From 6bc5edb36aa8440aef76a58e12ad75e0a37998cf Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 8 Jan 2025 11:27:53 -0700
Subject: [PATCH 1/5] test that this file is not needed anymore because RTD
 controls the version selector

---
 docs/_static/pop_ver.js | 18 ------------------
 docs/conf.py            |  2 +-
 2 files changed, 1 insertion(+), 19 deletions(-)
 delete mode 100644 docs/_static/pop_ver.js

diff --git a/docs/_static/pop_ver.js b/docs/_static/pop_ver.js
deleted file mode 100644
index ed70d7d141..0000000000
--- a/docs/_static/pop_ver.js
+++ /dev/null
@@ -1,18 +0,0 @@
-$(document).ready(function() {
-    // Add 8 to get to end of URL METplus/
-    var proj_end = document.baseURI.indexOf("METplus") + 8;
-    var end = document.baseURI.indexOf("/", proj_end);
-    var cur_ver = document.baseURI.substring(proj_end, end);
-    var name = cur_ver.startsWith('v') ? cur_ver.substring(1) : cur_ver;
-    var mylist = $("#version-list");
-    mylist.empty();
-    mylist.append($("<option>", {value: "../" + cur_ver, text: name}));
-    $.getJSON(version_json_loc, function(obj) {
-        $.each(obj.versions, function() {
-            if (this != cur_ver) {
-                name = this.startsWith('v') ? this.substring(1) : this;
-                mylist.append($("<option>", {value: DOCUMENTATION_OPTIONS.URL_ROOT + '../' + this, text: name}));
-            }
-        });
-    });
-});
diff --git a/docs/conf.py b/docs/conf.py
index a17adcd2ff..495411cf8b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -198,7 +198,7 @@
 #
 html_theme = 'sphinx_rtd_theme'
 html_theme_path = ["_themes", ]
-html_js_files = ['pop_ver.js']
+html_js_files = []
 html_css_files = ['theme_override.css']
 
 # Add any paths that contain custom static files (such as style sheets) here,

From 6ed470e39eac9ddc7421b106b1eda6c700284e08 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 8 Jan 2025 12:06:56 -0700
Subject: [PATCH 2/5] various changes to appease SonarQube complaints

---
 docs/build_docs.py                            |  13 +-
 .../compile_official_release_notes.py         |   4 +-
 internal/scripts/docker/Dockerfile            |   6 +-
 internal/tests/pytests/conftest.py            |   2 +-
 .../config_metplus/test_config_metplus.py     |  31 ++--
 .../util/config_util/test_config_util.py      |  15 +-
 .../pytests/util/diff_util/test_diff_util.py  |  12 +-
 .../util/met_config/test_met_config.py        | 147 +++++++++---------
 8 files changed, 113 insertions(+), 117 deletions(-)

diff --git a/docs/build_docs.py b/docs/build_docs.py
index 444d9bff7b..fe838172b3 100755
--- a/docs/build_docs.py
+++ b/docs/build_docs.py
@@ -31,7 +31,7 @@ def run_command(command, dir_to_run=None):
     log_text = f"Running {command}"
     if dir_to_run:
         log_text += f" under {dir_to_run}"
-
+    print(log_text)
     command_out = subprocess.run(shlex.split(command),
                                  cwd=dir_to_run)
     if command_out.returncode != 0:
@@ -103,8 +103,7 @@ def main():
                                'run')
 
     # run make to generate the documentation files
-    run_command(f"make clean html",
-                docs_dir)
+    run_command("make clean html", docs_dir)
 
     if not skip_doxygen:
         # build the doxygen documentation
@@ -157,14 +156,14 @@ def main():
     warning_file = os.path.join(docs_dir,
                                 '_build',
                                 'warnings.log')
-    if os.stat(warning_file).st_size == 0:
-        print(f"No warnings found, removing {warning_file}")
-        os.remove(warning_file)
-    else:
+    if os.stat(warning_file).st_size != 0:
         print('ERROR: Doc build contains warnings or errors. '
               f'Please review {warning_file}')
         sys.exit(1)
 
+    print(f"No warnings found, removing {warning_file}")
+    os.remove(warning_file)
+
     print("Documentation build completed")
 
 if __name__ == "__main__":
diff --git a/internal/scripts/dev_tools/compile_official_release_notes.py b/internal/scripts/dev_tools/compile_official_release_notes.py
index 1b797c3f7f..c66e548ff3 100644
--- a/internal/scripts/dev_tools/compile_official_release_notes.py
+++ b/internal/scripts/dev_tools/compile_official_release_notes.py
@@ -19,7 +19,7 @@
 items = {}
 # gather issues and organize them by category
 for line in content:
-    if match := re.match(r'  .. dropdown:: (.*)', line):
+    if match := re.match(r' {2}.. dropdown:: (.*)', line):
         category = match.group(1)
         if not items.get(category):
             items[category] = []
@@ -43,7 +43,7 @@
     if not issues.get(cat):
         issues[cat] = {}
     for issue in item_list:
-        match = re.match(r'.*\#(\d+).*', issue.replace('\n', ''))
+        match = re.match(r'.*#(\d+).*', issue.replace('\n', ''))
         if match:
             issues[cat][match.group(1)] = issue
 
diff --git a/internal/scripts/docker/Dockerfile b/internal/scripts/docker/Dockerfile
index 2df83a89c5..48931be5a3 100644
--- a/internal/scripts/docker/Dockerfile
+++ b/internal/scripts/docker/Dockerfile
@@ -18,7 +18,7 @@ ARG MET_DOCKER_REPO=met
 ARG MET_TAG=develop
 
 # if OBTAIN_SOURCE_CODE=copy, copy files from build context into image
-FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} as build_copy
+FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} AS build_copy
 ONBUILD WORKDIR /metplus
 ONBUILD RUN mkdir -p METplus
 ONBUILD COPY . METplus
@@ -28,7 +28,7 @@ ONBUILD RUN if [ ! -e "METplus/ush/run_metplus.py" ]; then \
   fi
 
 # if OBTAIN_SOURCE_CODE=clone, clone repository
-FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} as build_clone
+FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} AS build_clone
 ONBUILD WORKDIR /metplus
 ONBUILD ARG SOURCE_VERSION
 ONBUILD RUN echo "Cloning METplus repository"; \
@@ -40,7 +40,7 @@ ONBUILD RUN echo "Cloning METplus repository"; \
   fi
 
 # if OBTAIN_SOURCE_CODE=none, do not retrieve files
-FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} as build_none
+FROM dtcenter/${MET_DOCKER_REPO}:${MET_TAG} AS build_none
 ONBUILD WORKDIR /metplus
 
 # use build alias based on OBTAIN_SOURCE_CODE value
diff --git a/internal/tests/pytests/conftest.py b/internal/tests/pytests/conftest.py
index 4fdd602e8a..bf6396dcc9 100644
--- a/internal/tests/pytests/conftest.py
+++ b/internal/tests/pytests/conftest.py
@@ -185,7 +185,7 @@ def make_nc(tmp_path, lon, lat, z, data, variable='Temp', file_name='fake.nc'):
         latitude = rootgrp.createVariable("Latitude", "f4", "lat")
         levels = rootgrp.createVariable("Levels", "i4", "z")
         temp = rootgrp.createVariable(variable, "f4", ("time", "lon", "lat", "z"))
-        time = rootgrp.createVariable("Time", "i4", "time")
+        rootgrp.createVariable("Time", "i4", "time")
 
         longitude[:] = lon
         latitude[:] = lat
diff --git a/internal/tests/pytests/util/config_metplus/test_config_metplus.py b/internal/tests/pytests/util/config_metplus/test_config_metplus.py
index efb33d9b22..cb61841b0c 100644
--- a/internal/tests/pytests/util/config_metplus/test_config_metplus.py
+++ b/internal/tests/pytests/util/config_metplus/test_config_metplus.py
@@ -10,6 +10,10 @@
 from metplus.util.config_validate import validate_config_variables
 
 
+var1_levels = "LEVELS11, LEVELS12"
+var2_levels = "LEVELS21, LEVELS22"
+var1_options = 'ens_ssvar_bin_size = 0.1; ens_phist_bin_size = 0.05;'
+
 @pytest.mark.parametrize(
     'config_overrides,expected_logfile', [
         (['config.LOG_METPLUS={LOG_DIR}/metplus.log'], '<LOG_DIR>/metplus.log'),
@@ -267,9 +271,9 @@ def test_get_field_config_variables_synonyms(metplus_config,
 def test_parse_var_list_fcst_only(metplus_config, data_type, list_created):
     conf = metplus_config
     conf.set('config', 'FCST_VAR1_NAME', "NAME1")
-    conf.set('config', 'FCST_VAR1_LEVELS', "LEVELS11, LEVELS12")
+    conf.set('config', 'FCST_VAR1_LEVELS', var1_levels)
     conf.set('config', 'FCST_VAR2_NAME', "NAME2")
-    conf.set('config', 'FCST_VAR2_LEVELS', "LEVELS21, LEVELS22")
+    conf.set('config', 'FCST_VAR2_LEVELS', var2_levels)
 
     # this should not occur because OBS variables are missing
     assert not validate_config_variables(conf)[0]
@@ -303,9 +307,9 @@ def test_parse_var_list_fcst_only(metplus_config, data_type, list_created):
 def test_parse_var_list_obs(metplus_config, data_type, list_created):
     conf = metplus_config
     conf.set('config', 'OBS_VAR1_NAME', "NAME1")
-    conf.set('config', 'OBS_VAR1_LEVELS', "LEVELS11, LEVELS12")
+    conf.set('config', 'OBS_VAR1_LEVELS', var1_levels)
     conf.set('config', 'OBS_VAR2_NAME', "NAME2")
-    conf.set('config', 'OBS_VAR2_LEVELS', "LEVELS21, LEVELS22")
+    conf.set('config', 'OBS_VAR2_LEVELS', var2_levels)
 
     # this should not occur because FCST variables are missing
     if validate_config_variables(conf)[0]:
@@ -340,9 +344,9 @@ def test_parse_var_list_obs(metplus_config, data_type, list_created):
 def test_parse_var_list_both(metplus_config, data_type, list_created):
     conf = metplus_config
     conf.set('config', 'BOTH_VAR1_NAME', "NAME1")
-    conf.set('config', 'BOTH_VAR1_LEVELS', "LEVELS11, LEVELS12")
+    conf.set('config', 'BOTH_VAR1_LEVELS', var1_levels)
     conf.set('config', 'BOTH_VAR2_NAME', "NAME2")
-    conf.set('config', 'BOTH_VAR2_LEVELS', "LEVELS21, LEVELS22")
+    conf.set('config', 'BOTH_VAR2_LEVELS', var2_levels)
 
     # this should not occur because BOTH variables are used
     if not validate_config_variables(conf)[0]:
@@ -472,7 +476,7 @@ def test_parse_var_list_fcst_and_obs_and_both(metplus_config, data_type, list_le
 def test_parse_var_list_fcst_only_options(metplus_config, data_type, list_len):
     conf = metplus_config
     conf.set('config', 'FCST_VAR1_NAME', "NAME1")
-    conf.set('config', 'FCST_VAR1_LEVELS', "LEVELS11, LEVELS12")
+    conf.set('config', 'FCST_VAR1_LEVELS', var1_levels)
     conf.set('config', 'FCST_VAR1_THRESH', ">1, >2")
     conf.set('config', 'OBS_VAR1_OPTIONS', "OOPTIONS11")
 
@@ -533,13 +537,11 @@ def test_parse_var_list_ensemble(metplus_config):
     config.set('config', 'FCST_VAR1_NAME', 'APCP')
     config.set('config', 'FCST_VAR1_LEVELS', 'A24')
     config.set('config', 'FCST_VAR1_THRESH', '>0.01, >=10.0')
-    config.set('config', 'FCST_VAR1_OPTIONS', ('ens_ssvar_bin_size = 0.1; '
-                                               'ens_phist_bin_size = 0.05;'))
+    config.set('config', 'FCST_VAR1_OPTIONS', var1_options)
     config.set('config', 'OBS_VAR1_NAME', 'APCP')
     config.set('config', 'OBS_VAR1_LEVELS', 'A24')
     config.set('config', 'OBS_VAR1_THRESH', '>0.01, >=10.0')
-    config.set('config', 'OBS_VAR1_OPTIONS', ('ens_ssvar_bin_size = 0.1; '
-                                              'ens_phist_bin_size = 0.05;'))
+    config.set('config', 'OBS_VAR1_OPTIONS', var1_options)
     time_info = {}
 
     expected_ens_list = [{'index': 1,
@@ -567,14 +569,11 @@ def test_parse_var_list_ensemble(metplus_config):
                           'fcst_name': 'APCP',
                           'fcst_level': 'A24',
                           'fcst_thresh': ['>0.01', '>=10.0'],
-                          'fcst_extra': ('ens_ssvar_bin_size = 0.1; '
-                                         'ens_phist_bin_size = 0.05;'),
+                          'fcst_extra': var1_options,
                           'obs_name': 'APCP',
                           'obs_level': 'A24',
                           'obs_thresh': ['>0.01', '>=10.0'],
-                          'obs_extra': ('ens_ssvar_bin_size = 0.1; '
-                                        'ens_phist_bin_size = 0.05;')
-
+                          'obs_extra': var1_options
                           },
                         ]
 
diff --git a/internal/tests/pytests/util/config_util/test_config_util.py b/internal/tests/pytests/util/config_util/test_config_util.py
index 7409f62b4e..6054a947fc 100644
--- a/internal/tests/pytests/util/config_util/test_config_util.py
+++ b/internal/tests/pytests/util/config_util/test_config_util.py
@@ -3,10 +3,9 @@
 import pytest
 
 import pprint
-import os
 from datetime import datetime
 
-from metplus.util.config_util import *
+from metplus.util import config_util as cu
 from metplus.util.config_metplus import parse_var_list
 from metplus.util.time_util import ti_calculate
 
@@ -33,7 +32,7 @@ def test_get_custom_string_list(metplus_config, conf_items, met_tool, expected_r
     for conf_key, conf_value in conf_items.items():
         config.set('config', conf_key, conf_value)
 
-    assert get_custom_string_list(config, met_tool) == expected_result
+    assert cu.get_custom_string_list(config, met_tool) == expected_result
 
 
 @pytest.mark.parametrize(
@@ -72,7 +71,7 @@ def test_get_custom_string_list(metplus_config, conf_items, met_tool, expected_r
 def test_get_process_list(metplus_config, input_list, expected_list):
     conf = metplus_config
     conf.set('config', 'PROCESS_LIST', input_list)
-    process_list = get_process_list(conf)
+    process_list = cu.get_process_list(conf)
     output_list = [item[0] for item in process_list]
     assert output_list == expected_list
 
@@ -106,7 +105,7 @@ def test_get_process_list(metplus_config, input_list, expected_list):
 def test_get_process_list_instances(metplus_config, input_list, expected_list):
     conf = metplus_config
     conf.set('config', 'PROCESS_LIST', input_list)
-    output_list = get_process_list(conf)
+    output_list = cu.get_process_list(conf)
     assert output_list == expected_list
 
 
@@ -159,11 +158,11 @@ def test_sub_var_list(metplus_config, input_dict, expected_list):
     actual_temp = parse_var_list(config)
 
     pp = pprint.PrettyPrinter()
-    print(f'Actual var list (before sub):')
+    print('Actual var list (before sub):')
     pp.pprint(actual_temp)
 
-    actual_list = sub_var_list(actual_temp, time_info)
-    print(f'Actual var list (after sub):')
+    actual_list = cu.sub_var_list(actual_temp, time_info)
+    print('Actual var list (after sub):')
     pp.pprint(actual_list)
 
     assert len(actual_list) == len(expected_list)
diff --git a/internal/tests/pytests/util/diff_util/test_diff_util.py b/internal/tests/pytests/util/diff_util/test_diff_util.py
index 9222ed3388..b26dd8b6d7 100644
--- a/internal/tests/pytests/util/diff_util/test_diff_util.py
+++ b/internal/tests/pytests/util/diff_util/test_diff_util.py
@@ -1,8 +1,6 @@
 import pytest
 
-from netCDF4 import Dataset
 import os
-import shutil
 from unittest import mock
 from PIL import Image
 import numpy as np
@@ -214,7 +212,7 @@ def test_get_file_type(path, expected):
 
 
 @pytest.mark.util
-def test_get_file_type_netCDF4(dummy_nc1):
+def test_get_file_type_netcdf4(dummy_nc1):
     actual = du.get_file_type(dummy_nc1)
     assert actual == 'netcdf'
 
@@ -488,7 +486,7 @@ def test__handle_text_files(cmp_return, comp_txt_return, expected):
 
 
 @pytest.mark.parametrize(
-    'colour_A, colour_B, save_diff, expected, check_print',
+    "colour_a, colour_b, save_diff, expected, check_print",
     [
         (
             255,
@@ -515,7 +513,7 @@ def test__handle_text_files(cmp_return, comp_txt_return, expected):
 )
 @pytest.mark.util
 def test_compare_image_files(
-    capfd, tmp_path_factory, colour_A, colour_B, save_diff, expected, check_print
+    capfd, tmp_path_factory, colour_a, colour_b, save_diff, expected, check_print
 ):
     image_dir = tmp_path_factory.mktemp('images')
     image1 = image_dir / 'img1.jpg'
@@ -528,8 +526,8 @@ def _make_test_img(file_path, col):
         im.save(file_path)
         im.close()
 
-    _make_test_img(image1, colour_A)
-    _make_test_img(image2, colour_B)
+    _make_test_img(image1, colour_a)
+    _make_test_img(image2, colour_b)
 
     actual = du.compare_image_files(image1, image2, save_diff)
 
diff --git a/internal/tests/pytests/util/met_config/test_met_config.py b/internal/tests/pytests/util/met_config/test_met_config.py
index c42cfef14d..848fa73cef 100644
--- a/internal/tests/pytests/util/met_config/test_met_config.py
+++ b/internal/tests/pytests/util/met_config/test_met_config.py
@@ -2,32 +2,34 @@
 
 import pytest
 
-from metplus.util.met_config import *
+from metplus.util import met_config as mc
 from metplus.util.met_config import _read_climo_file_name, _read_climo_field
 from metplus.util import CLIMO_TYPES
 
+type_lower = '<type>'
+type_upper = '<TYPE>'
 
 @pytest.mark.parametrize(
     'config_overrides, expected_value', [
         # 0 no relevant config set
         ({}, ''),
         # 1 _FIELD set
-        ({'APP_CLIMO_<TYPE>_FIELD': '{name="TMP"; level="(*,*)";}'},
+        ({f'APP_CLIMO_{type_upper}_FIELD': '{name="TMP"; level="(*,*)";}'},
          '{name="TMP"; level="(*,*)";}'),
         # 2 VAR1 name/level set
-        ({'APP_CLIMO_<TYPE>_VAR1_NAME': 'TMP',
-          'APP_CLIMO_<TYPE>_VAR1_LEVELS': '"(*,*)"'},
+        ({f'APP_CLIMO_{type_upper}_VAR1_NAME': 'TMP',
+          f'APP_CLIMO_{type_upper}_VAR1_LEVELS': '"(*,*)"'},
          '{ name="TMP"; level="(*,*)"; }'),
         # 3 VAR1/2 name/level set
-        ({'APP_CLIMO_<TYPE>_VAR1_NAME': 'TMP',
-          'APP_CLIMO_<TYPE>_VAR1_LEVELS': '"(*,*)"',
-          'APP_CLIMO_<TYPE>_VAR2_NAME': 'PRES',
-          'APP_CLIMO_<TYPE>_VAR2_LEVELS': '"(0,*,*)"'},
+        ({f'APP_CLIMO_{type_upper}_VAR1_NAME': 'TMP',
+          f'APP_CLIMO_{type_upper}_VAR1_LEVELS': '"(*,*)"',
+          f'APP_CLIMO_{type_upper}_VAR2_NAME': 'PRES',
+          f'APP_CLIMO_{type_upper}_VAR2_LEVELS': '"(0,*,*)"'},
          '{ name="TMP"; level="(*,*)"; },{ name="PRES"; level="(0,*,*)"; }'),
         # 4 VAR1 name/level and FIELD set - prefer VAR<n>
-        ({'APP_CLIMO_<TYPE>_FIELD': '{name="TEMP"; level="(0,*,*)";}',
-          'APP_CLIMO_<TYPE>_VAR1_NAME': 'TMP',
-          'APP_CLIMO_<TYPE>_VAR1_LEVELS': '"(*,*)"'},
+        ({f'APP_CLIMO_{type_upper}_FIELD': '{name="TEMP"; level="(0,*,*)";}',
+          f'APP_CLIMO_{type_upper}_VAR1_NAME': 'TMP',
+          f'APP_CLIMO_{type_upper}_VAR1_LEVELS': '"(*,*)"'},
          '{ name="TMP"; level="(*,*)"; }'),
     ]
 )
@@ -40,9 +42,8 @@ def test_read_climo_field(metplus_config, config_overrides, expected_value):
 
         # set config values
         for key, value in config_overrides.items():
-            key_sub = key.replace('<TYPE>', climo_type)
-            value_sub = value.replace('<type>', climo_type.lower())
-            config.set('config', key_sub, value_sub)
+            key_sub = key.replace(type_upper, climo_type)
+            config.set('config', key_sub, value)
 
         _read_climo_field(climo_type, config, app_name)
         assert config.getraw('config', expected_var) == expected_value
@@ -53,75 +54,75 @@ def test_read_climo_field(metplus_config, config_overrides, expected_value):
         # 0 no relevant config set
         ({}, ''),
         # 1 file name single
-        ({'APP_CLIMO_<TYPE>_FILE_NAME': 'some/file/path'},
-         'climo_<type> = {file_name = ["some/file/path"];}'),
+        ({f'APP_CLIMO_{type_upper}_FILE_NAME': 'some/file/path'},
+         f'climo_{type_lower} = ' + '{file_name = ["some/file/path"];}'),
         # 2 file name multiple
-        ({'APP_CLIMO_<TYPE>_FILE_NAME': 'some/file/path, other/path'},
-         'climo_<type> = {file_name = ["some/file/path", "other/path"];}'),
+        ({f'APP_CLIMO_{type_upper}_FILE_NAME': 'some/file/path, other/path'},
+         f'climo_{type_lower} = ' + '{file_name = ["some/file/path", "other/path"];}'),
         # 3 field single
-        ({'APP_CLIMO_<TYPE>_FIELD': '{name="TMP"; level="(*,*)";}'},
-         'climo_<type> = {field = [{name="TMP"; level="(*,*)";}];}'),
+        ({f'APP_CLIMO_{type_upper}_FIELD': '{name="TMP"; level="(*,*)";}'},
+         f'climo_{type_lower} = ' + '{field = [{name="TMP"; level="(*,*)";}];}'),
         # 4 field multiple
-        ({'APP_CLIMO_<TYPE>_FIELD': ('{name="TMP"; level="(*,*)";},'
+        ({f'APP_CLIMO_{type_upper}_FIELD': ('{name="TMP"; level="(*,*)";},'
                                          '{name="TEMP"; level="P500";}')},
-         ('climo_<type> = {field = [{name="TMP"; level="(*,*)";}, '
+         (f'climo_{type_lower} = ' + '{field = [{name="TMP"; level="(*,*)";}, '
           '{name="TEMP"; level="P500";}];}')),
-        # 5 use fcst no other climo_<type>
-        ({'APP_CLIMO_<TYPE>_USE_FCST': 'TRUE'},
-         'climo_<type> = fcst;'),
-        # 6 use obs no other climo_<type>
-        ({'APP_CLIMO_<TYPE>_USE_OBS': 'TRUE'},
-         'climo_<type> = obs;'),
-        # 7 use fcst with other climo_<type>
-        ({'APP_CLIMO_<TYPE>_REGRID_METHOD': 'NEAREST',
-          'APP_CLIMO_<TYPE>_USE_FCST': 'TRUE'},
-         'climo_<type> = {regrid = {method = NEAREST;}}climo_<type> = fcst;'),
-        # 8 use obs with other climo_<type>
-        ({'APP_CLIMO_<TYPE>_REGRID_METHOD': 'NEAREST',
-          'APP_CLIMO_<TYPE>_USE_OBS': 'TRUE'},
-         'climo_<type> = {regrid = {method = NEAREST;}}climo_<type> = obs;'),
+        # 5 use fcst no other climo_{type_lower}
+        ({f'APP_CLIMO_{type_upper}_USE_FCST': 'TRUE'},
+         f'climo_{type_lower} = fcst;'),
+        # 6 use obs no other climo_{type_lower}
+        ({f'APP_CLIMO_{type_upper}_USE_OBS': 'TRUE'},
+         f'climo_{type_lower} = obs;'),
+        # 7 use fcst with other climo_{type_lower}
+        ({f'APP_CLIMO_{type_upper}_REGRID_METHOD': 'NEAREST',
+          f'APP_CLIMO_{type_upper}_USE_FCST': 'TRUE'},
+         f'climo_{type_lower} = ' + '{regrid = {method = NEAREST;}}' + f'climo_{type_lower} = fcst;'),
+        # 8 use obs with other climo_{type_lower}
+        ({f'APP_CLIMO_{type_upper}_REGRID_METHOD': 'NEAREST',
+          f'APP_CLIMO_{type_upper}_USE_OBS': 'TRUE'},
+         f'climo_{type_lower} = ' + '{regrid = {method = NEAREST;}}' + f'climo_{type_lower} = obs;'),
         # 9 regrid method
-        ({'APP_CLIMO_<TYPE>_REGRID_METHOD': 'NEAREST', },
-         'climo_<type> = {regrid = {method = NEAREST;}}'),
+        ({f'APP_CLIMO_{type_upper}_REGRID_METHOD': 'NEAREST', },
+         f'climo_{type_lower} = ' + '{regrid = {method = NEAREST;}}'),
         # 10 regrid width
-        ({'APP_CLIMO_<TYPE>_REGRID_WIDTH': '1', },
-         'climo_<type> = {regrid = {width = 1;}}'),
+        ({f'APP_CLIMO_{type_upper}_REGRID_WIDTH': '1', },
+         f'climo_{type_lower} = ' + '{regrid = {width = 1;}}'),
         # 11 regrid vld_thresh
-        ({'APP_CLIMO_<TYPE>_REGRID_VLD_THRESH': '0.5', },
-         'climo_<type> = {regrid = {vld_thresh = 0.5;}}'),
+        ({f'APP_CLIMO_{type_upper}_REGRID_VLD_THRESH': '0.5', },
+         f'climo_{type_lower} = ' + '{regrid = {vld_thresh = 0.5;}}'),
         # 12 regrid shape
-        ({'APP_CLIMO_<TYPE>_REGRID_SHAPE': 'SQUARE', },
-         'climo_<type> = {regrid = {shape = SQUARE;}}'),
+        ({f'APP_CLIMO_{type_upper}_REGRID_SHAPE': 'SQUARE', },
+         f'climo_{type_lower} = ' + '{regrid = {shape = SQUARE;}}'),
         # 13 time_interp_method
-        ({'APP_CLIMO_<TYPE>_TIME_INTERP_METHOD': 'NEAREST', },
-         'climo_<type> = {time_interp_method = NEAREST;}'),
+        ({f'APP_CLIMO_{type_upper}_TIME_INTERP_METHOD': 'NEAREST', },
+         f'climo_{type_lower} = ' + '{time_interp_method = NEAREST;}'),
         # 14 match_month
-        ({'APP_CLIMO_<TYPE>_MATCH_MONTH': 'True', },
-         'climo_<type> = {match_month = TRUE;}'),
+        ({f'APP_CLIMO_{type_upper}_MATCH_MONTH': 'True', },
+         f'climo_{type_lower} = ' + '{match_month = TRUE;}'),
         # 15 day_interval - int
-        ({'APP_CLIMO_<TYPE>_DAY_INTERVAL': '30', },
-         'climo_<type> = {day_interval = 30;}'),
+        ({f'APP_CLIMO_{type_upper}_DAY_INTERVAL': '30', },
+         f'climo_{type_lower} = ' + '{day_interval = 30;}'),
         # 16 day_interval - NA
-        ({'APP_CLIMO_<TYPE>_DAY_INTERVAL': 'NA', },
-         'climo_<type> = {day_interval = NA;}'),
+        ({f'APP_CLIMO_{type_upper}_DAY_INTERVAL': 'NA', },
+         f'climo_{type_lower} = ' + '{day_interval = NA;}'),
         # 17 hour_interval
-        ({'APP_CLIMO_<TYPE>_HOUR_INTERVAL': '12', },
-         'climo_<type> = {hour_interval = 12;}'),
+        ({f'APP_CLIMO_{type_upper}_HOUR_INTERVAL': '12', },
+         f'climo_{type_lower} = ' + '{hour_interval = 12;}'),
         # 18 all
         ({
-             'APP_CLIMO_<TYPE>_FILE_NAME': '/some/climo_<type>/file.txt',
-             'APP_CLIMO_<TYPE>_FIELD': '{name="CLM_NAME"; level="(0,0,*,*)";}',
-             'APP_CLIMO_<TYPE>_REGRID_METHOD': 'NEAREST',
-             'APP_CLIMO_<TYPE>_REGRID_WIDTH': '1',
-             'APP_CLIMO_<TYPE>_REGRID_VLD_THRESH': '0.5',
-             'APP_CLIMO_<TYPE>_REGRID_SHAPE': 'SQUARE',
-             'APP_CLIMO_<TYPE>_TIME_INTERP_METHOD': 'NEAREST',
-             'APP_CLIMO_<TYPE>_MATCH_MONTH': 'True',
-             'APP_CLIMO_<TYPE>_DAY_INTERVAL': '30',
-             'APP_CLIMO_<TYPE>_HOUR_INTERVAL': '12',
+             f'APP_CLIMO_{type_upper}_FILE_NAME': f'/some/climo_{type_lower}/file.txt',
+             f'APP_CLIMO_{type_upper}_FIELD': '{name="CLM_NAME"; level="(0,0,*,*)";}',
+             f'APP_CLIMO_{type_upper}_REGRID_METHOD': 'NEAREST',
+             f'APP_CLIMO_{type_upper}_REGRID_WIDTH': '1',
+             f'APP_CLIMO_{type_upper}_REGRID_VLD_THRESH': '0.5',
+             f'APP_CLIMO_{type_upper}_REGRID_SHAPE': 'SQUARE',
+             f'APP_CLIMO_{type_upper}_TIME_INTERP_METHOD': 'NEAREST',
+             f'APP_CLIMO_{type_upper}_MATCH_MONTH': 'True',
+             f'APP_CLIMO_{type_upper}_DAY_INTERVAL': '30',
+             f'APP_CLIMO_{type_upper}_HOUR_INTERVAL': '12',
          },
-         ('climo_<type> = {file_name = '
-          '["/some/climo_<type>/file.txt"];'
+         (f'climo_{type_lower} = ' + '{file_name = '
+          f'["/some/climo_{type_lower}/file.txt"];'
           'field = [{name="CLM_NAME"; level="(0,0,*,*)";}];'
           'regrid = {method = NEAREST;width = 1;'
           'vld_thresh = 0.5;shape = SQUARE;}'
@@ -141,13 +142,13 @@ def test_handle_climo_dict(metplus_config, config_overrides, expected_value):
 
         # set config values
         for key, value in config_overrides.items():
-            key_sub = key.replace('<TYPE>', climo_type)
-            value_sub = value.replace('<type>', climo_type.lower())
+            key_sub = key.replace(type_upper, climo_type)
+            value_sub = value.replace(type_lower, climo_type.lower())
             config.set('config', key_sub, value_sub)
 
-        handle_climo_dict(config, app_name, output_dict, sub_groups=sub_groups)
+        mc.handle_climo_dict(config, app_name, output_dict, sub_groups=sub_groups)
         print(output_dict)
-        expected_sub = expected_value.replace('<type>', climo_type.lower())
+        expected_sub = expected_value.replace(type_lower, climo_type.lower())
         assert output_dict[expected_var] == expected_sub
 
 
@@ -159,7 +160,7 @@ def test_handle_climo_dict(metplus_config, config_overrides, expected_value):
 )
 @pytest.mark.util
 def test_met_config_info(name, data_type, mp_configs, extra_args):
-    item = METConfig(name=name, data_type=data_type)
+    item = mc.METConfig(name=name, data_type=data_type)
 
     item.metplus_configs = mp_configs
     item.extra_args = extra_args
@@ -189,7 +190,7 @@ def test_met_config_info(name, data_type, mp_configs, extra_args):
 @pytest.mark.util
 def test_set_met_config_function(data_type, expected_function):
     try:
-        function_found = set_met_config_function(data_type)
+        function_found = mc.set_met_config_function(data_type)
         function_name = function_found.__name__ if function_found else None
         assert function_name == expected_function
     except ValueError:
@@ -207,7 +208,7 @@ def test_set_met_config_function(data_type, expected_function):
 )
 @pytest.mark.util
 def test_format_regrid_to_grid(input, output):
-    assert format_regrid_to_grid(input) == output
+    assert mc.format_regrid_to_grid(input) == output
 
 
 @pytest.mark.parametrize(

From 33668b294fd6c1c999424fedccdda818ad1344b3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 8 Jan 2025 13:36:04 -0700
Subject: [PATCH 3/5] remove deprecated docker command

---
 .github/jobs/free_disk_space.sh | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/jobs/free_disk_space.sh b/.github/jobs/free_disk_space.sh
index fc6c6bad0b..f4f86e8a7c 100755
--- a/.github/jobs/free_disk_space.sh
+++ b/.github/jobs/free_disk_space.sh
@@ -59,10 +59,6 @@ cmd="docker image prune -af"
 printf "\nRunning $cmd"
 $cmd
 
-cmd=docker system prune -af
-printf "\nRunning $cmd"
-$cmd
-
 cmd="docker images"
 printf "\nAFTER CLEANUP: $cmd"
 $cmd

From 1ba00fa346500466d0e70e734062b04762cf13f1 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 8 Jan 2025 15:03:43 -0700
Subject: [PATCH 4/5] resolve more SonarQube code smells

---
 .../pytests/util/run_util/test_run_util.py    | 33 ++++++++++---------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/internal/tests/pytests/util/run_util/test_run_util.py b/internal/tests/pytests/util/run_util/test_run_util.py
index 62d9e81497..e4e77e47a3 100644
--- a/internal/tests/pytests/util/run_util/test_run_util.py
+++ b/internal/tests/pytests/util/run_util/test_run_util.py
@@ -9,6 +9,7 @@
 from metplus.wrappers.ensemble_stat_wrapper import EnsembleStatWrapper
 from metplus.wrappers.grid_stat_wrapper import GridStatWrapper
 
+some_fake_dir = '/some/fake/dir'
 
 EXPECTED_CONFIG_KEYS = [
     'CLOCK_TIME',
@@ -158,7 +159,7 @@ def test_pre_run_setup_sed_file(capfd):
         assert actual is None
 
     # check sed file is written correctly
-    out, err = capfd.readouterr()
+    _, err = capfd.readouterr()
     sed_err_regex = r'.*Find/Replace commands have been generated in (.*)\n'
     sed_file = None
     match = re.match(sed_err_regex, err)
@@ -183,7 +184,7 @@ def test_pre_run_setup_deprecated(capfd):
     actual = get_config_from_file('sed_run_util.conf')
     assert actual is None
 
-    out, err = capfd.readouterr()
+    _, err = capfd.readouterr()
 
     expected_error_msgs = [
         'ERROR: DEPRECATED CONFIG ITEMS WERE FOUND. PLEASE FOLLOW THE INSTRUCTIONS TO UPDATE THE CONFIG FILES',
@@ -199,7 +200,7 @@ def test_pre_run_setup_no_install(capfd):
     actual = get_config_from_file('no_install_run_util.conf')
     assert actual is None
 
-    out, err = capfd.readouterr()
+    _, err = capfd.readouterr()
     assert 'MET_INSTALL_DIR must be set correctly to run METplus' in err
 
 
@@ -210,7 +211,7 @@ def test_run_metplus_usage(metplus_config, capfd):
     config.set('config', 'PROCESS_LIST', 'GridStat,Usage')
     actual = ru.run_metplus(config)
     assert actual == 0
-    out, err = capfd.readouterr()
+    out, _ = capfd.readouterr()
     assert "USAGE: This text is displayed when [config] PROCESS_LIST = Usage." in out
 
 
@@ -261,7 +262,7 @@ def test_run_metplus(capfd, config_dict, expected, check_err):
     actual = ru.run_metplus(config)
     assert actual == expected
 
-    out, err = capfd.readouterr()
+    _, err = capfd.readouterr()
     if check_err:
         for msg in check_err:
             assert msg in err
@@ -286,7 +287,7 @@ def test_run_metplus_errors(capfd, side_effect, return_value, check_err):
         config.set('config', 'PROCESS_LIST', 'GridStat')
         actual = ru.run_metplus(config)
         assert actual == 1
-        out, err = capfd.readouterr()
+        _, err = capfd.readouterr()
         if check_err:
             assert "Fatal error occurred" in err
         else:
@@ -315,7 +316,7 @@ def test_get_wrapper_instance_raises(capfd, side_effect, check_err):
     with mock.patch.object(wi, 'import_module', side_effect=side_effect):
         actual = wi.get_wrapper_instance(config, 'EnsembleStat')
     assert actual == None
-    out, err = capfd.readouterr()
+    _, err = capfd.readouterr()
     assert check_err in err
     remove_output_base(config)
 
@@ -338,7 +339,7 @@ def test__load_all_wrappers(metplus_config):
 
 
 @pytest.mark.parametrize(
-    'isOK_1, isOK_2, expected, reset_error',
+    "is_ok_1, is_ok_2, expected, reset_error",
     [
         (True, True, 0, False),
         (False, True, 2, False),
@@ -350,13 +351,13 @@ def test__load_all_wrappers(metplus_config):
 )
 @pytest.mark.util
 def test__check_wrapper_init_errors(
-    metplus_config, isOK_1, isOK_2, expected, reset_error
+    metplus_config, is_ok_1, is_ok_2, expected, reset_error
 ):
     process_list = [('EnsembleStat', 1), ('GridStat', None)]
     processes = ru._load_all_wrappers(metplus_config, process_list)
 
-    processes[0].isOK = isOK_1
-    processes[1].isOK = isOK_2
+    processes[0].isOK = is_ok_1
+    processes[1].isOK = is_ok_2
 
     if reset_error:
         processes[0].errors = 0
@@ -418,15 +419,15 @@ def _check_log_info(config, args, not_in=False):
 @pytest.mark.util
 def test_post_run_cleanup_scrubs(post_run_config):
     post_run_config.set('config', 'SCRUB_STAGING_DIR', True)
-    post_run_config.set('config', 'STAGING_DIR', '/some/fake/dir')
+    post_run_config.set('config', 'STAGING_DIR', some_fake_dir)
 
     with mock.patch.object(ru.shutil, 'rmtree') as mock_rm:
         with mock.patch.object(ru.os.path, 'exists', return_value=True):
             ru.post_run_cleanup(post_run_config, 'fake_app', 0)
 
-    assert mock_rm.called_once_with('/some/fake/dir')
+    assert mock_rm.called_once_with(some_fake_dir)
 
-    _check_log_info(post_run_config, ['Scrubbing staging dir: %s', '/some/fake/dir'])
+    _check_log_info(post_run_config, ['Scrubbing staging dir: %s', some_fake_dir])
     _check_log_info(
         post_run_config,
         ['Set SCRUB_STAGING_DIR to False to preserve intermediate files.'],
@@ -443,7 +444,7 @@ def test_post_run_cleanup_no_errors(post_run_config):
 
     with mock.patch.object(
         ru, 'get_user_info', return_value='Allan H. Murphy'
-    ) as mock_user:
+    ):
         with mock.patch.object(ru, 'get_logfile_info', return_value='/log/file.log'):
             actual = ru.post_run_cleanup(post_run_config, 'fake_app', 0)
 
@@ -463,7 +464,7 @@ def test_post_run_cleanup_errors(post_run_config):
     err_msg = 'fake_app has finished running as user Allan H. Murphy but had 5 errors.'
     with mock.patch.object(
         ru, 'get_user_info', return_value='Allan H. Murphy'
-    ) as mock_user:
+    ):
         with mock.patch.object(ru, 'get_logfile_info', return_value='/log/file.log'):
             actual = ru.post_run_cleanup(post_run_config, 'fake_app', 5)
 

From 99057cf73d6ba573f7de419575547c1a1e51b15b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 8 Jan 2025 15:04:00 -0700
Subject: [PATCH 5/5] update URL for posting sample data

---
 .github/ISSUE_TEMPLATE/bug_report.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 3e8ad837b1..f652d5b74a 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -28,7 +28,7 @@ Describe the steps to reproduce the behavior:
 *3. Scroll down to '....'*
 *4. See error*
 *Post relevant sample data following these instructions:*
-*https://dtcenter.org/community-code/model-evaluation-tools-met/met-help-desk#ftp*
+*https://github.com/dtcenter/METplus/discussions/954*
 
 ### Relevant Deadlines ###
 *List relevant project deadlines here or state NONE.*