data_src == 'OBS':
-            arg_dict['obs_path'] = single_list_path
-            arg_dict['model_path'] = None
-        else:
-            arg_dict['model_path'] = single_list_path
-            arg_dict['obs_path'] = None
-
-        self.process_fields_one_thresh(time_info, var_info, **arg_dict)
-
     def process_fields_one_thresh(self, time_info, var_info, model_path,
                                   obs_path):
         """! For each threshold, set up environment variables and run mode
@@ -507,3 +354,88 @@ def get_command(self):
             cmd += '-outdir {}'.format(self.outdir)
 
         return cmd
+
+    def get_input_templates(self, c_dict):
+        input_types = ['FCST', 'OBS']
+        if c_dict.get('SINGLE_RUN', False):
+            input_types = [c_dict['SINGLE_DATA_SRC']]
+
+        app = self.app_name.upper()
+        template_dict = {}
+        for in_type in input_types:
+            template_path = (
+                self.config.getraw('config',
+                                   f'{in_type}_{app}_INPUT_FILE_LIST')
+            )
+            if template_path:
+                c_dict['EXPLICIT_FILE_LIST'] = True
+            else:
+                in_dir = self.config.getdir(f'{in_type}_{app}_INPUT_DIR', '')
+                templates = getlist(
+                    self.config.getraw('config',
+                                       f'{in_type}_{app}_INPUT_TEMPLATE')
+                )
+                template_list = [os.path.join(in_dir, template)
+                                 for template in templates]
+                template_path = ','.join(template_list)
+
+            template_dict[in_type] = template_path
+
+        c_dict['TEMPLATE_DICT'] = template_dict
+
+    def get_files_from_time(self, time_info):
+        """! Create dictionary containing time information (key time_info) and
+             any relevant files for that runtime. The parent implementation of
+             this function creates a dictionary and adds the time_info to it.
+             This wrapper gets all files for the current runtime and adds it to
+             the dictionary with keys 'FCST' and 'OBS'
+
+             @param time_info dictionary containing time information
+             @returns dictionary containing time_info dict and any relevant
+             files with a key representing a description of that file
+        """
+        if self.c_dict.get('ONCE_PER_FIELD', False):
+            var_list = sub_var_list(self.c_dict.get('VAR_LIST_TEMP'), time_info)
+        else:
+            var_list = [None]
+
+        # create a dictionary for each field (var) with time_info and files
+        file_dict_list = []
+        for var_info in var_list:
+            file_dict = {'var_info': var_info}
+            if var_info:
+                add_field_info_to_time_info(time_info, var_info)
+
+            input_files = self.get_input_files(time_info, fill_missing=True)
+            # only add all input files if none are missing
+            no_missing = True
+            if input_files:
+                for key, value in input_files.items():
+                    if 'missing' in value:
+                        no_missing = False
+                    file_dict[key] = value
+            if no_missing:
+                file_dict_list.append(file_dict)
+
+        return file_dict_list
+
+    def _update_list_with_new_files(self, time_info, list_to_update):
+        new_files = self.get_files_from_time(time_info)
+        if not new_files:
+            return
+
+        # if list to update is empty, copy new items into list
+        if not list_to_update:
+            for new_file in new_files:
+                list_to_update.append(new_file.copy())
+            return
+
+        # if list to update is not empty, add new files to each file list,
+        # make sure new files correspond to the correct field (var)
+        assert len(list_to_update) == len(new_files)
+        for new_file, existing_item in zip(new_files, list_to_update):
+            assert new_file['var_info'] == existing_item['var_info']
+            for key, value in new_file.items():
+                if key == 'var_info':
+                    continue
+                existing_item[key].extend(value)

From a1ba59b47090676164db1f7d23771ae1ebc79f27 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 14:27:52 -0600
Subject: [PATCH 25/55] use f-strings for command, ci-run-all-diff

---
 metplus/wrappers/mtd_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index eeb4809dc..406d04261 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -337,7 +337,7 @@ def get_command(self):
            @rtype string
            @return Returns a MET command with arguments that you can run
         """
-        cmd = '{} -v {} '.format(self.app_path, self.c_dict['VERBOSITY'])
+        cmd = f"{self.app_path} -v {self.c_dict['VERBOSITY']} "
 
         for a in self.args:
             cmd += a + " "

From c9610e0623b7a01bb3e358da3ba0b892e1a16858 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:47:30 -0600
Subject: [PATCH 26/55] added unit test for case that happens in gfdl tracker
 wrapper

---
 internal/tests/pytests/util/time_util/test_time_util.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/internal/tests/pytests/util/time_util/test_time_util.py b/internal/tests/pytests/util/time_util/test_time_util.py
index 74d40d16d..553dc04d6 100644
--- a/internal/tests/pytests/util/time_util/test_time_util.py
+++ b/internal/tests/pytests/util/time_util/test_time_util.py
@@ -151,6 +151,8 @@ def test_time_string_to_met_time(time_string, default_unit, met_time):
         # RUN_ONCE_PER_LEAD: lead is time interval, init/valid are wildcards
         ({'init': '*', 'valid': '*', 'lead': relativedelta(hours=3)},
          {'init': '*', 'valid': '*', 'lead': relativedelta(hours=3), 'date': '*'}),
+        ({'init': datetime(2021, 7, 13, 0, 0), 'lead': 21600, 'offset_hours': 0},
+         {'init': datetime(2021, 7, 13, 0, 0), 'lead': 21600, 'valid': datetime(2021, 7, 13, 6, 0), 'offset': 0}),
         ]
 )
 @pytest.mark.util

From 95a245f1bcddc61a18c2f0c76d2b089886164b95 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:48:07 -0600
Subject: [PATCH 27/55] formatting

---
 metplus/wrappers/runtime_freq_wrapper.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 7f3831ecb..d899b05a6 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -334,8 +334,7 @@ def get_all_files_from_leads(self, time_input):
 
         lead_files = []
         # loop over all forecast leads
-        wildcard_if_empty = self.c_dict.get('WILDCARD_LEAD_IF_EMPTY',
-                                            False)
+        wildcard_if_empty = self.c_dict.get('WILDCARD_LEAD_IF_EMPTY', False)
         lead_seq = get_lead_sequence(self.config,
                                      time_input,
                                      wildcard_if_empty=wildcard_if_empty)

From 55dbcd8f2ed249080df0d151309ea244986b33c9 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:50:01 -0600
Subject: [PATCH 28/55] fixed failures when trying to format times that are
 wildcards, fix checks for lead not wildcard (relativedelta comparison
 operator to string '*' always reports False)

---
 metplus/util/time_util.py | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 67423d1ce..7fc75a9b5 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -357,17 +357,15 @@ def ti_calculate(input_dict):
     _set_init_valid_lead(out_dict)
 
     # set valid_fmt and init_fmt if they are not wildcard
-    if out_dict['valid'] != '*':
+    if out_dict.get('valid', '*') != '*':
         out_dict['valid_fmt'] = out_dict['valid'].strftime('%Y%m%d%H%M%S')
-
-    if out_dict['init'] != '*':
-        out_dict['init_fmt'] = out_dict['init'].strftime('%Y%m%d%H%M%S')
-
-    # calculate da_init from valid and offset
-    if out_dict['valid'] != '*':
+        # calculate da_init from valid and offset
         out_dict['da_init'] = out_dict['valid'] + out_dict['offset']
         out_dict['da_init_fmt'] = out_dict['da_init'].strftime('%Y%m%d%H%M%S')
 
+    if out_dict.get('init', '*') != '*':
+        out_dict['init_fmt'] = out_dict['init'].strftime('%Y%m%d%H%M%S')
+
     # convert offset to seconds and compute offset hours
     out_dict['offset'] = int(out_dict['offset'].total_seconds())
     out_dict['offset_hours'] = int(out_dict['offset'] // 3600)
@@ -379,8 +377,11 @@ def ti_calculate(input_dict):
     else:
         out_dict['date'] = out_dict['init']
 
-    # if any init/valid/lead are wildcard, skip updating other lead values
-    if out_dict['lead'] == '*' or out_dict['valid'] == '*' or out_dict['init'] == '*':
+    # if any init/valid/lead are unset or wildcard,
+    # skip converting lead to total seconds and computing lead hour, min, sec
+    if (isinstance(out_dict.get('lead', '*'), str) or
+            out_dict.get('valid', '*') == '*' or
+            out_dict.get('init', '*') == '*'):
         return out_dict
 
     # get difference between valid and init to get total seconds since relativedelta
@@ -466,6 +467,7 @@ def _set_loop_by(the_dict):
 def _set_init_valid_lead(the_dict):
     wildcard_items = [item for item in ('init', 'lead', 'valid')
                       if the_dict.get(item) == '*']
+
     # if 2 or more are wildcards, cannot compute init/valid/lead, so return
     if len(wildcard_items) >= 2:
         return
@@ -477,16 +479,18 @@ def _set_init_valid_lead(the_dict):
     loop_by = the_dict.get('loop_by')
 
     # if init and valid are both set and not wildcard, compute based on loop_by
+    # note: relativedelta == '*' and != '*' will always return False, so
+    # check if lead value is a string which implies it is '*'
     if init and valid and init != '*' and valid != '*':
         if loop_by == 'init':
             the_dict['valid'] = init + lead
         elif loop_by == 'valid':
             the_dict['init'] = valid - lead
-    elif init and init != '*':
+    elif init and init != '*' and not isinstance(lead, str):
         the_dict['valid'] = init + lead
         if not loop_by:
             the_dict['loop_by'] = 'init'
-    elif valid and valid != '*':
+    elif valid and valid != '*' and not isinstance(lead, str):
         the_dict['init'] = valid - lead
         if not loop_by:
             the_dict['loop_by'] = 'valid'

From c60b3eb1e9be1e838b89538d41b3acc196a4d61a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:50:19 -0600
Subject: [PATCH 29/55] set default runtime freq for TCPairs wrapper

---
 metplus/wrappers/tc_pairs_wrapper.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index 10ee11343..dd1884fc6 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -294,6 +294,9 @@ def create_c_dict(self):
                                 False)
         )
 
+        if c_dict['RUNTIME_FREQ'] == '':
+            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
+
         # check for settings that cause differences moving from v4.1 to v5.0
         # warn and update run setting to preserve old behavior
         if (self.config.has_option('config', 'LOOP_ORDER') and

From 9bac9087e2ee73be4685b096ffff2d404ed0f05f Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 14 Aug 2023 15:50:48 -0600
Subject: [PATCH 30/55] fix use case to use init instead of valid,
 ci-run-all-diff

---
 ...nalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf b/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
index c9b54fc87..8f9186f46 100644
--- a/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
+++ b/parm/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
@@ -46,13 +46,13 @@ OBS_MTD_INPUT_DIR = {FCST_MTD_INPUT_DIR}
 OBS_MTD_INPUT_TEMPLATE = {valid?fmt=%Y%m%d%H}/gfs.t{valid?fmt=%H}z.pgrb2.1p00.f000
 
 MTD_OUTPUT_DIR = {OUTPUT_BASE}/mtd
-MTD_OUTPUT_TEMPLATE = {valid?fmt=%Y%m%d%H}
+MTD_OUTPUT_TEMPLATE = {init?fmt=%Y%m%d%H}
 
 
 EXTRACT_TILES_SKIP_IF_OUTPUT_EXISTS = no
 
-EXTRACT_TILES_MTD_INPUT_DIR = {OUTPUT_BASE}/mtd
-EXTRACT_TILES_MTD_INPUT_TEMPLATE = {init?fmt=%Y%m%d%H}/mtd_{MODEL}_{FCST_VAR1_NAME}_vs_{OBTYPE}_{OBS_VAR1_NAME}_{OBS_VAR1_LEVELS}_{init?fmt=%Y%m%d_%H%M%S}V_2d.txt
+EXTRACT_TILES_MTD_INPUT_DIR = {MTD_OUTPUT_DIR}
+EXTRACT_TILES_MTD_INPUT_TEMPLATE = {MTD_OUTPUT_TEMPLATE}/mtd_{MODEL}_{FCST_VAR1_NAME}_vs_{OBTYPE}_{OBS_VAR1_NAME}_{OBS_VAR1_LEVELS}_{init?fmt=%Y%m%d_%H%M%S}V_2d.txt
 
 FCST_EXTRACT_TILES_INPUT_DIR = {FCST_MTD_INPUT_DIR}
 FCST_EXTRACT_TILES_INPUT_TEMPLATE = {FCST_MTD_INPUT_TEMPLATE}

From 9b7ee25aebd593783352032fc42e8d4376bdbf6a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:13:40 -0600
Subject: [PATCH 31/55] preserve old behavior by using init and first lead to
 compute valid time used to name output directories and file_list file names,
 change tests back to original values

---
 .../pytests/wrappers/mtd/test_mtd_wrapper.py  | 26 ++++++-------
 metplus/wrappers/mtd_wrapper.py               | 39 ++++++++++---------
 2 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
index 6c53d3bfb..1aa1b972d 100644
--- a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
+++ b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
@@ -71,7 +71,7 @@ def set_minimum_config_settings(config):
                '{valid?fmt=%Y%m%d%H}/obs_file')
     config.set('config', 'MTD_OUTPUT_DIR',
                '{OUTPUT_BASE}/MTD/output')
-    config.set('config', 'MTD_OUTPUT_TEMPLATE', '{init?fmt=%Y%m%d%H}')
+    config.set('config', 'MTD_OUTPUT_TEMPLATE', '{valid?fmt=%Y%m%d%H}')
 
     config.set('config', 'FCST_VAR1_NAME', fcst_name)
     config.set('config', 'FCST_VAR1_LEVELS', fcst_level)
@@ -175,11 +175,11 @@ def test_mode_single_field(metplus_config, config_overrides, env_var_values):
     out_dir = wrapper.c_dict.get('OUTPUT_DIR')
     expected_cmds = [(f"{app_path} {verbosity} "
                       f"-fcst {file_list_dir}/"
-                      f"init20050807000000_mtd_fcst_{fcst_name}.txt "
+                      f"20050807060000_mtd_fcst_{fcst_name}.txt "
                       f"-obs {file_list_dir}/"
-                      f"init20050807000000_mtd_obs_{obs_name}.txt "
+                      f"20050807060000_mtd_obs_{obs_name}.txt "
                       f"-config {config_file} "
-                      f"-outdir {out_dir}/2005080700"),
+                      f"-outdir {out_dir}/2005080706"),
                      ]
 
     all_cmds = wrapper.run_all_times()
@@ -224,8 +224,8 @@ def test_mtd_by_init_all_found(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -262,8 +262,8 @@ def test_mtd_by_valid_all_found(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'valid20170510030000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'valid20170510030000_mtd_obs_APCP.txt')
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510030000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510030000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -300,8 +300,8 @@ def test_mtd_by_init_miss_fcst(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510060000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510060000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -338,8 +338,8 @@ def test_mtd_by_init_miss_both(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
-    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_obs_APCP.txt')
+    fcst_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510090000_mtd_fcst_APCP.txt')
+    obs_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510090000_mtd_obs_APCP.txt')
     with open(fcst_list_file) as f:
         fcst_list = f.readlines()
     fcst_list = [x.strip() for x in fcst_list]
@@ -373,7 +373,7 @@ def test_mtd_single(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', 'init20170510030000_mtd_fcst_APCP.txt')
+    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_fcst_APCP.txt')
     with open(single_list_file) as f:
         single_list = f.readlines()
     single_list = [x.strip() for x in single_list]
diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index 406d04261..e6fd2f913 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -153,13 +153,17 @@ def read_field_values(self, c_dict, read_type, write_type):
             c_dict['OBS_CONV_THRESH'] = conf_value
 
     def run_at_time_once(self, time_info):
+        # calculate valid based on first forecast lead
+        lead_seq = get_lead_sequence(self.config, time_info)
+        if not lead_seq:
+            self.log_error('Could not get forecast lead list')
+            return
+        first_lead = lead_seq[0]
+        time_info['lead'] = first_lead
+        first_valid_time_info = ti_calculate(time_info)
+
         # get formatted time to use to name file list files
-        if 'valid_fmt' in time_info:
-            time_fmt = f"valid{time_info['valid_fmt']}"
-        elif 'init_fmt' in time_info:
-            time_fmt = f"init{time_info['init_fmt']}"
-        else:
-            time_fmt = 'all'
+        time_fmt = f"{first_valid_time_info['valid_fmt']}"
 
         # loop through the files found for each field (var_info)
         for file_dict in self.c_dict['ALL_FILES']:
@@ -194,13 +198,14 @@ def run_at_time_once(self, time_info):
                 'obs_path': inputs.get('OBS'),
                 'model_path': inputs.get('FCST'),
             }
-            self.process_fields_one_thresh(time_info, var_info, **arg_dict)
+            self.process_fields_one_thresh(first_valid_time_info, var_info,
+                                           **arg_dict)
 
-    def process_fields_one_thresh(self, time_info, var_info, model_path,
-                                  obs_path):
+    def process_fields_one_thresh(self, first_valid_time_info, var_info,
+                                  model_path, obs_path):
         """! For each threshold, set up environment variables and run mode
               Args:
-                @param time_info dictionary containing timing information
+                @param first_valid_time_info dictionary containing timing information
                 @param var_info object containing variable information
                 @param model_path forecast file list path
                 @param obs_path observation file list path
@@ -276,20 +281,16 @@ def process_fields_one_thresh(self, time_info, var_info, model_path,
 
         # loop through fields and call MTD
         for fcst_field, obs_field in zip(fcst_field_list, obs_field_list):
-            self.format_field('FCST',
-                              fcst_field,
-                              is_list=False)
-            self.format_field('OBS',
-                              obs_field,
-                              is_list=False)
+            self.format_field('FCST', fcst_field, is_list=False)
+            self.format_field('OBS',  obs_field,  is_list=False)
 
             self.param = do_string_sub(self.c_dict['CONFIG_FILE'],
-                                       **time_info)
+                                       **first_valid_time_info)
 
             self.set_current_field_config(var_info)
-            self.set_environment_variables(time_info)
+            self.set_environment_variables(first_valid_time_info)
 
-            if not self.find_and_check_output_file(time_info,
+            if not self.find_and_check_output_file(first_valid_time_info,
                                                    is_directory=True):
                 return
 

From c133bb417adc9f0203b7ed24b8cbe60466dc306b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:36:01 -0600
Subject: [PATCH 32/55] if [INIT/VALID]_BEG == [INIT/VALID]_END and runtime
 freq is RUN_ONCE, set init/valid to the time listed to allow TCPairs use
 cases to run with time info needed to preserve behavior

---
 metplus/wrappers/runtime_freq_wrapper.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index d899b05a6..34ee24db7 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -146,6 +146,13 @@ def run_once(self, custom):
         time_input['valid'] = '*'
         time_input['lead'] = '*'
 
+        # set init or valid to time if _BEG is equal to _END
+        start_dt, end_dt = get_start_and_end_times(self.config)
+        if start_dt == end_dt:
+            loop_by = get_time_prefix(self.config)
+            if loop_by:
+                time_input[loop_by.lower()] = start_dt
+
         time_info = time_util.ti_calculate(time_input)
 
         if not self.get_all_files(custom):

From 70fa3cbfdfd9bffbc103c4505b665df7dea424da Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:36:59 -0600
Subject: [PATCH 33/55] fix bug introduced by using RuntimeFreq that causes
 duplicate regex group

---
 metplus/wrappers/tc_pairs_wrapper.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index dd1884fc6..bf08e02d1 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -774,6 +774,7 @@ def _get_basin_cyclone_from_bdeck(self, bdeck_file, wildcard_used,
 
         # capture wildcard values in template - must replace ? wildcard
         # character after substitution because ? is used in template tags
+        bdeck_regex = bdeck_regex.replace('(*)', '*')
         bdeck_regex = bdeck_regex.replace('*', '(.*)').replace('?', '(.)')
         self.logger.debug(f'Regex to extract basin/cyclone: {bdeck_regex}')
 

From 9a433e2616081bb55d6e07b94efa0730fcd897c9 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:38:04 -0600
Subject: [PATCH 34/55] fix config to use same init beg/end for RUN_ONCE mode

---
 .../tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
index e45b93aa0..4825cd7a8 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
@@ -26,10 +26,8 @@ PROCESS_LIST = TCPairs, CyclonePlotter
 ###
 
 LOOP_BY = init
-INIT_TIME_FMT = %Y%m%d
-INIT_BEG = 20150301
-INIT_END = 20150330
-INIT_INCREMENT = 21600
+INIT_TIME_FMT = %Y%m
+INIT_BEG = 201503
 
 TC_PAIRS_RUN_ONCE = True
 
@@ -74,6 +72,8 @@ TC_PAIRS_REFORMAT_TYPE = SBU
 TC_PAIRS_MISSING_VAL_TO_REPLACE = -99
 TC_PAIRS_MISSING_VAL = -9999
 
+TC_PAIRS_INIT_BEG = {init?fmt=%Y%m}00
+TC_PAIRS_INIT_END = {init?fmt=%Y%m}30
 
 ###
 # CyclonePlotter Settings

From 4c903c691ddf3e6c6963a00600e0f46894aabd72 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:38:52 -0600
Subject: [PATCH 35/55] use RuntimeFreq time looping, preserve old behavior by
 setting runtime freq variables based on deprecated variables and warn that
 they are deprecated

---
 metplus/wrappers/tc_pairs_wrapper.py | 106 +++++++++++++++------------
 1 file changed, 59 insertions(+), 47 deletions(-)

diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index bf08e02d1..6b6087bc8 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -97,6 +97,8 @@ def create_c_dict(self):
                                                  c_dict['VERBOSITY'])
         c_dict['ALLOW_MULTIPLE_FILES'] = True
 
+        self._handle_time_looping(c_dict)
+
         c_dict['MISSING_VAL_TO_REPLACE'] = (
             self.config.getstr('config',
                                'TC_PAIRS_MISSING_VAL_TO_REPLACE', '-99')
@@ -207,12 +209,6 @@ def create_c_dict(self):
         if not c_dict['OUTPUT_DIR']:
             self.log_error('TC_PAIRS_OUTPUT_DIR must be set')
 
-        c_dict['READ_ALL_FILES'] = (
-            self.config.getbool('config',
-                                'TC_PAIRS_READ_ALL_FILES',
-                                False)
-        )
-
         # get list of models to process
         c_dict['MODEL_LIST'] = getlist(
             self.config.getraw('config', 'MODEL', '')
@@ -288,65 +284,81 @@ def create_c_dict(self):
 
         self.handle_description()
 
-        c_dict['SKIP_LEAD_SEQ'] = (
-            self.config.getbool('config',
-                                'TC_PAIRS_SKIP_LEAD_SEQ',
-                                False)
-        )
+        return c_dict
 
-        if c_dict['RUNTIME_FREQ'] == '':
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
+    def _handle_time_looping(self, c_dict):
+        """!Figure out time looping configuration based on legacy config
+         variables.
+         READ_ALL_FILES: Only pass directories to tc_pairs and
+         let the app handle all filtering. Force RUN_ONCE if set.
+         To preserve behavior when deprecated LOOP_ORDER=times and
+         TC_PAIRS_RUN_ONCE is not set,
+
+        @param c_dict dictionary to populate with values from METplusConfig
+        """
+        c_dict['READ_ALL_FILES'] = (
+            self.config.getbool('config', 'TC_PAIRS_READ_ALL_FILES', False)
+        )
+        if c_dict['READ_ALL_FILES']:
+            if c_dict['RUNTIME_FREQ'] != 'RUN_ONCE':
+                self.logger.debug('TC_PAIRS_READ_ALL_FILES=True. '
+                                  'Forcing TC_PAIRS_RUNTIME_FREQ=RUN_ONCE')
+                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
+            return
 
         # check for settings that cause differences moving from v4.1 to v5.0
         # warn and update run setting to preserve old behavior
         if (self.config.has_option('config', 'LOOP_ORDER') and
             self.config.getstr_nocheck('config', 'LOOP_ORDER') == 'times' and
-            not self.config.has_option('config', 'TC_PAIRS_RUN_ONCE')):
+            not (self.config.has_option('config', 'TC_PAIRS_RUN_ONCE') or
+                 self.config.has_option('config', 'TC_PAIRS_RUNTIME_FREQ'))):
             self.logger.warning(
                 'LOOP_ORDER has been deprecated. LOOP_ORDER has been set to '
-                '"times" and TC_PAIRS_RUN_ONCE is not set. '
-                'Forcing TC_PAIRS_RUN_ONCE=False to preserve behavior prior to '
-                'v5.0.0. Please remove LOOP_ORDER and set '
-                'TC_PAIRS_RUN_ONCE=False to preserve previous behavior and '
-                'remove this warning message.'
+                '"times" and TC_PAIRS_RUNTIME_FREQ is not set. '
+                'Forcing TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH to '
+                'preserve behavior prior to v5.0.0. Please remove LOOP_ORDER '
+                'and set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH to preserve '
+                'previous behavior and remove this warning message.'
             )
-            c_dict['RUN_ONCE'] = False
-            return c_dict
-
-        # only run once if True
-        c_dict['RUN_ONCE'] = self.config.getbool('config',
-                                                 'TC_PAIRS_RUN_ONCE',
-                                                 True)
-        return c_dict
-
-    def run_all_times(self):
-        """! Build up the command to invoke the MET tool tc_pairs.
-        """
-        # use first run time
-        input_dict = next(time_generator(self.config))
-        if not input_dict:
-            return self.all_commands
+            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
+
+        # check deprecated TC_PAIRS_RUN_ONCE, warn and handle if set
+        elif self.config.has_option('config', 'TC_PAIRS_RUN_ONCE'):
+            self.logger.warning('TC_PAIRS_RUN_ONCE is deprecated.')
+            run_once = self.config.getbool('config', 'TC_PAIRS_RUN_ONCE', True)
+            if run_once:
+                self.logger.warning('Setting TC_PAIRS_RUNTIME_FREQ=RUN_ONCE.'
+                                    'Please remove TC_PAIRS_RUN_ONCE and '
+                                    'set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE '
+                                    'to remove this warning')
+                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
+                return
 
-        add_to_time_input(input_dict, instance=self.instance)
+            self.logger.warning('Setting TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH.'
+                                'Please remove TC_PAIRS_RUN_ONCE and '
+                                'set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH '
+                                'to remove this warning')
+            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
 
-        # if running in READ_ALL_FILES mode, call tc_pairs once and exit
-        if self.c_dict['READ_ALL_FILES']:
-            return self._read_all_files(input_dict)
-
-        if not self.c_dict['RUN_ONCE']:
-            return super().run_all_times()
+        # set runtime frequency to RUN_ONCE if unset
+        if not c_dict['RUNTIME_FREQ']:
+            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
 
-        self.logger.debug('Only processing first run time. Set '
-                          'TC_PAIRS_RUN_ONCE=False to process all run times.')
-        log_runtime_banner(self.config, input_dict, self)
-        self.run_at_time(input_dict)
-        return self.all_commands
+        # if runtime frequency set to run once for each time, check skip lead
+        if c_dict['RUNTIME_FREQ'] == 'RUN_ONCE_FOR_EACH':
+            c_dict['SKIP_LEAD_SEQ'] = (
+                self.config.getbool('config', 'TC_PAIRS_SKIP_LEAD_SEQ', False)
+            )
 
     def run_at_time_once(self, time_info):
         """! Create the arguments to run MET tc_pairs
 
          @param time_info dictionary containing time information
         """
+        # if running in READ_ALL_FILES mode, call tc_pairs once and exit
+        if self.c_dict['READ_ALL_FILES']:
+            return self._read_all_files(time_info)
+
         # set output dir
         self.outdir = self.c_dict['OUTPUT_DIR']
 

From 95eac309021bf71f0aa8cbbd95cc916aadc9f4f7 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:39:14 -0600
Subject: [PATCH 36/55] turn on use case groups that were failing to test ,
 ci-run-diff

---
 .github/parm/use_case_groups.json | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index e8cc31f58..400cb4948 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -2,12 +2,12 @@
    {
     "category": "met_tool_wrapper",
     "index_list": "0-29,59-62",
-    "run": false
+    "run": true
   },
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": false
+    "run": true
   },
   {
     "category": "air_quality_and_comp",
@@ -112,7 +112,7 @@
   {
     "category": "medium_range",
     "index_list": "8",
-    "run": false
+    "run": true
   },
   {
     "category": "medium_range",
@@ -142,7 +142,7 @@
   {
     "category": "precipitation",
     "index_list": "3-7",
-    "run": false
+    "run": true
   },
   {
     "category": "precipitation",
@@ -157,7 +157,7 @@
   {
     "category": "s2s",
     "index_list": "0",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
@@ -262,12 +262,12 @@
   {
     "category": "tc_and_extra_tc",
     "index_list": "0-2",
-    "run": false
+    "run": true
   },
   {
     "category": "tc_and_extra_tc",
     "index_list": "3-5",
-    "run": false
+    "run": true
   },
   {
     "category": "unstructured_grids",

From 334f921843b72064611ad70ccde1720a647d0e74 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:40:53 -0600
Subject: [PATCH 37/55] add missing import, ci-run-diff

---
 metplus/wrappers/runtime_freq_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 34ee24db7..411ccc293 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -17,7 +17,7 @@
 from . import CommandBuilder
 from ..util import do_string_sub
 from ..util import log_runtime_banner, get_lead_sequence, is_loop_by_init
-from ..util import skip_time, getlist
+from ..util import skip_time, getlist, get_start_and_end_times, get_time_prefix
 from ..util import time_generator, add_to_time_input
 
 '''!@namespace RuntimeFreqWrapper

From 9e1eeab4c8bd8c1f37694be859bd3dcac465c79f Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:56:06 -0600
Subject: [PATCH 38/55] name file_list file with 'single' if MTD_SINGLE_RUN to
 prevent diffs in use case output

---
 internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py | 2 +-
 metplus/wrappers/mtd_wrapper.py                         | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
index 1aa1b972d..5c54a41ef 100644
--- a/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
+++ b/internal/tests/pytests/wrappers/mtd/test_mtd_wrapper.py
@@ -373,7 +373,7 @@ def test_mtd_single(metplus_config):
     }
     mw = mtd_wrapper(metplus_config, overrides)
     mw.run_all_times()
-    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_fcst_APCP.txt')
+    single_list_file = os.path.join(mw.config.getdir('STAGING_DIR'), 'file_lists', '20170510040000_mtd_single_APCP.txt')
     with open(single_list_file) as f:
         single_list = f.readlines()
     single_list = [x.strip() for x in single_list]
diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index e6fd2f913..a74282ff0 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -185,7 +185,8 @@ def run_at_time_once(self, time_info):
                 if not file_ext:
                     continue
 
-                outfile = f"{time_fmt}_mtd_{data_type.lower()}_{file_ext}.txt"
+                dt = 'single' if self.c_dict['SINGLE_RUN'] else data_type
+                outfile = f"{time_fmt}_mtd_{dt.lower()}_{file_ext}.txt"
                 inputs[data_type] = self.write_list_file(outfile, file_list)
 
             if not inputs:

From 0d53a0c05f1d3d13050f29ff3f0ddb42cccc3fbf Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:56:19 -0600
Subject: [PATCH 39/55] remove unused variable

---
 internal/tests/pytests/wrappers/tc_gen/test_tc_gen_wrapper.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/internal/tests/pytests/wrappers/tc_gen/test_tc_gen_wrapper.py b/internal/tests/pytests/wrappers/tc_gen/test_tc_gen_wrapper.py
index 84d9c9083..610b5573a 100644
--- a/internal/tests/pytests/wrappers/tc_gen/test_tc_gen_wrapper.py
+++ b/internal/tests/pytests/wrappers/tc_gen/test_tc_gen_wrapper.py
@@ -319,7 +319,6 @@ def test_tc_gen(metplus_config, config_overrides, env_var_values):
     config.set('config', 'LOOP_BY', 'INIT')
     config.set('config', 'INIT_TIME_FMT', '%Y')
     config.set('config', 'INIT_BEG', '2016')
-    config.set('config', 'LOOP_ORDER', 'processes')
 
     config.set('config', 'TC_GEN_TRACK_INPUT_DIR', track_dir)
     config.set('config', 'TC_GEN_TRACK_INPUT_TEMPLATE', track_template)

From 101f5d0462879dab85f196e39ba7eb34670e3e44 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:57:00 -0600
Subject: [PATCH 40/55] call self.clear before running in RUN_ONCE mode to
 clear out command line arguments for multiple runs via CUSTOM_LOOP_LIST

---
 metplus/wrappers/runtime_freq_wrapper.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 411ccc293..aa652daca 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -159,6 +159,7 @@ def run_once(self, custom):
             self.log_error("A problem occurred trying to obtain input files")
             return None
 
+        self.clear()
         return self.run_at_time_once(time_info)
 
     def run_once_per_init_or_valid(self, custom):

From 1e4a9535ced95f0e79415af50be2798fb47b722a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 11:57:50 -0600
Subject: [PATCH 41/55] change TCGen wrapper to RuntimeFreq

---
 metplus/wrappers/tc_gen_wrapper.py | 36 +++---------------------------
 1 file changed, 3 insertions(+), 33 deletions(-)

diff --git a/metplus/wrappers/tc_gen_wrapper.py b/metplus/wrappers/tc_gen_wrapper.py
index aae6c991c..cdfc2f387 100755
--- a/metplus/wrappers/tc_gen_wrapper.py
+++ b/metplus/wrappers/tc_gen_wrapper.py
@@ -17,7 +17,7 @@
 from ..util import time_util
 from ..util import do_string_sub, skip_time, get_lead_sequence
 from ..util import time_generator
-from . import CommandBuilder
+from . import RuntimeFreqWrapper
 
 '''!@namespace TCGenWrapper
 @brief Wraps the TC-Gen tool
@@ -25,7 +25,7 @@
 '''
 
 
-class TCGenWrapper(CommandBuilder):
+class TCGenWrapper(RuntimeFreqWrapper):
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_INIT_FREQ',
@@ -109,6 +109,7 @@ def create_c_dict(self):
                                c_dict['VERBOSITY'])
         )
         c_dict['ALLOW_MULTIPLE_FILES'] = True
+        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
 
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('TCGenConfig_wrapped')
@@ -279,11 +280,6 @@ def create_c_dict(self):
         )
         self.add_met_config_window('genesis_match_window')
 
-        # get INPUT_TIME_DICT values since wrapper doesn't loop over time
-        c_dict['INPUT_TIME_DICT'] = next(time_generator(self.config))
-        if not c_dict['INPUT_TIME_DICT']:
-            self.isOK = False
-
         return c_dict
 
     def handle_filter(self):
@@ -326,32 +322,6 @@ def get_command(self):
 
         return cmd
 
-    def run_all_times(self):
-        """!Runs tc_gen for the first run time"""
-        # run using input time dictionary
-        self.run_at_time(self.c_dict['INPUT_TIME_DICT'])
-        return self.all_commands
-
-    def run_at_time(self, input_dict):
-        """! Process runtime and try to build command to run ascii2nc
-             Args:
-                @param input_dict dictionary containing timing information
-        """
-        input_dict['instance'] = self.instance if self.instance else ''
-        for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            input_dict['custom'] = custom_string
-            time_info = time_util.ti_calculate(input_dict)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            self.clear()
-            self.run_at_time_once(time_info)
-
     def run_at_time_once(self, time_info):
         """! Process runtime and try to build command to run ascii2nc
              Args:

From df2d18a56fbbb87b0f9672aeb6b744909a7bc9dc Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 12:07:17 -0600
Subject: [PATCH 42/55] set lead_hours/minutes/seconds even if lead is months
 or years so relativedelta lead is still accurate if init/valid change but
 lead values can still be set from total seconds between init and valid, add
 unit test to ensure the case that broke a use case always works

---
 internal/tests/pytests/util/time_util/test_time_util.py | 5 +++++
 metplus/util/time_util.py                               | 7 ++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/internal/tests/pytests/util/time_util/test_time_util.py b/internal/tests/pytests/util/time_util/test_time_util.py
index 553dc04d6..242469c39 100644
--- a/internal/tests/pytests/util/time_util/test_time_util.py
+++ b/internal/tests/pytests/util/time_util/test_time_util.py
@@ -151,8 +151,13 @@ def test_time_string_to_met_time(time_string, default_unit, met_time):
         # RUN_ONCE_PER_LEAD: lead is time interval, init/valid are wildcards
         ({'init': '*', 'valid': '*', 'lead': relativedelta(hours=3)},
          {'init': '*', 'valid': '*', 'lead': relativedelta(hours=3), 'date': '*'}),
+        # case that failed in GFDLTracker wrapper
         ({'init': datetime(2021, 7, 13, 0, 0), 'lead': 21600, 'offset_hours': 0},
          {'init': datetime(2021, 7, 13, 0, 0), 'lead': 21600, 'valid': datetime(2021, 7, 13, 6, 0), 'offset': 0}),
+        # lead is months or years (relativedelta)
+        # allows lead to remain relativedelta in case init/valid change but still computes lead hours
+        ({'init': datetime(2021, 7, 13, 0, 0), 'lead': relativedelta(months=1)},
+         {'init': datetime(2021, 7, 13, 0, 0), 'lead': relativedelta(months=1), 'valid': datetime(2021, 8, 13, 0, 0), 'lead_hours': 744}),
         ]
 )
 @pytest.mark.util
diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 7fc75a9b5..f1d8aa9ab 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -392,9 +392,10 @@ def ti_calculate(input_dict):
     # if they are, keep lead as a relativedelta object to be handled differently
     if out_dict['lead'].months == 0 and out_dict['lead'].years == 0:
         out_dict['lead'] = total_seconds
-        out_dict['lead_hours'] = int(total_seconds // 3600)
-        out_dict['lead_minutes'] = int(total_seconds // 60)
-        out_dict['lead_seconds'] = total_seconds
+
+    out_dict['lead_hours'] = int(total_seconds // 3600)
+    out_dict['lead_minutes'] = int(total_seconds // 60)
+    out_dict['lead_seconds'] = total_seconds
 
     return out_dict
 

From 9a1a610148d05b707865c0ee1ee0afde9ad54e4d Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 12:13:42 -0600
Subject: [PATCH 43/55] update use case config to use single run time
 (RUN_ONCE) and set init_beg and init_end explicitly in TCPairs and TCStat MET
 config

---
 ...TCStat_fcstADECK_obsBDECK_ATCF_BasicExample.conf | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/TCPairs_TCStat_fcstADECK_obsBDECK_ATCF_BasicExample.conf b/parm/use_cases/model_applications/tc_and_extra_tc/TCPairs_TCStat_fcstADECK_obsBDECK_ATCF_BasicExample.conf
index 9847b29a1..854f18005 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/TCPairs_TCStat_fcstADECK_obsBDECK_ATCF_BasicExample.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/TCPairs_TCStat_fcstADECK_obsBDECK_ATCF_BasicExample.conf
@@ -26,10 +26,10 @@ PROCESS_LIST = TCPairs, TCStat
 ###
 
 LOOP_BY = INIT
-INIT_TIME_FMT = %Y%m%d%H
-INIT_BEG = 2021082500
-INIT_END = 2021083000
-INIT_INCREMENT = 21600
+INIT_TIME_FMT = %Y%m
+INIT_BEG = 202108
+
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
 
 ###
 # File I/O
@@ -67,6 +67,8 @@ TC_PAIRS_DLAND_FILE = MET_BASE/tc_data/dland_global_tenth_degree.nc
 
 TC_PAIRS_MATCH_POINTS = TRUE
 
+TC_PAIRS_INIT_BEG = {init?fmt=%Y%m}25_00
+TC_PAIRS_INIT_END = {init?fmt=%Y%m}30_00
 
 ###
 # TCStat Settings
@@ -81,3 +83,6 @@ TC_STAT_COLUMN_STRING_VAL = HU,SD,SS,TS,TD
 TC_STAT_WATER_ONLY = FALSE
 
 TC_STAT_JOB_ARGS = -job filter -dump_row {TC_STAT_OUTPUT_DIR}/tc_stat_summary.tcst
+
+TC_STAT_INIT_BEG = {init?fmt=%Y%m}25_00
+TC_STAT_INIT_END = {init?fmt=%Y%m}30_00

From 569c6cfebbca1c46c39176003ea4336aa8ddcbd4 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 12:15:15 -0600
Subject: [PATCH 44/55] turn off use cases that now pass and test if other
 cases will pass, ci-run-diff

---
 .github/parm/use_case_groups.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 400cb4948..6dde3d839 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -2,12 +2,12 @@
    {
     "category": "met_tool_wrapper",
     "index_list": "0-29,59-62",
-    "run": true
+    "run": false
   },
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": true
+    "run": false
   },
   {
     "category": "air_quality_and_comp",
@@ -112,7 +112,7 @@
   {
     "category": "medium_range",
     "index_list": "8",
-    "run": true
+    "run": false
   },
   {
     "category": "medium_range",

From 50fbe5a357b2b80fdca3714bdff57e089bdaff30 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 12:35:54 -0600
Subject: [PATCH 45/55] turn off all use cases

---
 .github/parm/use_case_groups.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 6dde3d839..e8cc31f58 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -142,7 +142,7 @@
   {
     "category": "precipitation",
     "index_list": "3-7",
-    "run": true
+    "run": false
   },
   {
     "category": "precipitation",
@@ -157,7 +157,7 @@
   {
     "category": "s2s",
     "index_list": "0",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
@@ -262,12 +262,12 @@
   {
     "category": "tc_and_extra_tc",
     "index_list": "0-2",
-    "run": true
+    "run": false
   },
   {
     "category": "tc_and_extra_tc",
     "index_list": "3-5",
-    "run": true
+    "run": false
   },
   {
     "category": "unstructured_grids",

From 438386963186b8417e7b1fa4d3977e0191ecfe2a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 15:32:10 -0600
Subject: [PATCH 46/55] Create class variables for RuntimeFreq wrappers to
 define default value to use for runtime frequency and list of supported
 frequencies (or 'ALL' if any are supported). Added function to validate
 RUNTIME_FREQ values to ensure the type selected is supported and the correct
 default if used if not set, ci-run-all-diff

---
 metplus/wrappers/ascii2nc_wrapper.py          |   3 +
 metplus/wrappers/command_builder.py           |   2 -
 metplus/wrappers/ensemble_stat_wrapper.py     |   3 +
 metplus/wrappers/example_wrapper.py           |   4 +
 metplus/wrappers/extract_tiles_wrapper.py     |   3 +
 metplus/wrappers/gempak_to_cf_wrapper.py      |   4 +
 metplus/wrappers/gen_ens_prod_wrapper.py      |   3 +
 metplus/wrappers/gen_vx_mask_wrapper.py       |   7 +-
 metplus/wrappers/gfdl_tracker_wrapper.py      |  28 ++--
 metplus/wrappers/grid_diag_wrapper.py         |   5 +-
 metplus/wrappers/grid_stat_wrapper.py         |  10 +-
 metplus/wrappers/ioda2nc_wrapper.py           |   3 +
 metplus/wrappers/met_db_load_wrapper.py       |   5 +
 metplus/wrappers/mode_wrapper.py              |   3 +
 metplus/wrappers/mtd_wrapper.py               |   8 +-
 metplus/wrappers/pb2nc_wrapper.py             |   2 +
 metplus/wrappers/pcp_combine_wrapper.py       |   3 +
 metplus/wrappers/plot_data_plane_wrapper.py   |   3 +
 metplus/wrappers/plot_point_obs_wrapper.py    |   2 +
 metplus/wrappers/point2grid_wrapper.py        |   2 +
 metplus/wrappers/point_stat_wrapper.py        |   3 +
 metplus/wrappers/py_embed_ingest_wrapper.py   |   3 +
 metplus/wrappers/regrid_data_plane_wrapper.py |   8 +-
 metplus/wrappers/runtime_freq_wrapper.py      |  51 +++++-
 metplus/wrappers/series_analysis_wrapper.py   |   3 +
 metplus/wrappers/stat_analysis_wrapper.py     |  41 +++--
 metplus/wrappers/tc_diag_wrapper.py           |   8 +-
 metplus/wrappers/tc_gen_wrapper.py            |   3 +-
 metplus/wrappers/tc_pairs_wrapper.py          |  34 ++--
 metplus/wrappers/tc_stat_wrapper.py           |   4 +-
 metplus/wrappers/tcrmw_wrapper.py             | 150 +++++++-----------
 metplus/wrappers/user_script_wrapper.py       |   3 +
 32 files changed, 227 insertions(+), 187 deletions(-)

diff --git a/metplus/wrappers/ascii2nc_wrapper.py b/metplus/wrappers/ascii2nc_wrapper.py
index b29cbf95c..df875575e 100755
--- a/metplus/wrappers/ascii2nc_wrapper.py
+++ b/metplus/wrappers/ascii2nc_wrapper.py
@@ -24,6 +24,9 @@
 
 class ASCII2NCWrapper(LoopTimesWrapper):
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_TIME_SUMMARY_DICT',
     ]
diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index 49f78acea..1f55e99b8 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -167,8 +167,6 @@ def create_c_dict(self):
         c_dict['VERBOSITY'] = self.config.getstr('config',
                                                  'LOG_MET_VERBOSITY',
                                                  '2')
-        c_dict['ALLOW_MULTIPLE_FILES'] = False
-
         app_name = ''
         if hasattr(self, 'app_name'):
             app_name = self.app_name
diff --git a/metplus/wrappers/ensemble_stat_wrapper.py b/metplus/wrappers/ensemble_stat_wrapper.py
index cadfab36c..21e48747e 100755
--- a/metplus/wrappers/ensemble_stat_wrapper.py
+++ b/metplus/wrappers/ensemble_stat_wrapper.py
@@ -27,6 +27,9 @@ class EnsembleStatWrapper(CompareGriddedWrapper):
     """!Wraps the MET tool ensemble_stat to compare ensemble datasets
     """
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_DESC',
diff --git a/metplus/wrappers/example_wrapper.py b/metplus/wrappers/example_wrapper.py
index c2dfcb332..d5290320a 100755
--- a/metplus/wrappers/example_wrapper.py
+++ b/metplus/wrappers/example_wrapper.py
@@ -18,6 +18,10 @@
 
 
 class ExampleWrapper(LoopTimesWrapper):
+
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     """!Wrapper can be used as a base to develop a new wrapper"""
     def __init__(self, config, instance=None):
         self.app_name = 'example'
diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index 8f8de6b97..246e5af68 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -24,6 +24,9 @@ class ExtractTilesWrapper(LoopTimesWrapper):
     """! Takes tc-pairs data and regrids paired data to an n x m grid as
          specified in the config file.
     """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     COLUMNS_OF_INTEREST = {
         'TC_STAT': [
             'INIT',
diff --git a/metplus/wrappers/gempak_to_cf_wrapper.py b/metplus/wrappers/gempak_to_cf_wrapper.py
index f54eb22b0..2270a703a 100755
--- a/metplus/wrappers/gempak_to_cf_wrapper.py
+++ b/metplus/wrappers/gempak_to_cf_wrapper.py
@@ -23,6 +23,10 @@
 
 
 class GempakToCFWrapper(LoopTimesWrapper):
+
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     def __init__(self, config, instance=None):
         self.app_name = "GempakToCF"
         self.app_path = config.getstr('exe', 'GEMPAKTOCF_JAR', '')
diff --git a/metplus/wrappers/gen_ens_prod_wrapper.py b/metplus/wrappers/gen_ens_prod_wrapper.py
index 27d79d0d8..26e4cd659 100755
--- a/metplus/wrappers/gen_ens_prod_wrapper.py
+++ b/metplus/wrappers/gen_ens_prod_wrapper.py
@@ -14,6 +14,9 @@
 class GenEnsProdWrapper(LoopTimesWrapper):
     """! Wrapper for gen_ens_prod MET application """
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_DESC',
diff --git a/metplus/wrappers/gen_vx_mask_wrapper.py b/metplus/wrappers/gen_vx_mask_wrapper.py
index 6338c9ec6..373284557 100755
--- a/metplus/wrappers/gen_vx_mask_wrapper.py
+++ b/metplus/wrappers/gen_vx_mask_wrapper.py
@@ -24,6 +24,9 @@
 
 class GenVxMaskWrapper(LoopTimesWrapper):
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     def __init__(self, config, instance=None):
         self.app_name = "gen_vx_mask"
         self.app_path = os.path.join(config.getdir('MET_BIN_DIR', ''),
@@ -40,12 +43,12 @@ def create_c_dict(self):
         # input and output files
         c_dict['INPUT_DIR'] = self.config.getdir('GEN_VX_MASK_INPUT_DIR',
                                                  '')
-        c_dict['INPUT_TEMPLATE'] = self.config.getraw('filename_templates',
+        c_dict['INPUT_TEMPLATE'] = self.config.getraw('config',
                                                       'GEN_VX_MASK_INPUT_TEMPLATE')
 
         c_dict['OUTPUT_DIR'] = self.config.getdir('GEN_VX_MASK_OUTPUT_DIR',
                                                   '')
-        c_dict['OUTPUT_TEMPLATE'] = self.config.getraw('filename_templates',
+        c_dict['OUTPUT_TEMPLATE'] = self.config.getraw('config',
                                                        'GEN_VX_MASK_OUTPUT_TEMPLATE')
 
         c_dict['MASK_INPUT_DIR'] = self.config.getdir('GEN_VX_MASK_INPUT_MASK_DIR',
diff --git a/metplus/wrappers/gfdl_tracker_wrapper.py b/metplus/wrappers/gfdl_tracker_wrapper.py
index 770093f4f..1e686109d 100755
--- a/metplus/wrappers/gfdl_tracker_wrapper.py
+++ b/metplus/wrappers/gfdl_tracker_wrapper.py
@@ -17,11 +17,15 @@
 
 from ..util import do_string_sub, ti_calculate, get_lead_sequence
 from ..util import remove_quotes, parse_template
-from . import CommandBuilder
+from . import RuntimeFreqWrapper
 
-class GFDLTrackerWrapper(CommandBuilder):
+
+class GFDLTrackerWrapper(RuntimeFreqWrapper):
     """!Configures and runs GFDL Tracker"""
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE', 'RUN_ONCE_PER_INIT_OR_VALID']
+
     CONFIG_NAMES = {
         "DATEIN_INP_MODEL": "int",
         "DATEIN_INP_MODTYP": "string",
@@ -241,20 +245,6 @@ def _read_gfdl_config_variables(self, c_dict):
             value = get_fct('config', f'GFDL_TRACKER_{name}', '')
             c_dict[f'REPLACE_CONF_{name}'] = value
 
-    def run_at_time(self, input_dict):
-        """! Do some processing for the current run time (init or valid)
-
-        @param input_dict dictionary containing time information of current run
-        """
-        for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            input_dict['custom'] = custom_string
-            self.run_at_time_once(input_dict)
-
-        self.c_dict['FIRST_RUN'] = False
-
     def run_at_time_once(self, input_dict):
         """! Do some processing for the current run time (init or valid)
 
@@ -547,8 +537,9 @@ def handle_templates(self, input_dict):
 
         # only fill out sgv template file if template is specified
         # and on a 0Z run that is not the first run time
-        if (not self.c_dict['SGV_TEMPLATE_FILE'] or
-                self.c_dict['FIRST_RUN'] or
+        first_run = self.c_dict['FIRST_RUN']
+        self.c_dict['FIRST_RUN'] = False
+        if (not self.c_dict['SGV_TEMPLATE_FILE'] or first_run or
                 input_dict['init'].strftime('%H') != '00'):
             return output_path
 
@@ -578,7 +569,6 @@ def sub_template(self, template_file, output_path, sub_dict):
             for line in output_lines:
                 file_handle.write(f'{line}\n')
 
-
     def populate_sub_dict(self, time_info):
         sub_dict = {}
 
diff --git a/metplus/wrappers/grid_diag_wrapper.py b/metplus/wrappers/grid_diag_wrapper.py
index bcdb52eb2..9d1f93d02 100755
--- a/metplus/wrappers/grid_diag_wrapper.py
+++ b/metplus/wrappers/grid_diag_wrapper.py
@@ -24,6 +24,9 @@
 
 class GridDiagWrapper(RuntimeFreqWrapper):
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_DESC',
         'METPLUS_REGRID_DICT',
@@ -150,8 +153,6 @@ def get_command(self):
         return cmd
 
     def run_at_time_once(self, time_info):
-        self.clear()
-
         # subset input files as appropriate
         input_list_dict = self.subset_input_files(time_info)
         if not input_list_dict:
diff --git a/metplus/wrappers/grid_stat_wrapper.py b/metplus/wrappers/grid_stat_wrapper.py
index c087cfc76..f9b9ca2fb 100755
--- a/metplus/wrappers/grid_stat_wrapper.py
+++ b/metplus/wrappers/grid_stat_wrapper.py
@@ -24,6 +24,9 @@
 class GridStatWrapper(CompareGriddedWrapper):
     """!Wraps the MET tool grid_stat to compare gridded datasets"""
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_DESC',
@@ -113,13 +116,6 @@ def create_c_dict(self):
                                                  'LOG_GRID_STAT_VERBOSITY',
                                                  c_dict['VERBOSITY'])
 
-        if c_dict['RUNTIME_FREQ'] != 'RUN_ONCE_FOR_EACH':
-            self.logger.warning(
-                f"GRID_STAT_RUNTIME_FREQ={c_dict['RUNTIME_FREQ']} not "
-                "supported. Using RUN_ONCE_FOR_EACH"
-            )
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
-
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('GridStatConfig_wrapped')
 
diff --git a/metplus/wrappers/ioda2nc_wrapper.py b/metplus/wrappers/ioda2nc_wrapper.py
index d8354144d..323fbbe0c 100755
--- a/metplus/wrappers/ioda2nc_wrapper.py
+++ b/metplus/wrappers/ioda2nc_wrapper.py
@@ -17,6 +17,9 @@
 
 class IODA2NCWrapper(LoopTimesWrapper):
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MESSAGE_TYPE',
         'METPLUS_MESSAGE_TYPE_GROUP_MAP',
diff --git a/metplus/wrappers/met_db_load_wrapper.py b/metplus/wrappers/met_db_load_wrapper.py
index 421d440ce..a837647f2 100755
--- a/metplus/wrappers/met_db_load_wrapper.py
+++ b/metplus/wrappers/met_db_load_wrapper.py
@@ -22,11 +22,16 @@
 @endcode
 '''
 
+
 class METDbLoadWrapper(RuntimeFreqWrapper):
     """! Config variable names - All names are prepended with MET_DB_LOAD_MV_
          and all c_dict values are prepended with MV_.
          The name is the key and string specifying the type is the value.
     """
+
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     CONFIG_NAMES = {
         'HOST': 'string',
         'DATABASE': 'string',
diff --git a/metplus/wrappers/mode_wrapper.py b/metplus/wrappers/mode_wrapper.py
index fc0d5bbaf..ece359d64 100755
--- a/metplus/wrappers/mode_wrapper.py
+++ b/metplus/wrappers/mode_wrapper.py
@@ -19,6 +19,9 @@
 class MODEWrapper(CompareGriddedWrapper):
     """!Wrapper for the mode MET tool"""
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_DESC',
diff --git a/metplus/wrappers/mtd_wrapper.py b/metplus/wrappers/mtd_wrapper.py
index a74282ff0..b3f3ef630 100755
--- a/metplus/wrappers/mtd_wrapper.py
+++ b/metplus/wrappers/mtd_wrapper.py
@@ -21,6 +21,9 @@
 
 class MTDWrapper(CompareGriddedWrapper):
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_DESC',
@@ -54,8 +57,6 @@ def create_c_dict(self):
         # set to prevent find_obs from getting multiple files within
         #  a time window. Does not refer to time series of files
         c_dict['ALLOW_MULTIPLE_FILES'] = False
-
-        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
         c_dict['ONCE_PER_FIELD'] = True
 
         c_dict['OUTPUT_DIR'] = (
@@ -156,8 +157,7 @@ def run_at_time_once(self, time_info):
         # calculate valid based on first forecast lead
         lead_seq = get_lead_sequence(self.config, time_info)
         if not lead_seq:
-            self.log_error('Could not get forecast lead list')
-            return
+            lead_seq = [0]
         first_lead = lead_seq[0]
         time_info['lead'] = first_lead
         first_valid_time_info = ti_calculate(time_info)
diff --git a/metplus/wrappers/pb2nc_wrapper.py b/metplus/wrappers/pb2nc_wrapper.py
index 42aad03a0..44bb7fd97 100755
--- a/metplus/wrappers/pb2nc_wrapper.py
+++ b/metplus/wrappers/pb2nc_wrapper.py
@@ -23,6 +23,8 @@ class PB2NCWrapper(LoopTimesWrapper):
     """! Wrapper to the MET tool pb2nc which converts prepbufr files
          to NetCDF for MET's point_stat tool can recognize.
     """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MESSAGE_TYPE',
diff --git a/metplus/wrappers/pcp_combine_wrapper.py b/metplus/wrappers/pcp_combine_wrapper.py
index b702e74a6..77b5b0b82 100755
--- a/metplus/wrappers/pcp_combine_wrapper.py
+++ b/metplus/wrappers/pcp_combine_wrapper.py
@@ -25,6 +25,9 @@ class PCPCombineWrapper(ReformatGriddedWrapper):
     """! Wraps the MET tool pcp_combine to combine or divide
          precipitation accumulations """
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     # valid values for [FCST/OBS]_PCP_COMBINE_METHOD
     valid_run_methods = ['ADD', 'SUM', 'SUBTRACT', 'DERIVE', 'USER_DEFINED']
 
diff --git a/metplus/wrappers/plot_data_plane_wrapper.py b/metplus/wrappers/plot_data_plane_wrapper.py
index 7e8c09ef2..b0efc8798 100755
--- a/metplus/wrappers/plot_data_plane_wrapper.py
+++ b/metplus/wrappers/plot_data_plane_wrapper.py
@@ -23,6 +23,9 @@
 
 
 class PlotDataPlaneWrapper(LoopTimesWrapper):
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     def __init__(self, config, instance=None):
         self.app_name = "plot_data_plane"
         self.app_path = os.path.join(config.getdir('MET_BIN_DIR', ''),
diff --git a/metplus/wrappers/plot_point_obs_wrapper.py b/metplus/wrappers/plot_point_obs_wrapper.py
index 071d71310..1a2ad6b43 100755
--- a/metplus/wrappers/plot_point_obs_wrapper.py
+++ b/metplus/wrappers/plot_point_obs_wrapper.py
@@ -19,6 +19,8 @@
 
 class PlotPointObsWrapper(LoopTimesWrapper):
     """! Wrapper used to build commands to call plot_point_obs """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_GRID_DATA_DICT',
diff --git a/metplus/wrappers/point2grid_wrapper.py b/metplus/wrappers/point2grid_wrapper.py
index 6443bcf18..e4cb356cd 100755
--- a/metplus/wrappers/point2grid_wrapper.py
+++ b/metplus/wrappers/point2grid_wrapper.py
@@ -25,6 +25,8 @@
 
 
 class Point2GridWrapper(LoopTimesWrapper):
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     def __init__(self, config, instance=None):
         self.app_name = "point2grid"
diff --git a/metplus/wrappers/point_stat_wrapper.py b/metplus/wrappers/point_stat_wrapper.py
index a5848b361..1836097d5 100755
--- a/metplus/wrappers/point_stat_wrapper.py
+++ b/metplus/wrappers/point_stat_wrapper.py
@@ -17,8 +17,11 @@
 from ..util import do_string_sub
 from . import CompareGriddedWrapper
 
+
 class PointStatWrapper(CompareGriddedWrapper):
     """! Wrapper to the MET tool, Point-Stat."""
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
diff --git a/metplus/wrappers/py_embed_ingest_wrapper.py b/metplus/wrappers/py_embed_ingest_wrapper.py
index 1d4fe7845..0f6d06917 100755
--- a/metplus/wrappers/py_embed_ingest_wrapper.py
+++ b/metplus/wrappers/py_embed_ingest_wrapper.py
@@ -24,6 +24,9 @@
 class PyEmbedIngestWrapper(LoopTimesWrapper):
     """!Wrapper to utilize Python Embedding in the MET tools to read in
     data using a python script"""
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     def __init__(self, config, instance=None):
         self.app_name = 'py_embed_ingest'
         super().__init__(config, instance=instance)
diff --git a/metplus/wrappers/regrid_data_plane_wrapper.py b/metplus/wrappers/regrid_data_plane_wrapper.py
index c4f93f0a5..7761d600e 100755
--- a/metplus/wrappers/regrid_data_plane_wrapper.py
+++ b/metplus/wrappers/regrid_data_plane_wrapper.py
@@ -23,9 +23,13 @@
 @brief Wraps the MET tool regrid_data_plane to reformat gridded datasets
 @endcode
 '''
+
+
 class RegridDataPlaneWrapper(ReformatGriddedWrapper):
-    '''! Wraps the MET tool regrid_data_plane to reformat gridded datasets
-    '''
+    """! Wraps the MET tool regrid_data_plane to reformat gridded datasets"""
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
+
     def __init__(self, config, instance=None):
         self.app_name = 'regrid_data_plane'
         self.app_path = os.path.join(config.getdir('MET_BIN_DIR', ''),
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index aa652daca..a3eec69b3 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -57,9 +57,52 @@ def create_c_dict(self):
                                        f'{app_name_upper}_RUNTIME_FREQ',
                                        '').upper()
         )
+        self.validate_runtime_freq(c_dict)
 
         return c_dict
 
+    def validate_runtime_freq(self, c_dict):
+        """!Check and update RUNTIME_FREQ. If RUNTIME_FREQ is unset and a
+        default value is set by the wrapper, use that value. If
+        """
+        if not c_dict['RUNTIME_FREQ']:
+            # use default if there is one
+            if (hasattr(self, 'RUNTIME_FREQ_DEFAULT') and
+                    self.RUNTIME_FREQ_DEFAULT is not None):
+                c_dict['RUNTIME_FREQ'] = self.RUNTIME_FREQ_DEFAULT
+                return
+
+            # otherwise error
+            self.log_error(f'Must set {self.app_name.upper()}_RUNTIME_FREQ')
+            return
+
+        # error if invalid value is set
+        if c_dict['RUNTIME_FREQ'] not in self.FREQ_OPTIONS:
+            self.log_error(f"Invalid value for "
+                           f"{self.app_name.upper()}_RUNTIME_FREQ: "
+                           f"({c_dict['RUNTIME_FREQ']}) "
+                           f"Valid options include:"
+                           f" {', '.join(self.FREQ_OPTIONS)}")
+            return
+
+        # if list of supported frequencies are set by wrapper,
+        # warn and use default if frequency is not supported
+        if hasattr(self, 'RUNTIME_FREQ_SUPPORTED'):
+            if self.RUNTIME_FREQ_SUPPORTED == 'ALL':
+                return
+
+            if c_dict['RUNTIME_FREQ'] not in self.RUNTIME_FREQ_SUPPORTED:
+                err_msg = (f"{self.app_name.upper()}_RUNTIME_FREQ="
+                           f"{c_dict['RUNTIME_FREQ']} not supported.")
+                if hasattr(self, 'RUNTIME_FREQ_DEFAULT'):
+                    self.logger.warning(
+                        f"{err_msg} Using {self.RUNTIME_FREQ_DEFAULT}"
+                    )
+                    c_dict['RUNTIME_FREQ'] = self.RUNTIME_FREQ_DEFAULT
+                else:
+                    self.log_error(err_msg)
+                    return
+
     def get_input_templates(self, c_dict):
         app_upper = self.app_name.upper()
         template_dict = {}
@@ -94,14 +137,6 @@ def get_input_templates(self, c_dict):
         c_dict['TEMPLATE_DICT'] = template_dict
 
     def run_all_times(self):
-        if self.c_dict['RUNTIME_FREQ'] not in self.FREQ_OPTIONS:
-            self.log_error(f"Invalid value for "
-                           f"{self.app_name.upper()}_RUNTIME_FREQ: "
-                           f"({self.c_dict['RUNTIME_FREQ']}) "
-                           f"Valid options include:"
-                           f" {', '.join(self.FREQ_OPTIONS)}")
-            return None
-
         wrapper_instance_name = self.get_wrapper_instance_name()
         self.logger.info(f'Running wrapper: {wrapper_instance_name}')
 
diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index e1394f425..1a3d0ae9d 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -34,9 +34,12 @@
 from .plot_data_plane_wrapper import PlotDataPlaneWrapper
 from . import RuntimeFreqWrapper
 
+
 class SeriesAnalysisWrapper(RuntimeFreqWrapper):
     """!  Performs series analysis with filtering options
     """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
diff --git a/metplus/wrappers/stat_analysis_wrapper.py b/metplus/wrappers/stat_analysis_wrapper.py
index 180908f54..7011ef77e 100755
--- a/metplus/wrappers/stat_analysis_wrapper.py
+++ b/metplus/wrappers/stat_analysis_wrapper.py
@@ -27,6 +27,9 @@ class StatAnalysisWrapper(RuntimeFreqWrapper):
          ensemble_stat, and wavelet_stat
     """
 
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
         'METPLUS_OBTYPE',
@@ -176,23 +179,6 @@ def create_c_dict(self):
             c_dict['DATE_BEG'] = start_dt
             c_dict['DATE_END'] = end_dt
 
-        if not c_dict['RUNTIME_FREQ']:
-            # if start and end times are not equal and
-            # LOOP_ORDER = times (legacy), set frequency to once per init/valid
-            if (start_dt != end_dt and
-                    self.config.has_option('config', 'LOOP_ORDER') and
-                    self.config.getraw('config', 'LOOP_ORDER') == 'times'):
-                self.logger.warning(
-                    'LOOP_ORDER has been deprecated. Please set '
-                    'STAT_ANALYSIS_RUNTIME_FREQ = RUN_ONCE_PER_INIT_OR_VALID '
-                    'instead.'
-                )
-                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
-            else:
-                self.logger.debug('Setting RUNTIME_FREQ to RUN_ONCE. Set '
-                                  'STAT_ANALYSIS_RUNTIME_FREQ to override.')
-                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
-
         # read jobs from STAT_ANALYSIS_JOB<n> or legacy JOB_NAME/ARGS if unset
         c_dict['JOBS'] = self._read_jobs_from_config()
 
@@ -219,6 +205,27 @@ def create_c_dict(self):
 
         return self._c_dict_error_check(c_dict, all_field_lists_empty)
 
+    def validate_runtime_freq(self, c_dict):
+        """!Check and update RUNTIME_FREQ. Performs additional checks for
+        deprecated LOOP_ORDER=times setting before calling parent class
+        version of function. This function will eventually be removed.
+        """
+        if not c_dict['RUNTIME_FREQ']:
+            # if start and end times are not equal and
+            # LOOP_ORDER = times (legacy), set frequency to once per init/valid
+            start_dt, end_dt = get_start_and_end_times(self.config)
+            if (start_dt != end_dt and
+                    self.config.has_option('config', 'LOOP_ORDER') and
+                    self.config.getraw('config', 'LOOP_ORDER') == 'times'):
+                self.logger.warning(
+                    'LOOP_ORDER has been deprecated. Please set '
+                    'STAT_ANALYSIS_RUNTIME_FREQ = RUN_ONCE_PER_INIT_OR_VALID '
+                    'instead.'
+                )
+                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
+
+        super().validate_runtime_freq(c_dict)
+
     def run_at_time_once(self, time_input):
         """! Function called when processing all times.
 
diff --git a/metplus/wrappers/tc_diag_wrapper.py b/metplus/wrappers/tc_diag_wrapper.py
index 1b8ebd8a7..56bf83bcc 100755
--- a/metplus/wrappers/tc_diag_wrapper.py
+++ b/metplus/wrappers/tc_diag_wrapper.py
@@ -26,6 +26,8 @@
 
 
 class TCDiagWrapper(RuntimeFreqWrapper):
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_PER_INIT_OR_VALID']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
@@ -80,12 +82,6 @@ def create_c_dict(self):
         # skip RuntimeFreq wrapper logic to find files
         c_dict['FIND_FILES'] = False
 
-        if not c_dict['RUNTIME_FREQ']:
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
-        if c_dict['RUNTIME_FREQ'] != 'RUN_ONCE_PER_INIT_OR_VALID':
-            self.log_error('Only RUN_ONCE_PER_INIT_OR_VALID is supported for '
-                           'TC_DIAG_RUNTIME_FREQ.')
-
         # get command line arguments domain and tech id list for -data
         self._read_data_inputs(c_dict)
 
diff --git a/metplus/wrappers/tc_gen_wrapper.py b/metplus/wrappers/tc_gen_wrapper.py
index cdfc2f387..6f3a9a9f7 100755
--- a/metplus/wrappers/tc_gen_wrapper.py
+++ b/metplus/wrappers/tc_gen_wrapper.py
@@ -26,6 +26,8 @@
 
 
 class TCGenWrapper(RuntimeFreqWrapper):
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_INIT_FREQ',
@@ -109,7 +111,6 @@ def create_c_dict(self):
                                c_dict['VERBOSITY'])
         )
         c_dict['ALLOW_MULTIPLE_FILES'] = True
-        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
 
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('TCGenConfig_wrapped')
diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index 6b6087bc8..a95bd925c 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -42,6 +42,8 @@ class TCPairsWrapper(RuntimeFreqWrapper):
     """!Wraps the MET tool, tc_pairs to parse and match ATCF_by_pairs adeck and
        bdeck files.  Pre-processes extra tropical cyclone data.
     """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE'
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
@@ -97,8 +99,6 @@ def create_c_dict(self):
                                                  c_dict['VERBOSITY'])
         c_dict['ALLOW_MULTIPLE_FILES'] = True
 
-        self._handle_time_looping(c_dict)
-
         c_dict['MISSING_VAL_TO_REPLACE'] = (
             self.config.getstr('config',
                                'TC_PAIRS_MISSING_VAL_TO_REPLACE', '-99')
@@ -286,7 +286,7 @@ def create_c_dict(self):
 
         return c_dict
 
-    def _handle_time_looping(self, c_dict):
+    def validate_runtime_freq(self, c_dict):
         """!Figure out time looping configuration based on legacy config
          variables.
          READ_ALL_FILES: Only pass directories to tc_pairs and
@@ -304,14 +304,13 @@ def _handle_time_looping(self, c_dict):
                 self.logger.debug('TC_PAIRS_READ_ALL_FILES=True. '
                                   'Forcing TC_PAIRS_RUNTIME_FREQ=RUN_ONCE')
                 c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
-            return
 
         # check for settings that cause differences moving from v4.1 to v5.0
         # warn and update run setting to preserve old behavior
-        if (self.config.has_option('config', 'LOOP_ORDER') and
-            self.config.getstr_nocheck('config', 'LOOP_ORDER') == 'times' and
-            not (self.config.has_option('config', 'TC_PAIRS_RUN_ONCE') or
-                 self.config.has_option('config', 'TC_PAIRS_RUNTIME_FREQ'))):
+        elif (self.config.has_option('config', 'LOOP_ORDER') and
+              self.config.getstr_nocheck('config', 'LOOP_ORDER') == 'times' and
+              not (self.config.has_option('config', 'TC_PAIRS_RUN_ONCE') or
+                   self.config.has_option('config', 'TC_PAIRS_RUNTIME_FREQ'))):
             self.logger.warning(
                 'LOOP_ORDER has been deprecated. LOOP_ORDER has been set to '
                 '"times" and TC_PAIRS_RUNTIME_FREQ is not set. '
@@ -332,17 +331,12 @@ def _handle_time_looping(self, c_dict):
                                     'set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE '
                                     'to remove this warning')
                 c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
-                return
-
-            self.logger.warning('Setting TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH.'
-                                'Please remove TC_PAIRS_RUN_ONCE and '
-                                'set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH '
-                                'to remove this warning')
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
-
-        # set runtime frequency to RUN_ONCE if unset
-        if not c_dict['RUNTIME_FREQ']:
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE'
+            else:
+                self.logger.warning('Setting TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH.'
+                                    'Please remove TC_PAIRS_RUN_ONCE and '
+                                    'set TC_PAIRS_RUNTIME_FREQ=RUN_ONCE_FOR_EACH '
+                                    'to remove this warning')
+                c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
 
         # if runtime frequency set to run once for each time, check skip lead
         if c_dict['RUNTIME_FREQ'] == 'RUN_ONCE_FOR_EACH':
@@ -350,6 +344,8 @@ def _handle_time_looping(self, c_dict):
                 self.config.getbool('config', 'TC_PAIRS_SKIP_LEAD_SEQ', False)
             )
 
+        super().validate_runtime_freq(c_dict)
+
     def run_at_time_once(self, time_info):
         """! Create the arguments to run MET tc_pairs
 
diff --git a/metplus/wrappers/tc_stat_wrapper.py b/metplus/wrappers/tc_stat_wrapper.py
index 027637cd9..0a133a861 100755
--- a/metplus/wrappers/tc_stat_wrapper.py
+++ b/metplus/wrappers/tc_stat_wrapper.py
@@ -33,6 +33,8 @@ class TCStatWrapper(RuntimeFreqWrapper):
     """! Wrapper for the MET tool, tc_stat, which is used to filter tropical
          cyclone pair data.
     """
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_PER_INIT_OR_VALID']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_AMODEL',
@@ -111,8 +113,6 @@ def create_c_dict(self):
                                                  'LOG_TC_STAT_VERBOSITY',
                                                  c_dict['VERBOSITY'])
 
-        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
-
         c_dict['LOOKIN_DIR'] = self.config.getdir('TC_STAT_LOOKIN_DIR', '')
 
         # support LOOKIN_DIR and INPUT_DIR
diff --git a/metplus/wrappers/tcrmw_wrapper.py b/metplus/wrappers/tcrmw_wrapper.py
index 990e93f22..0f021e6e0 100755
--- a/metplus/wrappers/tcrmw_wrapper.py
+++ b/metplus/wrappers/tcrmw_wrapper.py
@@ -12,10 +12,10 @@
 
 import os
 
-from ..util import time_util
-from . import RuntimeFreqWrapper
+from ..util import ti_calculate, ti_get_hours_from_relativedelta
 from ..util import do_string_sub, skip_time, get_lead_sequence
 from ..util import parse_var_list, sub_var_list
+from . import RuntimeFreqWrapper
 
 '''!@namespace TCRMWWrapper
 @brief Wraps the TC-RMW tool
@@ -24,6 +24,8 @@
 
 
 class TCRMWWrapper(RuntimeFreqWrapper):
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_PER_INIT_OR_VALID'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_PER_INIT_OR_VALID']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_MODEL',
@@ -60,8 +62,6 @@ def create_c_dict(self):
                                                  c_dict['VERBOSITY'])
         c_dict['ALLOW_MULTIPLE_FILES'] = True
 
-        c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_PER_INIT_OR_VALID'
-
         # get the MET config file path or use default
         c_dict['CONFIG_FILE'] = self.get_config_file('TCRMWConfig_wrapped')
 
@@ -164,6 +164,8 @@ def create_c_dict(self):
         c_dict['VAR_LIST_TEMP'] = parse_var_list(self.config,
                                                  data_type='FCST',
                                                  met_tool=self.app_name)
+        if not c_dict['VAR_LIST_TEMP']:
+            self.log_error("Could not get field information from config.")
 
         return c_dict
 
@@ -198,87 +200,6 @@ def get_command(self):
         cmd += ' -v ' + self.c_dict['VERBOSITY']
         return cmd
 
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-              loops over the list of forecast leads and runs the
-               application for each.
-              Args:
-                @param input_dict dictionary containing timing information
-        """
-        for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            input_dict['custom'] = custom_string
-            time_info = time_util.ti_calculate(input_dict)
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            self.clear()
-            self.run_at_time_once(time_info)
-
-    def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run ascii2nc
-             Args:
-                @param time_info dictionary containing timing information
-        """
-        # get input files
-        if self.find_input_files(time_info) is None:
-            return
-
-        # get output path
-        if not self.find_and_check_output_file(time_info):
-            return
-
-        # get field information to set in MET config
-        if not self.set_data_field(time_info):
-            return
-
-        # get other configurations for command
-        self.set_command_line_arguments(time_info)
-
-        # set environment variables if using config file
-        self.set_environment_variables(time_info)
-
-        # build command and run
-        cmd = self.get_command()
-        if cmd is None:
-            self.log_error("Could not generate command")
-            return
-
-        self.build()
-
-    def set_data_field(self, time_info):
-        """!Get list of fields from config to process. Build list of field info
-            that are formatted to be read by the MET config file. Set DATA_FIELD
-            item of c_dict with the formatted list of fields.
-            Args:
-                @param time_info time dictionary to use for string substitution
-                @returns True if field list could be built, False if not.
-        """
-        field_list = sub_var_list(self.c_dict['VAR_LIST_TEMP'], time_info)
-        if not field_list:
-            self.log_error("Could not get field information from config.")
-            return False
-
-        all_fields = []
-        for field in field_list:
-            field_list = self.get_field_info(d_type='FCST',
-                                             v_name=field['fcst_name'],
-                                             v_level=field['fcst_level'],
-                                             )
-            if field_list is None:
-                return False
-
-            all_fields.extend(field_list)
-
-        data_field = ','.join(all_fields)
-        self.env_var_dict['METPLUS_DATA_FIELD'] = f'field = [{data_field}];'
-
-        return True
-
     def find_input_files(self, time_info):
         """!Get DECK file and list of input data files and set c_dict items.
             Args:
@@ -310,7 +231,7 @@ def find_input_files(self, time_info):
                 self.clear()
                 time_info['lead'] = lead
 
-                time_info = time_util.ti_calculate(time_info)
+                time_info = ti_calculate(time_info)
 
                 # get a list of the input data files,
                 # write to an ascii file if there are more than one
@@ -329,20 +250,57 @@ def find_input_files(self, time_info):
 
         self.infiles.append(list_file)
 
-        # set LEAD_LIST to list of forecast leads used
-        if lead_seq != [0]:
-            lead_list = []
-            for lead in lead_seq:
-                lead_hours = (
-                    time_util.ti_get_hours_from_relativedelta(lead,
-                                                              valid_time=time_info['valid'])
-                    )
-                lead_list.append(f'"{str(lead_hours).zfill(2)}"')
+        if not self._set_data_field(time_info):
+            return None
 
-            self.env_var_dict['METPLUS_LEAD_LIST'] = f"lead = [{', '.join(lead_list)}];"
+        self._set_lead_list(time_info, lead_seq)
 
         return self.infiles
 
+    def _set_data_field(self, time_info):
+        """!Get list of fields from config to process. Build list of field info
+            that are formatted to be read by the MET config file. Set DATA_FIELD
+            item of c_dict with the formatted list of fields.
+            Args:
+                @param time_info time dictionary to use for string substitution
+                @returns True if field list could be built, False if not.
+        """
+        field_list = sub_var_list(self.c_dict['VAR_LIST_TEMP'], time_info)
+        if not field_list:
+            self.log_error("Could not get field information from config.")
+            return False
+
+        all_fields = []
+        for field in field_list:
+            field_list = self.get_field_info(d_type='FCST',
+                                             v_name=field['fcst_name'],
+                                             v_level=field['fcst_level'],
+                                             )
+            if field_list is None:
+                self.log_error(f'Could not get field info from {field}')
+                return False
+
+            all_fields.extend(field_list)
+
+        data_field = ','.join(all_fields)
+        self.env_var_dict['METPLUS_DATA_FIELD'] = f'field = [{data_field}];'
+        return True
+
+    def _set_lead_list(self, time_info, lead_seq):
+        # set LEAD_LIST to list of forecast leads used
+        if lead_seq == [0]:
+            return
+
+        lead_list = []
+        for lead in lead_seq:
+            lead_hours = (
+                ti_get_hours_from_relativedelta(lead,
+                                                valid_time=time_info['valid'])
+            )
+            lead_list.append(f'"{str(lead_hours).zfill(2)}"')
+
+        self.env_var_dict['METPLUS_LEAD_LIST'] = f"lead = [{', '.join(lead_list)}];"
+
     def set_command_line_arguments(self, time_info):
         if self.c_dict['CONFIG_FILE']:
             config_file = do_string_sub(self.c_dict['CONFIG_FILE'],
diff --git a/metplus/wrappers/user_script_wrapper.py b/metplus/wrappers/user_script_wrapper.py
index aba672b69..dae9bdf0a 100755
--- a/metplus/wrappers/user_script_wrapper.py
+++ b/metplus/wrappers/user_script_wrapper.py
@@ -24,6 +24,9 @@
 
 
 class UserScriptWrapper(RuntimeFreqWrapper):
+    RUNTIME_FREQ_DEFAULT = None
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
     def __init__(self, config, instance=None):
         self.app_name = "user_script"
         super().__init__(config, instance=instance)

From 2bcda339122b1a6d89c3851d3b16ea800510cec1 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 16:18:09 -0600
Subject: [PATCH 47/55] error and return if start and end times cannot be read,
 e.g. if end time comes before start time

---
 metplus/wrappers/runtime_freq_wrapper.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index a3eec69b3..3f6edfd0c 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -183,6 +183,10 @@ def run_once(self, custom):
 
         # set init or valid to time if _BEG is equal to _END
         start_dt, end_dt = get_start_and_end_times(self.config)
+        if not start_dt:
+            self.log_error('Could not read begin and end times')
+            return None
+
         if start_dt == end_dt:
             loop_by = get_time_prefix(self.config)
             if loop_by:

From 8f308ff9d820a5bb4a02d8759e47600500f5c63a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 16:26:04 -0600
Subject: [PATCH 48/55] update config files to use current config options,
 ci-run-all-diff

---
 ...alysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py | 1 -
 .../met_tool_wrapper/TCPairs/TCPairs_extra_tropical.conf | 3 +--
 .../met_tool_wrapper/TCPairs/TCPairs_tropical.conf       | 4 +---
 ...ysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf | 6 ++----
 ...lative_SeriesByLead_PyEmbed_Multiple_Diagnostics.conf | 5 ++---
 .../METdbLoad_fcstFV3_obsGoes_BrightnessTemp.conf        | 4 ++--
 ...CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf | 9 ++++-----
 .../tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf  | 2 +-
 8 files changed, 13 insertions(+), 21 deletions(-)

diff --git a/docs/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py b/docs/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py
index 5cac8f53c..4ff1b3526 100644
--- a/docs/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py
+++ b/docs/use_cases/model_applications/medium_range/MTD_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.py
@@ -190,7 +190,6 @@
 # .. note::
 #
 #   * MediumRangeAppUseCase
-#   * TCPairsToolUseCase
 #   * SeriesByLeadUseCase
 #   * MTDToolUseCase
 #   * RegridDataPlaneToolUseCase
diff --git a/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_extra_tropical.conf b/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_extra_tropical.conf
index 23c81e647..e2db24760 100644
--- a/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_extra_tropical.conf
+++ b/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_extra_tropical.conf
@@ -31,7 +31,7 @@ INIT_BEG = 2014121318
 INIT_END = 2014121318
 INIT_INCREMENT = 21600
 
-TC_PAIRS_RUN_ONCE = True
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
 
 
 ###
@@ -59,7 +59,6 @@ TC_PAIRS_SKIP_IF_OUTPUT_EXISTS = yes
 TC_PAIRS_SKIP_IF_REFORMAT_EXISTS = yes
 
 TC_PAIRS_READ_ALL_FILES = no
-#TC_PAIRS_SKIP_LEAD_SEQ = False
 
 TC_PAIRS_REFORMAT_DECK = yes
 TC_PAIRS_REFORMAT_TYPE = SBU
diff --git a/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_tropical.conf b/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_tropical.conf
index ab9d64900..2df99931c 100644
--- a/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_tropical.conf
+++ b/parm/use_cases/met_tool_wrapper/TCPairs/TCPairs_tropical.conf
@@ -31,9 +31,7 @@ INIT_BEG = 2018083006
 INIT_END = 2018083018
 INIT_INCREMENT = 21600
 
-#TC_PAIRS_SKIP_LEAD_SEQ = False
-
-TC_PAIRS_RUN_ONCE = False
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE_FOR_EACH
 
 
 ###
diff --git a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
index dd0fc4827..23af3130e 100644
--- a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
+++ b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
@@ -28,8 +28,6 @@ PROCESS_LIST = TCPairs, TCStat, ExtractTiles, TCStat(for_series_analysis), Serie
 LOOP_BY = INIT
 INIT_TIME_FMT = %Y%m%d
 INIT_BEG = 20141214
-INIT_END = 20141214
-INIT_INCREMENT = 21600 ;; set to every 6 hours=21600 seconds
 
 LEAD_SEQ_1 = begin_end_incr(0,18,6)
 LEAD_SEQ_1_LABEL = Day1
@@ -37,6 +35,8 @@ LEAD_SEQ_1_LABEL = Day1
 LEAD_SEQ_2 = begin_end_incr(24,42,6)
 LEAD_SEQ_2_LABEL = Day2
 
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
+
 
 ###
 # File I/O
@@ -109,8 +109,6 @@ BOTH_VAR1_LEVELS = Z2
 # https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#tcpairs
 ###
 
-TC_PAIRS_SKIP_LEAD_SEQ = True
-
 TC_PAIRS_INIT_INCLUDE =
 TC_PAIRS_INIT_EXCLUDE =
 
diff --git a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.conf b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.conf
index 6cf9ba3c7..ea00e6493 100644
--- a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.conf
+++ b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead_PyEmbed_Multiple_Diagnostics.conf
@@ -33,6 +33,7 @@ INIT_INCREMENT = 21600
 
 LEAD_SEQ = 90, 96, 102, 108, 114
 
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
 SERIES_ANALYSIS_RUNTIME_FREQ = RUN_ONCE_PER_LEAD
 
 SERIES_ANALYSIS_RUN_ONCE_PER_STORM_ID = False
@@ -60,7 +61,7 @@ TC_PAIRS_REFORMAT_DIR = {OUTPUT_BASE}/track_data_atcf
 TC_PAIRS_SKIP_IF_REFORMAT_EXISTS = no
 
 TC_PAIRS_OUTPUT_DIR = {OUTPUT_BASE}/tc_pairs
-TC_PAIRS_OUTPUT_TEMPLATE = {date?fmt=%Y%m}/{basin?fmt=%s}q{date?fmt=%Y%m%d%H}.dorian
+TC_PAIRS_OUTPUT_TEMPLATE = {basin?fmt=%s}q{INIT_BEG}.dorian
 TC_PAIRS_SKIP_IF_OUTPUT_EXISTS = no
 
 
@@ -169,8 +170,6 @@ PY_EMBED_INGEST_2_OUTPUT_GRID = {MODEL_DIR}/{valid?fmt=%Y%m%d}/gfs_4_{valid?fmt=
 # https://metplus.readthedocs.io/en/latest/Users_Guide/wrappers.html#tcpairs
 ###
 
-TC_PAIRS_SKIP_LEAD_SEQ = True
-
 TC_PAIRS_INIT_INCLUDE =
 TC_PAIRS_INIT_EXCLUDE =
 
diff --git a/parm/use_cases/model_applications/short_range/METdbLoad_fcstFV3_obsGoes_BrightnessTemp.conf b/parm/use_cases/model_applications/short_range/METdbLoad_fcstFV3_obsGoes_BrightnessTemp.conf
index 3ac50c4d4..35cb1522c 100644
--- a/parm/use_cases/model_applications/short_range/METdbLoad_fcstFV3_obsGoes_BrightnessTemp.conf
+++ b/parm/use_cases/model_applications/short_range/METdbLoad_fcstFV3_obsGoes_BrightnessTemp.conf
@@ -28,8 +28,8 @@ PROCESS_LIST = METDbLoad
 LOOP_BY = VALID
 
 VALID_TIME_FMT = %Y%m%d%H
-VALID_BEG = 2019052112
-VALID_END = 2019052100
+VALID_BEG = 2019052100
+VALID_END = 2019052112
 VALID_INCREMENT = 12H
 
 MET_DB_LOAD_RUNTIME_FREQ = RUN_ONCE
diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf b/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
index 1e3b3fc45..807619631 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/CyclonePlotter_fcstGFS_obsGFS_UserScript_ExtraTC.conf
@@ -26,12 +26,11 @@ PROCESS_LIST = UserScript, TCPairs, CyclonePlotter
 ###
 
 LOOP_BY = INIT
-INIT_TIME_FMT = %Y%m%d%H
-INIT_BEG = 2020100700
-INIT_END = 2020100700
-INIT_INCREMENT = 21600
+INIT_TIME_FMT = %Y%m%d
+INIT_BEG = 20201007
 
-USER_SCRIPT_RUNTIME_FREQ = RUN_ONCE_PER_INIT_OR_VALID
+USER_SCRIPT_RUNTIME_FREQ = RUN_ONCE
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
 
 
 ###
diff --git a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
index 4825cd7a8..52f2e39ac 100644
--- a/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
+++ b/parm/use_cases/model_applications/tc_and_extra_tc/Plotter_fcstGFS_obsGFS_ExtraTC.conf
@@ -29,7 +29,7 @@ LOOP_BY = init
 INIT_TIME_FMT = %Y%m
 INIT_BEG = 201503
 
-TC_PAIRS_RUN_ONCE = True
+TC_PAIRS_RUNTIME_FREQ = RUN_ONCE
 
 
 ###

From 74e52bd96c4808e495fc8dc461cfd6aecf0bcdac Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 15 Aug 2023 16:34:28 -0600
Subject: [PATCH 49/55] fixed bug  when beg/end times are not set and aren't
 needed, ci-run-all-diff

---
 metplus/wrappers/runtime_freq_wrapper.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 3f6edfd0c..127fd9a20 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -183,11 +183,7 @@ def run_once(self, custom):
 
         # set init or valid to time if _BEG is equal to _END
         start_dt, end_dt = get_start_and_end_times(self.config)
-        if not start_dt:
-            self.log_error('Could not read begin and end times')
-            return None
-
-        if start_dt == end_dt:
+        if start_dt and start_dt == end_dt:
             loop_by = get_time_prefix(self.config)
             if loop_by:
                 time_input[loop_by.lower()] = start_dt

From b9eef8f6404bd47e50e39961c1cf737265b83751 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 16 Aug 2023 09:02:16 -0600
Subject: [PATCH 50/55] fix use case reference to init time

---
 ...iesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
index 23af3130e..c73754b67 100644
--- a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
+++ b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
@@ -211,7 +211,7 @@ EXTRACT_TILES_LAT_ADJ = 15
 # the value set outside of this section
 [for_series_analysis]
 
-TC_STAT_JOB_ARGS = -job filter -init_beg {INIT_BEG} -init_end {INIT_END} -dump_row {TC_STAT_OUTPUT_DIR}/{TC_STAT_DUMP_ROW_TEMPLATE}
+TC_STAT_JOB_ARGS = -job filter -init_beg {init?fmt=%Y%m%d_%H} -init_end {init?fmt=%Y%m%d_%H} -dump_row {TC_STAT_OUTPUT_DIR}/{TC_STAT_DUMP_ROW_TEMPLATE}
 
 TC_STAT_OUTPUT_DIR = {SERIES_ANALYSIS_OUTPUT_DIR}
 TC_STAT_LOOKIN_DIR = {EXTRACT_TILES_OUTPUT_DIR}

From 75da7abe9bc9ee2f6b2cc612dbeb27b5efe34c88 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 16 Aug 2023 11:40:26 -0600
Subject: [PATCH 51/55] update contrib guide

---
 docs/Contributors_Guide/basic_components.rst | 176 +++++++++++++++----
 docs/Contributors_Guide/create_wrapper.rst   | 108 ++++--------
 docs/Contributors_Guide/deprecation.rst      |  71 ++++----
 3 files changed, 213 insertions(+), 142 deletions(-)

diff --git a/docs/Contributors_Guide/basic_components.rst b/docs/Contributors_Guide/basic_components.rst
index 441bb9320..34fbfce51 100644
--- a/docs/Contributors_Guide/basic_components.rst
+++ b/docs/Contributors_Guide/basic_components.rst
@@ -4,15 +4,13 @@
 Basic Components of METplus Python Wrappers
 *******************************************
 
-CommandBuilder
-==============
+.. _bc_class_hierarchy:
+
+Class Hierarchy
+===============
 
-CommandBuilder is the parent class of all METplus wrappers.
-Every wrapper is a subclass of CommandBuilder or
-another subclass of CommandBuilder.
-For example, GridStatWrapper, PointStatWrapper, EnsembleStatWrapper,
-and MODEWrapper are all subclasses of CompareGriddedWrapper.
-CompareGriddedWrapper is a subclass of CommandBuilder.
+**CommandBuilder** is the parent class of all METplus wrappers.
+Every wrapper is a subclass of CommandBuilder or a subclass of CommandBuilder.
 CommandBuilder contains instance variables that are common to every wrapper,
 such as config (METplusConfig object), errors (a counter of the number of
 errors that have occurred in the wrapper), and
@@ -20,6 +18,105 @@ c_dict (a dictionary containing common information).
 CommandBuilder also contains use class functions that can be called within
 each wrapper, such as create_c_dict, clear, and find_data.
 
+**RuntimeFreqWrapper** is a subclass of **CommandBuilder** that contains all
+of the logic to handle time looping.
+See :ref:`Runtime_Freq` for more information on time looping.
+Unless a wrapper is very basic and does not need to loop over time, then
+the wrapper should inherit directly or indirectly from **RuntimeFreqWrapper**.
+
+**LoopTimesWrapper** is a subclass of **RuntimeFreqWrapper**.
+This wrapper simply sets the default runtime frequency to **RUN_ONCE_FOR_EACH**
+for its subclasses.
+
+**CompareGriddedWrapper** is a subclass of **LoopTimesWrapper** that contains
+functions that are common to multiple wrappers that compare forecast (FCST)
+and observation (OBS) data. Subclasses of this wrapper include
+**GridStatWrapper**, **PointStatWrapper**, **EnsembleStatWrapper**,
+**MODEWrapper**, and **MTDWrapper**.
+
+**MTDWrapper** in an exception from the rest of the **CompareGriddeWrapper**
+subclasses because it typically runs once for each init or valid time and
+reads and processes all forecast leads at once. This wrapper inherits from
+**CompareGriddedWrapper** because it still uses many of its functions.
+
+
+.. _bc_class_vars:
+
+Class Variables
+===============
+
+RUNTIME_FREQ_DEFAULT
+--------------------
+
+Wrappers that inherit from **RuntimeFreqWrapper** should include a class
+variable called **RUNTIME_FREQ_DEFAULT** that lists the default runtime
+frequency that should be used if it is not explicitly defined in the METplus
+configuration.
+
+Example::
+
+    RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
+
+If no clear default value exists, then *None* can be set in place of a string.
+The **UserScriptWrapper** wrapper is an example::
+
+    RUNTIME_FREQ_DEFAULT = None
+
+
+RUNTIME_FREQ_SUPPORTED
+----------------------
+
+Wrappers that inherit from **RuntimeFreqWrapper** should include a class
+variable called **RUNTIME_FREQ_SUPPORTED**  that defines the a list of the
+runtime frequency settings that are supported by the wrapper. Example::
+
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_PER_INIT_OR_VALID']
+
+If all runtime frequency values are supported by the wrapper, then the string
+*'ALL'* can be set instead of a list of strings::
+
+    RUNTIME_FREQ_SUPPORTED = 'ALL'
+
+
+WRAPPER_ENV_VAR_KEYS
+--------------------
+
+This class variable lists all of the environment variables that are set by
+the wrapper. These variables are typically referenced in the wrapped MET
+config file for the tool and are named with a *METPLUS\_* prefix.
+All of the variables that are referenced in the wrapped MET config file must
+be listed here so that they will always be set to prevent an error when MET
+reads the config file. An empty string will be set if they are not set to
+another value by the wrapper.
+
+DEPRECATED_WRAPPER_ENV_VAR_KEYS
+--------------------------------
+
+(Optional)
+This class variable lists any environment variables that were
+previously set by the wrapper and referenced in an old version of the
+wrapped MET config file.
+This list serves as a developer reference of the variables that were
+previously used but are now deprecated. When support for setting these
+variables are eventually removed, then the values in this list should also
+be removed.
+
+Flags
+-----
+
+(Optional)
+For wrappers that set a dictionary of flags in the wrapped MET config file,
+class variables that contain a list of variable names can be defined.
+This makes it easier to add/change these variables.
+
+The list is read by the **self.handle_flags** function.
+The name of the variable corresponds to the argument passed to the function.
+For example, **EnsembleStatWrapper** includes **OUTPUT_FLAGS** and a call
+to **self.handle_flags('OUTPUT')**.
+
+Existing \*_FLAG class variables include **OUTPUT_FLAGS**, **NC_PAIRS_FLAGS**, **NC_ORANK_FLAGS**, and **ENSEMBLE_FLAGS**.
+
+
 .. _bc_init_function:
 
 Init Function
@@ -116,45 +213,62 @@ wrappers in the process list are initialized correctly.
 
 See MODEWrapper (ush/mode_wrapper.py) for other examples.
 
+.. _bc_run_at_time_once:
 
-run_at_time function
-====================
+run_at_time_once function
+=========================
 
-run_at_time runs a process for one specific time.
-This is defined in CommandBuilder.
+**run_at_time_once** runs a process for one specific time. The time depends
+on the value of {APP_NAME}_RUNTIME_FREQ. Most wrappers run once per each
+init or valid and forecast lead time. This function is often defined in each
+wrapper to handle command setup specific to the wrapper. There is a generic
+version of the function in **runtime_freq_wrapper.py** that can be used by
+other wrappers:
 
 .. code-block:: python
 
-    def run_at_time(self, input_dict):
-        """! Loop over each forecast lead and build pb2nc command """
-         # loop of forecast leads and process each
-        lead_seq = util.get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            input_dict['lead'] = lead
+    def run_at_time_once(self, time_info):
+        """! Process runtime and try to build command to run. Most wrappers
+        should be able to call this function to perform all of the actions
+        needed to build the commands using this template. This function can
+        be overridden if necessary.
 
-            lead_string = time_util.ti_calculate(input_dict)['lead_string']
-            self.logger.info("Processing forecast lead {}".format(lead_string))
+        @param time_info dictionary containing timing information
+        @returns True if command was built/run successfully or
+         False if something went wrong
+        """
+        # get input files
+        if not self.find_input_files(time_info):
+            return False
 
-            # Run for given init/valid time and forecast lead combination
-            self.run_at_time_once(input_dict)
+        # get output path
+        if not self.find_and_check_output_file(time_info):
+            return False
 
-See ush/pb2nc_wrapper.py for an example.
+        # get other configurations for command
+        self.set_command_line_arguments(time_info)
+
+        # set environment variables if using config file
+        self.set_environment_variables(time_info)
+
+        # build command and run
+        return self.build()
+
+Typically the **find_input_files** and **set_command_line_arguments**
+functions need to be implemented in the wrapper to handle the wrapper-specific
+functionality.
 
 run_all_times function
 ======================
 
-run_all_times loops over a series of times calling run_at_time for one
-process for each time. Defined in CommandBuilder but overridden in
-wrappers that process all of the data from every run time at once.
-
-See SeriesByLeadWrapper (ush/series_by_lead_wrapper.py) for an example of
-overriding the function.
+If a wrapper is not inheriting from RuntimeFreqWrapper or one of its child
+classes, then the **run_all_times** function can be implemented in the wrapper.
+This function is called when the wrapper is called.
 
 get_command function
 ====================
 
-get_command assembles a MET command with arguments that can be run via the
-shell or the wrapper.
+**get_command** assembles the command that will be run.
 It is defined in CommandBuilder but is overridden in most wrappers because
 the command line arguments differ for each MET tool.
 
diff --git a/docs/Contributors_Guide/create_wrapper.rst b/docs/Contributors_Guide/create_wrapper.rst
index d9849dcc2..f5280e3a1 100644
--- a/docs/Contributors_Guide/create_wrapper.rst
+++ b/docs/Contributors_Guide/create_wrapper.rst
@@ -7,7 +7,7 @@ Naming
 File Name
 ^^^^^^^^^
 
-Create the new wrapper in the *METplus/metplus/wrappers* directory and
+Create the new wrapper in the *metplus/wrappers* directory and
 name it to reflect the wrapper's function, e.g.: new_tool_wrapper.py is
 a wrapper around an application named "new_tool."
 Copy the **example_wrapper.py** to start the process.
@@ -65,12 +65,12 @@ Naming
 ^^^^^^
 
 Rename the class to match the wrapper's class from the above sections.
-Most wrappers should be a subclass of the CommandBuilder wrapper::
+Most wrappers should be a subclass of the RuntimeFreqWrapper::
 
-    class NewToolWrapper(CommandBuilder)
+    class NewToolWrapper(RuntimeFreqWrapper)
 
-The text 'CommandBuilder' in parenthesis makes NewToolWrapper a subclass
-of CommandBuilder.
+The text *RuntimeFreqWrapper* in parenthesis makes NewToolWrapper a subclass
+of RuntimeFreqWrapper.
 
 Find and replace can be used to rename all instances of the wrapper name in
 the file. For example, to create IODA2NC wrapper from ASCII2NC, replace
@@ -85,7 +85,18 @@ Parent Class
 If the new tool falls under one of the existing tool categories,
 then make the tool a subclass of one of the existing classes.
 This should only be done if the functions in the parent class are needed
-by the new wrapper. When in doubt, use the CommandBuilder.
+by the new wrapper. When in doubt, use the **RuntimeFreqWrapper**.
+
+See :ref:`bc_class_hierarchy` for more information on existing classes to
+determine which class to use as the parent class.
+
+Class Variables for Runtime Frequency
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+**RUNTIME_FREQ_DEFAULT** and **RUNTIME_FREQ_SUPPORTED** should be set for all
+wrappers that inherit from **RuntimeFreqWrapper**.
+
+See :ref:`bc_class_vars` for more information.
 
 Init Function
 ^^^^^^^^^^^^^
@@ -142,69 +153,20 @@ then the wrapper will produce an error and not build the command.
 Run Functions
 ^^^^^^^^^^^^^
 
-* Override the run_at_time method if the wrapper will be called once for each
-  valid or init time specified in the configuration file.
-  If the wrapper will loop over each forecast lead
-  (LEAD_SEQ in the METplus config file) and process once for each, then
-  override run_at_time with the following method and put the logic to build
-  the MET command for each run in a run_at_time_once method::
-
-    def run_at_time(self, input_dict):
-        """! Runs the MET application for a given run time. This function
-        loops over the list of forecast leads and runs the application for
-        each.
-          @param input_dict dictionary containing timing information
-          @returns None
-          """
-        lead_seq = util.get_lead_sequence(self.config, input_dict)
-            for lead in lead_seq:
-            self.clear()
-            input_dict['lead'] = lead
-
-            time_info = time_util.ti_calculate(input_dict)
-            for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
-                if custom_string:
-                    self.logger.info(f"Processing custom string: {custom_string}")
-
-                time_info['custom'] = custom_string
-
-                self.run_at_time_once(time_info)
-
-    def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run ascii2nc
-                @param time_info dictionary containing timing information
-        """
-        # get input files
-        if self.find_input_files(time_info) is None:
-            return
-
-        # get output path
-        if not self.find_and_check_output_file(time_info):
-            return
-
-        # get other configurations for command
-        self.set_command_line_arguments(time_info)
-
-        # set environment variables if using config file
-        self.set_environment_variables(time_info)
-
-        # build command and run
-        self.build_and_run_command()
-
-
-If the wrapper will not loop and process for each forecast lead,
-put the logic to build the command in the run_at_time method.
+* The **run_at_time_once** function or some the functions that it calls will
+  need to be overridden in the wrapper.
+  See :ref:`bc_run_at_time_once` for more information.
 
-* It is recommended to divide up the logic into components, as illustrated
-  above, to make the code more readable and easier to test.
+* It is recommended to divide up the logic into small functions to make
+  the code more readable and easier to test.
 
 * The function self.set_environment_variables should be called by all
-  wrappers even if the MET tool does not have a config file. This is done
-  to set environment variables that MET expects to be set when running, such
-  as MET_TMP_DIR and MET_PYTHON_EXE. If no environment variables need to be
-  set specific to the wrapper, then no
-  implementation of the function in the wrapper needs to be written.
-  Call the
+  wrappers even if the MET tool does not have a config file.
+  This function is typically called from the run_at_time_once function.
+  This is done to set environment variables that MET expects to be set when
+  running, such as MET_TMP_DIR and MET_PYTHON_EXE.
+  If no environment variables need to be set specific to the wrapper, then no
+  implementation of the function in the wrapper needs to be written. Call the
   implementation of the function from CommandBuilder, which sets the
   environment variables defined in the [user_env_vars] section of the
   configuration file and outputs DEBUG logs for each environment variable
@@ -212,7 +174,7 @@ put the logic to build the command in the run_at_time method.
   each wrapper.
 
 * Once all the necessary information has been provided to create the MET
-  command, call self.build_and_run_command(). This calls self.get_command()
+  command, call self.build(). This calls self.get_command()
   to assemble the command and verify that the command wrapper generated
   contains all of the required arguments. The get_command() in the wrapper
   may need to be overridden if the MET application is different from
@@ -224,7 +186,9 @@ put the logic to build the command in the run_at_time method.
 
 * Call self.clear() at the beginning of each loop iteration that tries to
   build/run a MET command to prevent inadvertently reusing/re-running
-  commands that were previously created.
+  commands that were previously created. This is called in the RuntimeFreq
+  wrapper before each call to run_at_time_once, but an additional call may be
+  needed if multiple commands are built and run in this function.
 
 * To allow the use case to use the specific wrapper, assign the wrapper name to
   PROCESS_LIST::
@@ -262,12 +226,12 @@ put the logic to build the command in the run_at_time method.
   documentation for that use case and a README file to create a header for
   the documentation page.
 
-This new uuse case/example configuration file is located in a directory structure
+This new use case/example configuration file is located in a directory structure
 like the following::
 
-    METplus/parm/use_cases/met_tool_wrapper/NewTool/NewTool.conf
-    METplus/docs/use_cases/met_tool_wrapper/NewTool/NewTool.py
-    METplus/docs/use_cases/met_tool_wrapper/NewTool/README.md
+    parm/use_cases/met_tool_wrapper/NewTool/NewTool.conf
+    docs/use_cases/met_tool_wrapper/NewTool/NewTool.py
+    docs/use_cases/met_tool_wrapper/NewTool/README.rst
 
 Note the documentation file is in METplus/docs while the use case conf file
 is in METplus/parm.
diff --git a/docs/Contributors_Guide/deprecation.rst b/docs/Contributors_Guide/deprecation.rst
index 6c6d63e2f..1703d7a2c 100644
--- a/docs/Contributors_Guide/deprecation.rst
+++ b/docs/Contributors_Guide/deprecation.rst
@@ -26,60 +26,53 @@ wrong variable and it is using WGRIB2 = wgrib2.
 
 check_for_deprecated_config()
 -----------------------------
-In **metplus/util/config_metplus.py** there is a function called
-check_for_deprecated_config. It contains a dictionary of dictionaries
-called deprecated_dict that specifies the old config name, the section
-it was found in, and a suggested alternative (None if no alternative
-exists).
+In **metplus/util/constants.py** there is a dictionary called
+DEPRECATED_DICT that specifies the old config name as the key.
+The value is a dictionary of info that is used to help users update their
+config files.
+
+* **alt**: optional suggested alternative name for the deprecated config.
+  This can be a single variable name or text to describe multiple variables
+  or how to handle it.
+  Set to None or leave unset to tell the user to just remove the variable.
+* **copy**: optional item (defaults to True). Set this to False if one
+  cannot simply replace the deprecated variable name with the value in *alt*.
+  If True, easy-to-run sed commands are generated to help replace variables.
+* **upgrade**: optional item where the value is a keyword that will output
+  additional instructions for the user, e.g. *ensemble*.
+
+If any of these old variables are found in any config file passed to
+METplus by the user, an error report will be displayed with the old
+variables and suggested new ones if applicable.
 
 **Example 1**
 ::
 
-'WGRIB2_EXE' : {'sec' : 'exe', 'alt' : 'WGRIB2'}
+'WGRIB2_EXE' : {'alt' : 'WGRIB2'}
 
-This says that WGRIB2_EXE was found in the [exe] section and should
-be replaced with WGRIB2.
+This means WGRIB2_EXE was found in the config and should be replaced with WGRIB2.
 
 **Example 2**
 ::
 
-'PREPBUFR_DIR_REGEX' : {'sec' : 'regex_pattern', 'alt' : None}
-
-This says that [regex_pattern] PREPBUFR_DIR_REGEX is no longer used
-and there is no alternative (because the wrapper uses filename
-templates instead of regex now).
-
+'PREPBUFR_DIR_REGEX' : {'alt' : None}
 
-If any of these old variables are found in any config file passed to
-METplus by the user, an error report will be displayed with the old
-variables and suggested new ones if applicable.
+This means PREPBUFR_DIR_REGEX is no longer used and there is no alternative.
+The variable can simply be removed from the config file.
 
-If support for an old config variable is temporarily needed, the
-user should be warned to update their config file because the
-variable will be phased out in the future. In this case, add the
-‘req’ item to the dictionary and set it to False.  This will provide
-a warning to the user but will not stop the execution of the code.
-If this is done, be sure to modify the code to check for the new
-config variable, and if it is not set, check the old config variable
-to see if it is set. 
-
-**Example**
+**Example 3**
 ::
 
-'LOOP_METHOD' : {'sec' : 'config', 'alt' : 'LOOP_ORDER', 'req' : False}
-
-This says that [config] LOOP_METHOD is deprecated and the user
-should use LOOP_ORDER, but it is not required to change
-immediately. If this is done, it is important to
-check for LOOP_ORDER and then
-check for LOOP_METHOD if it is not set.
+'SOME_VAR' : {'alt': 'OTHER_VAR', 'copy' : None}
 
-In run_metplus.py:
+This means SOME_VAR is no longer used. OTHER_VAR is the variable that should
+be set instead, but the value must change slightly.
+The variable name SOME_VAR cannot simply be replaced with OTHER_VAR.
 
+**Example 4**
 ::
 
-    loop_order = config.getstr('config', 'LOOP_ORDER', '')
-    if loop_order == '':
-        loop_order = config.getstr('config', 'LOOP_METHOD')
-
+'ENSEMBLE_STAT_ENSEMBLE_FLAG_LATLON': {'upgrade': 'ensemble'},
 
+This means that ENSEMBLE_STAT_ENSEMBLE_FLAG_LATLON is no longer used and can
+be removed. Additional text will be output to describe how to upgrade.

From 407aba4a91014fa615f5e1f40061cb926fddf173 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 16 Aug 2023 12:00:13 -0600
Subject: [PATCH 52/55] clean up contrib guide additions

---
 docs/Contributors_Guide/basic_components.rst | 25 ++++++++++++--------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/docs/Contributors_Guide/basic_components.rst b/docs/Contributors_Guide/basic_components.rst
index 34fbfce51..6ac70dbcf 100644
--- a/docs/Contributors_Guide/basic_components.rst
+++ b/docs/Contributors_Guide/basic_components.rst
@@ -58,6 +58,8 @@ Example::
     RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
 
 If no clear default value exists, then *None* can be set in place of a string.
+This means that a use case will report an error if the frequency is not
+defined in the METplus configuration file.
 The **UserScriptWrapper** wrapper is an example::
 
     RUNTIME_FREQ_DEFAULT = None
@@ -161,16 +163,17 @@ create_c_dict (ExampleWrapper)::
     def create_c_dict(self):
         c_dict = super().create_c_dict()
         # get values from config object and set them to be accessed by wrapper
-        c_dict['INPUT_TEMPLATE'] = self.config.getraw('filename_templates',
-                                                      'EXAMPLE_INPUT_TEMPLATE', '')
+        c_dict['INPUT_TEMPLATE'] = self.config.getraw('config',
+                                                      'EXAMPLE_INPUT_TEMPLATE')
         c_dict['INPUT_DIR'] = self.config.getdir('EXAMPLE_INPUT_DIR', '')
 
-        if c_dict['INPUT_TEMPLATE'] == '':
-            self.logger.info('[filename_templates] EXAMPLE_INPUT_TEMPLATE was not set. '
-                             'You should set this variable to see how the runtime is '
-                             'substituted. For example: {valid?fmt=%Y%m%d%H}.ext')
+        if not c_dict['INPUT_TEMPLATE']:
+            self.logger.info('EXAMPLE_INPUT_TEMPLATE was not set. '
+                             'You should set this variable to see how the '
+                             'runtime is substituted. '
+                             'For example: {valid?fmt=%Y%m%d%H}.ext')
 
-        if c_dict['INPUT_DIR'] == '':
+        if not c_dict['INPUT_DIR']:
             self.logger.debug('EXAMPLE_INPUT_DIR was not set')
 
         return c_dict
@@ -192,7 +195,7 @@ create_c_dict (CommandBuilder)::
 isOK class variable
 ===================
 
-isOK is defined in CommandBuilder (ush/command_builder.py).
+isOK is defined in CommandBuilder (metplus/wrappers/command_builder.py).
 
 Its function is to note a failed process while not stopping a parent process.
 Instead of instantly exiting a larger wrapper script once one subprocess has
@@ -203,16 +206,18 @@ At the end of the wrapper initialization step, all isOK=false will be
 collected and reported. Execution of the wrappers will not occur unless all
 wrappers in the process list are initialized correctly.
 
+The **self.log_error** function logs an error and sets self.isOK to False, so
+it is not necessary to set *self.isOK = False* if this function is called.
+
 .. code-block:: python
 
     c_dict['CONFIG_FILE'] = self.config.getstr('config', 'MODE_CONFIG_FILE', '')
     if not c_dict['CONFIG_FILE']:
         self.log_error('MODE_CONFIG_FILE must be set')
+    if something_else_goes_wrong:
         self.isOK = False
 
 
-See MODEWrapper (ush/mode_wrapper.py) for other examples.
-
 .. _bc_run_at_time_once:
 
 run_at_time_once function

From cef425de14ba8297b4d968913fc7eca42e1f3ab0 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 16 Aug 2023 12:18:12 -0600
Subject: [PATCH 53/55] change supported runtime frequency values for wrappers
 that need enhancements to actually support running different frequencies

---
 metplus/wrappers/ascii2nc_wrapper.py       |  2 +-
 metplus/wrappers/example_wrapper.py        |  2 +-
 metplus/wrappers/gempak_to_cf_wrapper.py   |  2 +-
 metplus/wrappers/gen_vx_mask_wrapper.py    |  2 +-
 metplus/wrappers/plot_point_obs_wrapper.py | 24 ----------------------
 5 files changed, 4 insertions(+), 28 deletions(-)

diff --git a/metplus/wrappers/ascii2nc_wrapper.py b/metplus/wrappers/ascii2nc_wrapper.py
index df875575e..4cb65ffb7 100755
--- a/metplus/wrappers/ascii2nc_wrapper.py
+++ b/metplus/wrappers/ascii2nc_wrapper.py
@@ -25,7 +25,7 @@
 class ASCII2NCWrapper(LoopTimesWrapper):
 
     RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
-    RUNTIME_FREQ_SUPPORTED = 'ALL'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     WRAPPER_ENV_VAR_KEYS = [
         'METPLUS_TIME_SUMMARY_DICT',
diff --git a/metplus/wrappers/example_wrapper.py b/metplus/wrappers/example_wrapper.py
index d5290320a..1802ee01f 100755
--- a/metplus/wrappers/example_wrapper.py
+++ b/metplus/wrappers/example_wrapper.py
@@ -20,7 +20,7 @@
 class ExampleWrapper(LoopTimesWrapper):
 
     RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
-    RUNTIME_FREQ_SUPPORTED = 'ALL'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     """!Wrapper can be used as a base to develop a new wrapper"""
     def __init__(self, config, instance=None):
diff --git a/metplus/wrappers/gempak_to_cf_wrapper.py b/metplus/wrappers/gempak_to_cf_wrapper.py
index 2270a703a..f0ddd57a6 100755
--- a/metplus/wrappers/gempak_to_cf_wrapper.py
+++ b/metplus/wrappers/gempak_to_cf_wrapper.py
@@ -25,7 +25,7 @@
 class GempakToCFWrapper(LoopTimesWrapper):
 
     RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
-    RUNTIME_FREQ_SUPPORTED = 'ALL'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     def __init__(self, config, instance=None):
         self.app_name = "GempakToCF"
diff --git a/metplus/wrappers/gen_vx_mask_wrapper.py b/metplus/wrappers/gen_vx_mask_wrapper.py
index 373284557..6f9018598 100755
--- a/metplus/wrappers/gen_vx_mask_wrapper.py
+++ b/metplus/wrappers/gen_vx_mask_wrapper.py
@@ -25,7 +25,7 @@
 class GenVxMaskWrapper(LoopTimesWrapper):
 
     RUNTIME_FREQ_DEFAULT = 'RUN_ONCE_FOR_EACH'
-    RUNTIME_FREQ_SUPPORTED = 'ALL'
+    RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_FOR_EACH']
 
     def __init__(self, config, instance=None):
         self.app_name = "gen_vx_mask"
diff --git a/metplus/wrappers/plot_point_obs_wrapper.py b/metplus/wrappers/plot_point_obs_wrapper.py
index 1a2ad6b43..bf6f2798f 100755
--- a/metplus/wrappers/plot_point_obs_wrapper.py
+++ b/metplus/wrappers/plot_point_obs_wrapper.py
@@ -182,30 +182,6 @@ def get_command(self):
                 f' "{self.infiles[0]}" {self.get_output_path()}'
                 f" {' '.join(self.args)}")
 
-    def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run plot_point_obs.
-
-        @param time_info dictionary containing timing information
-        @returns True if command was built/run successfully or
-         False if something went wrong
-        """
-        # get input files
-        if not self.find_input_files(time_info):
-            return False
-
-        # get output path
-        if not self.find_and_check_output_file(time_info):
-            return False
-
-        # get other configurations for command
-        self.set_command_line_arguments(time_info)
-
-        # set environment variables if using config file
-        self.set_environment_variables(time_info)
-
-        # build command and run
-        return self.build()
-
     def find_input_files(self, time_info):
         """! Get all input files for plot_point_obs. Sets self.infiles list.
 

From 4ed89d6af9e0cb8c3c45944b246eb214be49ab7d Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 16 Aug 2023 13:59:32 -0600
Subject: [PATCH 54/55] fix job args to remove hours from -init_beg and
 -init_end

---
 ...esAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
index c73754b67..3ac8a6f08 100644
--- a/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
+++ b/parm/use_cases/model_applications/medium_range/TCStat_SeriesAnalysis_fcstGFS_obsGFS_FeatureRelative_SeriesByLead.conf
@@ -28,6 +28,7 @@ PROCESS_LIST = TCPairs, TCStat, ExtractTiles, TCStat(for_series_analysis), Serie
 LOOP_BY = INIT
 INIT_TIME_FMT = %Y%m%d
 INIT_BEG = 20141214
+INIT_END = 20141214
 
 LEAD_SEQ_1 = begin_end_incr(0,18,6)
 LEAD_SEQ_1_LABEL = Day1
@@ -211,7 +212,7 @@ EXTRACT_TILES_LAT_ADJ = 15
 # the value set outside of this section
 [for_series_analysis]
 
-TC_STAT_JOB_ARGS = -job filter -init_beg {init?fmt=%Y%m%d_%H} -init_end {init?fmt=%Y%m%d_%H} -dump_row {TC_STAT_OUTPUT_DIR}/{TC_STAT_DUMP_ROW_TEMPLATE}
+TC_STAT_JOB_ARGS = -job filter -init_beg {INIT_BEG} -init_end {INIT_END} -dump_row {TC_STAT_OUTPUT_DIR}/{TC_STAT_DUMP_ROW_TEMPLATE}
 
 TC_STAT_OUTPUT_DIR = {SERIES_ANALYSIS_OUTPUT_DIR}
 TC_STAT_LOOKIN_DIR = {EXTRACT_TILES_OUTPUT_DIR}

From 25b0d4ca25ba80d94684cb64f5b473881971ae65 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 30 Aug 2023 08:52:53 -0600
Subject: [PATCH 55/55] Update docs/Contributors_Guide/basic_components.rst

Co-authored-by: John Halley Gotway <johnhg@ucar.edu>
---
 docs/Contributors_Guide/basic_components.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Contributors_Guide/basic_components.rst b/docs/Contributors_Guide/basic_components.rst
index 6ac70dbcf..0b24209d8 100644
--- a/docs/Contributors_Guide/basic_components.rst
+++ b/docs/Contributors_Guide/basic_components.rst
@@ -69,7 +69,7 @@ RUNTIME_FREQ_SUPPORTED
 ----------------------
 
 Wrappers that inherit from **RuntimeFreqWrapper** should include a class
-variable called **RUNTIME_FREQ_SUPPORTED**  that defines the a list of the
+variable called **RUNTIME_FREQ_SUPPORTED** that defines a list of the
 runtime frequency settings that are supported by the wrapper. Example::
 
     RUNTIME_FREQ_SUPPORTED = ['RUN_ONCE_PER_INIT_OR_VALID']