From f9ad43ff42f7ae129432329133d7544a3b26f958 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 26 Sep 2022 14:14:31 -0600
Subject: [PATCH 01/34] removed logic to save user env to file

---
 metplus/util/met_util.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/metplus/util/met_util.py b/metplus/util/met_util.py
index a8c337b8f4..2c33a3d537 100644
--- a/metplus/util/met_util.py
+++ b/metplus/util/met_util.py
@@ -396,12 +396,6 @@ def write_final_conf(config):
 
         @param config METplusConfig object to write to file
      """
-    # write out os environment to file for debugging
-    env_file = os.path.join(config.getdir('LOG_DIR'), '.metplus_user_env')
-    with open(env_file, 'w') as env_file:
-        for key, value in os.environ.items():
-            env_file.write('{}={}\n'.format(key, value))
-
     final_conf = config.getstr('config', 'METPLUS_CONF')
 
     # remove variables that start with CURRENT

From c544f7d338bce708010c6cae927b94913f9fee39 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 26 Sep 2022 14:14:43 -0600
Subject: [PATCH 02/34] modified logic to set self.env to be more efficient

---
 metplus/wrappers/command_builder.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index f16dc01eff..44b20090e5 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -88,10 +88,7 @@ def __init__(self, config, instance=None):
             )
 
         self.instance = instance
-
-        self.env = os.environ.copy()
-        if hasattr(config, 'env'):
-            self.env = config.env
+        self.env = config.env if hasattr(config, 'env') else os.environ.copy()
 
         # populate c_dict dictionary
         self.c_dict = self.create_c_dict()

From 2604114ab9d4af15bf042b534d6b5c302e753b6c Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Mon, 26 Sep 2022 14:19:41 -0600
Subject: [PATCH 03/34] set LOOP_ORDER to always be processes, ci-run-all-diff

---
 metplus/util/met_util.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/metplus/util/met_util.py b/metplus/util/met_util.py
index 2c33a3d537..257e8ceb4b 100644
--- a/metplus/util/met_util.py
+++ b/metplus/util/met_util.py
@@ -137,6 +137,7 @@ def run_metplus(config, process_list):
             return 1
 
         loop_order = config.getstr('config', 'LOOP_ORDER', '').lower()
+        loop_order = 'processes'
 
         if loop_order == "processes":
             all_commands = []

From 751f30444c0b3805c089a4bc270ab92f7ed005fc Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 27 Sep 2022 11:36:57 -0600
Subject: [PATCH 04/34] added function to easily get string of wrapper name and
 instance if it is set

---
 metplus/wrappers/command_builder.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index 44b20090e5..148061d3d4 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -1624,3 +1624,8 @@ def handle_climo_cdf_dict(self, write_bins=True):
 
         items['direct_prob'] = 'bool'
         self.add_met_config_dict('climo_cdf', items)
+
+    def get_wrapper_instance_name(self):
+        if not self.instance:
+            return self.app_name
+        return f'{self.app_name}({self.instance})'

From f41630b22f31a3800d4e94d5459d3e965f365b74 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 27 Sep 2022 11:37:10 -0600
Subject: [PATCH 05/34] fix indentation

---
 metplus/wrappers/runtime_freq_wrapper.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 8488f2072a..c785b1381c 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -28,11 +28,12 @@
 class RuntimeFreqWrapper(CommandBuilder):
 
     # valid options for run frequency
-    FREQ_OPTIONS = ['RUN_ONCE',
-                    'RUN_ONCE_PER_INIT_OR_VALID',
-                    'RUN_ONCE_PER_LEAD',
-                    'RUN_ONCE_FOR_EACH'
-                    ]
+    FREQ_OPTIONS = [
+        'RUN_ONCE',
+        'RUN_ONCE_PER_INIT_OR_VALID',
+        'RUN_ONCE_PER_LEAD',
+        'RUN_ONCE_FOR_EACH'
+    ]
 
     def __init__(self, config, instance=None):
         super().__init__(config, instance=instance)

From 8c29a406efcb86c80daaa32333f1ec747dbdb7db Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 27 Sep 2022 11:37:42 -0600
Subject: [PATCH 06/34] log which wrapper is being run at start of each wrapper
 execution

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

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index c785b1381c..a0634641e4 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -110,6 +110,9 @@ def run_all_times(self):
                                "mode unless LOOP_ORDER = processes")
                 return None
 
+        wrapper_instance_name = self.get_wrapper_instance_name()
+        self.logger.info(f'Running wrapper: {wrapper_instance_name}')
+
         # loop over all custom strings
         for custom_string in self.c_dict['CUSTOM_LOOP_LIST']:
             if custom_string:

From 2422b6ca09bb00708ac7cb16a941ba597dbe00f1 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 27 Sep 2022 13:28:27 -0600
Subject: [PATCH 07/34] per #1687, modified runtime freq logic to get relevant
 files for each time iteration instead of gathering all files and subsetting
 them for each time. Modified logic in SeriesAnalysis wrapper to handle
 writing of file list files using RuntimeFreq logic to prevent 2 different
 approaches for handling file lists. SeriesAnalysis file list files will still
 be written to the appropriate directory but the file name will no longer
 include the range of forecasts used. This is OK because the other output
 files contain this info and it is not necessary for the file lists since they
 are found in the directory for each forecast time range

---
 metplus/wrappers/runtime_freq_wrapper.py    |  99 ++++++++++++-----
 metplus/wrappers/series_analysis_wrapper.py | 115 ++++++++------------
 2 files changed, 117 insertions(+), 97 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index a0634641e4..5e34fbcd12 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -129,11 +129,6 @@ def run_all_times_custom(self, custom):
 
              @returns True on success, False on failure
         """
-        # get a list of all input files that are available
-        if not self.get_all_files(custom):
-            self.log_error("A problem occurred trying to obtain input files")
-            return None
-
         runtime_freq = self.c_dict['RUNTIME_FREQ']
         if runtime_freq == 'RUN_ONCE':
             self.run_once(custom)
@@ -159,6 +154,10 @@ def run_once(self, custom):
         time_input['valid'] = '*'
         time_input['lead'] = '*'
 
+        if not self.get_all_files(custom):
+            self.log_error("A problem occurred trying to obtain input files")
+            return None
+
         return self.run_at_time_once(time_input)
 
     def run_once_per_init_or_valid(self, custom):
@@ -182,6 +181,8 @@ def run_once_per_init_or_valid(self, custom):
 
             time_input['lead'] = '*'
 
+            self.c_dict['ALL_FILES'] = self.get_all_files_from_leads(time_input)
+
             self.clear()
             if not self.run_at_time_once(time_input):
                 success = False
@@ -209,6 +210,8 @@ def run_once_per_lead(self, custom):
             time_input['init'] = '*'
             time_input['valid'] = '*'
 
+            self.c_dict['ALL_FILES'] = self.get_all_files_for_lead(time_input)
+
             self.clear()
             if not self.run_at_time_once(time_input):
                 success = False
@@ -272,27 +275,8 @@ def get_all_files(self, custom=None):
                               instance=self.instance,
                               custom=custom)
 
-            # 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:
-                time_input['lead'] = lead
-
-                # set current lead time config and environment variables
-                time_info = time_util.ti_calculate(time_input)
-
-                if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
-                    continue
-
-                file_dict = self.get_files_from_time(time_info)
-                if file_dict:
-                    if isinstance(file_dict, list):
-                        all_files.extend(file_dict)
-                    else:
-                        all_files.append(file_dict)
+            lead_files = self.get_all_files_from_leads(time_input)
+            all_files.extend(lead_files)
 
         if not all_files:
             return False
@@ -300,6 +284,58 @@ def get_all_files(self, custom=None):
         self.c_dict['ALL_FILES'] = all_files
         return True
 
+    def get_all_files_from_leads(self, time_input):
+        lead_files = []
+        # loop over all forecast leads
+        wildcard_if_empty = self.c_dict.get('WILDCARD_LEAD_IF_EMPTY',
+                                            False)
+        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
+
+            # set current lead time config and environment variables
+            time_info = time_util.ti_calculate(current_time_input)
+
+            if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
+                continue
+
+            file_dict = self.get_files_from_time(time_info)
+            if file_dict:
+                if isinstance(file_dict, list):
+                    lead_files.extend(file_dict)
+                else:
+                    lead_files.append(file_dict)
+
+        return lead_files
+
+    def get_all_files_for_lead(self, time_input):
+        new_files = []
+        for run_time in time_generator(self.config):
+            if run_time is None:
+                continue
+
+            current_time_input = time_input.copy()
+            if 'valid' in run_time:
+                current_time_input['valid'] = run_time['valid']
+                del current_time_input['init']
+            elif 'init' in run_time:
+                current_time_input['init'] = run_time['init']
+                del current_time_input['valid']
+            time_info = time_util.ti_calculate(current_time_input)
+            if skip_time(time_info, self.c_dict.get('SKIP_TIMES')):
+                continue
+            file_dict = self.get_files_from_time(time_info)
+            if file_dict:
+                if isinstance(file_dict, list):
+                    new_files.extend(file_dict)
+                else:
+                    new_files.append(file_dict)
+
+        return new_files
+
     def get_files_from_time(self, time_info):
         """! Create dictionary containing time information (key time_info) and
              any relevant files for that runtime.
@@ -322,12 +358,13 @@ def compare_time_info(self, runtime, filetime):
              @returns True if file's info matches the requirements for current
              runtime or False if not.
         """
+        # False if init/valid is not wildcard and the file time doesn't match
         for time_val in ['init', 'valid']:
             if (runtime[time_val] != '*' and
                     filetime[time_val] != runtime[time_val]):
                 return False
 
-        if runtime['lead'] == '*':
+        if runtime.get('lead', '*') == '*':
             return True
 
         # convert each value to seconds to compare
@@ -377,7 +414,7 @@ def find_input_files(self, time_info, fill_missing=False):
 
         return all_input_files
 
-    def subset_input_files(self, time_info):
+    def subset_input_files(self, time_info, output_dir=None):
         """! Obtain a subset of input files from the c_dict ALL_FILES based on
              the time information for the current run.
 
@@ -414,7 +451,9 @@ def subset_input_files(self, time_info):
         list_file_dict = {}
         for identifier, input_files in all_input_files.items():
             list_file_name = self.get_list_file_name(time_info, identifier)
-            list_file_path = self.write_list_file(list_file_name, input_files)
+            list_file_path = self.write_list_file(list_file_name,
+                                                  input_files,
+                                                  output_dir=output_dir)
             list_file_dict[identifier] = list_file_path
 
         return list_file_dict
@@ -439,7 +478,7 @@ def get_list_file_name(self, time_info, identifier):
         else:
             valid = time_info['valid'].strftime('%Y%m%d%H%M%S')
 
-        if time_info['lead'] == '*':
+        if time_info.get('lead', '*') == '*':
             lead = 'ALL'
         else:
             lead = time_util.ti_get_seconds_from_lead(time_info['lead'],
diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index cc45658217..380c8dfc88 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -26,7 +26,7 @@
 from ..util import do_string_sub, parse_template, get_tags
 from ..util import get_lead_sequence, get_lead_sequence_groups
 from ..util import ti_get_hours_from_lead, ti_get_seconds_from_lead
-from ..util import ti_get_lead_string
+from ..util import ti_get_lead_string, ti_calculate
 from ..util import parse_var_list
 from ..util import add_to_time_input
 from ..util import field_read_prob_info
@@ -460,16 +460,29 @@ def run_once_per_lead(self, custom):
 
             input_dict['init'] = '*'
             input_dict['valid'] = '*'
-            lead_hours = [ti_get_lead_string(item, plural=False) for
-                          item in lead_group[1]]
+            lead_hours_str = [ti_get_lead_string(item, plural=False) for
+                              item in lead_group[1]]
 
             self.logger.debug(f"Processing {lead_group[0]} - forecast leads: "
-                              f"{', '.join(lead_hours)}")
+                              f"{', '.join(lead_hours_str)}")
+
+            lead_hours = [ti_get_hours_from_lead(item) for item in lead_group[1]]
+            self.c_dict['ALL_FILES'] = self.get_all_files_for_leads(input_dict,
+                                                                    lead_hours)
             if not self.run_at_time_once(input_dict, lead_group):
                 success = False
 
         return success
 
+    def get_all_files_for_leads(self, input_dict, lead_hours):
+        all_files = []
+        current_input_dict = input_dict.copy()
+        for lead_hour in lead_hours:
+            current_input_dict['lead_hours'] = lead_hour
+            new_files = self.get_all_files_for_lead(current_input_dict)
+            all_files.extend(new_files)
+        return all_files
+
     def run_at_time_once(self, time_info, lead_group=None):
         """! Attempt to build series_analysis command for run time
 
@@ -577,12 +590,23 @@ def get_files_from_time(self, time_info):
             if fcst_files is None or obs_files is None:
                 return None
 
-            file_dict['fcst'] = fcst_files
-            file_dict['obs'] = obs_files
+            fcst_key, obs_key = self._get_fcst_obs_keys(storm_id)
+
+            file_dict[fcst_key] = fcst_files
+            file_dict[obs_key] = obs_files
             file_dict_list.append(file_dict)
 
         return file_dict_list
 
+    @staticmethod
+    def _get_fcst_obs_keys(storm_id):
+        fcst_key = 'fcst'
+        obs_key = 'obs'
+        if storm_id != '*':
+            fcst_key = f'{fcst_key}_{storm_id}'
+            obs_key = f'{obs_key}_{storm_id}'
+        return fcst_key, obs_key
+
     def find_input_files(self, time_info, data_type):
         """! Loop over list of input templates and find files for each
 
@@ -596,27 +620,6 @@ def find_input_files(self, time_info, data_type):
                                      mandatory=False)
         return input_files
 
-    def subset_input_files(self, time_info):
-        """! Obtain a subset of input files from the c_dict ALL_FILES based on
-             the time information for the current run.
-
-              @param time_info dictionary containing time information
-              @returns the path to a ascii file containing the list of files
-               or None if could not find any files
-        """
-        fcst_files = []
-        obs_files = []
-        for file_dict in self.c_dict['ALL_FILES']:
-            # compare time information for each input file
-            # add file to list of files to use if it matches
-            if not self.compare_time_info(time_info, file_dict['time_info']):
-                continue
-
-            fcst_files.extend(file_dict['fcst'])
-            obs_files.extend(file_dict['obs'])
-
-        return fcst_files, obs_files
-
     def compare_time_info(self, runtime, filetime):
         """! Call parents implementation then if the current run time and file
               time may potentially still not match, use storm_id to check
@@ -696,48 +699,20 @@ def _get_fcst_and_obs_path(self, time_info, storm_id, lead_group):
 
             return fcst_path, obs_path
 
-        all_fcst_files = []
-        all_obs_files = []
-        lead_loop = leads if leads else [None]
-        for lead in lead_loop:
-            if lead is not None:
-                time_info['lead'] = lead
-
-            fcst_files, obs_files = self.subset_input_files(time_info)
-            if fcst_files and obs_files:
-                all_fcst_files.extend(fcst_files)
-                all_obs_files.extend(obs_files)
-
-        # skip if no files were found
-        if not all_fcst_files or not all_obs_files:
-            return None, None
-
         output_dir = self.get_output_dir(time_info, storm_id, label)
 
-        # create forecast (or both) file list
-        if self.c_dict['USING_BOTH']:
-            data_type = 'BOTH'
-        else:
-            data_type = 'FCST'
+        list_file_dict = self.subset_input_files(time_info, output_dir)
+        if not list_file_dict:
+            return None, None
 
-        fcst_ascii_filename = self._get_ascii_filename(data_type,
-                                                       storm_id,
-                                                       leads)
-        fcst_path = self.write_list_file(fcst_ascii_filename,
-                                         all_fcst_files,
-                                         output_dir=output_dir)
+        # add storm_id and label to time_info for output filename
+        self._add_storm_id_and_label(time_info, storm_id, label)
 
+        fcst_key, obs_key = self._get_fcst_obs_keys(storm_id)
+        fcst_path = list_file_dict[fcst_key]
         if self.c_dict['USING_BOTH']:
             return fcst_path, fcst_path
-
-        # create analysis file list
-        obs_ascii_filename = self._get_ascii_filename('OBS',
-                                                      storm_id,
-                                                      leads)
-        obs_path = self.write_list_file(obs_ascii_filename,
-                                        all_obs_files,
-                                        output_dir=output_dir)
-
+        obs_path = list_file_dict[obs_key]
         return fcst_path, obs_path
 
     def _check_python_embedding(self):
@@ -818,17 +793,23 @@ def get_output_dir(self, time_info, storm_id, label):
         output_dir_template = os.path.join(self.c_dict['OUTPUT_DIR'],
                                            self.c_dict['OUTPUT_TEMPLATE'])
         output_dir_template = os.path.dirname(output_dir_template)
+
+        # get output directory including storm ID and label
+        current_time_info = time_info.copy()
+        self._add_storm_id_and_label(current_time_info, storm_id, label)
+        output_dir = do_string_sub(output_dir_template,
+                                   **current_time_info)
+        return output_dir
+
+    @staticmethod
+    def _add_storm_id_and_label(time_info, storm_id, label):
         if storm_id == '*':
             storm_id_out = 'all_storms'
         else:
             storm_id_out = storm_id
 
-        # get output directory including storm ID and label
         time_info['storm_id'] = storm_id_out
         time_info['label'] = label
-        output_dir = do_string_sub(output_dir_template,
-                                   **time_info)
-        return output_dir
 
     def build_and_run_series_request(self, time_info, fcst_path, obs_path):
         """! Build up the -obs, -fcst, -out necessary for running the

From f386fb7c7885ac9561d43d7ae008fbc1848185e7 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Tue, 27 Sep 2022 13:30:40 -0600
Subject: [PATCH 08/34] turn on use cases that run SeriesAnalysis and diff with
 ci-run-diff

---
 .github/parm/use_case_groups.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 3bb687f2c8..4a60113665 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -7,7 +7,7 @@
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": false
+    "run": true
   },
   {
     "category": "air_quality_and_comp",
@@ -77,7 +77,7 @@
   {
     "category": "medium_range",
     "index_list": "1-2",
-    "run": false
+    "run": true
   },
   {
     "category": "medium_range",
@@ -92,12 +92,12 @@
   {
     "category": "medium_range",
     "index_list": "7",
-    "run": false
+    "run": true
   },
   {
     "category": "medium_range",
     "index_list": "8",
-    "run": false
+    "run": true
   },
   {
     "category": "precipitation",
@@ -127,7 +127,7 @@
   {
     "category": "s2s",
     "index_list": "0",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
@@ -152,7 +152,7 @@
   {
     "category": "s2s",
     "index_list": "5",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",

From ca702253d44c7d94c3a59ffccb4bf79eb3129cfe Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 09:17:34 -0600
Subject: [PATCH 09/34] removed function that is no longer used

---
 .../series_analysis/test_series_analysis.py   | 51 +------------------
 metplus/wrappers/series_analysis_wrapper.py   | 44 ----------------
 2 files changed, 1 insertion(+), 94 deletions(-)

diff --git a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
index 5259e03ef1..b8a3c4d35d 100644
--- a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
+++ b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
@@ -798,61 +798,12 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
         actual_obs_files = file_handle.readlines()
     actual_obs_files = [item.strip() for item in actual_obs_files[1:]]
 
+    assert len(actual_obs_files) == len(expect_obs_subset)
     for actual_file, expected_file in zip(actual_obs_files, expect_obs_subset):
         actual_file = actual_file.replace(tile_input_dir, '').lstrip('/')
         assert actual_file == expected_file
 
 
-@pytest.mark.parametrize(
-        'storm_id, leads, expected_result', [
-        # storm ID, no leads
-        ('ML1221072014', None, '_FILES_ML1221072014'),
-        # no storm ID no leads
-        ('*', None, '_FILES'),
-        # storm ID, 1 lead
-        ('ML1221072014', [relativedelta(hours=12)], '_FILES_ML1221072014_F012'),
-        # no storm ID, 1 lead
-        ('*', [relativedelta(hours=12)], '_FILES_F012'),
-        # storm ID, 2 leads
-        ('ML1221072014', [relativedelta(hours=18),
-                                  relativedelta(hours=12)],
-         '_FILES_ML1221072014_F012_to_F018'),
-        # no storm ID, 2 leads
-        ('*', [relativedelta(hours=18),
-                       relativedelta(hours=12)],
-         '_FILES_F012_to_F018'),
-        # storm ID, 3 leads
-        ('ML1221072014', [relativedelta(hours=15),
-                                  relativedelta(hours=18),
-                                  relativedelta(hours=12)],
-         '_FILES_ML1221072014_F012_to_F018'),
-        # no storm ID, 3 leads
-        ('*', [relativedelta(hours=15),
-                       relativedelta(hours=18),
-                       relativedelta(hours=12)],
-         '_FILES_F012_to_F018'),
-    ]
-)
-@pytest.mark.wrapper_a
-def test_get_ascii_filename(metplus_config, storm_id, leads,
-                            expected_result):
-    wrapper = series_analysis_wrapper(metplus_config)
-    for data_type in ['FCST', 'OBS']:
-        actual_result = wrapper._get_ascii_filename(data_type,
-                                                   storm_id,
-                                                   leads)
-        assert actual_result == f"{data_type}{expected_result}"
-
-        if leads is None:
-            return
-
-        lead_seconds = [ti_get_seconds_from_lead(item) for item in leads]
-        actual_result = wrapper._get_ascii_filename(data_type,
-                                                   storm_id,
-                                                   lead_seconds)
-        assert actual_result == f"{data_type}{expected_result}"
-
-
 @pytest.mark.parametrize(
         # no storm ID, label
         'template, storm_id, label, expected_result', [
diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index 380c8dfc88..5c773a4caa 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -733,50 +733,6 @@ def _check_python_embedding(self):
 
         return True
 
-    @staticmethod
-    def _get_ascii_filename(data_type, storm_id, leads=None):
-        """! Build filename for ASCII file list file
-
-             @param data_type FCST, OBS, or BOTH
-             @param storm_id current storm ID or wildcard character
-             @param leads list of forecast leads to use add the forecast hour
-              string to the filename or the minimum and maximum forecast hour
-              strings if there are more than one lead
-             @returns string containing filename to use
-        """
-        prefix = f"{data_type}_FILES"
-
-        # of storm ID is set (not wildcard), then add it to filename
-        if storm_id == '*':
-            filename = ''
-        else:
-            filename = f"_{storm_id}"
-
-        # add forecast leads if specified
-        if leads is not None:
-            lead_hours_list = []
-            for lead in leads:
-                lead_hours = ti_get_hours_from_lead(lead)
-                if lead_hours is None:
-                    lead_hours = ti_get_lead_string(lead,
-                                                    letter_only=True)
-                lead_hours_list.append(lead_hours)
-
-            # get first forecast lead, convert to hours, and add to filename
-            lead_hours = min(lead_hours_list)
-
-            lead_str = str(lead_hours).zfill(3)
-            filename += f"_F{lead_str}"
-
-            # if list of forecast leads, get min and max and add them to name
-            if len(lead_hours_list) > 1:
-                max_lead_hours = max(lead_hours_list)
-                max_lead_str = str(max_lead_hours).zfill(3)
-                filename += f"_to_F{max_lead_str}"
-
-        ascii_filename = f"{prefix}{filename}"
-        return ascii_filename
-
     def get_output_dir(self, time_info, storm_id, label):
         """! Determine directory that will contain output data from the
               OUTPUT_DIR and OUTPUT_TEMPLATE. This will include any

From 4c8e2ec604c24c7bbb716f6cb77fca7a9e038424 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 09:18:00 -0600
Subject: [PATCH 10/34] fixed support for processing a group of multiple
 forecast leads

---
 metplus/wrappers/runtime_freq_wrapper.py    | 35 ++++++++++++++-------
 metplus/wrappers/series_analysis_wrapper.py | 23 +++++++++-----
 2 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 5e34fbcd12..862c676bbc 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -414,7 +414,7 @@ def find_input_files(self, time_info, fill_missing=False):
 
         return all_input_files
 
-    def subset_input_files(self, time_info, output_dir=None):
+    def subset_input_files(self, time_info, output_dir=None, leads=None):
         """! Obtain a subset of input files from the c_dict ALL_FILES based on
              the time information for the current run.
 
@@ -427,21 +427,34 @@ def subset_input_files(self, time_info, output_dir=None):
         if not self.c_dict.get('ALL_FILES'):
             return all_input_files
 
+        if leads is None:
+            lead_loop = [None]
+        else:
+            lead_loop = leads
+
         for file_dict in self.c_dict['ALL_FILES']:
-            # compare time information for each input file
-            # add file to list of files to use if it matches
-            if not self.compare_time_info(time_info, file_dict['time_info']):
-                continue
+            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
 
-            for input_key in file_dict:
-                # skip time info key
-                if input_key == '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
 
-                if input_key not in all_input_files:
-                    all_input_files[input_key] = []
+                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])
+                    all_input_files[input_key].extend(file_dict[input_key])
 
         # return None if no matching input files were found
         if not all_input_files:
diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index 5c773a4caa..5ec6da50d4 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -27,6 +27,7 @@
 from ..util import get_lead_sequence, get_lead_sequence_groups
 from ..util import ti_get_hours_from_lead, ti_get_seconds_from_lead
 from ..util import ti_get_lead_string, ti_calculate
+from ..util import ti_get_seconds_from_relativedelta
 from ..util import parse_var_list
 from ..util import add_to_time_input
 from ..util import field_read_prob_info
@@ -466,19 +467,24 @@ def run_once_per_lead(self, custom):
             self.logger.debug(f"Processing {lead_group[0]} - forecast leads: "
                               f"{', '.join(lead_hours_str)}")
 
-            lead_hours = [ti_get_hours_from_lead(item) for item in lead_group[1]]
-            self.c_dict['ALL_FILES'] = self.get_all_files_for_leads(input_dict,
-                                                                    lead_hours)
+            self.c_dict['ALL_FILES'] = (
+                self.get_all_files_for_leads(input_dict, lead_group[1])
+            )
+
+            # if only 1 forecast lead is being processed, set it in time dict
+            if len(lead_group[1]) == 1:
+                input_dict['lead'] = lead_group[1][0]
+
             if not self.run_at_time_once(input_dict, lead_group):
                 success = False
 
         return success
 
-    def get_all_files_for_leads(self, input_dict, lead_hours):
+    def get_all_files_for_leads(self, input_dict, leads):
         all_files = []
         current_input_dict = input_dict.copy()
-        for lead_hour in lead_hours:
-            current_input_dict['lead_hours'] = lead_hour
+        for lead in leads:
+            current_input_dict['lead'] = lead
             new_files = self.get_all_files_for_lead(current_input_dict)
             all_files.extend(new_files)
         return all_files
@@ -701,13 +707,14 @@ def _get_fcst_and_obs_path(self, time_info, storm_id, lead_group):
 
         output_dir = self.get_output_dir(time_info, storm_id, label)
 
-        list_file_dict = self.subset_input_files(time_info, output_dir)
+        list_file_dict = self.subset_input_files(time_info,
+                                                 output_dir=output_dir,
+                                                 leads=leads)
         if not list_file_dict:
             return None, None
 
         # add storm_id and label to time_info for output filename
         self._add_storm_id_and_label(time_info, storm_id, label)
-
         fcst_key, obs_key = self._get_fcst_obs_keys(storm_id)
         fcst_path = list_file_dict[fcst_key]
         if self.c_dict['USING_BOTH']:

From f0758f61305af3d4b6b08a8e0af8f51bc5330fae Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 09:18:45 -0600
Subject: [PATCH 11/34] updated unit tests to conform to new method of
 gathering input files for series_analysis to be consistent with other
 runtime_freq

---
 .../series_analysis/test_series_analysis.py   | 128 ++++++++----------
 1 file changed, 60 insertions(+), 68 deletions(-)

diff --git a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
index b8a3c4d35d..b189a37c14 100644
--- a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
+++ b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
@@ -313,9 +313,13 @@ def test_series_analysis_single_field(metplus_config, config_overrides,
 
     config_file = wrapper.c_dict.get('CONFIG_FILE')
     out_dir = wrapper.c_dict.get('OUTPUT_DIR')
+    prefix = 'series_analysis_files_'
+    suffix = '_init_20050807000000_valid_ALL_lead_ALL.txt'
+    fcst_file = f'{prefix}fcst{suffix}'
+    obs_file = f'{prefix}obs{suffix}'
     expected_cmds = [(f"{app_path} "
-                      f"-fcst {out_dir}/FCST_FILES "
-                      f"-obs {out_dir}/OBS_FILES "
+                      f"-fcst {out_dir}/{fcst_file} "
+                      f"-obs {out_dir}/{obs_file} "
                       f"-out {out_dir}/2005080700 "
                       f"-config {config_file} {verbosity}"),
                      ]
@@ -356,8 +360,6 @@ def test_get_fcst_file_info(metplus_config):
     expected_beg = '000'
     expected_end = '048'
 
-    time_info = {'storm_id': storm_id, 'lead': 0, 'valid': '', 'init': ''}
-
     wrapper = series_analysis_wrapper(metplus_config)
     wrapper.c_dict['FCST_INPUT_DIR'] = '/fake/path/of/file'
     wrapper.c_dict['FCST_INPUT_TEMPLATE'] = (
@@ -404,29 +406,6 @@ def test_get_storms_list(metplus_config):
     assert storm_list == expected_storm_list
 
 
-# added list of all files for reference for creating subsets
-all_fake_fcst = ['fcst/20141214_00/ML1201072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
-                 'fcst/20141214_00/ML1221072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
-                 'fcst/20141214_00/ML1201072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
-                 'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
-                 'fcst/20141214_00/ML1201072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
-                 'fcst/20141214_00/ML1221072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
-                 'fcst/20141215_00/ML1291072014/FCST_TILE_F000_gfs_4_20141215_0000_000.nc',
-                 'fcst/20141215_00/ML1291072014/FCST_TILE_F006_gfs_4_20141215_0000_006.nc',
-                 'fcst/20141215_00/ML1291072014/FCST_TILE_F012_gfs_4_20141215_0000_012.nc',
-                  ]
-all_fake_obs = ['obs/20141214_00/ML1201072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
-                 'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
-                 'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
-                 'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
-                 'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
-                 'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
-                 'obs/20141215_00/ML1291072014/OBS_TILE_F000_gfs_4_20141215_0000_000.nc',
-                 'obs/20141215_00/ML1291072014/OBS_TILE_F006_gfs_4_20141215_0000_006.nc',
-                 'obs/20141215_00/ML1291072014/OBS_TILE_F012_gfs_4_20141215_0000_012.nc',
-                  ]
-
-
 @pytest.mark.parametrize(
         'time_info, expect_fcst_subset, expect_obs_subset', [
         # filter by init all storms
@@ -435,16 +414,16 @@ def test_get_storms_list(metplus_config):
           'lead': '*',
           'storm_id': '*'},
          ['fcst/20141214_00/ML1201072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
-          'fcst/20141214_00/ML1221072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
           'fcst/20141214_00/ML1201072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
-          'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
           'fcst/20141214_00/ML1201072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
+          'fcst/20141214_00/ML1221072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
+          'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
           'fcst/20141214_00/ML1221072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',],
          ['obs/20141214_00/ML1201072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
-          'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
           'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
-          'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
+          'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
+          'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',]),
         # filter by init single storm
         ({'init': datetime(2014, 12, 14, 0, 0),
@@ -526,10 +505,10 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
 
     expected_fcst = [
         'fcst/20141214_00/ML1201072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
-        'fcst/20141214_00/ML1221072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
         'fcst/20141214_00/ML1201072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
-        'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
         'fcst/20141214_00/ML1201072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
+        'fcst/20141214_00/ML1221072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
+        'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
         'fcst/20141214_00/ML1221072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
     ]
     expected_fcst_files = []
@@ -539,10 +518,10 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
 
     expected_obs = [
         'obs/20141214_00/ML1201072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
-        'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
         'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
-        'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
         'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
+        'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
+        'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
         'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
     ]
     expected_obs_files = []
@@ -550,15 +529,33 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
         expected_obs_files.append(os.path.join(tile_input_dir, expected))
 
     # convert list of lists into a single list to compare to expected results
-    fcst_files = [item['fcst'] for item in wrapper.c_dict['ALL_FILES']]
+    fcst_files = []
+    obs_files = []
+    for item in wrapper.c_dict['ALL_FILES']:
+        for key, value in item.items():
+            if key.startswith('fcst'):
+                fcst_files.append(value)
+            if key.startswith('obs'):
+                obs_files.append(value)
     fcst_files = [item for sub in fcst_files for item in sub]
-    obs_files = [item['obs'] for item in wrapper.c_dict['ALL_FILES']]
     obs_files = [item for sub in obs_files for item in sub]
-
+    fcst_files.sort()
+    obs_files.sort()
     assert fcst_files == expected_fcst_files
     assert obs_files == expected_obs_files
 
-    fcst_files_sub, obs_files_sub = wrapper.subset_input_files(time_info)
+    list_file_dict = wrapper.subset_input_files(time_info)
+    fcst_files_sub = []
+    obs_files_sub = []
+    for key, value in list_file_dict.items():
+        if key.startswith('fcst'):
+            with open(value, 'r') as file_handle:
+                fcst_files_sub.extend(file_handle.read().splitlines()[1:])
+        if key.startswith('obs'):
+            with open(value, 'r') as file_handle:
+                obs_files_sub.extend(file_handle.read().splitlines()[1:])
+    fcst_files_sub.sort()
+    obs_files_sub.sort()
     assert fcst_files_sub and obs_files_sub
     assert len(fcst_files_sub) == len(obs_files_sub)
 
@@ -571,7 +568,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
 
 @pytest.mark.parametrize(
         'config_overrides, time_info, storm_id, lead_group, expect_fcst_subset, expect_obs_subset', [
-        # filter by init all storms
+        # 0: filter by init all storms
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "{init?fmt=%Y%m%d_%H}/{storm_id}/series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byinitallstorms'},
@@ -593,7 +590,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
           'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',]),
-        # filter by init single storm
+        # 1: filter by init single storm
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "{init?fmt=%Y%m%d_%H}/{storm_id}/series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byinitstormA'},
@@ -611,7 +608,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
           'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
          ]),
-        # filter by init another single storm
+        # 2: filter by init another single storm
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "{init?fmt=%Y%m%d_%H}/{storm_id}/series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byinitstormB'},
@@ -629,7 +626,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
           'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
          ]),
-        # filter by lead all storms
+        # 3: filter by lead all storms
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byleadallstorms'},
@@ -645,7 +642,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
          ['obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
          ]),
-        # filter by lead 1 storm
+        # 4: filter by lead 1 storm
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byleadstormA'},
@@ -659,7 +656,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
          ],
          ['obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
          ]),
-        # filter by lead another storm
+        # 5: filter by lead another storm
         ({'LEAD_SEQ': '0H, 6H, 12H',
           'SERIES_ANALYSIS_OUTPUT_TEMPLATE': "series_{fcst_name}_{fcst_level}.nc",
           'TEST_OUTPUT_DIRNAME': 'byleadstormB'},
@@ -673,7 +670,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
          ],
          ['obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
          ]),
-        # filter by lead groups A all storms
+        # 6: filter by lead groups A all storms
         ({'LEAD_SEQ_1': '0H, 6H',
           'LEAD_SEQ_1_LABEL': 'Group1',
           'LEAD_SEQ_2': '12H',
@@ -695,7 +692,7 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
           'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
          ]),
-        # filter by lead groups B all storms
+        # 7: filter by lead groups B all storms
         ({'LEAD_SEQ_1': '0H, 6H',
           'LEAD_SEQ_1_LABEL': 'Group1',
           'LEAD_SEQ_2': '12H',
@@ -730,32 +727,34 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
     all_config_overrides.update(config_overrides)
     wrapper = series_analysis_wrapper(metplus_config, all_config_overrides)
     stat_input_dir, tile_input_dir = get_input_dirs(wrapper.config)
-    fcst_input_dir = os.path.join(tile_input_dir,
-                                  'fcst')
-    obs_input_dir = os.path.join(tile_input_dir,
-                                 'obs')
+    fcst_input_dir = os.path.join(tile_input_dir, 'fcst')
+    obs_input_dir = os.path.join(tile_input_dir, 'obs')
 
     stat_input_template = 'another_fake_filter_{init?fmt=%Y%m%d_%H}.tcst'
 
     wrapper.c_dict['TC_STAT_INPUT_DIR'] = stat_input_dir
     wrapper.c_dict['TC_STAT_INPUT_TEMPLATE'] = stat_input_template
-    wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = True
     wrapper.c_dict['FCST_INPUT_DIR'] = fcst_input_dir
     wrapper.c_dict['OBS_INPUT_DIR'] = obs_input_dir
     test_out_dirname = wrapper.config.getstr('config', 'TEST_OUTPUT_DIRNAME')
     output_dir = os.path.join(wrapper.config.getdir('OUTPUT_BASE'),
-                              'series_by',
-                              'output',
-                              test_out_dirname)
+                              'series_by', 'output', test_out_dirname)
     wrapper.c_dict['OUTPUT_DIR'] = output_dir
 
-    assert wrapper.get_all_files()
+    fcst_id = 'fcst'
+    obs_id = 'obs'
 
     # read output files and compare to expected list
     if storm_id == '*':
         storm_dir = 'all_storms'
+        wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = False
     else:
         storm_dir = storm_id
+        wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = True
+        fcst_id = f'{fcst_id}_{storm_id}'
+        obs_id = f'{obs_id}_{storm_id}'
+
+    assert wrapper.get_all_files()
 
     templates = config_overrides['SERIES_ANALYSIS_OUTPUT_TEMPLATE'].split('/')
     if len(templates) == 1:
@@ -763,21 +762,13 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
     else:
         output_prefix = os.path.join('20141214_00', storm_dir)
 
-    if lead_group:
-        leads = lead_group[1]
-    else:
-        leads = None
-    fcst_list_file = wrapper._get_ascii_filename('FCST', storm_id, leads)
-    fcst_file_path = os.path.join(output_dir,
-                                  output_prefix,
-                                  fcst_list_file)
+    fcst_list_file = wrapper.get_list_file_name(time_info, fcst_id)
+    fcst_file_path = os.path.join(output_dir, output_prefix, fcst_list_file)
     if os.path.exists(fcst_file_path):
         os.remove(fcst_file_path)
 
-    obs_list_file = wrapper._get_ascii_filename('OBS', storm_id, leads)
-    obs_file_path = os.path.join(output_dir,
-                                  output_prefix,
-                                  obs_list_file)
+    obs_list_file = wrapper.get_list_file_name(time_info, obs_id)
+    obs_file_path = os.path.join(output_dir, output_prefix, obs_list_file)
     if os.path.exists(obs_file_path):
         os.remove(obs_file_path)
 
@@ -790,6 +781,7 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
         actual_fcsts = file_handle.readlines()
     actual_fcsts = [item.strip() for item in actual_fcsts[1:]]
 
+    assert len(actual_fcsts) == len(expect_fcst_subset)
     for actual_file, expected_file in zip(actual_fcsts, expect_fcst_subset):
         actual_file = actual_file.replace(tile_input_dir, '').lstrip('/')
         assert actual_file == expected_file

From f5187a833f8a265e7e2070035993fbcb005e74f5 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 09:20:46 -0600
Subject: [PATCH 12/34] renamed variable back to original and ci-run-diff

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

diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index 5ec6da50d4..068d6d6943 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -461,11 +461,11 @@ def run_once_per_lead(self, custom):
 
             input_dict['init'] = '*'
             input_dict['valid'] = '*'
-            lead_hours_str = [ti_get_lead_string(item, plural=False) for
+            lead_hours = [ti_get_lead_string(item, plural=False) for
                               item in lead_group[1]]
 
             self.logger.debug(f"Processing {lead_group[0]} - forecast leads: "
-                              f"{', '.join(lead_hours_str)}")
+                              f"{', '.join(lead_hours)}")
 
             self.c_dict['ALL_FILES'] = (
                 self.get_all_files_for_leads(input_dict, lead_group[1])

From bae19ff9f9abb1f09f1bfa075869d7bb9f9d69ce Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 09:39:39 -0600
Subject: [PATCH 13/34] updated tests to more closely match what would actually
 run in the wrapper and use _get_fcst_obs_keys function to determine fcst/obs
 dictionary keys instead of formatting them by hand

---
 .../series_analysis/test_series_analysis.py   | 40 ++++++++++---------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
index b189a37c14..d588d2425f 100644
--- a/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
+++ b/internal/tests/pytests/wrappers/series_analysis/test_series_analysis.py
@@ -408,7 +408,7 @@ def test_get_storms_list(metplus_config):
 
 @pytest.mark.parametrize(
         'time_info, expect_fcst_subset, expect_obs_subset', [
-        # filter by init all storms
+        # 0: filter by init all storms
         ({'init': datetime(2014, 12, 14, 0, 0),
           'valid': '*',
           'lead': '*',
@@ -425,7 +425,7 @@ def test_get_storms_list(metplus_config):
           'obs/20141214_00/ML1221072014/OBS_TILE_F000_gfs_4_20141214_0000_000.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
           'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',]),
-        # filter by init single storm
+        # 1: filter by init single storm
         ({'init': datetime(2014, 12, 14, 0, 0),
           'valid': '*',
           'lead': '*',
@@ -440,7 +440,7 @@ def test_get_storms_list(metplus_config):
              'obs/20141214_00/ML1201072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
              'obs/20141214_00/ML1201072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
          ]),
-        # filter by init another single storm
+        # 2: filter by init another single storm
         ({'init': datetime(2014, 12, 14, 0, 0),
           'valid': '*',
           'lead': '*',
@@ -455,7 +455,7 @@ def test_get_storms_list(metplus_config):
              'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
              'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
          ]),
-        # filter by lead all storms
+        # 3: filter by lead all storms
         ({'init': '*',
           'valid': '*',
           'lead': 21600,
@@ -489,7 +489,6 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
     stat_input_dir, tile_input_dir = get_input_dirs(wrapper.config)
     stat_input_template = 'another_fake_filter_{init?fmt=%Y%m%d_%H}.tcst'
 
-    wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = True
     wrapper.c_dict['TC_STAT_INPUT_DIR'] = stat_input_dir
     wrapper.c_dict['TC_STAT_INPUT_TEMPLATE'] = stat_input_template
 
@@ -501,8 +500,13 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
     wrapper.c_dict['FCST_INPUT_DIR'] = fcst_input_dir
     wrapper.c_dict['OBS_INPUT_DIR'] = obs_input_dir
 
-    assert wrapper.get_all_files()
+    if time_info['storm_id'] == '*':
+        wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = False
+    else:
+        wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = True
 
+    assert wrapper.get_all_files()
+    print(f"ALL FILES: {wrapper.c_dict['ALL_FILES']}")
     expected_fcst = [
         'fcst/20141214_00/ML1201072014/FCST_TILE_F000_gfs_4_20141214_0000_000.nc',
         'fcst/20141214_00/ML1201072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
@@ -511,6 +515,9 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
         'fcst/20141214_00/ML1221072014/FCST_TILE_F006_gfs_4_20141214_0000_006.nc',
         'fcst/20141214_00/ML1221072014/FCST_TILE_F012_gfs_4_20141214_0000_012.nc',
     ]
+    if time_info['storm_id'] != '*':
+        expected_fcst = [item for item in expected_fcst
+                         if time_info['storm_id'] in item]
     expected_fcst_files = []
     for expected in expected_fcst:
         expected_fcst_files.append(os.path.join(tile_input_dir, expected))
@@ -524,19 +531,19 @@ def test_get_all_files_and_subset(metplus_config, time_info, expect_fcst_subset,
         'obs/20141214_00/ML1221072014/OBS_TILE_F006_gfs_4_20141214_0000_006.nc',
         'obs/20141214_00/ML1221072014/OBS_TILE_F012_gfs_4_20141214_0000_012.nc',
     ]
+    if time_info['storm_id'] != '*':
+        expected_obs = [item for item in expected_obs
+                        if time_info['storm_id'] in item]
     expected_obs_files = []
     for expected in expected_obs:
         expected_obs_files.append(os.path.join(tile_input_dir, expected))
 
+    fcst_key, obs_key = wrapper._get_fcst_obs_keys(time_info['storm_id'])
+    fcst_files = [item[fcst_key] for item in wrapper.c_dict['ALL_FILES']
+                  if fcst_key in item]
+    obs_files = [item[obs_key] for item in wrapper.c_dict['ALL_FILES']
+                 if obs_key in item]
     # convert list of lists into a single list to compare to expected results
-    fcst_files = []
-    obs_files = []
-    for item in wrapper.c_dict['ALL_FILES']:
-        for key, value in item.items():
-            if key.startswith('fcst'):
-                fcst_files.append(value)
-            if key.startswith('obs'):
-                obs_files.append(value)
     fcst_files = [item for sub in fcst_files for item in sub]
     obs_files = [item for sub in obs_files for item in sub]
     fcst_files.sort()
@@ -741,8 +748,7 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
                               'series_by', 'output', test_out_dirname)
     wrapper.c_dict['OUTPUT_DIR'] = output_dir
 
-    fcst_id = 'fcst'
-    obs_id = 'obs'
+    fcst_id, obs_id = wrapper._get_fcst_obs_keys(storm_id)
 
     # read output files and compare to expected list
     if storm_id == '*':
@@ -751,8 +757,6 @@ def test_get_fcst_and_obs_path(metplus_config, config_overrides,
     else:
         storm_dir = storm_id
         wrapper.c_dict['RUN_ONCE_PER_STORM_ID'] = True
-        fcst_id = f'{fcst_id}_{storm_id}'
-        obs_id = f'{obs_id}_{storm_id}'
 
     assert wrapper.get_all_files()
 

From 9c1365c31d326862565721f9cb085f9c46710b35 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:06:37 -0600
Subject: [PATCH 14/34] added logic to add forecast lead to file name if the
 number of seconds cannot be computed, which happens when valid time is not
 available and the lead is a non-uniform interval like month or year

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

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 862c676bbc..9efbdc9ef6 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -493,6 +493,11 @@ def get_list_file_name(self, time_info, identifier):
 
         if time_info.get('lead', '*') == '*':
             lead = 'ALL'
+        # use lead with letter if seconds cannot be computed e.g. 3m
+        elif time_info['valid'] == '*':
+            lead = time_util.ti_get_lead_string(time_info['lead'],
+                                                plural=False,
+                                                letter_only=True)
         else:
             lead = time_util.ti_get_seconds_from_lead(time_info['lead'],
                                                       time_info['valid'])

From d272e88b42b25a3158af83d8c815d2b5a85a1b39 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:09:10 -0600
Subject: [PATCH 15/34] turn off series_analysis use cases after confirmed they
 work as expeceted after changes

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

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 4a60113665..0e9a05056c 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -7,7 +7,7 @@
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": true
+    "run": false
   },
   {
     "category": "air_quality_and_comp",
@@ -77,7 +77,7 @@
   {
     "category": "medium_range",
     "index_list": "1-2",
-    "run": true
+    "run": false
   },
   {
     "category": "medium_range",
@@ -92,12 +92,12 @@
   {
     "category": "medium_range",
     "index_list": "7",
-    "run": true
+    "run": false
   },
   {
     "category": "medium_range",
     "index_list": "8",
-    "run": true
+    "run": false
   },
   {
     "category": "precipitation",
@@ -117,7 +117,7 @@
   {
     "category": "precipitation",
     "index_list": "3-7",
-    "run": true
+    "run": false
   },
   {
     "category": "precipitation",
@@ -127,7 +127,7 @@
   {
     "category": "s2s",
     "index_list": "0",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
@@ -152,7 +152,7 @@
   {
     "category": "s2s",
     "index_list": "5",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",

From d9fa4647619bd02b85898449e72c590a3c62d415 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:17:13 -0600
Subject: [PATCH 16/34] fixed indent

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

diff --git a/metplus/wrappers/series_analysis_wrapper.py b/metplus/wrappers/series_analysis_wrapper.py
index 068d6d6943..8d24ea0c30 100755
--- a/metplus/wrappers/series_analysis_wrapper.py
+++ b/metplus/wrappers/series_analysis_wrapper.py
@@ -462,7 +462,7 @@ def run_once_per_lead(self, custom):
             input_dict['init'] = '*'
             input_dict['valid'] = '*'
             lead_hours = [ti_get_lead_string(item, plural=False) for
-                              item in lead_group[1]]
+                          item in lead_group[1]]
 
             self.logger.debug(f"Processing {lead_group[0]} - forecast leads: "
                               f"{', '.join(lead_hours)}")

From 3aadc48a9bedacdb15dc65afeeedd5d45c64e8be Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:17:35 -0600
Subject: [PATCH 17/34] moved LOWER_TO_WRAPPER_NAME to constants file

---
 docs/Contributors_Guide/create_wrapper.rst |  2 +-
 metplus/util/constants.py                  | 40 +++++++++++++++++++++
 metplus/util/doc_util.py                   | 41 ++--------------------
 3 files changed, 43 insertions(+), 40 deletions(-)

diff --git a/docs/Contributors_Guide/create_wrapper.rst b/docs/Contributors_Guide/create_wrapper.rst
index 9ce44eceee..d9849dcc20 100644
--- a/docs/Contributors_Guide/create_wrapper.rst
+++ b/docs/Contributors_Guide/create_wrapper.rst
@@ -22,7 +22,7 @@ For example, the new_tool wrapper would be named **NewToolWrapper**.
 Add Entry to LOWER_TO_WRAPPER_NAME Dictionary
 ---------------------------------------------
 
-In *metplus/util/doc_util.py*, add entries to the LOWER_TO_WRAPPER_NAME
+In *metplus/util/constants.py*, add entries to the LOWER_TO_WRAPPER_NAME
 dictionary so that the wrapper can be found in the PROCESS_LIST even if
 it is formatted differently. The key should be the wrapper name in all
 lower-case letters without any underscores. The value should be the class name
diff --git a/metplus/util/constants.py b/metplus/util/constants.py
index 7e7d9cd9f0..57284b209a 100644
--- a/metplus/util/constants.py
+++ b/metplus/util/constants.py
@@ -1,3 +1,43 @@
+# dictionary used by get_wrapper_name function to easily convert wrapper
+# name in many formats to the correct name of the wrapper class
+LOWER_TO_WRAPPER_NAME = {
+    'ascii2nc': 'ASCII2NC',
+    'cycloneplotter': 'CyclonePlotter',
+    'ensemblestat': 'EnsembleStat',
+    'example': 'Example',
+    'extracttiles': 'ExtractTiles',
+    'gempaktocf': 'GempakToCF',
+    'genvxmask': 'GenVxMask',
+    'genensprod': 'GenEnsProd',
+    'gfdltracker': 'GFDLTracker',
+    'griddiag': 'GridDiag',
+    'gridstat': 'GridStat',
+    'ioda2nc': 'IODA2NC',
+    'makeplots': 'MakePlots',
+    'metdbload': 'METDbLoad',
+    'mode': 'MODE',
+    'mtd': 'MTD',
+    'modetimedomain': 'MTD',
+    'pb2nc': 'PB2NC',
+    'pcpcombine': 'PCPCombine',
+    'plotdataplane': 'PlotDataPlane',
+    'plotpointobs': 'PlotPointObs',
+    'point2grid': 'Point2Grid',
+    'pointtogrid': 'Point2Grid',
+    'pointstat': 'PointStat',
+    'pyembedingest': 'PyEmbedIngest',
+    'regriddataplane': 'RegridDataPlane',
+    'seriesanalysis': 'SeriesAnalysis',
+    'statanalysis': 'StatAnalysis',
+    'tcgen': 'TCGen',
+    'tcpairs': 'TCPairs',
+    'tcrmw': 'TCRMW',
+    'tcstat': 'TCStat',
+    'tcmprplotter': 'TCMPRPlotter',
+    'usage': 'Usage',
+    'userscript': 'UserScript',
+}
+
 # supported file extensions that will automatically be uncompressed
 COMPRESSION_EXTENSIONS = [
     '.gz',
diff --git a/metplus/util/doc_util.py b/metplus/util/doc_util.py
index 44ee50ad8a..d32e42f778 100755
--- a/metplus/util/doc_util.py
+++ b/metplus/util/doc_util.py
@@ -3,45 +3,8 @@
 import sys
 import os
 
-# dictionary used by get_wrapper_name function to easily convert wrapper
-# name in many formats to the correct name of the wrapper class
-LOWER_TO_WRAPPER_NAME = {
-    'ascii2nc': 'ASCII2NC',
-    'cycloneplotter': 'CyclonePlotter',
-    'ensemblestat': 'EnsembleStat',
-    'example': 'Example',
-    'extracttiles': 'ExtractTiles',
-    'gempaktocf': 'GempakToCF',
-    'genvxmask': 'GenVxMask',
-    'genensprod': 'GenEnsProd',
-    'gfdltracker': 'GFDLTracker',
-    'griddiag': 'GridDiag',
-    'gridstat': 'GridStat',
-    'ioda2nc': 'IODA2NC',
-    'makeplots': 'MakePlots',
-    'metdbload': 'METDbLoad',
-    'mode': 'MODE',
-    'mtd': 'MTD',
-    'modetimedomain': 'MTD',
-    'pb2nc': 'PB2NC',
-    'pcpcombine': 'PCPCombine',
-    'plotdataplane': 'PlotDataPlane',
-    'plotpointobs': 'PlotPointObs',
-    'point2grid': 'Point2Grid',
-    'pointtogrid': 'Point2Grid',
-    'pointstat': 'PointStat',
-    'pyembedingest': 'PyEmbedIngest',
-    'regriddataplane': 'RegridDataPlane',
-    'seriesanalysis': 'SeriesAnalysis',
-    'statanalysis': 'StatAnalysis',
-    'tcgen': 'TCGen',
-    'tcpairs': 'TCPairs',
-    'tcrmw': 'TCRMW',
-    'tcstat': 'TCStat',
-    'tcmprplotter': 'TCMPRPlotter',
-    'usage': 'Usage',
-    'userscript': 'UserScript',
-}
+from . import LOWER_TO_WRAPPER_NAME
+
 
 def get_wrapper_name(process_name):
     """! Determine name of wrapper from string that may not contain the correct

From 7eb11271df7cdbafe1f39b8667f3084c1e72a39d Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:21:38 -0600
Subject: [PATCH 18/34] added description of file content

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

diff --git a/metplus/util/constants.py b/metplus/util/constants.py
index 57284b209a..d2a5380b18 100644
--- a/metplus/util/constants.py
+++ b/metplus/util/constants.py
@@ -1,3 +1,5 @@
+# Constant variables used throughout the METplus wrappers source code
+
 # dictionary used by get_wrapper_name function to easily convert wrapper
 # name in many formats to the correct name of the wrapper class
 LOWER_TO_WRAPPER_NAME = {

From 7e4c521a5a7be9f4a75e47e1e121492fde6f77ca Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 10:22:12 -0600
Subject: [PATCH 19/34] fixed wrapper instance name string to use correct
 formatting of wrapper name instead of application name

---
 metplus/wrappers/command_builder.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index 148061d3d4..0b2a7b48f5 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -30,6 +30,7 @@
 from ..util import get_wrapped_met_config_file, add_met_config_item, format_met_config
 from ..util import remove_quotes
 from ..util import get_field_info, format_field_info
+from ..util import get_wrapper_name
 from ..util.met_config import add_met_config_dict, handle_climo_dict
 
 # pylint:disable=pointless-string-statement
@@ -1626,6 +1627,7 @@ def handle_climo_cdf_dict(self, write_bins=True):
         self.add_met_config_dict('climo_cdf', items)
 
     def get_wrapper_instance_name(self):
+        wrapper_name = get_wrapper_name(self.app_name)
         if not self.instance:
-            return self.app_name
-        return f'{self.app_name}({self.instance})'
+            return wrapper_name
+        return f'{wrapper_name}({self.instance})'

From cc1a011de56a3a96cb3a949ddf2877c0e496ade6 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:04:25 -0600
Subject: [PATCH 20/34] per #1687, added a function to handle running once for
 each init/valid and lead combination instead of logic outside of RuntimeFreq
 wrapper

---
 metplus/wrappers/runtime_freq_wrapper.py | 51 +++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 9efbdc9ef6..81e01d7dbd 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -137,7 +137,7 @@ def run_all_times_custom(self, custom):
         elif runtime_freq == 'RUN_ONCE_PER_LEAD':
             self.run_once_per_lead(custom)
         elif runtime_freq == 'RUN_ONCE_FOR_EACH':
-            self.all_commands = super().run_all_times(custom)
+            self.run_once_for_each(custom)
 
     def run_once(self, custom):
         self.logger.debug("Running once for all files")
@@ -218,6 +218,55 @@ 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")
+
+        success = True
+        for time_input in time_generator(self.config):
+            if time_input is None:
+                success = False
+                continue
+
+            log_runtime_banner(self.config, time_input, self)
+            add_to_time_input(time_input,
+                              instance=self.instance,
+                              custom=custom)
+
+            # loop of forecast leads and process each
+            lead_seq = get_lead_sequence(self.config, time_input)
+            for lead in lead_seq:
+                time_input['lead'] = lead
+
+                # set current lead time config and environment variables
+                time_info = time_util.ti_calculate(time_input)
+
+                self.logger.info(
+                    f"Processing forecast lead {time_info['lead_string']}"
+                )
+
+                if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
+                    self.logger.debug('Skipping run time')
+                    continue
+
+                # since run_all_times was not called (LOOP_BY=times) then
+                # get files for current run time
+                file_dict = self.get_files_from_time(time_info)
+                all_files = []
+                if file_dict:
+                    if isinstance(file_dict, list):
+                        all_files = file_dict
+                    else:
+                        all_files = [file_dict]
+
+                self.c_dict['ALL_FILES'] = all_files
+
+                # Run for given init/valid time and forecast lead combination
+                self.clear()
+                if not self.run_at_time_once(time_info):
+                    success = False
+
+        return success
+
     def run_at_time(self, input_dict):
         """! Runs the command for a given run time. This function loops
               over the list of forecast leads and list of custom loops

From 5390c08662799b565fbb72c2b947f84ba5f21f7b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:04:41 -0600
Subject: [PATCH 21/34] turn on UserScript and GridDiag use cases to test
 ci-run-diff

---
 .github/parm/use_case_groups.json | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 0e9a05056c..7843bfd6d7 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -2,12 +2,12 @@
   {
     "category": "met_tool_wrapper",
     "index_list": "0-29,59-61",
-    "run": false
+    "run": true
   },
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": false
+    "run": true
   },
   {
     "category": "air_quality_and_comp",
@@ -82,7 +82,7 @@
   {
     "category": "medium_range",
     "index_list": "3-5",
-    "run": false
+    "run": true
   },
   {
     "category": "medium_range",
@@ -132,22 +132,22 @@
   {
     "category": "s2s",
     "index_list": "1",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
     "index_list": "2",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
     "index_list": "3",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
     "index_list": "4",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s",
@@ -162,27 +162,27 @@
   {
     "category": "s2s_mid_lat",
     "index_list": "0-2",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s_mid_lat",
     "index_list": "3",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s_mjo",
     "index_list": "0-2",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s_mjo",
     "index_list": "3",
-    "run": false
+    "run": true
   },
   {
     "category": "s2s_mjo",
     "index_list": "4",
-    "run": false
+    "run": true
   },
   {
     "category": "space_weather",
@@ -192,11 +192,11 @@
   {
     "category": "tc_and_extra_tc",
     "index_list": "0-2",
-    "run": false
+    "run": true
   },
   {
     "category": "tc_and_extra_tc",
     "index_list": "3-5",
-    "run": false
+    "run": true
   }
 ]

From 0cf3650289bd811af6452920154e83a9e9827f90 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:26:22 -0600
Subject: [PATCH 22/34] removed custom loop logic in GridDiag wrapper because
 it will always be handled by RuntimeFreq wrapper

---
 metplus/wrappers/grid_diag_wrapper.py | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/metplus/wrappers/grid_diag_wrapper.py b/metplus/wrappers/grid_diag_wrapper.py
index afe63f4480..d44026af25 100755
--- a/metplus/wrappers/grid_diag_wrapper.py
+++ b/metplus/wrappers/grid_diag_wrapper.py
@@ -152,26 +152,6 @@ def get_command(self):
         return cmd
 
     def run_at_time_once(self, time_info):
-        """! Process runtime and try to build command to run ascii2nc
-             Args:
-                @param time_info dictionary containing timing information
-        """
-
-        # if custom is already set in time info, run for only that item
-        # if not, loop over the CUSTOM_LOOP_LIST and process once for each
-        if 'custom' in time_info:
-            custom_loop_list = [time_info['custom']]
-        else:
-            custom_loop_list = self.c_dict['CUSTOM_LOOP_LIST']
-
-        for custom_string in custom_loop_list:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            time_info['custom'] = custom_string
-            self.run_at_time_custom(time_info)
-
-    def run_at_time_custom(self, time_info):
         self.clear()
 
         # subset input files as appropriate

From ecbc2345a7c70535bd68fa1bcb1c0bd565b0967e Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:27:43 -0600
Subject: [PATCH 23/34] skip finding files for wrappers that don't need to find
 files instead of overriding get_all_files function to return True always

---
 metplus/wrappers/met_db_load_wrapper.py  |  3 ++
 metplus/wrappers/runtime_freq_wrapper.py | 48 +++++-------------------
 2 files changed, 12 insertions(+), 39 deletions(-)

diff --git a/metplus/wrappers/met_db_load_wrapper.py b/metplus/wrappers/met_db_load_wrapper.py
index e5a8783935..b12ac87b9a 100755
--- a/metplus/wrappers/met_db_load_wrapper.py
+++ b/metplus/wrappers/met_db_load_wrapper.py
@@ -94,6 +94,9 @@ def create_c_dict(self):
                 self.log_error(f"Must set MET_DB_LOAD_MV_{name}")
             c_dict[f'MV_{name}'] = value
 
+        # set variable to skip finding input files
+        c_dict['FIND_FILES'] = False
+
         return c_dict
 
     def get_command(self):
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 81e01d7dbd..2c1326b4fb 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -267,51 +267,15 @@ def run_once_for_each(self, custom):
 
         return success
 
-    def run_at_time(self, input_dict):
-        """! Runs the command for a given run time. This function loops
-              over the list of forecast leads and list of custom loops
-              and runs once for each combination
-
-            @param input_dict dictionary containing time information
-        """
-        # loop of forecast leads and process each
-        lead_seq = get_lead_sequence(self.config, input_dict)
-        for lead in lead_seq:
-            input_dict['lead'] = lead
-
-            # set current lead time config and environment variables
-            time_info = time_util.ti_calculate(input_dict)
-
-            self.logger.info(
-                f"Processing forecast lead {time_info['lead_string']}"
-            )
-
-            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                self.logger.debug('Skipping run time')
-                continue
-
-            # since run_all_times was not called (LOOP_BY=times) then
-            # get files for current run time
-            file_dict = self.get_files_from_time(time_info)
-            all_files = []
-            if file_dict:
-                if isinstance(file_dict, list):
-                    all_files = file_dict
-                else:
-                    all_files = [file_dict]
-
-            self.c_dict['ALL_FILES'] = all_files
-
-            # Run for given init/valid time and forecast lead combination
-            self.clear()
-            self.run_at_time_once(time_info)
-
     def get_all_files(self, custom=None):
         """! Get all files that can be processed with the app.
         @returns A dictionary where the key is the type of data that was found,
         i.e. fcst or obs, and the value is a list of files that fit in that
         category
         """
+        if not self.c_dict.get('FIND_FILES', True):
+            return True
+
         self.logger.debug("Finding all input files")
         all_files = []
 
@@ -334,6 +298,9 @@ def get_all_files(self, custom=None):
         return True
 
     def get_all_files_from_leads(self, time_input):
+        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',
@@ -361,6 +328,9 @@ def get_all_files_from_leads(self, time_input):
         return lead_files
 
     def get_all_files_for_lead(self, time_input):
+        if not self.c_dict.get('FIND_FILES', True):
+            return True
+
         new_files = []
         for run_time in time_generator(self.config):
             if run_time is None:

From 012a652aa120e1daa57f3251714361fe3f14e207 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:28:32 -0600
Subject: [PATCH 24/34] removed custom loop logic in wrappers because it will
 always be handled by RuntimeFreq wrapper

---
 metplus/wrappers/met_db_load_wrapper.py | 59 +++++++++----------------
 metplus/wrappers/user_script_wrapper.py | 56 ++++++++---------------
 2 files changed, 39 insertions(+), 76 deletions(-)

diff --git a/metplus/wrappers/met_db_load_wrapper.py b/metplus/wrappers/met_db_load_wrapper.py
index b12ac87b9a..1ed678cb9f 100755
--- a/metplus/wrappers/met_db_load_wrapper.py
+++ b/metplus/wrappers/met_db_load_wrapper.py
@@ -114,48 +114,29 @@ def run_at_time_once(self, time_info):
         """
         success = True
 
-        # if custom is already set in time info, run for only that item
-        # if not, loop over the CUSTOM_LOOP_LIST and process once for each
-        if 'custom' in time_info:
-            custom_loop_list = [time_info['custom']]
-        else:
-            custom_loop_list = self.c_dict['CUSTOM_LOOP_LIST']
-
-        for custom_string in custom_loop_list:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            time_info['custom'] = custom_string
-            # if lead and either init or valid are set, compute other string sub
-            if time_info.get('lead') != '*':
-                if (time_info.get('init') != '*'
-                        or time_info.get('valid') != '*'):
-                    time_info = time_util.ti_calculate(time_info)
-
-            self.set_environment_variables(time_info)
-
-            if not self.replace_values_in_xml(time_info):
-                return
-
-            # run command
-            if not self.build():
-                success = False
-
-            # remove tmp file
-            if self.c_dict.get('REMOVE_TMP_XML', True):
-                xml_file = self.c_dict.get('XML_TMP_FILE')
-                if xml_file and os.path.exists(xml_file):
-                    self.logger.debug(f"Removing tmp file: {xml_file}")
-                    os.remove(xml_file)
+        # if lead and either init or valid are set, compute other string sub
+        if time_info.get('lead') != '*':
+            if (time_info.get('init') != '*'
+                    or time_info.get('valid') != '*'):
+                time_info = time_util.ti_calculate(time_info)
 
-        return success
+        self.set_environment_variables(time_info)
 
-    def get_all_files(self, custom=None):
-        """! Don't get list of all files for METdbLoad wrapper
+        if not self.replace_values_in_xml(time_info):
+            return
 
-            @returns True to report that no failures occurred
-        """
-        return True
+        # run command
+        if not self.build():
+            success = False
+
+        # remove tmp file
+        if self.c_dict.get('REMOVE_TMP_XML', True):
+            xml_file = self.c_dict.get('XML_TMP_FILE')
+            if xml_file and os.path.exists(xml_file):
+                self.logger.debug(f"Removing tmp file: {xml_file}")
+                os.remove(xml_file)
+
+        return success
 
     def get_stat_directories(self, input_paths):
         """! Traverse through files under input path and find all directories
diff --git a/metplus/wrappers/user_script_wrapper.py b/metplus/wrappers/user_script_wrapper.py
index a64cfbdefa..50384c0190 100755
--- a/metplus/wrappers/user_script_wrapper.py
+++ b/metplus/wrappers/user_script_wrapper.py
@@ -63,43 +63,25 @@ def run_at_time_once(self, time_info):
              @param time_info dictionary containing time information
              @returns True if command was run successfully, False otherwise
         """
-        success = True
-
-        # if custom is already set in time info, run for only that item
-        # if not, loop over the CUSTOM_LOOP_LIST and process once for each
-        if 'custom' in time_info:
-            custom_loop_list = [time_info['custom']]
-        else:
-            custom_loop_list = self.c_dict['CUSTOM_LOOP_LIST']
-
-        for custom_string in custom_loop_list:
-            if custom_string:
-                self.logger.info(f"Processing custom string: {custom_string}")
-
-            time_info['custom'] = custom_string
-            # if lead and either init or valid are set, compute other string sub
-            if time_info.get('lead') != '*':
-                if (time_info.get('init') != '*'
-                        or time_info.get('valid') != '*'):
-                    time_info = time_util.ti_calculate(time_info)
-
-            # create file list text files for the current run time criteria
-            # set c_dict to the input file dict to set as environment vars
-            self.c_dict['INPUT_LIST_DICT'] = self.subset_input_files(time_info)
-
-            self.set_environment_variables(time_info)
-
-            # substitute values from dictionary into command
-            self.c_dict['COMMAND'] = (
-                do_string_sub(self.c_dict['COMMAND_TEMPLATE'],
-                              **time_info)
-            )
-
-            # run command
-            if not self.build():
-                success = False
-
-        return success
+        # if lead and either init or valid are set, compute other string sub
+        if time_info.get('lead') != '*':
+            if (time_info.get('init') != '*'
+                    or time_info.get('valid') != '*'):
+                time_info = time_util.ti_calculate(time_info)
+
+        # create file list text files for the current run time criteria
+        # set c_dict to the input file dict to set as environment vars
+        self.c_dict['INPUT_LIST_DICT'] = self.subset_input_files(time_info)
+
+        self.set_environment_variables(time_info)
+
+        # substitute values from dictionary into command
+        self.c_dict['COMMAND'] = (
+            do_string_sub(self.c_dict['COMMAND_TEMPLATE'],
+                          **time_info)
+        )
+
+        return self.build()
 
     def get_files_from_time(self, time_info):
         """! Create dictionary containing time information (key time_info) and

From 1b4b0c88b4c5b1a9efa06abf6e95afc90eef69f4 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:28:45 -0600
Subject: [PATCH 25/34] changed functions to static methods

---
 metplus/wrappers/runtime_freq_wrapper.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 2c1326b4fb..199e4e5682 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -355,7 +355,8 @@ def get_all_files_for_lead(self, time_input):
 
         return new_files
 
-    def get_files_from_time(self, time_info):
+    @staticmethod
+    def get_files_from_time(time_info):
         """! Create dictionary containing time information (key time_info) and
              any relevant files for that runtime.
              @param time_info dictionary containing time information
@@ -366,7 +367,8 @@ def get_files_from_time(self, time_info):
         file_dict['time_info'] = time_info.copy()
         return file_dict
 
-    def compare_time_info(self, runtime, filetime):
+    @staticmethod
+    def compare_time_info(runtime, filetime):
         """! Compare current runtime dictionary to current file time dictionary
              If runtime value for init, valid, or lead is not a wildcard and
              it doesn't match the file's time value, return False. Otherwise

From 63603860e3e90ff67e7697d6b3b59d9d61f9a1e2 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:32:23 -0600
Subject: [PATCH 26/34] changed logic to get file list filename to only use
 string forecast lead if lead seconds cannot be calculated because some time
 intervals do not need a valid time to compute. If the lead cannot be
 converted to seconds, then run the logic to get the lead string

---
 metplus/wrappers/runtime_freq_wrapper.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 199e4e5682..f38587a11c 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -514,14 +514,14 @@ def get_list_file_name(self, time_info, identifier):
 
         if time_info.get('lead', '*') == '*':
             lead = 'ALL'
+        else:
+            lead = time_util.ti_get_seconds_from_lead(time_info['lead'],
+                                                      time_info['valid'])
         # use lead with letter if seconds cannot be computed e.g. 3m
-        elif time_info['valid'] == '*':
+        if lead is None:
             lead = time_util.ti_get_lead_string(time_info['lead'],
                                                 plural=False,
                                                 letter_only=True)
-        else:
-            lead = time_util.ti_get_seconds_from_lead(time_info['lead'],
-                                                      time_info['valid'])
 
         return (f"{self.app_name}_files_{identifier}_"
                 f"init_{init}_valid_{valid}_lead_{lead}.txt")

From 478ca2964fbe8394e85922812559a43f5830f320 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:36:12 -0600
Subject: [PATCH 27/34] changed warning to error if required variable is not
 set, ci-run-diff

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

diff --git a/metplus/wrappers/plot_point_obs_wrapper.py b/metplus/wrappers/plot_point_obs_wrapper.py
index 3648003c87..4d90c691ec 100755
--- a/metplus/wrappers/plot_point_obs_wrapper.py
+++ b/metplus/wrappers/plot_point_obs_wrapper.py
@@ -70,8 +70,8 @@ def create_c_dict(self):
         c_dict['INPUT_DIR'] = self.config.getdir(f'{app}_INPUT_DIR', '')
 
         if not c_dict['INPUT_TEMPLATE']:
-            self.logger.warning(f'{app}_INPUT_TEMPLATE is required '
-                                'to run PlotPointObs wrapper.')
+            self.log_error(f'{app}_INPUT_TEMPLATE is required '
+                           'to run PlotPointObs wrapper.')
 
         # get optional grid input files
         c_dict['GRID_INPUT_TEMPLATE'] = self.config.getraw(

From 67a4c1eba4f519e01ae84d67e3584ff6799e0adc Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 11:43:49 -0600
Subject: [PATCH 28/34] change PlotPointObs wrapper to be a LoopTimes wrapper
 since it defaults to runtime freq RUN_ONCE_FOR_EACH if
 PLOT_POINT_OBS_RUNTIME_FREQ is unset, which is what LoopTimes wrapper
 accomplishes

---
 metplus/wrappers/plot_point_obs_wrapper.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/metplus/wrappers/plot_point_obs_wrapper.py b/metplus/wrappers/plot_point_obs_wrapper.py
index 4d90c691ec..2a0ec4373b 100755
--- a/metplus/wrappers/plot_point_obs_wrapper.py
+++ b/metplus/wrappers/plot_point_obs_wrapper.py
@@ -14,10 +14,10 @@
 
 from ..util import do_string_sub, ti_calculate, get_lead_sequence
 from ..util import skip_time
-from . import RuntimeFreqWrapper
+from . import LoopTimesWrapper
 
 
-class PlotPointObsWrapper(RuntimeFreqWrapper):
+class PlotPointObsWrapper(LoopTimesWrapper):
     """! Wrapper used to build commands to call plot_point_obs """
 
     WRAPPER_ENV_VAR_KEYS = [
@@ -56,10 +56,6 @@ def create_c_dict(self):
         c_dict = super().create_c_dict()
         app = self.app_name.upper()
 
-        # set default runtime frequency if unset explicitly
-        if not c_dict['RUNTIME_FREQ']:
-            c_dict['RUNTIME_FREQ'] = 'RUN_ONCE_FOR_EACH'
-
         c_dict['VERBOSITY'] = self.config.getstr('config',
                                                  f'LOG_{app}_VERBOSITY',
                                                  c_dict['VERBOSITY'])

From d4c5c3d598f422ecbe1b7d5c37b7217fac9a3721 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 12:38:03 -0600
Subject: [PATCH 29/34] turn off all use cases after testing

---
 .github/parm/use_case_groups.json | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 7843bfd6d7..0e9a05056c 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -2,12 +2,12 @@
   {
     "category": "met_tool_wrapper",
     "index_list": "0-29,59-61",
-    "run": true
+    "run": false
   },
   {
     "category": "met_tool_wrapper",
     "index_list": "30-58",
-    "run": true
+    "run": false
   },
   {
     "category": "air_quality_and_comp",
@@ -82,7 +82,7 @@
   {
     "category": "medium_range",
     "index_list": "3-5",
-    "run": true
+    "run": false
   },
   {
     "category": "medium_range",
@@ -132,22 +132,22 @@
   {
     "category": "s2s",
     "index_list": "1",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
     "index_list": "2",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
     "index_list": "3",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
     "index_list": "4",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s",
@@ -162,27 +162,27 @@
   {
     "category": "s2s_mid_lat",
     "index_list": "0-2",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s_mid_lat",
     "index_list": "3",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s_mjo",
     "index_list": "0-2",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s_mjo",
     "index_list": "3",
-    "run": true
+    "run": false
   },
   {
     "category": "s2s_mjo",
     "index_list": "4",
-    "run": true
+    "run": false
   },
   {
     "category": "space_weather",
@@ -192,11 +192,11 @@
   {
     "category": "tc_and_extra_tc",
     "index_list": "0-2",
-    "run": true
+    "run": false
   },
   {
     "category": "tc_and_extra_tc",
     "index_list": "3-5",
-    "run": true
+    "run": false
   }
 ]

From 1514f4e591459b883e5273615645acfda014c8e8 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 28 Sep 2022 12:42:43 -0600
Subject: [PATCH 30/34] Commented line to force LOOP_ORDER to always be
 processes. After the first PR for #1687 that changes the logic for
 SeriesAnalysis wrapper to use the same logic to build file lists as the other
 RuntimeFreq wrappers which produces differences in some filenames, uncomment
 this to prove that there are no differences in any use cases if LOOP_ORDER is
 always processes (removing LOOP_ORDER=times). A test already proved this but
 additional work is needed for this issue

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

diff --git a/metplus/util/met_util.py b/metplus/util/met_util.py
index 257e8ceb4b..4d3f796bb5 100644
--- a/metplus/util/met_util.py
+++ b/metplus/util/met_util.py
@@ -137,7 +137,7 @@ def run_metplus(config, process_list):
             return 1
 
         loop_order = config.getstr('config', 'LOOP_ORDER', '').lower()
-        loop_order = 'processes'
+        #loop_order = 'processes'
 
         if loop_order == "processes":
             all_commands = []

From 05f10af7fb989837518bc7e1088f92daa36766f4 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Thu, 29 Sep 2022 08:15:49 -0600
Subject: [PATCH 31/34] added back run_at_time function

---
 metplus/wrappers/runtime_freq_wrapper.py | 62 +++++++++++++-----------
 1 file changed, 35 insertions(+), 27 deletions(-)

diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index f38587a11c..05ff099cbf 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -233,37 +233,45 @@ def run_once_for_each(self, custom):
                               custom=custom)
 
             # loop of forecast leads and process each
-            lead_seq = get_lead_sequence(self.config, time_input)
-            for lead in lead_seq:
-                time_input['lead'] = lead
+            if not self.run_at_time(time_input):
+                success = False
 
-                # set current lead time config and environment variables
-                time_info = time_util.ti_calculate(time_input)
+        return success
 
-                self.logger.info(
-                    f"Processing forecast lead {time_info['lead_string']}"
-                )
+    def run_at_time(self, input_dict):
+        success = True
+        # loop of forecast leads and process each
+        lead_seq = get_lead_sequence(self.config, input_dict)
+        for lead in lead_seq:
+            input_dict['lead'] = lead
 
-                if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
-                    self.logger.debug('Skipping run time')
-                    continue
+            # set current lead time config and environment variables
+            time_info = time_util.ti_calculate(input_dict)
 
-                # since run_all_times was not called (LOOP_BY=times) then
-                # get files for current run time
-                file_dict = self.get_files_from_time(time_info)
-                all_files = []
-                if file_dict:
-                    if isinstance(file_dict, list):
-                        all_files = file_dict
-                    else:
-                        all_files = [file_dict]
-
-                self.c_dict['ALL_FILES'] = all_files
-
-                # Run for given init/valid time and forecast lead combination
-                self.clear()
-                if not self.run_at_time_once(time_info):
-                    success = False
+            self.logger.info(
+                f"Processing forecast lead {time_info['lead_string']}"
+            )
+
+            if skip_time(time_info, self.c_dict.get('SKIP_TIMES', {})):
+                self.logger.debug('Skipping run time')
+                continue
+
+            # since run_all_times was not called (LOOP_BY=times) then
+            # get files for current run time
+            file_dict = self.get_files_from_time(time_info)
+            all_files = []
+            if file_dict:
+                if isinstance(file_dict, list):
+                    all_files = file_dict
+                else:
+                    all_files = [file_dict]
+
+            self.c_dict['ALL_FILES'] = all_files
+
+            # Run for given init/valid time and forecast lead combination
+            self.clear()
+            if not self.run_at_time_once(time_info):
+                success = False
 
         return success
 

From 6d0604628ce01714fc86fa9cd5ef496b1bde1376 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Thu, 29 Sep 2022 12:25:35 -0600
Subject: [PATCH 32/34] per #1687, remove LOOP_ORDER from the source code and
 documentation

---
 docs/Users_Guide/glossary.rst                 | 29 ++++---
 docs/Users_Guide/systemconfiguration.rst      | 43 ++---------
 docs/Users_Guide/wrappers.rst                 | 75 +++----------------
 .../stat_analysis/test_stat_analysis.py       |  1 -
 metplus/util/config_metplus.py                |  1 -
 metplus/util/met_util.py                      | 21 ++----
 metplus/wrappers/command_builder.py           | 10 ---
 metplus/wrappers/make_plots_wrapper.py        |  1 -
 metplus/wrappers/runtime_freq_wrapper.py      |  9 ---
 metplus/wrappers/stat_analysis_wrapper.py     |  3 +-
 metplus/wrappers/tc_pairs_wrapper.py          |  2 +-
 11 files changed, 39 insertions(+), 156 deletions(-)

diff --git a/docs/Users_Guide/glossary.rst b/docs/Users_Guide/glossary.rst
index dbe419ef6e..9c7ad67f9b 100644
--- a/docs/Users_Guide/glossary.rst
+++ b/docs/Users_Guide/glossary.rst
@@ -1620,12 +1620,12 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`FCST_THRESH_LIST` instead.
 
    FCST_THRESH_LIST
-     Specify the values of the FCST_THRESH column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the FCST_THRESH column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
    OBS_THRESH_LIST
-     Specify the values of the OBS_THRESH column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the OBS_THRESH column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
@@ -1647,7 +1647,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`FCST_LEVEL_LIST` instead.
 
    FCST_LEVEL_LIST
-     Specify the values of the FCST_LEV column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the FCST_LEV column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
@@ -1655,12 +1655,12 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`FCST_VAR_LIST` instead.
 
    FCST_VAR_LIST
-     Specify the values of the FCST_VAR column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the FCST_VAR column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
    FCST_UNITS_LIST
-     Specify the values of the FCST_UNITS column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the FCST_UNITS column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
@@ -2319,7 +2319,7 @@ METplus Configuration Glossary
 
 
    LINE_TYPE_LIST
-     Specify the MET STAT line types to be considered. For TCMPRPlotter, this is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the MET STAT line types to be considered.
 
      | *Used by:*  MakePlots, StatAnalysis, TCMPRPlotter
 
@@ -2395,7 +2395,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`LOOP_BY` instead.
 
    LOOP_ORDER
-     Control the looping order for METplus. Valid options are "times" or "processes". "times" runs all items in the :term:`PROCESS_LIST` for a single run time, then repeat until all times have been evaluated. "processes" runs each item in the :term:`PROCESS_LIST` for all times specified, then repeat for the next item in the :term:`PROCESS_LIST`.
+     .. warning:: **DEPRECATED:** This previously controlled the looping order for METplus. This was removed in v5.0.0. The wrappers will always execute the logic that was previously run when LOOP_ORDER = processes, which runs each item in the :term:`PROCESS_LIST` for all times specified, then repeat for the next item in the :term:`PROCESS_LIST`.
 
      | *Used by:*  All
 
@@ -3207,7 +3207,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`OBS_LEVEL_LIST` instead.
 
    OBS_LEVEL_LIST
-     Specify the values of the OBS_LEV column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the OBS_LEV column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
@@ -3215,12 +3215,12 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`OBS_VAR_LIST` instead.
 
    OBS_VAR_LIST
-     Specify the values of the OBS_VAR column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the OBS_VAR column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
    OBS_UNITS_LIST
-     Specify the values of the OBS_UNITS column in the MET .stat file to use. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the values of the OBS_UNITS column in the MET .stat file to use.
 
      | *Used by:*  StatAnalysis
 
@@ -3837,7 +3837,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`MODEL<n>_STAT_ANALYSIS_DUMP_ROW_TEMPLATE` instead.
 
    MODEL<n>_STAT_ANALYSIS_DUMP_ROW_TEMPLATE
-     Specify the template to use for the stat_analysis dump_row file. A user customized template to use for the dump_row file. If left blank and a dump_row file is requested, a default version will be used. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the template to use for the stat_analysis dump_row file. A user customized template to use for the dump_row file. If left blank and a dump_row file is requested, a default version will be used.
 
      | *Used by:*  StatAnalysis
 
@@ -3853,7 +3853,7 @@ METplus Configuration Glossary
      .. warning:: **DEPRECATED:** Please use :term:`MODEL<n>_STAT_ANALYSIS_OUT_STAT_TEMPLATE` instead.
 
    MODEL<n>_STAT_ANALYSIS_OUT_STAT_TEMPLATE
-     Specify the template to use for the stat_analysis out_stat file. A user customized template to use for the out_stat file. If left blank and a out_stat file is requested, a default version will be used. This is optional in the METplus configuration file for running with :term:`LOOP_ORDER` = times.
+     Specify the template to use for the stat_analysis out_stat file. A user customized template to use for the out_stat file. If left blank and a out_stat file is requested, a default version will be used.
 
      | *Used by:*  StatAnalysis
 
@@ -7636,12 +7636,11 @@ METplus Configuration Glossary
      | *Used by:*  UserScript
 
    TC_PAIRS_RUN_ONCE
-     If True and LOOP_ORDER = processes, TCPairs will be run once using the
+     If True, TCPairs will be run once using the
      INIT_BEG or VALID_BEG value (depending on the value of LOOP_BY).
      This is the default setting and preserves the original logic of the
      wrapper. If this variable is set to False, then TCPairs will run once
-     for each run time iteration. If LOOP_ORDER = times, then TCPairs will
-     still run for each run time. The preferred configuration settings to
+     for each run time iteration. The preferred configuration settings to
      run TCPairs once for a range of init or valid times is to set INIT_BEG
      to INIT_END (if LOOP_BY = INIT) and define the range of init times to
      filter the data inside TCPairs with TC_PAIRS_INIT_BEG and
diff --git a/docs/Users_Guide/systemconfiguration.rst b/docs/Users_Guide/systemconfiguration.rst
index e9e3868f2d..4d9b1a31e3 100644
--- a/docs/Users_Guide/systemconfiguration.rst
+++ b/docs/Users_Guide/systemconfiguration.rst
@@ -1078,38 +1078,14 @@ the output directory.
 Loop Order
 ----------
 
-The METplus wrappers can be configured to loop first by times then
-processes or vice-versa. Looping by times first will run each process in
-the process list for a given run time, increment to the next run time, run
-each process in the process list, and so on. Looping by processes first
-will run all times for the first process, then run all times for the
-second process, and so on.
+The METplus wrappers will run all times for the first process defined in the
+:term:`PROCESS_LIST, then run all times for the second process, and so on.
+The :term:`LOOP_ORDER` variable has been deprecated in v5.0.0.
+This is the behavior that was previously executed when LOOP_ORDER = processes.
 
-**Example 1 Configuration**::
-
-  [config]
-  LOOP_ORDER = times
-
-  PROCESS_LIST = PCPCombine, GridStat
-
-  VALID_BEG = 20190201
-  VALID_END = 20190203
-  VALID_INCREMENT = 1d
-
-will run in the following order::
-
-  * PCPCombine at 2019-02-01
-  * GridStat   at 2019-02-01
-  * PCPCombine at 2019-02-02
-  * GridStat   at 2019-02-02
-  * PCPCombine at 2019-02-03
-  * GridStat   at 2019-02-03
-
-
-**Example 2 Configuration**::
+**Example Configuration**::
 
   [config]
-  LOOP_ORDER = processes
 
   PROCESS_LIST = PCPCombine, GridStat
 
@@ -1126,12 +1102,7 @@ will run in the following order::
   * GridStat   at 2019-02-02
   * GridStat   at 2019-02-03
 
-.. note::
-    If running a MET tool that processes data over a time range, such as
-    SeriesAnalysis or StatAnalysis, the tool must be run with
-    LOOP_ORDER = processes.
 
-    
 .. _Custom_Looping:
 
 Custom Looping
@@ -1782,15 +1753,13 @@ The possible values for the \*_RUNTIME_FREQ variables are:
   (init or valid and forecast lead combination).
   All filename templates are substituted with values.
 
-Note that :term:`LOOP_ORDER` must be set to processes to run these wrappers.
-Also note that the following example may not contain all of the configuration
+Note that the following example may not contain all of the configuration
 variables that are required for a successful run. The are intended to show
 how these variables affect how the data is processed.
 
 **SeriesAnalysis Examples**::
 
     [config]
-    LOOP_ORDER = processes
 
     LOOP_BY = INIT
     INIT_TIME_FMT = %Y%m%d%H
diff --git a/docs/Users_Guide/wrappers.rst b/docs/Users_Guide/wrappers.rst
index 0956b88bef..8850e47abe 100644
--- a/docs/Users_Guide/wrappers.rst
+++ b/docs/Users_Guide/wrappers.rst
@@ -3693,9 +3693,9 @@ Description
 -----------
 
 The MakePlots wrapper creates various statistical plots using python
-scripts for the various METplus Wrappers use cases. This can only be run
-following StatAnalysis wrapper when LOOP_ORDER = processes. To run
-MakePlots wrapper, include MakePlots in PROCESS_LIST.
+scripts for the various METplus Wrappers use cases.
+This can only be run following StatAnalysis wrapper.
+To run MakePlots wrapper, include MakePlots in PROCESS_LIST.
 
 METplus Configuration
 ---------------------
@@ -6829,74 +6829,18 @@ Description
 
 The StatAnalysis wrapper encapsulates the behavior of the MET
 stat_analysis tool. It provides the infrastructure to summarize and
-filter the MET .stat files. StatAnalysis wrapper can be run in two
-different methods. First is to look at the STAT lines for a single date,
-to use this method set LOOP_ORDER = times. Second is to look at the STAT
-lines over a span of dates, to use this method set LOOP_ORDER =
-processes. To run StatAnalysis wrapper, include StatAnalysis in
-PROCESS_LIST.
+filter the MET .stat files.
 
 METplus Configuration
 ---------------------
 
-The following values must be defined in the METplus Wrappers
-configuration file for running with LOOP_ORDER = times:
+The following values **must** be defined in the METplus configuration file:
 
 | :term:`STAT_ANALYSIS_OUTPUT_DIR`
-| :term:`MODEL<n>_STAT_ANALYSIS_DUMP_ROW_TEMPLATE`
-| :term:`MODEL<n>_STAT_ANALYSIS_OUT_STAT_TEMPLATE`
 | :term:`LOG_STAT_ANALYSIS_VERBOSITY`
 | :term:`MODEL\<n\>`
 | :term:`MODEL<n>_OBTYPE`
 | :term:`MODEL<n>_STAT_ANALYSIS_LOOKIN_DIR`
-| :term:`MODEL_LIST`
-| :term:`GROUP_LIST_ITEMS`
-| :term:`LOOP_LIST_ITEMS`
-| :term:`STAT_ANALYSIS_CONFIG_FILE`
-| :term:`STAT_ANALYSIS_JOB_NAME`
-| :term:`STAT_ANALYSIS_JOB_ARGS`
-| :term:`STAT_ANALYSIS_MET_CONFIG_OVERRIDES`
-|
-
-The following values are **optional** in the METplus Wrappers
-configuration file for running with LOOP_ORDER = times:
-
-| :term:`DESC_LIST`
-| :term:`FCST_VALID_HOUR_LIST`
-| :term:`OBS_VALID_HOUR_LIST`
-| :term:`FCST_INIT_HOUR_LIST`
-| :term:`OBS_INIT_HOUR_LIST`
-| :term:`FCST_VAR_LIST`
-| :term:`OBS_VAR_LIST`
-| :term:`FCST_LEVEL_LIST`
-| :term:`OBS_LEVEL_LIST`
-| :term:`FCST_UNITS_LIST`
-| :term:`OBS_UNITS_LIST`
-| :term:`FCST_THRESH_LIST`
-| :term:`OBS_THRESH_LIST`
-| :term:`FCST_LEAD_LIST`
-| :term:`OBS_LEAD_LIST`
-| :term:`VX_MASK_LIST`
-| :term:`INTERP_MTHD_LIST`
-| :term:`INTERP_PNTS_LIST`
-| :term:`ALPHA_LIST`
-| :term:`COV_THRESH_LIST`
-| :term:`LINE_TYPE_LIST`
-| :term:`STAT_ANALYSIS_SKIP_IF_OUTPUT_EXISTS`
-| :term:`STAT_ANALYSIS_HSS_EC_VALUE`
-| :term:`STAT_ANALYSIS_OUTPUT_TEMPLATE`
-|
-
-The following values **must** be defined in the METplus Wrappers
-configuration file for running with LOOP_ORDER = processes:
-
-| :term:`STAT_ANALYSIS_OUTPUT_DIR`
-| :term:`LOG_STAT_ANALYSIS_VERBOSITY`
-| :term:`DATE_TYPE`
-| :term:`STAT_ANALYSIS_CONFIG_FILE`
-| :term:`MODEL\<n\>`
-| :term:`MODEL<n>_OBTYPE`
-| :term:`MODEL<n>_STAT_ANALYSIS_LOOKIN_DIR`
 | :term:`MODEL<n>_REFERENCE_NAME`
 | :term:`GROUP_LIST_ITEMS`
 | :term:`LOOP_LIST_ITEMS`
@@ -6904,11 +6848,14 @@ configuration file for running with LOOP_ORDER = processes:
 | :term:`VX_MASK_LIST`
 | :term:`FCST_LEAD_LIST`
 | :term:`LINE_TYPE_LIST`
+| :term:`STAT_ANALYSIS_JOB_NAME`
+| :term:`STAT_ANALYSIS_JOB_ARGS`
+| :term:`STAT_ANALYSIS_MET_CONFIG_OVERRIDES`
 |
 
-The following values are optional in the METplus Wrappers configuration
-file for running with LOOP_ORDER = processes:
+The following values are optional in the METplus configuration file:
 
+| :term:`STAT_ANALYSIS_CONFIG_FILE`
 | :term:`VAR<n>_FOURIER_DECOMP`
 | :term:`VAR<n>_WAVE_NUM_LIST`
 | :term:`FCST_VALID_HOUR_LIST`
@@ -6923,6 +6870,8 @@ file for running with LOOP_ORDER = processes:
 | :term:`ALPHA_LIST`
 | :term:`STAT_ANALYSIS_HSS_EC_VALUE`
 | :term:`STAT_ANALYSIS_OUTPUT_TEMPLATE`
+| :term:`MODEL<n>_STAT_ANALYSIS_DUMP_ROW_TEMPLATE`
+| :term:`MODEL<n>_STAT_ANALYSIS_OUT_STAT_TEMPLATE`
 |
 
 .. warning:: **DEPRECATED:**
diff --git a/internal/tests/pytests/wrappers/stat_analysis/test_stat_analysis.py b/internal/tests/pytests/wrappers/stat_analysis/test_stat_analysis.py
index 054e167bc5..8a5755d263 100644
--- a/internal/tests/pytests/wrappers/stat_analysis/test_stat_analysis.py
+++ b/internal/tests/pytests/wrappers/stat_analysis/test_stat_analysis.py
@@ -54,7 +54,6 @@ def test_create_c_dict(metplus_config):
     st = stat_analysis_wrapper(metplus_config)
     # Test 1
     c_dict = st.create_c_dict()
-    assert c_dict['LOOP_ORDER'] == 'times'
     assert(os.path.realpath(c_dict['CONFIG_FILE']) == (METPLUS_BASE+'/internal/tests/'
                                                        +'config/STATAnalysisConfig'))
     assert(c_dict['OUTPUT_DIR'] == (st.config.getdir('OUTPUT_BASE')
diff --git a/metplus/util/config_metplus.py b/metplus/util/config_metplus.py
index feea916bc2..654063212a 100644
--- a/metplus/util/config_metplus.py
+++ b/metplus/util/config_metplus.py
@@ -1000,7 +1000,6 @@ def check_for_deprecated_config(config):
     #     modify the code to handle both variables accordingly
     deprecated_dict = {
         'LOOP_BY_INIT' : {'sec' : 'config', 'alt' : 'LOOP_BY', 'copy': False},
-        'LOOP_METHOD' : {'sec' : 'config', 'alt' : 'LOOP_ORDER'},
         'PREPBUFR_DIR_REGEX' : {'sec' : 'regex_pattern', 'alt' : None},
         'PREPBUFR_FILE_REGEX' : {'sec' : 'regex_pattern', 'alt' : None},
         'OBS_INPUT_DIR_REGEX' : {'sec' : 'regex_pattern', 'alt' : 'OBS_POINT_STAT_INPUT_DIR', 'copy': False},
diff --git a/metplus/util/met_util.py b/metplus/util/met_util.py
index 4d3f796bb5..32eecab662 100644
--- a/metplus/util/met_util.py
+++ b/metplus/util/met_util.py
@@ -136,22 +136,11 @@ def run_metplus(config, process_list):
             logger.info("Refer to ERROR messages above to resolve issues.")
             return 1
 
-        loop_order = config.getstr('config', 'LOOP_ORDER', '').lower()
-        #loop_order = 'processes'
-
-        if loop_order == "processes":
-            all_commands = []
-            for process in processes:
-                new_commands = process.run_all_times()
-                if new_commands:
-                    all_commands.extend(new_commands)
-
-        elif loop_order == "times":
-            all_commands = loop_over_times_and_call(config, processes)
-        else:
-            logger.error("Invalid LOOP_ORDER defined. "
-                         "Options are processes, times")
-            return 1
+        all_commands = []
+        for process in processes:
+            new_commands = process.run_all_times()
+            if new_commands:
+                all_commands.extend(new_commands)
 
         # if process list contains any wrapper that should run commands
         if any([item[0] not in NO_COMMAND_WRAPPERS for item in process_list]):
diff --git a/metplus/wrappers/command_builder.py b/metplus/wrappers/command_builder.py
index 0b2a7b48f5..31cf9da942 100755
--- a/metplus/wrappers/command_builder.py
+++ b/metplus/wrappers/command_builder.py
@@ -1278,16 +1278,6 @@ def run_command(self, cmd, cmd_name=None):
 
         return True
 
-    # argument needed to match call
-    # pylint:disable=unused-argument
-    def run_at_time(self, input_dict):
-        """! Used to output error and exit if wrapper is attempted to be run
-         with LOOP_ORDER = times and the run_at_time method is not implemented
-        """
-        self.log_error(f'run_at_time not implemented for {self.log_name} '
-                       'wrapper. Cannot run with LOOP_ORDER = times')
-        return None
-
     def run_all_times(self, custom=None):
         """! Loop over time range specified in conf file and
         call METplus wrapper for each time
diff --git a/metplus/wrappers/make_plots_wrapper.py b/metplus/wrappers/make_plots_wrapper.py
index 29bbcc8aac..88ba564fb7 100755
--- a/metplus/wrappers/make_plots_wrapper.py
+++ b/metplus/wrappers/make_plots_wrapper.py
@@ -105,7 +105,6 @@ def create_c_dict(self):
             self.config.getstr('config', 'LOG_MAKE_PLOTS_VERBOSITY',
                                c_dict['VERBOSITY'])
         )
-        c_dict['LOOP_ORDER'] = self.config.getstr('config', 'LOOP_ORDER')
         c_dict['INPUT_BASE_DIR'] = self.config.getdir('MAKE_PLOTS_INPUT_DIR')
         c_dict['OUTPUT_BASE_DIR'] = self.config.getdir('MAKE_PLOTS_OUTPUT_DIR')
         c_dict['SCRIPTS_BASE_DIR'] = self.config.getdir('MAKE_PLOTS_SCRIPTS_DIR')
diff --git a/metplus/wrappers/runtime_freq_wrapper.py b/metplus/wrappers/runtime_freq_wrapper.py
index 05ff099cbf..2812e81e15 100755
--- a/metplus/wrappers/runtime_freq_wrapper.py
+++ b/metplus/wrappers/runtime_freq_wrapper.py
@@ -101,15 +101,6 @@ def run_all_times(self):
                            f" {', '.join(self.FREQ_OPTIONS)}")
             return None
 
-        # if not running once for each runtime and loop order is not set to
-        # 'processes' report an error
-        if self.c_dict['RUNTIME_FREQ'] != 'RUN_ONCE_FOR_EACH':
-            loop_order = self.config.getstr('config', 'LOOP_ORDER', '').lower()
-            if loop_order != 'processes':
-                self.log_error(f"Cannot run using {self.c_dict['RUNTIME_FREQ']} "
-                               "mode unless LOOP_ORDER = processes")
-                return None
-
         wrapper_instance_name = self.get_wrapper_instance_name()
         self.logger.info(f'Running wrapper: {wrapper_instance_name}')
 
diff --git a/metplus/wrappers/stat_analysis_wrapper.py b/metplus/wrappers/stat_analysis_wrapper.py
index de313014ca..ffde04030a 100755
--- a/metplus/wrappers/stat_analysis_wrapper.py
+++ b/metplus/wrappers/stat_analysis_wrapper.py
@@ -158,7 +158,6 @@ def create_c_dict(self):
             self.config.getstr('config', 'LOG_STAT_ANALYSIS_VERBOSITY',
                                c_dict['VERBOSITY'])
         )
-        c_dict['LOOP_ORDER'] = self.config.getstr('config', 'LOOP_ORDER')
 
         # STATAnalysis config file is optional, so
         # don't provide wrapped config file name as default value
@@ -436,7 +435,7 @@ def set_lists_loop_or_group(self, c_dict):
         for missing_config in missing_config_list:
 
             # if running MakePlots
-            if (c_dict['LOOP_ORDER'] == 'processes' and self.runMakePlots):
+            if self.runMakePlots:
 
                 # if LINE_TYPE_LIST is missing, add it to group list
                 if missing_config == 'LINE_TYPE_LIST':
diff --git a/metplus/wrappers/tc_pairs_wrapper.py b/metplus/wrappers/tc_pairs_wrapper.py
index e4870b7e06..c86cc01ab8 100755
--- a/metplus/wrappers/tc_pairs_wrapper.py
+++ b/metplus/wrappers/tc_pairs_wrapper.py
@@ -285,7 +285,7 @@ def create_c_dict(self):
                                 False)
         )
 
-        # if LOOP_ORDER = processes, only run once if True
+        # only run once if True
         c_dict['RUN_ONCE'] = self.config.getbool('config',
                                                  'TC_PAIRS_RUN_ONCE',
                                                  True)

From c0f66fb8a95bbd03ca86e2bc43bb0f074e63e668 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Thu, 29 Sep 2022 12:49:21 -0600
Subject: [PATCH 33/34] fixed typo in docs

---
 docs/Users_Guide/systemconfiguration.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Users_Guide/systemconfiguration.rst b/docs/Users_Guide/systemconfiguration.rst
index 4d9b1a31e3..c0ff3ef4dd 100644
--- a/docs/Users_Guide/systemconfiguration.rst
+++ b/docs/Users_Guide/systemconfiguration.rst
@@ -1079,7 +1079,7 @@ Loop Order
 ----------
 
 The METplus wrappers will run all times for the first process defined in the
-:term:`PROCESS_LIST, then run all times for the second process, and so on.
+:term:`PROCESS_LIST`, then run all times for the second process, and so on.
 The :term:`LOOP_ORDER` variable has been deprecated in v5.0.0.
 This is the behavior that was previously executed when LOOP_ORDER = processes.
 

From ed6213f1bc0192ec5d257f29963cad37559e17c2 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Thu, 29 Sep 2022 12:51:08 -0600
Subject: [PATCH 34/34] removed loop order from another test

---
 .../tests/pytests/plotting/make_plots/test_make_plots_wrapper.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/internal/tests/pytests/plotting/make_plots/test_make_plots_wrapper.py b/internal/tests/pytests/plotting/make_plots/test_make_plots_wrapper.py
index 5ee62c781a..5c6b08c910 100644
--- a/internal/tests/pytests/plotting/make_plots/test_make_plots_wrapper.py
+++ b/internal/tests/pytests/plotting/make_plots/test_make_plots_wrapper.py
@@ -47,7 +47,6 @@ def test_create_c_dict(metplus_config):
     mp = make_plots_wrapper(metplus_config)
     # Test 1
     c_dict = mp.create_c_dict()
-    assert(c_dict['LOOP_ORDER'] == 'processes')
     # NOTE: MakePlots relies on output from StatAnalysis
     #       so its input resides in the output of StatAnalysis
     assert(c_dict['INPUT_BASE_DIR'] == mp.config.getdir('OUTPUT_BASE')