From 98382e4a05650a26028b461855683f26eac077ab Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 09:59:37 -0600
Subject: [PATCH 01/26] Refactor to prevent calling sys.exit from functions
 that could cause the calling script to exit unintentionally. Instead return
 None or False and only sys.exit a non-zero value from a script that is called
 explicitly. Refactored validate config logic to reduce cognitive complexity
 to satisfy SonarQube

---
 .../config_validate/test_config_validate.py   |   6 +-
 metplus/util/config_metplus.py                |  19 ++-
 metplus/util/config_validate.py               |  54 ++++----
 metplus/util/run_util.py                      |   2 +
 metplus/wrappers/cyclone_plotter_wrapper.py   |   7 +-
 ush/validate_config.py                        | 128 ++++++++----------
 6 files changed, 107 insertions(+), 109 deletions(-)

diff --git a/internal/tests/pytests/util/config_validate/test_config_validate.py b/internal/tests/pytests/util/config_validate/test_config_validate.py
index f93adbc14b..aa2ffe16fa 100644
--- a/internal/tests/pytests/util/config_validate/test_config_validate.py
+++ b/internal/tests/pytests/util/config_validate/test_config_validate.py
@@ -104,9 +104,9 @@ def test_is_var_item_valid_levels(metplus_config, item_list, configs_to_set, is_
 @pytest.mark.parametrize(
     'met_config_file, expected',
     [
-        ('GridStatConfig_good', (True, [])),
-        ('GridStatConfig_bad', (False, [])),
-        ('GridStatConfig_fake', (False, [])),
+        ('GridStatConfig_good', True),
+        ('GridStatConfig_bad', False),
+        ('GridStatConfig_fake', False),
     ]
 )
 @pytest.mark.util
diff --git a/metplus/util/config_metplus.py b/metplus/util/config_metplus.py
index c842f96840..b92a70a133 100644
--- a/metplus/util/config_metplus.py
+++ b/metplus/util/config_metplus.py
@@ -98,12 +98,16 @@ def setup(args, base_confs=None):
     if base_confs is None:
         base_confs = _get_default_config_list()
 
+    if base_confs is None:
+        return None
+
     override_list = _parse_launch_args(args)
+    if override_list is None:
+        return None
 
     # add default config files to override list
     override_list = base_confs + override_list
     config = launch(override_list)
-
     return config
 
 
@@ -132,7 +136,7 @@ def _get_default_config_list(parm_base=None):
 
     if not default_config_list:
         print(f"FATAL: No default config files found in {conf_dir}")
-        sys.exit(1)
+        return None
 
     return default_config_list
 
@@ -195,9 +199,9 @@ def _parse_launch_args(args):
         # add file path to override list
         override_list.append(filepath)
 
-    # exit if anything went wrong reading config arguments
+    # return None if anything went wrong reading config arguments
     if bad:
-        sys.exit(2)
+        return None
 
     return override_list
 
@@ -249,7 +253,8 @@ def launch(config_list):
     mkdir_p(config.getdir('OUTPUT_BASE'))
 
     # set and log variables to the config object
-    get_logger(config)
+    if not get_logger(config):
+        return None
 
     final_conf = config.getstr('config', 'METPLUS_CONF')
 
@@ -337,14 +342,14 @@ def get_logger(config):
         log_level_val = logging.getLevelName(log_level)
     except ValueError:
         print(f'ERROR: Invalid value set for LOG_LEVEL: {log_level}')
-        sys.exit(1)
+        return None
 
     try:
         log_level_terminal_val = logging.getLevelName(log_level_terminal)
     except ValueError:
         print('ERROR: Invalid value set for LOG_LEVEL_TERMINAL:'
               f' {log_level_terminal}')
-        sys.exit(1)
+        return None
 
     # create log formatter from config settings
     formatter = METplusLogFormatter(config)
diff --git a/metplus/util/config_validate.py b/metplus/util/config_validate.py
index 2941733cfc..438cd344c6 100644
--- a/metplus/util/config_validate.py
+++ b/metplus/util/config_validate.py
@@ -17,8 +17,7 @@ def validate_config_variables(config):
 
     # check for deprecated env vars in MET config files and
     # warn user to remove/replace them
-    deprecated_met_is_ok, sed_cmds = check_for_deprecated_met_config(config)
-    all_sed_cmds.extend(sed_cmds)
+    deprecated_met_is_ok = check_for_deprecated_met_config(config)
 
     # validate configuration variables
     field_is_ok, sed_cmds = validate_field_info_configs(config)
@@ -133,7 +132,6 @@ def handle_deprecated(old, alt, depr_info, config, all_sed_cmds, e_list,
 
 
 def check_for_deprecated_met_config(config):
-    sed_cmds = []
     all_good = True
 
     # check if *_CONFIG_FILE if set in the METplus config file and check for
@@ -159,7 +157,7 @@ def check_for_deprecated_met_config(config):
                                                         met_tool):
                 all_good = False
 
-    return all_good, sed_cmds
+    return all_good
 
 
 def check_for_deprecated_met_config_file(config, met_config, met_tool):
@@ -184,31 +182,31 @@ def check_for_deprecated_met_config_file(config, met_config, met_tool):
                 continue
             error_logs.append(f"Deprecated environment variable ${{{deprecated_item}}} found")
 
-    if error_logs:
-        config.logger.error(f"Deprecated environment variables found in {met_tool}_CONFIG_FILE: {met_config}")
-        for error_log in error_logs:
-            config.logger.error(error_log)
-
-        met_install_dir = config.getdir('MET_INSTALL_DIR')
-        config_dir = os.path.join(met_install_dir, 'share', 'met', 'config')
-        default_config = f"{get_wrapper_name(met_tool)}Config_default"
-        default_path = os.path.join(config_dir, default_config)
-        config.logger.error(
-            "Please set values that differ from the defaults in a METplus "
-            f"config file and unset {met_tool}_CONFIG_FILE to use the "
-            "wrapped MET config that is provided with the METplus wrappers."
-        )
-        config.logger.error(
-            f"Compare values set in {met_config} to {default_path}"
-        )
-        config.logger.error(
-            "See https://metplus.readthedocs.io/en/latest/Users_Guide/"
-            "release-notes.html#metplus-wrappers-upgrade-instructions"
-            " for more information."
-        )
-        return False
+    if not error_logs:
+        return True
 
-    return True
+    config.logger.error(f"Deprecated environment variables found in {met_tool}_CONFIG_FILE: {met_config}")
+    for error_log in error_logs:
+        config.logger.error(error_log)
+
+    met_install_dir = config.getdir('MET_INSTALL_DIR')
+    config_dir = os.path.join(met_install_dir, 'share', 'met', 'config')
+    default_config = f"{get_wrapper_name(met_tool)}Config_default"
+    default_path = os.path.join(config_dir, default_config)
+    config.logger.error(
+        "Please set values that differ from the defaults in a METplus "
+        f"config file and unset {met_tool}_CONFIG_FILE to use the "
+        "wrapped MET config that is provided with the METplus wrappers."
+    )
+    config.logger.error(
+        f"Compare values set in {met_config} to {default_path}"
+    )
+    config.logger.error(
+        "See https://metplus.readthedocs.io/en/latest/Users_Guide/"
+        "release-notes.html#metplus-wrappers-upgrade-instructions"
+        " for more information."
+    )
+    return False
 
 
 def _get_deprecated_met_list(config, met_tool):
diff --git a/metplus/util/run_util.py b/metplus/util/run_util.py
index cb61e05aaa..145468c5a6 100644
--- a/metplus/util/run_util.py
+++ b/metplus/util/run_util.py
@@ -121,6 +121,8 @@ def pre_run_setup(config_inputs):
 
     # Read config inputs and return a config instance
     config = setup(config_inputs)
+    if not config:
+        return None
 
     logger = config.logger
 
diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
index 8b7ceb53a4..45e6ac3bd1 100644
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -331,6 +331,8 @@ def retrieve_data(self):
             if not self.is_global_extent:
                 self.logger.debug(f"Subset the data based on the region of interest.")
                 subset_by_region_df = self.subset_by_region(sanitized_df)
+                if not subset_by_region_df:
+                    return None
                 final_df = subset_by_region_df.copy(deep=True)
             else:
                 final_df = sanitized_df.copy(deep=True)
@@ -607,8 +609,9 @@ def subset_by_region(self, sanitized_df):
         masked = sanitized_by_region_df[sanitized_by_region_df['INSIDE'] == True]
         masked.reset_index(drop=True,inplace=True)
 
-        if len(masked) == 0:
-            sys.exit("No data in region specified, please check your lon and lat values in the config file.")
+        if not masked:
+            self.log_error("No data in region specified, please check your lon and lat values in the config file.")
+            return None
 
         return masked
 
diff --git a/ush/validate_config.py b/ush/validate_config.py
index 015d36662d..efdf84a440 100755
--- a/ush/validate_config.py
+++ b/ush/validate_config.py
@@ -33,6 +33,9 @@ def main():
 
     # Parse arguments, options and return a config instance.
     config = config_metplus.setup(config_inputs)
+    if config is None:
+        print("ERROR: Could not parse config")
+        return False
 
     # validate configuration variables
     is_ok, sed_commands = validate_config_variables(config)
@@ -40,78 +43,65 @@ def main():
     # if everything is valid, report success and exit
     if is_ok:
         print("SUCCESS: Configuration passed all of the validation tests.")
-        sys.exit(0)
+        return True
+
+    _prompt_sed_commands(sed_commands)
+    return True
+
+
+def _prompt_sed_commands(sed_commands):
 
     # if sed commands can be run, output lines that will be changed and ask
     # user if they want to run the sed command
-    if sed_commands:
-        for cmd in sed_commands:
-            if cmd.startswith('#Add'):
-                add_line = cmd.replace('#Add ', '')
-                met_tool = None
-                for suffix in ['_REGRID_TO_GRID', '_OUTPUT_PREFIX']:
-                    if suffix in add_line:
-                        met_tool = add_line.split(suffix)[0]
-                        section = 'config'
-
-                for suffix in ['_CLIMO_MEAN_INPUT_TEMPLATE']:
-                    if suffix in add_line:
-                        met_tool = add_line.split(suffix)[0]
-                        section = 'filename_templates'
-
-                if met_tool:
-                    print(f"\nIMPORTANT: If it is not already set, add the following in the [{section}] section to "
-                          f"your METplus configuration file that sets {met_tool}_CONFIG_FILE:\n")
-                    print(add_line)
-                    input("Make this change before continuing! [OK]")
-                else:
-                    print("ERROR: Something went wrong in the validate_config.py script. Please send an email to met_help@ucar.edu.")
-
-                continue
-
-            # remove -i from sed command to avoid replacing in the file
-            cmd_no_inline = cmd.replace('sed -i', 'sed')
-            split_cmd = shlex.split(cmd_no_inline)
-            original_file = split_cmd[-1]
-
-            # call sed command to get result of find/replace
-            result = subprocess.check_output(split_cmd, encoding='utf-8').splitlines()
-
-            # compare the result to the original file and show the differences
-            with open(original_file, 'r') as f:
-                original = [i.replace('\n', '') for i in f.readlines()]
-
-            # if no differences, continue
-            if result == original:
-                continue
-
-            print(f"\nThe following replacement is suggested for {original_file}\n")
-
-            # loop over before and after files line by line and 
-            for old, new in zip(original, result):
-
-                if old != new:
-                    print(f"Before:\n{old}\n")
-                    print(f"After:\n{new}\n")
-
-            # ask the user if they want to make the changes to their file (y/n default is no)
-            run_sed = False
-            user_answer = input(f"Would you like the make this change to {original_file}? (y/n)[n]")
-
-            if user_answer and user_answer[0] == 'y':
-                run_sed = True
-
-            # if yes, run original sed command
-            if run_sed:
-                print(f"Running command: {cmd}")
-                subprocess.run(shlex.split(cmd))
-            else:
-                print(f"Skipping sed command for {original_file}")
-
-        print("\nFinished running sed commands.")
-        print("\nRerun this script to ensure no other deprecated variables need to be replaced.")
-        print("See METplus User's Guide for more information on how to change deprecated variables")
+    if not sed_commands:
+        return
+
+    for cmd in sed_commands:
+        # remove -i from sed command to avoid replacing in the file
+        cmd_no_inline = cmd.replace('sed -i', 'sed')
+        split_cmd = shlex.split(cmd_no_inline)
+        original_file = split_cmd[-1]
+
+        # call sed command to get result of find/replace
+        result = subprocess.check_output(split_cmd, encoding='utf-8').splitlines()
+
+        # compare the result to the original file and show the differences
+        with open(original_file, 'r') as f:
+            original = f.read().splitlines()
+
+        # if no differences, continue
+        if result == original:
+            continue
+
+        print(f"\nThe following replacement is suggested for {original_file}\n")
+
+        # loop over before and after files line by line and
+        for old, new in zip(original, result):
+
+            if old != new:
+                print(f"Before:\n{old}\n")
+                print(f"After:\n{new}\n")
+
+        # ask the user if they want to make the changes to their file (y/n default is no)
+        run_sed = False
+        user_answer = input(f"Would you like the make this change to {original_file}? (y/n)[n]")
+
+        if user_answer and user_answer[0] == 'y':
+            run_sed = True
+
+        # if yes, run original sed command
+        if run_sed:
+            print(f"Running command: {cmd}")
+            subprocess.run(shlex.split(cmd))
+        else:
+            print(f"Skipping sed command for {original_file}")
+
+    print("\nFinished running sed commands.")
+    print("\nRerun this script to ensure no other deprecated variables need to be replaced.")
+    print("See METplus User's Guide for more information on how to change deprecated variables")
 
 
 if __name__ == "__main__":
-    main()
+    status = main()
+    if not status:
+        sys.exit(1)

From ef8520f079fa3c2104444d8bf884ce509b831273 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 10:06:39 -0600
Subject: [PATCH 02/26] per #2596, ensure the same RUN_ID is set for a given
 METplus run even if instances are used in the PROCESS_LIST

---
 metplus/util/config_metplus.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/metplus/util/config_metplus.py b/metplus/util/config_metplus.py
index b92a70a133..c0d25deea6 100644
--- a/metplus/util/config_metplus.py
+++ b/metplus/util/config_metplus.py
@@ -415,7 +415,7 @@ def replace_config_from_section(config, section, required=True):
         # if not required, return input config object
         return config
 
-    new_config = METplusConfig()
+    new_config = METplusConfig(run_id=config.run_id)
 
     # copy over all key/values from sections
     for section_to_copy in ['config', 'user_env_vars']:
@@ -449,9 +449,11 @@ class METplusConfig(ProdConfig):
         'regex_pattern',
     )
 
-    def __init__(self, conf=None):
+    def __init__(self, conf=None, run_id=None):
         """!Creates a new METplusConfig
         @param conf The configuration file
+        @param run_id 8 character identifier for the run or None if ID should
+        be created. Defaults to None.
         """
         # set interpolation to None so you can supply filename template
         # that contain % to config.set
@@ -460,7 +462,7 @@ def __init__(self, conf=None):
                             interpolation=None) if (conf is None) else conf
         super().__init__(conf)
         self._cycle = None
-        self.run_id = str(uuid.uuid4())[0:8]
+        self.run_id = run_id if run_id else str(uuid.uuid4())[0:8]
         self._logger = logging.getLogger(f'metplus.{self.run_id}')
         # config.logger is called in wrappers, so set this name
         # so the code doesn't break

From 13da8d07ea2525445051921747b4c4a936281b5a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 12:06:26 -0600
Subject: [PATCH 03/26] fixed linter complaints

---
 metplus/util/time_looping.py | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/metplus/util/time_looping.py b/metplus/util/time_looping.py
index 045c6e6ced..dc0bc0dc95 100644
--- a/metplus/util/time_looping.py
+++ b/metplus/util/time_looping.py
@@ -12,7 +12,7 @@
 def time_generator(config):
     """! Generator used to read METplusConfig variables for time looping
 
-    @param METplusConfig object to read
+    @param config METplusConfig object to read
     @returns None if not enough information is available on config.
      Yields the next run time dictionary or None if something went wrong
     """
@@ -414,16 +414,16 @@ def get_lead_sequence(config, input_dict=None, wildcard_if_empty=False):
             return lead_seq
 
         out_leads = _handle_lead_seq(config,
-                                    lead_seq,
-                                    lead_min,
-                                    lead_max)
+                                     lead_seq,
+                                     lead_min,
+                                     lead_max)
 
     # use INIT_SEQ to build lead list based on the valid time
     elif init_seq:
         out_leads = _handle_init_seq(init_seq,
-                                    input_dict,
-                                    lead_min,
-                                    lead_max)
+                                     input_dict,
+                                     lead_min,
+                                     lead_max)
     elif lead_groups:
         out_leads = _handle_lead_groups(lead_groups)
 
@@ -435,6 +435,7 @@ def get_lead_sequence(config, input_dict=None, wildcard_if_empty=False):
 
     return out_leads
 
+
 def _are_lead_configs_ok(lead_seq, init_seq, lead_groups,
                          config, input_dict, no_max):
     if lead_groups is None:
@@ -476,8 +477,9 @@ def _are_lead_configs_ok(lead_seq, init_seq, lead_groups,
 
     return True
 
+
 def _get_lead_min_max(config):
-    # remove any items that are outside of the range specified
+    # remove any items that are outside the range specified
     #  by LEAD_SEQ_MIN and LEAD_SEQ_MAX
     # convert min and max to relativedelta objects, then use current time
     # to compare them to each forecast lead
@@ -491,6 +493,7 @@ def _get_lead_min_max(config):
     lead_max = get_relativedelta(lead_max_str, 'H')
     return lead_min, lead_max, no_max
 
+
 def _handle_lead_seq(config, lead_strings, lead_min=None, lead_max=None):
     out_leads = []
     leads = []
@@ -511,11 +514,12 @@ def _handle_lead_seq(config, lead_strings, lead_min=None, lead_max=None):
     lead_max_approx = now_time + lead_max
     for lead in leads:
         lead_approx = now_time + lead
-        if lead_approx >= lead_min_approx and lead_approx <= lead_max_approx:
+        if lead_min_approx <= lead_approx <= lead_max_approx:
             out_leads.append(lead)
 
     return out_leads
 
+
 def _handle_init_seq(init_seq, input_dict, lead_min, lead_max):
     out_leads = []
     lead_min_hours = ti_get_hours_from_relativedelta(lead_min)
@@ -533,14 +537,14 @@ def _handle_init_seq(init_seq, input_dict, lead_min, lead_max):
                 out_leads.append(get_relativedelta(current_lead, default_unit='H'))
             current_lead += 24
 
-    out_leads = sorted(out_leads, key=lambda
-        rd: ti_get_seconds_from_relativedelta(rd, input_dict['valid']))
+    out_leads = sorted(out_leads, key=lambda rd: ti_get_seconds_from_relativedelta(rd, input_dict['valid']))
     return out_leads
 
+
 def _handle_lead_groups(lead_groups):
     """! Read groups of forecast leads and create a list with all unique items
 
-         @param lead_group dictionary where the values are lists of forecast
+         @param lead_groups dictionary where the values are lists of forecast
          leads stored as relativedelta objects
          @returns list of forecast leads stored as relativedelta objects
     """
@@ -552,6 +556,7 @@ def _handle_lead_groups(lead_groups):
 
     return out_leads
 
+
 def get_lead_sequence_groups(config):
     # output will be a dictionary where the key will be the
     #  label specified and the value will be the list of forecast leads

From e6d2f718b5d66c6d9b8e145d943e691c2a694380 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:23:16 -0600
Subject: [PATCH 04/26] remove unused imports

---
 metplus/wrappers/example_wrapper.py          | 3 +--
 metplus/wrappers/extract_tiles_wrapper.py    | 4 ++--
 metplus/wrappers/gempak_to_cf_wrapper.py     | 3 +--
 metplus/wrappers/gen_ens_prod_wrapper.py     | 4 +---
 metplus/wrappers/gen_vx_mask_wrapper.py      | 4 ++--
 metplus/wrappers/loop_times_wrapper.py       | 1 -
 metplus/wrappers/mode_wrapper.py             | 3 +--
 metplus/wrappers/plot_data_plane_wrapper.py  | 3 +--
 metplus/wrappers/plot_point_obs_wrapper.py   | 3 +--
 metplus/wrappers/py_embed_ingest_wrapper.py  | 4 +---
 metplus/wrappers/reformat_gridded_wrapper.py | 4 ----
 11 files changed, 11 insertions(+), 25 deletions(-)

diff --git a/metplus/wrappers/example_wrapper.py b/metplus/wrappers/example_wrapper.py
index 1802ee01fc..4d3ab77f00 100755
--- a/metplus/wrappers/example_wrapper.py
+++ b/metplus/wrappers/example_wrapper.py
@@ -12,8 +12,7 @@
 
 import os
 
-from ..util import do_string_sub, ti_calculate, get_lead_sequence
-from ..util import skip_time
+from ..util import do_string_sub
 from . import LoopTimesWrapper
 
 
diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index fc091a4e5b..fe08e124dc 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -13,8 +13,8 @@
 from datetime import datetime
 import re
 
-from ..util import do_string_sub, ti_calculate, skip_time
-from ..util import get_lead_sequence, sub_var_list
+from ..util import do_string_sub, ti_calculate
+from ..util import sub_var_list
 from ..util import parse_var_list, round_0p5, get_storms, prune_empty
 from .regrid_data_plane_wrapper import RegridDataPlaneWrapper
 from . import LoopTimesWrapper
diff --git a/metplus/wrappers/gempak_to_cf_wrapper.py b/metplus/wrappers/gempak_to_cf_wrapper.py
index 6c6108dac8..9519da51fc 100755
--- a/metplus/wrappers/gempak_to_cf_wrapper.py
+++ b/metplus/wrappers/gempak_to_cf_wrapper.py
@@ -12,8 +12,7 @@
 
 import os
 
-from ..util import do_string_sub, skip_time, get_lead_sequence
-from ..util import time_util
+from ..util import do_string_sub
 from . import LoopTimesWrapper
 
 '''!@namespace GempakToCFWrapper
diff --git a/metplus/wrappers/gen_ens_prod_wrapper.py b/metplus/wrappers/gen_ens_prod_wrapper.py
index 3ed3fcd643..3fbde580f7 100755
--- a/metplus/wrappers/gen_ens_prod_wrapper.py
+++ b/metplus/wrappers/gen_ens_prod_wrapper.py
@@ -5,9 +5,7 @@
 
 import os
 
-from ..util import do_string_sub, ti_calculate, get_lead_sequence
-from ..util import skip_time, parse_var_list, sub_var_list
-
+from ..util import do_string_sub, parse_var_list, sub_var_list
 from . import LoopTimesWrapper
 
 
diff --git a/metplus/wrappers/gen_vx_mask_wrapper.py b/metplus/wrappers/gen_vx_mask_wrapper.py
index 9d971537c6..59ef9e2f4c 100755
--- a/metplus/wrappers/gen_vx_mask_wrapper.py
+++ b/metplus/wrappers/gen_vx_mask_wrapper.py
@@ -12,9 +12,9 @@
 
 import os
 
-from ..util import getlist, get_lead_sequence, skip_time, ti_calculate, mkdir_p
-from . import LoopTimesWrapper
+from ..util import getlist
 from ..util import do_string_sub, remove_quotes
+from . import LoopTimesWrapper
 
 '''!@namespace GenVxMaskWrapper
 @brief Wraps the GenVxMask tool to reformat ascii format to NetCDF
diff --git a/metplus/wrappers/loop_times_wrapper.py b/metplus/wrappers/loop_times_wrapper.py
index 09570364cc..c58f1f093a 100755
--- a/metplus/wrappers/loop_times_wrapper.py
+++ b/metplus/wrappers/loop_times_wrapper.py
@@ -4,7 +4,6 @@
 """
 
 from . import RuntimeFreqWrapper
-from ..util import get_lead_sequence, skip_time, ti_calculate
 
 '''!@namespace LoopTimesWrapper
 @brief parent class for any wrapper that will loop over init/valid times
diff --git a/metplus/wrappers/mode_wrapper.py b/metplus/wrappers/mode_wrapper.py
index 13190a3b33..a4ab535f21 100755
--- a/metplus/wrappers/mode_wrapper.py
+++ b/metplus/wrappers/mode_wrapper.py
@@ -12,9 +12,8 @@
 
 import os
 
-from . import CompareGriddedWrapper
 from ..util import do_string_sub
-
+from . import CompareGriddedWrapper
 
 class MODEWrapper(CompareGriddedWrapper):
     """!Wrapper for the mode MET tool"""
diff --git a/metplus/wrappers/plot_data_plane_wrapper.py b/metplus/wrappers/plot_data_plane_wrapper.py
index 6145324128..da5dee031a 100755
--- a/metplus/wrappers/plot_data_plane_wrapper.py
+++ b/metplus/wrappers/plot_data_plane_wrapper.py
@@ -12,8 +12,7 @@
 
 import os
 
-from ..util import time_util
-from ..util import do_string_sub, remove_quotes, skip_time, get_lead_sequence
+from ..util import do_string_sub, remove_quotes
 from . import LoopTimesWrapper
 
 '''!@namespace PlotDataPlaneWrapper
diff --git a/metplus/wrappers/plot_point_obs_wrapper.py b/metplus/wrappers/plot_point_obs_wrapper.py
index 076811804b..97f62a2880 100755
--- a/metplus/wrappers/plot_point_obs_wrapper.py
+++ b/metplus/wrappers/plot_point_obs_wrapper.py
@@ -12,8 +12,7 @@
 
 import os
 
-from ..util import do_string_sub, ti_calculate, get_lead_sequence
-from ..util import skip_time
+from ..util import do_string_sub
 from . import LoopTimesWrapper
 
 
diff --git a/metplus/wrappers/py_embed_ingest_wrapper.py b/metplus/wrappers/py_embed_ingest_wrapper.py
index 2f86694e33..0dcef33132 100755
--- a/metplus/wrappers/py_embed_ingest_wrapper.py
+++ b/metplus/wrappers/py_embed_ingest_wrapper.py
@@ -10,11 +10,9 @@
 Condition codes: 0 for success, 1 for failure
 """
 
-import os
 import re
 
-from ..util import time_util
-from ..util import do_string_sub, get_lead_sequence
+from ..util import do_string_sub
 from . import LoopTimesWrapper
 from . import RegridDataPlaneWrapper
 
diff --git a/metplus/wrappers/reformat_gridded_wrapper.py b/metplus/wrappers/reformat_gridded_wrapper.py
index 92aa3ce162..58afa6936c 100755
--- a/metplus/wrappers/reformat_gridded_wrapper.py
+++ b/metplus/wrappers/reformat_gridded_wrapper.py
@@ -10,10 +10,6 @@
 Condition codes: 0 for success, 1 for failure
 '''
 
-import os
-
-from ..util import get_lead_sequence
-from ..util import time_util, skip_time
 from . import LoopTimesWrapper
 
 # pylint:disable=pointless-string-statement

From e17cdb426a2407ea86d9e1f365996e9204b687e0 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:26:17 -0600
Subject: [PATCH 05/26] cleanup for SonarQube and linter

---
 metplus/wrappers/runtime_freq_wrapper.py | 40 ++++++++++--------------
 1 file changed, 17 insertions(+), 23 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 308e4ec711..c635a0ce74 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -95,21 +95,20 @@ def validate_runtime_freq(self, c_dict):
 
         # 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 (not hasattr(self, 'RUNTIME_FREQ_SUPPORTED') or
+                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
+        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)
 
     def get_input_templates(self, c_dict, input_info=None):
         """!Read input templates from config.
@@ -252,7 +251,7 @@ def run_once(self, custom):
         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")
+        self.logger.debug("Running once for each init/valid time")
 
         success = True
         for time_input in time_generator(self.config):
@@ -317,7 +316,7 @@ def run_once_per_lead(self, custom):
         return success
 
     def run_once_for_each(self, custom):
-        self.logger.debug(f"Running once for each init/valid and lead time")
+        self.logger.debug("Running once for each init/valid and lead time")
 
         success = True
         for time_input in time_generator(self.config):
@@ -508,10 +507,9 @@ def get_files_from_time(self, time_info):
              @returns dictionary containing time_info dict and any relevant
              files with a key representing a description of that file
         """
+        var_list = [None]
         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 = []
@@ -661,11 +659,7 @@ def subset_input_files(self, time_info, output_dir=None, leads=None,
         if not self.c_dict.get('ALL_FILES') or self.c_dict.get('ALL_FILES') is True:
             return all_input_files
 
-        if leads is None:
-            lead_loop = [None]
-        else:
-            lead_loop = leads
-
+        lead_loop = [None] if leads is None else leads
         for file_dict in self.c_dict['ALL_FILES']:
             for lead in lead_loop:
                 if lead is not None:

From b8a43b2b00d92cfe7b12658a0d8668e19d415b5b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:40:10 -0600
Subject: [PATCH 06/26] remove unused imports

---
 metplus/wrappers/cyclone_plotter_wrapper.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
index 45e6ac3bd1..f987597424 100644
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -8,8 +8,6 @@
 import os
 import time
 import datetime
-import re
-import sys
 from collections import namedtuple
 
 

From 386c67f67efc4ae9d4ed24653a0d55a754818491 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:42:21 -0600
Subject: [PATCH 07/26] import parent wrappers directly so that PyCharm can
 follow class hierarchy

---
 metplus/wrappers/__init__.py | 27 +++++++++++----------------
 1 file changed, 11 insertions(+), 16 deletions(-)

diff --git a/metplus/wrappers/__init__.py b/metplus/wrappers/__init__.py
index c9d53693ba..ae8a1c3aae 100644
--- a/metplus/wrappers/__init__.py
+++ b/metplus/wrappers/__init__.py
@@ -5,27 +5,22 @@
 from importlib import import_module
 from ..util.metplus_check import plot_wrappers_are_enabled
 
+# import parent classes to other wrappers
+from .command_builder import CommandBuilder
+from .runtime_freq_wrapper import RuntimeFreqWrapper
+from .loop_times_wrapper import LoopTimesWrapper
+from .reformat_gridded_wrapper import ReformatGriddedWrapper
+from .reformat_point_wrapper import ReformatPointWrapper
+from .compare_gridded_wrapper import CompareGriddedWrapper
+
+# import RegridDataPlane wrapper because it is used by other wrappers
+from .regrid_data_plane_wrapper import RegridDataPlaneWrapper
+
 # these wrappers should not be imported if plotting is disabled
 plotting_wrappers = [
     'cyclone_plotter_wrapper',
 ]
 
-# import classes that other wrappers import
-parent_classes = {
-    'command_builder': 'CommandBuilder',
-    'runtime_freq_wrapper': 'RuntimeFreqWrapper',
-    'loop_times_wrapper': 'LoopTimesWrapper',
-    'reformat_gridded_wrapper': 'ReformatGriddedWrapper',
-    'reformat_point_wrapper': 'ReformatPointWrapper',
-    'compare_gridded_wrapper': 'CompareGriddedWrapper',
-    'regrid_data_plane_wrapper': 'RegridDataPlaneWrapper',
-}
-
-for module_name, attribute_name in parent_classes.items():
-    module = import_module(f"{__name__}.{module_name}")
-    attribute = getattr(module, attribute_name)
-    globals()[attribute_name] = attribute
-
 # iterate through the modules in the current package
 package_dir = str(Path(__file__).resolve().parent)
 for (_, module_name, _) in iter_modules([package_dir]):

From f744c9695c8352894dc9002545ffd88fc65fd3f3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:43:39 -0600
Subject: [PATCH 08/26] per #2612, add support for processing groups of
 forecast leads

---
 metplus/wrappers/runtime_freq_wrapper.py | 42 ++++++++++++++++--------
 1 file changed, 29 insertions(+), 13 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index c635a0ce74..37416b7934 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -13,7 +13,7 @@
 import os
 
 from ..util import time_util
-from ..util import log_runtime_banner, get_lead_sequence
+from ..util import log_runtime_banner, get_lead_sequence, get_lead_sequence_groups
 from ..util import skip_time, getlist, get_start_and_end_times, get_time_prefix
 from ..util import time_generator, add_to_time_input
 from ..util import sub_var_list, add_field_info_to_time_info
@@ -272,16 +272,32 @@ def run_once_per_init_or_valid(self, custom):
             time_input['lead'] = '*'
             time_info = time_util.ti_calculate(time_input)
 
-            self.c_dict['ALL_FILES'] = self.get_all_files_from_leads(time_info)
-            if not self._check_input_files():
-                continue
+            lead_groups = self._get_leads_as_group(time_info)
+            for label, lead_seq in lead_groups.items():
+                time_info['label'] = label
+                self.c_dict['ALL_FILES'] = (
+                    self.get_all_files_from_leads(time_info, lead_seq)
+                )
+                if not self._check_input_files():
+                    continue
 
-            self.clear()
-            if not self.run_at_time_once(time_info):
-                success = False
+                self.clear()
+                if not self.run_at_time_once(time_info):
+                    success = False
 
         return success
 
+    def _get_leads_as_group(self, time_input):
+        """!"""
+        lead_groups = get_lead_sequence_groups(self.config)
+        if lead_groups:
+            return lead_groups
+
+        use_wildcard = self.c_dict.get('WILDCARD_LEAD_IF_EMPTY')
+        lead_seq = get_lead_sequence(self.config, time_input,
+                                     wildcard_if_empty=use_wildcard)
+        return {'': lead_seq}
+
     def run_once_per_lead(self, custom):
         self.logger.debug("Running once for forecast lead time")
         success = True
@@ -421,7 +437,11 @@ def get_all_files(self, custom=None):
                               instance=self.instance,
                               custom=custom)
 
-            lead_files = self.get_all_files_from_leads(time_input)
+            use_wildcard = self.c_dict.get('WILDCARD_LEAD_IF_EMPTY')
+            lead_seq = get_lead_sequence(self.config,
+                                         time_input,
+                                         wildcard_if_empty=use_wildcard)
+            lead_files = self.get_all_files_from_leads(time_input, lead_seq)
             all_files.extend(lead_files)
 
         return all_files
@@ -440,16 +460,12 @@ def _check_input_files(self):
             return False
         return True
 
-    def get_all_files_from_leads(self, time_input):
+    def get_all_files_from_leads(self, time_input, lead_seq):
         if not self.c_dict.get('FIND_FILES', True):
             return True
 
         lead_files = []
         # loop over all forecast leads
-        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)
         for lead in lead_seq:
             current_time_input = time_input.copy()
             current_time_input['lead'] = lead

From 027feca797d3cee4c6fc35fc19e9c31a7d342543 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 13:44:54 -0600
Subject: [PATCH 09/26] remove call to prune_empty function and ci-run-all-diff

---
 metplus/wrappers/extract_tiles_wrapper.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/metplus/wrappers/extract_tiles_wrapper.py b/metplus/wrappers/extract_tiles_wrapper.py
index fe08e124dc..c0d15276fe 100755
--- a/metplus/wrappers/extract_tiles_wrapper.py
+++ b/metplus/wrappers/extract_tiles_wrapper.py
@@ -15,7 +15,7 @@
 
 from ..util import do_string_sub, ti_calculate
 from ..util import sub_var_list
-from ..util import parse_var_list, round_0p5, get_storms, prune_empty
+from ..util import parse_var_list, round_0p5, get_storms
 from .regrid_data_plane_wrapper import RegridDataPlaneWrapper
 from . import LoopTimesWrapper
 
@@ -235,8 +235,6 @@ def run_at_time_once(self, time_info):
         else:
             self.use_tc_stat_input(storm_dict, idx_dict)
 
-        prune_empty(self.c_dict['OUTPUT_DIR'], self.logger)
-
     def use_tc_stat_input(self, storm_dict, idx_dict):
         """! Find storms in TCStat input file and create tiles using the storm.
 

From eb39f3ad0afa86c463c2afced48791929675219f Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 16:05:05 -0600
Subject: [PATCH 10/26] fixed check on DataFrame to properly check for an empty
 one

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

diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
index f987597424..8c5fa18526 100644
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -607,7 +607,7 @@ def subset_by_region(self, sanitized_df):
         masked = sanitized_by_region_df[sanitized_by_region_df['INSIDE'] == True]
         masked.reset_index(drop=True,inplace=True)
 
-        if not masked:
+        if len(masked) == 0:
             self.log_error("No data in region specified, please check your lon and lat values in the config file.")
             return None
 

From 2e1d3a46aca39fccd1a788c93d6c57c98137acae Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 12 Jun 2024 16:08:25 -0600
Subject: [PATCH 11/26] remove prune_empty function that is no longer used

---
 .../util/system_util/test_system_util.py      | 23 -------------
 metplus/util/system_util.py                   | 34 -------------------
 2 files changed, 57 deletions(-)

diff --git a/internal/tests/pytests/util/system_util/test_system_util.py b/internal/tests/pytests/util/system_util/test_system_util.py
index ed370f2e1b..cf239cbbf5 100644
--- a/internal/tests/pytests/util/system_util/test_system_util.py
+++ b/internal/tests/pytests/util/system_util/test_system_util.py
@@ -228,29 +228,6 @@ def test_write_list_to_file(tmp_path_factory):
     assert actual == '\n'.join(output_list) + '\n'
 
 
-@pytest.mark.util
-def test_prune_empty(tmp_path_factory):
-    prune_dir = tmp_path_factory.mktemp('prune')
-   
-    dir1 = prune_dir / 'empty_file_dir'
-    dir2 = prune_dir / 'not_empty_file_dir'
-    dir3 = prune_dir / 'empty_dir'
-    for d in [dir1, dir2, dir3]:
-        os.makedirs(d)
-    
-    # make two files, one empty one not.
-    open(os.path.join(dir1, 'empty.txt'), 'a').close()
-    file_with_content = os.path.join(dir2, 'not_empty.txt')
-    with open(file_with_content, 'w') as f:
-        f.write('Fee fi fo fum.')
-    
-    su.prune_empty(prune_dir, mock.Mock())
-    
-    assert not os.path.exists(dir1)
-    assert os.path.exists(file_with_content)
-    assert not os.path.exists(dir3)
-
-
 @pytest.mark.parametrize(
     'regex, expected', [
         (r'\d', ['bigfoot/123.txt', 'yeti/234.txt']),
diff --git a/metplus/util/system_util.py b/metplus/util/system_util.py
index 29f4e8bc19..ec192a4a86 100644
--- a/metplus/util/system_util.py
+++ b/metplus/util/system_util.py
@@ -109,40 +109,6 @@ def get_storms(filter_filename, id_only=False, sort_column='STORM_ID'):
     return storm_dict
 
 
-def prune_empty(output_dir, logger):
-    """! Start from the output_dir, and recursively check
-        all directories and files.  If there are any empty
-        files or directories, delete/remove them so they
-        don't cause performance degradation or errors
-        when performing subsequent tasks.
-
-        @param output_dir The directory from which searching should begin.
-        @param logger The logger to which all logging is directed.
-    """
-
-    # Check for empty files.
-    for root, dirs, files in os.walk(output_dir):
-        # Create a full file path by joining the path
-        # and filename.
-        for a_file in files:
-            a_file = os.path.join(root, a_file)
-            if os.stat(a_file).st_size == 0:
-                logger.debug("Empty file: " + a_file +
-                             "...removing")
-                os.remove(a_file)
-
-    # Now check for any empty directories, some
-    # may have been created when removing
-    # empty files.
-    for root, dirs, files in os.walk(output_dir):
-        for direc in dirs:
-            full_dir = os.path.join(root, direc)
-            if not os.listdir(full_dir):
-                logger.debug("Empty directory: " + full_dir +
-                             "...removing")
-                os.rmdir(full_dir)
-
-
 def get_files(filedir, filename_regex):
     """! Get all the files (with a particular naming format) by walking
         through the directories. Note this uses re.match and will only

From 70c59136b93bdcd59afee639341ae4c8d6063b01 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 18 Jun 2024 12:44:18 -0600
Subject: [PATCH 12/26] update conda environment requirements for metdataio

---
 internal/scripts/docker_env/scripts/metdataio_env.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/internal/scripts/docker_env/scripts/metdataio_env.sh b/internal/scripts/docker_env/scripts/metdataio_env.sh
index a0eac3a869..012f64f352 100755
--- a/internal/scripts/docker_env/scripts/metdataio_env.sh
+++ b/internal/scripts/docker_env/scripts/metdataio_env.sh
@@ -23,4 +23,5 @@ BASE_ENV=metplus_base.${METPLUS_VERSION}
 
 mamba create -y --clone ${BASE_ENV} --name ${ENV_NAME}
 
-mamba install -y --name ${ENV_NAME} -c conda-forge lxml==4.9.1 pymysql==1.0.2 pandas==1.5.1
+#mamba install -y --name ${ENV_NAME} -c conda-forge lxml==4.9.1 pymysql==1.0.2 pandas==1.5.1
+mamba install -y --name ${ENV_NAME} -c conda-forge pymysql==1.1.0 pyyaml==6.0 "xarray>=2023.1.0" lxml==4.9.1 netcdf4==1.6.2

From d103d483b10577257ef9c658b3ff86017bb96441 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 21 Jun 2024 16:34:55 -0600
Subject: [PATCH 13/26] set label to Group<n> for LEAD_SEQ_<n> if
 LEAD_SEQ_<n>_LABEL is not set (instead of erroring), use forecast lead label
 for lead if set, log lead group label and formatted list of leads for each
 run

---
 metplus/util/time_looping.py             | 5 +----
 metplus/util/time_util.py                | 8 ++++++++
 metplus/wrappers/grid_diag_wrapper.py    | 2 +-
 metplus/wrappers/runtime_freq_wrapper.py | 9 +++++++--
 4 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/metplus/util/time_looping.py b/metplus/util/time_looping.py
index dc0bc0dc95..5cb6635edd 100644
--- a/metplus/util/time_looping.py
+++ b/metplus/util/time_looping.py
@@ -575,10 +575,7 @@ def get_lead_sequence_groups(config):
         if config.has_option('config', f"LEAD_SEQ_{index}_LABEL"):
             label = config.getstr('config', f"LEAD_SEQ_{index}_LABEL")
         else:
-            log_msg = (f'Need to set LEAD_SEQ_{index}_LABEL to describe '
-                       f'LEAD_SEQ_{index}')
-            config.logger.error(log_msg)
-            return None
+            label = f"Group{index}"
 
         # get forecast list for n
         lead_string_list = getlist(config.getstr('config', f'LEAD_SEQ_{index}'))
diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 6dc305b4b6..2d0997189e 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -276,6 +276,14 @@ def ti_get_lead_string(lead, plural=True, letter_only=False):
     return f"{negative}{output}"
 
 
+def format_lead_seq(lead_seq, plural=True, letter_only=False):
+    leads = []
+    for lead in lead_seq:
+        lead_fmt = ti_get_lead_string(lead, plural=plural, letter_only=letter_only)
+        leads.append(lead_fmt)
+    return ', '.join(leads)
+
+
 def get_met_time_list(string_value, sort_list=True):
     """! Convert a string into a list of strings in MET time format HHMMSS.
 
diff --git a/metplus/wrappers/grid_diag_wrapper.py b/metplus/wrappers/grid_diag_wrapper.py
index c95ab75d9a..f2228cde14 100755
--- a/metplus/wrappers/grid_diag_wrapper.py
+++ b/metplus/wrappers/grid_diag_wrapper.py
@@ -107,7 +107,7 @@ def create_c_dict(self):
 
         return c_dict
 
-    def set_environment_variables(self, time_info):
+    def set_environment_variables(self, time_info=None):
         """!Set environment variables that will be read by the MET config file.
              Reformat as needed. Print list of variables that were set and
               their values.
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 37416b7934..20f11153c2 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -15,7 +15,7 @@
 from ..util import time_util
 from ..util import log_runtime_banner, get_lead_sequence, get_lead_sequence_groups
 from ..util import skip_time, getlist, get_start_and_end_times, get_time_prefix
-from ..util import time_generator, add_to_time_input
+from ..util import time_generator, add_to_time_input, format_lead_seq
 from ..util import sub_var_list, add_field_info_to_time_info
 from . import CommandBuilder
 
@@ -274,6 +274,11 @@ def run_once_per_init_or_valid(self, custom):
 
             lead_groups = self._get_leads_as_group(time_info)
             for label, lead_seq in lead_groups.items():
+                if label:
+                    self.logger.info(
+                        f"Processing lead group {label}:"
+                        f" {format_lead_seq(lead_seq, plural=False)}"
+                    )
                 time_info['label'] = label
                 self.c_dict['ALL_FILES'] = (
                     self.get_all_files_from_leads(time_info, lead_seq)
@@ -740,7 +745,7 @@ def get_list_file_name(self, time_info, identifier):
             valid = time_info['valid'].strftime('%Y%m%d%H%M%S')
 
         if time_info.get('lead', '*') == '*':
-            lead = 'ALL'
+            lead = time_info.get('label') if time_info.get('label') else 'ALL'
         else:
             lead = time_util.ti_get_seconds_from_lead(time_info['lead'],
                                                       time_info['valid'])

From 97f7bd274feea78ba655951281cebf9245c26ea3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:11:30 -0600
Subject: [PATCH 14/26] increase timeout for request from 60 to 90

---
 .github/jobs/docker_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/jobs/docker_utils.py b/.github/jobs/docker_utils.py
index edf0b00167..b5a102d99d 100644
--- a/.github/jobs/docker_utils.py
+++ b/.github/jobs/docker_utils.py
@@ -39,7 +39,7 @@ def get_dockerhub_url(branch_name):
 def docker_get_volumes_last_updated(current_branch):
     import requests
     dockerhub_url = get_dockerhub_url(current_branch)
-    dockerhub_request = requests.get(dockerhub_url, timeout=60)
+    dockerhub_request = requests.get(dockerhub_url, timeout=90)
     if dockerhub_request.status_code != 200:
         print(f"Could not find DockerHub URL: {dockerhub_url}")
         return None

From e8cdb6183619f0ef1f5047138f2de22d8ca7619c Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:14:33 -0600
Subject: [PATCH 15/26] handle exception and output an error message with a
 suggestion to rerun the failed GHA jobs when a hiccup with DockerHub prevents
 the list of available Docker data volumes from being obtained. FYI @jprestop

---
 .github/jobs/get_data_volumes.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/jobs/get_data_volumes.py b/.github/jobs/get_data_volumes.py
index e492711710..2ce0ccf7d5 100755
--- a/.github/jobs/get_data_volumes.py
+++ b/.github/jobs/get_data_volumes.py
@@ -54,7 +54,12 @@ def main(args):
         branch_name = branch_name[5:]
 
     # get all docker data volumes associated with current branch
-    available_volumes = docker_get_volumes_last_updated(branch_name).keys()
+    try:
+        available_volumes = docker_get_volumes_last_updated(branch_name).keys()
+    except AttributeError:
+        print("ERROR: Could not get available Docker data volumes "
+              f"for {branch_name}. Try rerunning failed jobs in GitHub Actions")
+        return None
 
     # loop through arguments and get data volume for each category
     for model_app_name in args:

From 4b22607ac16e811609a2580b326756403b937347 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:16:07 -0600
Subject: [PATCH 16/26] cleanup to address SonarQube complaints, move call to
 exit out of main function so a script calling the function does not exit when
 the function errors

---
 .github/jobs/get_data_volumes.py        | 10 ++-
 .github/jobs/setup_and_run_use_cases.py | 81 +++++++++++++------------
 2 files changed, 45 insertions(+), 46 deletions(-)

diff --git a/.github/jobs/get_data_volumes.py b/.github/jobs/get_data_volumes.py
index 2ce0ccf7d5..cbf3a4e01d 100755
--- a/.github/jobs/get_data_volumes.py
+++ b/.github/jobs/get_data_volumes.py
@@ -7,8 +7,6 @@
 
 import sys
 import os
-import subprocess
-import shlex
 
 from docker_utils import docker_get_volumes_last_updated, get_branch_name
 from docker_utils import get_data_repo, DOCKERHUB_METPLUS_DATA_DEV
@@ -83,7 +81,7 @@ def main(args):
             volume_name = f'{prefix}-{model_app_name}'
 
             # add output- to model app name
-            model_app_name=f'output-{model_app_name}'
+            model_app_name = f'output-{model_app_name}'
 
             # set DockerHub repo to dev version because all output data
             # should be in dev repository
@@ -113,11 +111,11 @@ def main(args):
 
 if __name__ == "__main__":
     # split up command line args that have commas before passing into main
-    args = []
+    arg_list = []
 
     for arg in sys.argv[1:]:
-        args.extend(arg.split(','))
-    out = main(args)
+        arg_list.extend(arg.split(','))
+    out = main(arg_list)
     if out is None:
         print("ERROR: Something went wrong")
         sys.exit(1)
diff --git a/.github/jobs/setup_and_run_use_cases.py b/.github/jobs/setup_and_run_use_cases.py
index a2e55f8fa0..37b47537f6 100755
--- a/.github/jobs/setup_and_run_use_cases.py
+++ b/.github/jobs/setup_and_run_use_cases.py
@@ -63,7 +63,7 @@ def main():
     # use BuildKit to build image
     os.environ['DOCKER_BUILDKIT'] = '1'
 
-    isOK = True
+    is_ok = True
     failed_use_cases = []
     for setup_commands, use_case_commands, requirements in all_commands:
         # get environment image tag
@@ -79,45 +79,38 @@ def main():
             f"-f {DOCKERFILE_DIR}/{dockerfile_name} ."
         )
 
-        print(f'Building Docker environment/branch image...')
+        print('Building Docker environment/branch image...')
         if not run_commands(docker_build_cmd):
-            isOK = False
+            is_ok = False
             continue
 
-        commands = []
-
-        # print list of existing docker images
-        commands.append('docker images')
-
+        # print list of existing docker images,
         # remove docker image after creating run env or prune untagged images
-        commands.append(f'docker image rm dtcenter/metplus-dev:{branch_name} -f')
-        commands.append('docker image prune -f')
-        run_commands(commands)
-
-        commands = []
-
-        # list docker images again after removal
-        commands.append('docker images')
-
-        # start interactive container in the background
-        commands.append(
-            f"docker run -d --rm -it -e GITHUB_WORKSPACE "
-            f"--name {RUN_TAG} "
-            f"{os.environ.get('NETWORK_ARG', '')} "
-            f"{' '.join(VOLUME_MOUNTS)} "
-            f"{volumes_from} --workdir {GITHUB_WORKSPACE} "
-            f'{RUN_TAG} bash'
-        )
-
-        # list running containers
-        commands.append('docker ps -a')
-
-        # execute setup commands in running docker container
-        commands.append(_format_docker_exec_command(setup_commands))
+        run_commands([
+            'docker images',
+            f'docker image rm dtcenter/metplus-dev:{branch_name} -f',
+            'docker image prune -f',
+        ])
+
+        # list docker images again after removal,
+        # start interactive container in the background,
+        # list running containers,
+        # then execute setup commands in running docker container
+        commands = [
+            'docker images',
+            (f"docker run -d --rm -it -e GITHUB_WORKSPACE "
+             f"--name {RUN_TAG} "
+             f"{os.environ.get('NETWORK_ARG', '')} "
+             f"{' '.join(VOLUME_MOUNTS)} "
+             f"{volumes_from} --workdir {GITHUB_WORKSPACE} "
+             f'{RUN_TAG} bash'),
+            'docker ps -a',
+            _format_docker_exec_command(setup_commands),
+        ]
 
         # run docker commands and skip running cases if something went wrong
         if not run_commands(commands):
-            isOK = False
+            is_ok = False
 
             # force remove container if setup step fails
             run_commands(f'docker rm -f {RUN_TAG}')
@@ -132,7 +125,7 @@ def main():
         for use_case_command in use_case_commands:
             if not run_commands(_format_docker_exec_command(use_case_command)):
                 failed_use_cases.append(use_case_command)
-                isOK = False
+                is_ok = False
 
         # print bashrc file to see what was added by setup commands
         # then force remove container to stop and remove it
@@ -140,15 +133,20 @@ def main():
             _format_docker_exec_command('cat /root/.bashrc'),
             f'docker rm -f {RUN_TAG}',
         ]):
-            isOK = False
+            is_ok = False
 
     # print summary of use cases that failed
-    for failed_use_case in failed_use_cases:
-        print(f'ERROR: Use case failed: {failed_use_case}')
+    _print_failed_use_cases(failed_use_cases)
 
-    if not isOK:
+    if not is_ok:
         print("ERROR: Some commands failed.")
-        sys.exit(1)
+
+    return is_ok
+
+
+def _print_failed_use_cases(failed_use_cases):
+    for failed_use_case in failed_use_cases:
+        print(f'ERROR: Use case failed: {failed_use_case}')
 
 
 def _format_docker_exec_command(command):
@@ -201,4 +199,7 @@ def _get_dockerfile_name(requirements):
 
 
 if __name__ == '__main__':
-    main()
+    ret = main()
+    # exit non-zero if anything went wrong
+    if not ret:
+        sys.exit(1)

From 848436254a78a27f4cb1622a4741df75083f99ba Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 13:47:30 -0600
Subject: [PATCH 17/26] cleanup to appease SonarQube

---
 metplus/wrappers/runtime_freq_wrapper.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 20f11153c2..d4f1f7d8e3 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -10,8 +10,6 @@
 Condition codes: 0 for success, 1 for failure
 """
 
-import os
-
 from ..util import time_util
 from ..util import log_runtime_banner, get_lead_sequence, get_lead_sequence_groups
 from ..util import skip_time, getlist, get_start_and_end_times, get_time_prefix
@@ -274,11 +272,7 @@ def run_once_per_init_or_valid(self, custom):
 
             lead_groups = self._get_leads_as_group(time_info)
             for label, lead_seq in lead_groups.items():
-                if label:
-                    self.logger.info(
-                        f"Processing lead group {label}:"
-                        f" {format_lead_seq(lead_seq, plural=False)}"
-                    )
+                self._log_lead_group(label, lead_seq)
                 time_info['label'] = label
                 self.c_dict['ALL_FILES'] = (
                     self.get_all_files_from_leads(time_info, lead_seq)
@@ -303,6 +297,12 @@ def _get_leads_as_group(self, time_input):
                                      wildcard_if_empty=use_wildcard)
         return {'': lead_seq}
 
+    def _log_lead_group(self, label, lead_seq):
+        if not label:
+            return
+        self.logger.info(f"Processing lead group {label}:"
+                         f" {format_lead_seq(lead_seq, plural=False)}")
+
     def run_once_per_lead(self, custom):
         self.logger.debug("Running once for forecast lead time")
         success = True

From d7b942e389c075f0b1c850588e4fd270591ddd2d Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:52:33 -0600
Subject: [PATCH 18/26] per #2612, add support for creating groups of forecast
 leads by specifying a list of forecast leads and a time interval to create
 groups of leads

---
 metplus/util/time_looping.py | 74 ++++++++++++++++++++++++++++++------
 1 file changed, 62 insertions(+), 12 deletions(-)

diff --git a/metplus/util/time_looping.py b/metplus/util/time_looping.py
index 5cb6635edd..7bab6f52a9 100644
--- a/metplus/util/time_looping.py
+++ b/metplus/util/time_looping.py
@@ -560,30 +560,80 @@ def _handle_lead_groups(lead_groups):
 def get_lead_sequence_groups(config):
     # output will be a dictionary where the key will be the
     #  label specified and the value will be the list of forecast leads
-    lead_seq_dict = {}
-    # used in plotting
+    lead_seq_dict = _get_lead_groups_from_indices(config)
+    if lead_seq_dict is not None:
+        return lead_seq_dict
+
+    # if no indices were found, check if divisions are requested
+    return _get_lead_groups_from_divisions(config)
+
+
+def _get_lead_groups_from_indices(config):
     all_conf = config.keys('config')
     indices = []
-    regex = re.compile(r"LEAD_SEQ_(\d+)")
+    regex = re.compile(r"LEAD_SEQ_(\d+)$")
     for conf in all_conf:
         result = regex.match(conf)
         if result is not None:
             indices.append(result.group(1))
 
+    if not indices:
+        return None
+
+    lead_seq_dict = {}
     # loop over all possible variables and add them to list
     for index in indices:
-        if config.has_option('config', f"LEAD_SEQ_{index}_LABEL"):
-            label = config.getstr('config', f"LEAD_SEQ_{index}_LABEL")
-        else:
-            label = f"Group{index}"
-
+        label = _get_label_from_index(config, index)
         # get forecast list for n
         lead_string_list = getlist(config.getstr('config', f'LEAD_SEQ_{index}'))
-        lead_seq = _handle_lead_seq(config,
-                                    lead_string_list,
-                                    lead_min=None,
-                                    lead_max=None)
+        lead_seq = _handle_lead_seq(config, lead_string_list,
+                                    lead_min=None, lead_max=None)
         # add to output dictionary
         lead_seq_dict[label] = lead_seq
 
     return lead_seq_dict
+
+
+def _get_lead_groups_from_divisions(config):
+    if not config.has_option('config', 'LEAD_SEQ_DIVISIONS'):
+        return {}
+
+    lead_list = getlist(config.getstr('config', 'LEAD_SEQ', ''))
+    divisions = config.getstr('config', 'LEAD_SEQ_DIVISIONS')
+    divisions = get_relativedelta(divisions, default_unit='H')
+    lead_min = get_relativedelta('0')
+    lead_max = divisions - get_relativedelta('1S')
+    index = 1
+    now = datetime.now()
+    # maximum 1000 divisions can be created to prevent infinite loop
+    num_leads = 0
+    lead_groups = {}
+    while now + lead_max < now + (divisions * 1000):
+        lead_seq = _handle_lead_seq(config, lead_list,
+                                    lead_min=lead_min, lead_max=lead_max)
+        if lead_seq:
+            label = _get_label_from_index(config, index)
+            lead_groups[label] = lead_seq
+            num_leads += len(lead_seq)
+
+        # if all forecast leads have been handled, break out of while loop
+        if num_leads >= len(lead_list):
+            break
+
+        index += 1
+        lead_min += divisions
+        lead_max += divisions
+
+    if num_leads < len(lead_list):
+        config.logger.warning('Could not split LEAD_SEQ using LEAD_SEQ_DIVISIONS')
+        return None
+
+    return lead_groups
+
+
+def _get_label_from_index(config, index):
+    if config.has_option('config', f"LEAD_SEQ_{index}_LABEL"):
+        return config.getstr('config', f"LEAD_SEQ_{index}_LABEL")
+    if config.has_option('config', "LEAD_SEQ_DIVISIONS_LABEL"):
+        return f"{config.getstr('config', 'LEAD_SEQ_DIVISIONS_LABEL')}{index}"
+    return f"Group{index}"

From 9c2e258749e8565bcd3253d7a7145aec3d853c1a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:53:10 -0600
Subject: [PATCH 19/26] per #2612, add unit tests for function that gets groups
 of forecast leads and added tests for new groups capabilities

---
 .../util/time_looping/test_time_looping.py    | 75 +++++++++++++++++++
 1 file changed, 75 insertions(+)

diff --git a/internal/tests/pytests/util/time_looping/test_time_looping.py b/internal/tests/pytests/util/time_looping/test_time_looping.py
index 53689acce0..847f6c929f 100644
--- a/internal/tests/pytests/util/time_looping/test_time_looping.py
+++ b/internal/tests/pytests/util/time_looping/test_time_looping.py
@@ -7,6 +7,81 @@
 from metplus.util.time_util import ti_calculate, ti_get_hours_from_relativedelta
 
 
+@pytest.mark.parametrize(
+    'config_dict, expected_output', [
+        # 1 group
+        ({'LEAD_SEQ_1': "0, 1, 2, 3",
+          'LEAD_SEQ_1_LABEL': 'Day1',
+          },  {'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)]}),
+        # 2 groups, no overlap
+        ({'LEAD_SEQ_1': "0, 1, 2, 3",
+          'LEAD_SEQ_1_LABEL': 'Day1',
+          'LEAD_SEQ_2': "8, 9, 10, 11",
+          'LEAD_SEQ_2_LABEL': 'Day2',
+          },  {'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)],
+               'Day2': [relativedelta(hours=+8), relativedelta(hours=+9), relativedelta(hours=+10),
+                        relativedelta(hours=+11)]}),
+        # 2 groups, overlap
+        ({'LEAD_SEQ_1': "0, 1, 2, 3",
+          'LEAD_SEQ_1_LABEL': 'Day1',
+          'LEAD_SEQ_2': "3, 4, 5, 6",
+          'LEAD_SEQ_2_LABEL': 'Day2',
+          }, {'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)],
+              'Day2': [relativedelta(hours=+3), relativedelta(hours=+4), relativedelta(hours=+5),
+                       relativedelta(hours=+6)]}),
+        # 2 groups, no overlap, out of order
+        ({'LEAD_SEQ_1': "8, 9, 10, 11",
+          'LEAD_SEQ_1_LABEL': 'Day2',
+          'LEAD_SEQ_2': "0, 1, 2, 3",
+          'LEAD_SEQ_2_LABEL': 'Day1',
+          },  {'Day2': [relativedelta(hours=+8), relativedelta(hours=+9), relativedelta(hours=+10),
+                        relativedelta(hours=+11)],
+               'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)]}),
+        # 2 groups, overlap, out of order
+        ({'LEAD_SEQ_1': "3, 4, 5, 6",
+          'LEAD_SEQ_1_LABEL': 'Day2',
+          'LEAD_SEQ_2': "0, 1, 2, 3",
+          'LEAD_SEQ_2_LABEL': 'Day1',
+          }, {'Day2': [relativedelta(hours=+3), relativedelta(hours=+4), relativedelta(hours=+5),
+                       relativedelta(hours=+6)],
+              'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)]}),
+        # divisions without labels
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d"},
+         {'Group1': [relativedelta(), relativedelta(hours=+12)],
+          'Group2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
+        # divisions with divisions label
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+         {'Day1': [relativedelta(), relativedelta(hours=+12)],
+          'Day2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
+        # divisions with explicit labels
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d",
+          'LEAD_SEQ_1_LABEL': 'One', 'LEAD_SEQ_2_LABEL': 'Two'},
+         {'One': [relativedelta(), relativedelta(hours=+12)],
+          'Two': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
+        # divisions with one explicit label, one no label
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_1_LABEL': 'One'},
+         {'One': [relativedelta(), relativedelta(hours=+12)],
+          'Group2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
+        # divisions with one explicit label, one division label
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d",
+          'LEAD_SEQ_1_LABEL': 'One', 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+         {'One': [relativedelta(), relativedelta(hours=+12)],
+          'Day2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
+        # divisions with skipped index
+        ({'LEAD_SEQ': "0, 12, 48, 60", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+         {'Day1': [relativedelta(), relativedelta(hours=+12)],
+          'Day3': [relativedelta(days=+2), relativedelta(days=+2, hours=+12)]}),
+    ]
+)
+@pytest.mark.util
+def test_get_lead_sequence_groups(metplus_config, config_dict, expected_output):
+    config = metplus_config
+    for key, value in config_dict.items():
+        config.set('config', key, value)
+
+    assert tl.get_lead_sequence_groups(config) == expected_output
+
+
 @pytest.mark.parametrize(
     'run_time, skip_times, inc_times, expected_result', [
         (datetime(2019, 12, 30), {'%d': ['30', '31']}, None, True),

From ab1f3dbe827412ffe376292452479b5a06936179 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:53:43 -0600
Subject: [PATCH 20/26] various refactoring to satisfy SonarQube complaints

---
 .../util/time_looping/test_time_looping.py    | 106 +++++++-----------
 metplus/util/time_util.py                     |  85 +++++++-------
 metplus/wrappers/runtime_freq_wrapper.py      |  53 +++++----
 3 files changed, 116 insertions(+), 128 deletions(-)

diff --git a/internal/tests/pytests/util/time_looping/test_time_looping.py b/internal/tests/pytests/util/time_looping/test_time_looping.py
index 847f6c929f..db0e1e8242 100644
--- a/internal/tests/pytests/util/time_looping/test_time_looping.py
+++ b/internal/tests/pytests/util/time_looping/test_time_looping.py
@@ -88,9 +88,12 @@ def test_get_lead_sequence_groups(metplus_config, config_dict, expected_output):
         (datetime(2019, 12, 30), {'%d': ['29', '31']}, None, False),
         (datetime(2019, 2, 27), {'%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, False),
         (datetime(2019, 3, 30), {'%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, True),
-        (datetime(2019, 3, 30), {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, True),
-        (datetime(2019, 3, 29), {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, True),
-        (datetime(2019, 1, 29), {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, False),
+        (datetime(2019, 3, 30),
+         {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, True),
+        (datetime(2019, 3, 29),
+         {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, True),
+        (datetime(2019, 1, 29),
+         {'%d': ['30', '31'], '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}, None, False),
         (datetime(2020, 10, 31), {'%Y%m%d': ['20201031']}, None, True),
         (datetime(2020, 3, 31), {'%Y%m%d': ['20201031']}, None, False),
         (datetime(2020, 10, 30), {'%Y%m%d': ['20201031']}, None, False),
@@ -121,6 +124,7 @@ def test_skip_time(run_time, skip_times, inc_times, expected_result):
     print(time_info)
     assert tl.skip_time(time_info, c_dict) == expected_result
 
+
 @pytest.mark.parametrize(
     'inc_init_times, skip_init_times, inc_valid_times, skip_valid_times, expected_result', [
         # nothing set
@@ -165,7 +169,7 @@ def test_skip_time(run_time, skip_times, inc_times, expected_result):
         (None, {'%m': ['12']}, None, {'%d': ['29', '30']}, True),
         # include/skip init/valid
         ({'%m': ['12']}, {'%d': ['29', '31']}, {'%m': ['11', '12']}, {'%d': ['29', '30']}, False),
-        ({'%m': ['10,' '11']}, {'%d': ['29', '31']}, {'%m': ['11', '12']}, {'%d': ['29', '30']}, True),
+        ({'%m': ['10', '11']}, {'%d': ['29', '31']}, {'%m': ['11', '12']}, {'%d': ['29', '30']}, True),
         ({'%m': ['12']}, {'%d': ['29', '30']}, {'%m': ['11', '12']}, {'%d': ['29', '30']}, True),
         ({'%m': ['12']}, {'%d': ['29', '31']}, {'%m': ['10', '11']}, {'%d': ['29', '30']}, True),
         ({'%m': ['12']}, {'%d': ['29', '31']}, {'%m': ['11', '12']}, {'%d': ['29', '31']}, True),
@@ -182,15 +186,15 @@ def test_skip_time_init_and_valid(inc_init_times, skip_init_times, inc_valid_tim
 
 @pytest.mark.util
 def test_skip_time_no_valid():
-    input_dict ={'init': datetime(2019, 1, 29)}
-    assert tl.skip_time(input_dict, {'SKIP_VALID_TIMES': {'%Y': ['2019']}}) == False
+    input_dict = {'init': datetime(2019, 1, 29)}
+    assert not tl.skip_time(input_dict, {'SKIP_VALID_TIMES': {'%Y': ['2019']}})
 
 
 @pytest.mark.parametrize(
     'skip_times_conf, expected_dict', [
-        ('"%d:30,31"', {'%d': ['30','31']}),
+        ('"%d:30,31"', {'%d': ['30', '31']}),
         ('"%m:begin_end_incr(3,11,1)"', {'%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
-        ('"%d:30,31", "%m:begin_end_incr(3,11,1)"', {'%d': ['30','31'],
+        ('"%d:30,31", "%m:begin_end_incr(3,11,1)"', {'%d': ['30', '31'],
                                                      '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
         ('"%Y%m%d:20201031"', {'%Y%m%d': ['20201031']}),
         ('"%Y%m%d:20201031", "%Y:2019"', {'%Y%m%d': ['20201031'],
@@ -199,52 +203,26 @@ def test_skip_time_no_valid():
     ]
 )
 @pytest.mark.util
-def test_get_skip_times(metplus_config, skip_times_conf, expected_dict):
-    conf = metplus_config
-    conf.set('config', 'SKIP_VALID_TIMES', skip_times_conf)
-
-    assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'T') == expected_dict
-
-
-@pytest.mark.parametrize(
-    'skip_times_conf, expected_dict', [
-        ('"%d:30,31"', {'%d': ['30','31']}),
-        ('"%m:begin_end_incr(3,11,1)"', {'%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
-        ('"%d:30,31", "%m:begin_end_incr(3,11,1)"', {'%d': ['30','31'],
-                                                     '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
-        ('"%Y%m%d:20201031"', {'%Y%m%d': ['20201031']}),
-        ('"%Y%m%d:20201031", "%Y:2019"', {'%Y%m%d': ['20201031'],
-                                          '%Y': ['2019']}),
-    ]
-)
-@pytest.mark.util
-def test_get_skip_times_wrapper(metplus_config, skip_times_conf, expected_dict):
-    conf = metplus_config
+class TestSkipTimes:
 
-    # set wrapper specific skip times, then ensure it is found
-    conf.set('config', 'GRID_STAT_SKIP_VALID_TIMES', skip_times_conf)
-    assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'grid_stat') == expected_dict
+    def test_get_skip_times(self, metplus_config, skip_times_conf, expected_dict):
+        conf = metplus_config
+        conf.set('config', 'SKIP_VALID_TIMES', skip_times_conf)
+        assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'T') == expected_dict
 
+    def test_get_skip_times_wrapper(self, metplus_config, skip_times_conf, expected_dict):
+        conf = metplus_config
+        # set wrapper specific skip times, then ensure it is found
+        conf.set('config', 'GRID_STAT_SKIP_VALID_TIMES', skip_times_conf)
+        assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'grid_stat') == expected_dict
 
-@pytest.mark.parametrize(
-    'skip_times_conf, expected_dict', [
-        ('"%d:30,31"', {'%d': ['30','31']}),
-        ('"%m:begin_end_incr(3,11,1)"', {'%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
-        ('"%d:30,31", "%m:begin_end_incr(3,11,1)"', {'%d': ['30','31'],
-                                                     '%m': ['3', '4', '5', '6', '7', '8', '9', '10', '11']}),
-        ('"%Y%m%d:20201031"', {'%Y%m%d': ['20201031']}),
-        ('"%Y%m%d:20201031", "%Y:2019"', {'%Y%m%d': ['20201031'],
-                                          '%Y': ['2019']}),
-    ]
-)
-@pytest.mark.util
-def test_get_skip_times_wrapper_not_used(metplus_config, skip_times_conf, expected_dict):
-    conf = metplus_config
+    def test_get_skip_times_wrapper_not_used(self, metplus_config, skip_times_conf, expected_dict):
+        conf = metplus_config
 
-    # set generic SKIP_TIMES, then request grid_stat to ensure it uses generic
-    conf.set('config', 'SKIP_VALID_TIMES', skip_times_conf)
+        # set generic SKIP_TIMES, then request grid_stat to ensure it uses generic
+        conf.set('config', 'SKIP_VALID_TIMES', skip_times_conf)
 
-    assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'grid_stat') == expected_dict
+        assert tl.get_skip_times(conf, 'SKIP', 'VALID', 'grid_stat') == expected_dict
 
 
 @pytest.mark.util
@@ -319,7 +297,7 @@ def test_time_generator_list(metplus_config):
             next(generator)
             assert False
         except StopIteration:
-            assert True
+            pass
 
 
 @pytest.mark.util
@@ -346,7 +324,7 @@ def test_time_generator_increment(metplus_config):
             next(generator)
             assert False
         except StopIteration:
-            assert True
+            pass
 
 
 @pytest.mark.parametrize(
@@ -467,21 +445,23 @@ def test_get_lead_sequence_lead(metplus_config):
 
 @pytest.mark.parametrize(
     'key, value', [
-        ('begin_end_incr(3,12,3)',  [ 3, 6, 9, 12]),
-        ('begin_end_incr( 3,12 , 3)',  [ 3, 6, 9, 12]),
-        ('begin_end_incr(0,10,2)',  [ 0, 2, 4, 6, 8, 10]),
-        ('begin_end_incr(10,0,-2)',  [ 10, 8, 6, 4, 2, 0]),
-        ('begin_end_incr(2,2,20)',  [ 2 ]),
-        ('begin_end_incr(72,72,6)',  [ 72 ]),
-        ('begin_end_incr(0,12,1), begin_end_incr(15,60,3)', [0,1,2,3,4,5,6,7,8,9,10,11,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60]),
-        ('begin_end_incr(0,10,2), 12',  [ 0, 2, 4, 6, 8, 10, 12]),
-        ('begin_end_incr(0,10,2)H, 12',  [ 0, 2, 4, 6, 8, 10, 12]),
-        ('begin_end_incr(0,10800,3600)S, 4H',  [ 0, 1, 2, 3, 4]),
+        ('begin_end_incr(3,12,3)',  [3, 6, 9, 12]),
+        ('begin_end_incr( 3,12 , 3)',  [3, 6, 9, 12]),
+        ('begin_end_incr(0,10,2)',  [0, 2, 4, 6, 8, 10]),
+        ('begin_end_incr(10,0,-2)',  [10, 8, 6, 4, 2, 0]),
+        ('begin_end_incr(2,2,20)',  [2]),
+        ('begin_end_incr(72,72,6)',  [72]),
+        ('begin_end_incr(0,12,1), begin_end_incr(15,60,3)',
+         [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 18, 21, 24, 27, 30, 33,
+          36, 39, 42, 45, 48, 51, 54, 57, 60]),
+        ('begin_end_incr(0,10,2), 12',  [0, 2, 4, 6, 8, 10, 12]),
+        ('begin_end_incr(0,10,2)H, 12',  [0, 2, 4, 6, 8, 10, 12]),
+        ('begin_end_incr(0,10800,3600)S, 4H',  [0, 1, 2, 3, 4]),
     ]
 )
 @pytest.mark.util
 def test_get_lead_sequence_lead_list(metplus_config, key, value):
-    input_dict = { 'valid' : datetime(2019, 2, 1, 13) }
+    input_dict = {'valid': datetime(2019, 2, 1, 13)}
     conf = metplus_config
     conf.set('config', 'LEAD_SEQ', key)
     test_seq = tl.get_lead_sequence(conf, input_dict)
@@ -526,7 +506,7 @@ def test_get_lead_sequence_lead_list(metplus_config, key, value):
     ]
 )
 @pytest.mark.util
-def test_get_lead_sequence_groups(metplus_config, config_dict, expected_list):
+def test_get_lead_sequence_from_groups(metplus_config, config_dict, expected_list):
     config = metplus_config
     for key, value in config_dict.items():
         config.set('config', key, value)
diff --git a/metplus/util/time_util.py b/metplus/util/time_util.py
index 2d0997189e..cc19485911 100755
--- a/metplus/util/time_util.py
+++ b/metplus/util/time_util.py
@@ -13,15 +13,8 @@
 from dateutil.relativedelta import relativedelta
 import re
 
-from .string_manip import split_level, format_thresh
+from .string_manip import format_thresh
 
-'''!@namespace TimeInfo
-@brief Utility to handle timing in METplus wrappers
-@code{.sh}
-Cannot be called directly. These are helper functions
-to be used in other METplus wrappers
-@endcode
-'''
 
 # dictionary where key is letter of time unit, i.e. Y and value is
 # the string representation of it, i.e. year
@@ -60,48 +53,52 @@ def get_relativedelta(value, default_unit='S'):
     mult = 1
     reg = r'(-*)(\d+)([a-zA-Z]*)'
     match = re.match(reg, value)
-    if match:
-        if match.group(1) == '-':
-            mult = -1
-        time_value = int(match.group(2)) * mult
-        unit_value = match.group(3)
-
-        # create relativedelta (dateutil) object for unit
-        # if no units specified, use seconds unless default_unit is specified
-        if unit_value == '':
-            if default_unit == 'S':
-                return relativedelta(seconds=time_value)
-            else:
-                unit_value = default_unit
-
-        if unit_value == 'H':
-            return relativedelta(hours=time_value)
-
-        if unit_value == 'M':
-            return relativedelta(minutes=time_value)
-
-        if unit_value == 'S':
+    if not match:
+        return None
+
+    if match.group(1) == '-':
+        mult = -1
+    time_value = int(match.group(2)) * mult
+    unit_value = match.group(3)
+
+    # create relativedelta (dateutil) object for unit
+    # if no units specified, use seconds unless default_unit is specified
+    if unit_value == '':
+        if default_unit == 'S':
             return relativedelta(seconds=time_value)
+        else:
+            unit_value = default_unit
 
-        if unit_value == 'd':
-            return relativedelta(days=time_value)
+    if unit_value == 'H':
+        return relativedelta(hours=time_value)
 
-        if unit_value == 'm':
-            return relativedelta(months=time_value)
+    if unit_value == 'M':
+        return relativedelta(minutes=time_value)
 
-        if unit_value == 'Y':
-            return relativedelta(years=time_value)
+    if unit_value == 'S':
+        return relativedelta(seconds=time_value)
 
-        # unsupported time unit specified, return None
-        return None
+    if unit_value == 'd':
+        return relativedelta(days=time_value)
+
+    if unit_value == 'm':
+        return relativedelta(months=time_value)
+
+    if unit_value == 'Y':
+        return relativedelta(years=time_value)
+
+    # unsupported time unit specified, return None
+    return None
 
 
 def get_seconds_from_string(value, default_unit='S', valid_time=None):
-    """!Convert string of time (optionally ending with time letter, i.e. HMSyMD to seconds
-        Args:
-          @param value string to convert, i.e. 3M, 4H, 17
-          @param default_unit units to apply if not specified at end of string
-          @returns time in seconds if successfully parsed, None if not"""
+    """!Convert string of time, optionally ending with time letter, e.g. HMSyMD to seconds
+
+      @param value string to convert, i.e. 3M, 4H, 17
+      @param default_unit units to apply if not specified at end of string
+      @param valid_time optional valid time to compute seconds if units to
+      convert are months or years
+      @returns time in seconds if successfully parsed, None if not"""
     rd_obj = get_relativedelta(value, default_unit)
     return ti_get_seconds_from_relativedelta(rd_obj, valid_time)
 
@@ -135,7 +132,7 @@ def ti_get_hours_from_relativedelta(lead, valid_time=None):
          @param lead relativedelta object to convert
          @param valid_time (optional) valid time required to convert values
           that contain months or years
-         @returns integer value of hours or None if cannot compute
+         @returns integer value of hours or None if it cannot be computed
     """
     lead_seconds = ti_get_seconds_from_relativedelta(lead, valid_time)
     if lead_seconds is None:
@@ -514,7 +511,7 @@ def add_to_time_input(time_input, clock_time=None, instance=None, custom=None):
     time_input['instance'] = instance if instance else ''
 
     # if custom is specified, set it
-    # otherwise leave it unset so it can be set within the wrapper
+    # otherwise leave it unset, so it can be set within the wrapper
     if custom:
         time_input['custom'] = custom
 
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index d4f1f7d8e3..f2cf83d26f 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -683,27 +683,8 @@ def subset_input_files(self, time_info, output_dir=None, leads=None,
         lead_loop = [None] if leads is None else leads
         for file_dict in self.c_dict['ALL_FILES']:
             for lead in lead_loop:
-                if lead is not None:
-                    current_time_info = time_info.copy()
-                    current_time_info['lead'] = lead
-                else:
-                    current_time_info = time_info
-
-                # compare time information for each input file
-                # add file to list of files to use if it matches
-                if not self.compare_time_info(current_time_info,
-                                              file_dict['time_info']):
-                    continue
-
-                for input_key in file_dict:
-                    # skip time info key
-                    if input_key == 'time_info':
-                        continue
-
-                    if input_key not in all_input_files:
-                        all_input_files[input_key] = []
-
-                    all_input_files[input_key].extend(file_dict[input_key])
+                self._add_files_that_match_time(all_input_files, time_info,
+                                                file_dict, lead)
 
         # return None if no matching input files were found
         if not all_input_files:
@@ -724,6 +705,36 @@ def subset_input_files(self, time_info, output_dir=None, leads=None,
 
         return list_file_dict
 
+    def _add_files_that_match_time(self, all_input_files, time_info, file_dict, lead):
+        """!Check if time info of input files matches current time info. If it
+        is a match, add the file info to the all_input_files dictionary.
+
+        @param all_input_files dictionary to add file info if there is a time match
+        @param time_info dictionary of time info to compare to file times
+        @param file_dict dictionary containing file information including file times
+        @param lead forecast lead to check
+        """
+        current_time_info = time_info
+        if lead is not None:
+            current_time_info = time_info.copy()
+            current_time_info['lead'] = lead
+
+        # compare time information for each input file
+        # add file to list of files to use if it matches
+        if not self.compare_time_info(current_time_info,
+                                      file_dict['time_info']):
+            return
+
+        for input_key in file_dict:
+            # skip time info key
+            if input_key == 'time_info':
+                continue
+
+            if input_key not in all_input_files:
+                all_input_files[input_key] = []
+
+            all_input_files[input_key].extend(file_dict[input_key])
+
     def get_list_file_name(self, time_info, identifier):
         """! Build name of ascii file that contains a list of files to process.
              If wildcard is set for init, valid, or lead then use the text ALL

From 5231f4c8d46dad0372bdae7eca7682f5f251ae2a Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:57:20 -0600
Subject: [PATCH 21/26] renamed config LEAD_SEQ_DIVISIONS to
 LEAD_SEQ_GROUP_SIZE and LEAD_SEQ_DIVISIONS_LABEL to LEAD_SEQ_GROUP_LABEL

---
 .../pytests/util/time_looping/test_time_looping.py | 14 +++++++-------
 metplus/util/time_looping.py                       | 10 +++++-----
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/internal/tests/pytests/util/time_looping/test_time_looping.py b/internal/tests/pytests/util/time_looping/test_time_looping.py
index db0e1e8242..90159f142b 100644
--- a/internal/tests/pytests/util/time_looping/test_time_looping.py
+++ b/internal/tests/pytests/util/time_looping/test_time_looping.py
@@ -46,29 +46,29 @@
                        relativedelta(hours=+6)],
               'Day1': [relativedelta(), relativedelta(hours=+1), relativedelta(hours=+2), relativedelta(hours=+3)]}),
         # divisions without labels
-        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d"},
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_GROUP_SIZE': "1d"},
          {'Group1': [relativedelta(), relativedelta(hours=+12)],
           'Group2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
         # divisions with divisions label
-        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_GROUP_SIZE': "1d", 'LEAD_SEQ_GROUP_LABEL': 'Day'},
          {'Day1': [relativedelta(), relativedelta(hours=+12)],
           'Day2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
         # divisions with explicit labels
-        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d",
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_GROUP_SIZE': "1d",
           'LEAD_SEQ_1_LABEL': 'One', 'LEAD_SEQ_2_LABEL': 'Two'},
          {'One': [relativedelta(), relativedelta(hours=+12)],
           'Two': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
         # divisions with one explicit label, one no label
-        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_1_LABEL': 'One'},
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_GROUP_SIZE': "1d", 'LEAD_SEQ_1_LABEL': 'One'},
          {'One': [relativedelta(), relativedelta(hours=+12)],
           'Group2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
         # divisions with one explicit label, one division label
-        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_DIVISIONS': "1d",
-          'LEAD_SEQ_1_LABEL': 'One', 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+        ({'LEAD_SEQ': "begin_end_incr(0,36,12)", 'LEAD_SEQ_GROUP_SIZE': "1d",
+          'LEAD_SEQ_1_LABEL': 'One', 'LEAD_SEQ_GROUP_LABEL': 'Day'},
          {'One': [relativedelta(), relativedelta(hours=+12)],
           'Day2': [relativedelta(days=+1), relativedelta(days=+1, hours=+12)]}),
         # divisions with skipped index
-        ({'LEAD_SEQ': "0, 12, 48, 60", 'LEAD_SEQ_DIVISIONS': "1d", 'LEAD_SEQ_DIVISIONS_LABEL': 'Day'},
+        ({'LEAD_SEQ': "0, 12, 48, 60", 'LEAD_SEQ_GROUP_SIZE': "1d", 'LEAD_SEQ_GROUP_LABEL': 'Day'},
          {'Day1': [relativedelta(), relativedelta(hours=+12)],
           'Day3': [relativedelta(days=+2), relativedelta(days=+2, hours=+12)]}),
     ]
diff --git a/metplus/util/time_looping.py b/metplus/util/time_looping.py
index 7bab6f52a9..eee0be20d2 100644
--- a/metplus/util/time_looping.py
+++ b/metplus/util/time_looping.py
@@ -595,11 +595,11 @@ def _get_lead_groups_from_indices(config):
 
 
 def _get_lead_groups_from_divisions(config):
-    if not config.has_option('config', 'LEAD_SEQ_DIVISIONS'):
+    if not config.has_option('config', 'LEAD_SEQ_GROUP_SIZE'):
         return {}
 
     lead_list = getlist(config.getstr('config', 'LEAD_SEQ', ''))
-    divisions = config.getstr('config', 'LEAD_SEQ_DIVISIONS')
+    divisions = config.getstr('config', 'LEAD_SEQ_GROUP_SIZE')
     divisions = get_relativedelta(divisions, default_unit='H')
     lead_min = get_relativedelta('0')
     lead_max = divisions - get_relativedelta('1S')
@@ -625,7 +625,7 @@ def _get_lead_groups_from_divisions(config):
         lead_max += divisions
 
     if num_leads < len(lead_list):
-        config.logger.warning('Could not split LEAD_SEQ using LEAD_SEQ_DIVISIONS')
+        config.logger.warning('Could not split LEAD_SEQ using LEAD_SEQ_GROUP_SIZE')
         return None
 
     return lead_groups
@@ -634,6 +634,6 @@ def _get_lead_groups_from_divisions(config):
 def _get_label_from_index(config, index):
     if config.has_option('config', f"LEAD_SEQ_{index}_LABEL"):
         return config.getstr('config', f"LEAD_SEQ_{index}_LABEL")
-    if config.has_option('config', "LEAD_SEQ_DIVISIONS_LABEL"):
-        return f"{config.getstr('config', 'LEAD_SEQ_DIVISIONS_LABEL')}{index}"
+    if config.has_option('config', "LEAD_SEQ_GROUP_LABEL"):
+        return f"{config.getstr('config', 'LEAD_SEQ_GROUP_LABEL')}{index}"
     return f"Group{index}"

From fe1d748e08605bacac0cd437a364a9f65436b6e0 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 17:22:58 -0600
Subject: [PATCH 22/26] per #2612, add documentation for new config variables
 including examples

---
 docs/Users_Guide/glossary.rst            | 17 ++++++-
 docs/Users_Guide/systemconfiguration.rst | 63 ++++++++++++++++++++++--
 2 files changed, 73 insertions(+), 7 deletions(-)

diff --git a/docs/Users_Guide/glossary.rst b/docs/Users_Guide/glossary.rst
index 29890ccfcf..dff37c4efa 100644
--- a/docs/Users_Guide/glossary.rst
+++ b/docs/Users_Guide/glossary.rst
@@ -2247,10 +2247,23 @@ METplus Configuration Glossary
      | *Used by:*  SeriesAnalysis
 
    LEAD_SEQ_<n>_LABEL
-     Required when SERIES_BY_LEAD_GROUP_FCSTS=True. Specify the label of the corresponding bin of series by lead results.
+     Specify the label for the :term:`LEAD_SEQ_<n>` group of forecast leads.
 
      | *Used by:*  SeriesAnalysis
 
+   LEAD_SEQ_GROUP_SIZE
+     Defines the size of forecast lead groups to create from :term:`LEAD_SEQ`.
+     See :ref:`grouping_forecast_leads` for more information.
+
+     | *Used by:*  All
+
+   LEAD_SEQ_GROUP_LABEL
+     Defines the label to apply for each forecast lead group that are created
+     using :term:`LEAD_SEQ` and :term:`LEAD_SEQ_GROUP_SIZE`.
+     See :ref:`grouping_forecast_leads` for more information.
+
+     | *Used by:*  All
+
    LINE_TYPE
      .. warning:: **DEPRECATED:** Please use :term:`LINE_TYPE_LIST` instead.
 
@@ -3545,7 +3558,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`LEAD_SEQ_\<n>` and :term:`SERIES_ANALYSIS_RUNTIME_FREQ` instead.
 
    SERIES_BY_LEAD_GROUP_FCSTS
-     .. warning:: **DEPRECATED:** Please use :term:`SERIES_ANALYSIS_GROUP_FCSTS` instead.
+     .. warning:: **DEPRECATED:** Please use :term:`LEAD_SEQ_\<n>` and :term:`SERIES_ANALYSIS_RUNTIME_FREQ` instead.
 
    SERIES_INIT_FILTERED_OUT_DIR
      .. warning:: **DEPRECATED:** Please use :term:`SERIES_ANALYSIS_FILTERED_OUTPUT_DIR` instead.
diff --git a/docs/Users_Guide/systemconfiguration.rst b/docs/Users_Guide/systemconfiguration.rst
index bca6adb1db..cdffb1ffc6 100644
--- a/docs/Users_Guide/systemconfiguration.rst
+++ b/docs/Users_Guide/systemconfiguration.rst
@@ -795,11 +795,16 @@ is equivalent to setting::
   [config]
   LEAD_SEQ = 0, 3, 6, 9, 12
 
+.. _grouping_forecast_leads:
+
+Grouping Forecast Leads
+"""""""""""""""""""""""
+
 Grouping forecast leads is possible as well using a special version of
-the :term:`LEAD_SEQ` variable for the
-**SeriesByLead Wrapper Only**.
-If :term:`SERIES_BY_LEAD_GROUP_FCSTS` = True, then groups of
-forecast leads can be defined to be evaluated together.
+the :term:`LEAD_SEQ` variable.
+If {APP_NAME}_RUNTIME_FREQ, e.g. SERIES_ANALYSIS_RUNTIME_FREQ, is set to
+**RUN_ONCE_PER_INIT_OR_VALID**,
+then groups of forecast leads can be defined to be evaluated together.
 Any number of these groups can be defined by setting
 configuration variables LEAD_SEQ_1, LEAD_SEQ_2, ..., :term:`LEAD_SEQ_\<n\>`.
 The value can be defined with a
@@ -807,13 +812,61 @@ comma-separated list of integers (currently only hours are supported here)
 or using :ref:`begin_end_incr`. Each :term:`LEAD_SEQ_\<n\>` must have a
 corresponding variable :term:`LEAD_SEQ_<n>_LABEL`. For example::
 
-
   [config]
   LEAD_SEQ_1 = 0, 6, 12, 18
   LEAD_SEQ_1_LABEL = Day1
   LEAD_SEQ_2 = begin_end_incr(24,42,6)
   LEAD_SEQ_2_LABEL = Day2
 
+In this example, the label **Day1** will be used for 0, 6, 12, 18 and
+the label **Day2** will be used for 24, 30, 36, 42.
+
+Forecast leads can also be grouped by defining a single list of forecast leads
+with :term:`LEAD_SEQ`, then specifying the size of each group using
+:term:`LEAD_SEQ_GROUP_SIZE`. For example::
+
+    [config]
+    LEAD_SEQ = 0, 12, 24, 36
+    LEAD_SEQ_GROUP_SIZE = 1d
+
+This configuration will create groups of forecast leads that each contain 1 day.
+This is the equivalent of setting::
+
+    [config]
+    LEAD_SEQ_1 = 0, 12
+    LEAD_SEQ_2 = 24, 36
+
+Each group will be labeled Group<INDEX> where <INDEX> is the group number.
+In this example, the label **Group1** will be used for 0, 12 and
+the label **Group2** will be used for 24, 36.
+The label can be referenced in filename templates using {label}.
+
+To change the text "Group" to something else, set :term:`LEAD_SEQ_GROUP_LABEL`.
+Setting::
+
+    LEAD_SEQ_GROUP_LABEL = Day
+
+will label the groups **Day1** and **Day2**.
+
+:term:`LEAD_SEQ_<n>_LABEL` can also be used to change the label for a specific
+group. From the previous example, setting::
+
+    LEAD_SEQ_2_LABEL = SecondDay
+
+will label the groups **Day1** and **SecondDay**.
+
+If the list of forecast leads contain a gap where there are no leads that fall
+within a given group, that group will be skipped. For example::
+
+    [config]
+    LEAD_SEQ = 0, 12, 48, 60
+    LEAD_SEQ_GROUP_SIZE = 1d
+    LEAD_SEQ_GROUP_LABEL = Day
+
+The label **Day1** will be used for 0, 12 and
+the label **Day3** will be used for 48, 60.
+Notice that a **Day2** label is not created.
+
 :term:`INIT_SEQ`
 """"""""""""""""
 

From d7288b655eba510136201c893f4da84b54783ffb Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 17:27:06 -0600
Subject: [PATCH 23/26] fix empty check for DataFrame

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

diff --git a/metplus/wrappers/cyclone_plotter_wrapper.py b/metplus/wrappers/cyclone_plotter_wrapper.py
index 8c5fa18526..1bd26b8e2d 100644
--- a/metplus/wrappers/cyclone_plotter_wrapper.py
+++ b/metplus/wrappers/cyclone_plotter_wrapper.py
@@ -329,7 +329,7 @@ def retrieve_data(self):
             if not self.is_global_extent:
                 self.logger.debug(f"Subset the data based on the region of interest.")
                 subset_by_region_df = self.subset_by_region(sanitized_df)
-                if not subset_by_region_df:
+                if subset_by_region_df.empty:
                     return None
                 final_df = subset_by_region_df.copy(deep=True)
             else:

From 597b952d8f89e8ca054deb45bd6ee16d9c3201db Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Fri, 28 Jun 2024 17:30:07 -0600
Subject: [PATCH 24/26] fix rst typo

---
 docs/Users_Guide/glossary.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/Users_Guide/glossary.rst b/docs/Users_Guide/glossary.rst
index dff37c4efa..1bd9595b17 100644
--- a/docs/Users_Guide/glossary.rst
+++ b/docs/Users_Guide/glossary.rst
@@ -2244,12 +2244,12 @@ METplus Configuration Glossary
    LEAD_SEQ_<n>
      Specify the sequence of forecast lead times to include in the analysis. Comma separated list format, e.g.:0, 6, 12. <n> corresponds to the bin in which the user wishes to aggregate series by lead results.
 
-     | *Used by:*  SeriesAnalysis
+     | *Used by:*  All
 
    LEAD_SEQ_<n>_LABEL
-     Specify the label for the :term:`LEAD_SEQ_<n>` group of forecast leads.
+     Specify the label for the :term:`LEAD_SEQ_\<n>` group of forecast leads.
 
-     | *Used by:*  SeriesAnalysis
+     | *Used by:*  All
 
    LEAD_SEQ_GROUP_SIZE
      Defines the size of forecast lead groups to create from :term:`LEAD_SEQ`.

From d36faaa82e379a97878332d33ca0b3ca19a769a0 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 3 Jul 2024 12:35:00 -0600
Subject: [PATCH 25/26] minor cleanup to satisfy linter

---
 metplus/wrappers/compare_gridded_wrapper.py | 2 +-
 metplus/wrappers/mode_wrapper.py            | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/metplus/wrappers/compare_gridded_wrapper.py b/metplus/wrappers/compare_gridded_wrapper.py
index 9e27757b55..86ef774cdc 100755
--- a/metplus/wrappers/compare_gridded_wrapper.py
+++ b/metplus/wrappers/compare_gridded_wrapper.py
@@ -76,7 +76,7 @@ def create_c_dict(self):
 
         return c_dict
 
-    def set_environment_variables(self, time_info):
+    def set_environment_variables(self, time_info=None):
         """! Set environment variables that will be set when running this tool.
             Wrappers can override this function to set wrapper-specific values,
             then call this (super) version to handle user configs and printing
diff --git a/metplus/wrappers/mode_wrapper.py b/metplus/wrappers/mode_wrapper.py
index a4ab535f21..f650b26a29 100755
--- a/metplus/wrappers/mode_wrapper.py
+++ b/metplus/wrappers/mode_wrapper.py
@@ -15,6 +15,7 @@
 from ..util import do_string_sub
 from . import CompareGriddedWrapper
 
+
 class MODEWrapper(CompareGriddedWrapper):
     """!Wrapper for the mode MET tool"""
 

From c94c495bec52cfa6f0125c54994bbe302a8402ce Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 3 Jul 2024 12:39:58 -0600
Subject: [PATCH 26/26] Per #2612, if runtime freq is RUN_ONCE_PER_LEAD and
 groups of forecast leads are specified, then the wrapper will be run once per
 lead GROUP instead of once for each unique lead in the lead groups. Update
 unit test to reflect new behavior

---
 .../wrappers/user_script/test_user_script.py  | 10 +--
 metplus/util/time_looping.py                  |  2 +-
 metplus/wrappers/runtime_freq_wrapper.py      | 66 +++++++++++--------
 3 files changed, 43 insertions(+), 35 deletions(-)

diff --git a/internal/tests/pytests/wrappers/user_script/test_user_script.py b/internal/tests/pytests/wrappers/user_script/test_user_script.py
index 64e0b765d4..5102d3c94c 100644
--- a/internal/tests/pytests/wrappers/user_script/test_user_script.py
+++ b/internal/tests/pytests/wrappers/user_script/test_user_script.py
@@ -168,14 +168,8 @@ def set_run_type_info(config, run_type):
                   'echo init_{init?fmt=%Y%m%d%H%M%S}_'
                   'valid_{valid?fmt=%Y%m%d%H%M%S}_lead_{lead?fmt=%3H}.nc')},
          ['LEAD_GROUPS'],
-         ['echo init_*_valid_*_lead_000.nc',
-          'echo init_*_valid_*_lead_024.nc',
-          'echo init_*_valid_*_lead_048.nc',
-          'echo init_*_valid_*_lead_072.nc',
-          'echo init_*_valid_*_lead_096.nc',
-          'echo init_*_valid_*_lead_120.nc',
-          'echo init_*_valid_*_lead_144.nc',
-          'echo init_*_valid_*_lead_168.nc',
+         ['echo init_*_valid_*_lead_*.nc',
+          'echo init_*_valid_*_lead_*.nc',
           ]),
         # run all init/lead sequence - simple
         ({'USER_SCRIPT_RUNTIME_FREQ': 'RUN_ONCE_FOR_EACH',
diff --git a/metplus/util/time_looping.py b/metplus/util/time_looping.py
index eee0be20d2..736b359538 100644
--- a/metplus/util/time_looping.py
+++ b/metplus/util/time_looping.py
@@ -464,7 +464,7 @@ def _are_lead_configs_ok(lead_seq, init_seq, lead_groups,
             return False
 
         # if looping by init, fail and exit
-        if 'valid' not in input_dict.keys():
+        if 'valid' not in input_dict.keys() or input_dict['valid'] == '*':
             log_msg = ('INIT_SEQ specified while looping by init time.'
                        ' Use LEAD_SEQ or change to loop by valid time')
             config.logger.error(log_msg)
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index f2cf83d26f..57a3f76d26 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -271,18 +271,8 @@ def run_once_per_init_or_valid(self, custom):
             time_info = time_util.ti_calculate(time_input)
 
             lead_groups = self._get_leads_as_group(time_info)
-            for label, lead_seq in lead_groups.items():
-                self._log_lead_group(label, lead_seq)
-                time_info['label'] = label
-                self.c_dict['ALL_FILES'] = (
-                    self.get_all_files_from_leads(time_info, lead_seq)
-                )
-                if not self._check_input_files():
-                    continue
-
-                self.clear()
-                if not self.run_at_time_once(time_info):
-                    success = False
+            if not self.run_once_per_lead_group(lead_groups, time_info):
+                success = False
 
         return success
 
@@ -303,27 +293,51 @@ def _log_lead_group(self, label, lead_seq):
         self.logger.info(f"Processing lead group {label}:"
                          f" {format_lead_seq(lead_seq, plural=False)}")
 
+    def run_once_per_lead_group(self, lead_groups, time_input):
+        success = True
+        for label, lead_seq in lead_groups.items():
+            self._log_lead_group(label, lead_seq)
+            time_input['label'] = label
+            self.c_dict['ALL_FILES'] = (
+                self.get_all_files_from_leads(time_input, lead_seq)
+            )
+            if not self._check_input_files():
+                continue
+
+            self.clear()
+            if not self.run_at_time_once(time_input):
+                success = False
+
+        return success
+
     def run_once_per_lead(self, custom):
-        self.logger.debug("Running once for forecast lead time")
+        # create input dict and only set 'now' item
+        time_input = {
+            'init': '*',
+            'valid': '*',
+        }
+        add_to_time_input(time_input,
+                          clock_time=self.config.getstr('config', 'CLOCK_TIME'),
+                          instance=self.instance, custom=custom)
+
+        # check if forecast lead groups are specified and
+        # run once per group of leads if they are
+        lead_groups = get_lead_sequence_groups(self.config)
+        if lead_groups:
+            self.logger.debug("Running once per forecast lead group")
+            time_input['lead'] = '*'
+            return self.run_once_per_lead_group(lead_groups, time_input)
+
+        self.logger.debug("Running once per forecast lead time")
         success = True
 
         lead_seq = get_lead_sequence(self.config, input_dict=None)
         for lead in lead_seq:
-            # create input dict and only set 'now' item
-            # create a new dictionary each iteration in case the function
-            # that it is passed into modifies it
-            time_input = {}
-            add_to_time_input(time_input,
-                              clock_time=self.config.getstr('config',
-                                                            'CLOCK_TIME'),
-                              instance=self.instance,
-                              custom=custom)
-
-            # add forecast lead
+            # add forecast lead to time input
             time_input['lead'] = lead
-            time_input['init'] = '*'
-            time_input['valid'] = '*'
 
+            # create a new dictionary each iteration in case the function
+            # that it is passed into modifies it
             time_info = time_util.ti_calculate(time_input)
 
             self.c_dict['ALL_FILES'] = self.get_all_files_for_lead(time_info)