Feature #2578 PCPCombine -input_thresh for missing inputs (#2609)

* refactoring to reduce duplicate/redundant code, reduce cognitive complexity to satisfy SonarQube, etc

* change wording of error log to satisfy test

* set -input_thresh argument if set for add, derive, and sum methods. refactor setting of method arguments, e.g. -add, -sum, etc., cleanup

* refactor how level is handled in find_data function so that if the level has already been set, it will use that value, otherwise try to get it from {data_type}_level, e.g. fcst_level, otherwise set it to 0 to prevent errors

* refactor duplicate code into function to satisfy SonarQube

* removed unused variable

* use find_data function to find input files to be consistent with other wrappers, only allow multiple input files to be found for a given call to find_data if using the -derive method

* fix typo in key

* suppress warnings when files aren't found because it is expected

* formatting to be consistent in doc string

* per #2578, add MISSING before file path that is not found if input_thresh is set and less than 1.0, added unit test to ensure correct behavior occurs

* add documentation blocks for new functions, ci-run-all-diff

* use pytest fixture instead of local function

* add support for setting -vld_thresh argument

* per #2578, added documentation and tests for setting -input_thresh and -vld_thresh

* moved verbosity argument to end of command to more easily change it when debugging

* refactor to reduce cognitive complexity to satisfy SonarQube

* update usage statement to include METplus version number

docs/Users_Guide/glossary.rst

@@ -11979,3 +11979,29 @@ METplus Configuration Glossary
      There is no default, so a value must be specified. All runtime frequencies are supported.
 
      | *Used by:*  UserScript
+
+   FCST_PCP_COMBINE_INPUT_THRESH
+     Specify the value for the command line argument '-input_thresh' for the
+     forecast run of PCPCombine, e.g. :term:`FCST_PCP_COMBINE_RUN` is True.
+     Not used when :term:`FCST_PCP_COMBINE_METHOD` is SUBTRACT or USER_DEFINED.
+
+     | *Used by:* PCPCombine
+
+   OBS_PCP_COMBINE_INPUT_THRESH
+     Specify the value for the command line argument '-input_thresh' for the
+     observation run of PCPCombine, e.g. :term:`OBS_PCP_COMBINE_RUN` is True.
+     Not used when :term:`OBS_PCP_COMBINE_METHOD` is SUBTRACT or USER_DEFINED.
+
+     | *Used by:* PCPCombine
+
+   FCST_PCP_COMBINE_VLD_THRESH
+     Specify the value for the command line argument '-vld_thresh' for the
+     forecast run of PCPCombine, e.g. :term:`FCST_PCP_COMBINE_RUN` is True.
+
+     | *Used by:* PCPCombine
+
+   OBS_PCP_COMBINE_VLD_THRESH
+     Specify the value for the command line argument '-vld_thresh' for the
+     observation run of PCPCombine, e.g. :term:`OBS_PCP_COMBINE_RUN` is True.
+
+     | *Used by:* PCPCombine

docs/Users_Guide/wrappers.rst

@@ -6027,6 +6027,10 @@ METplus Configuration
 | :term:`PCP_COMBINE_INC_VALID_TIMES`
 | :term:`PCP_COMBINE_SKIP_INIT_TIMES`
 | :term:`PCP_COMBINE_INC_INIT_TIMES`
+| :term:`FCST_PCP_COMBINE_INPUT_THRESH`
+| :term:`FCST_PCP_COMBINE_VLD_THRESH`
+| :term:`OBS_PCP_COMBINE_INPUT_THRESH`
+| :term:`OBS_PCP_COMBINE_VLD_THRESH`
 |
 
 .. warning:: **DEPRECATED:**

internal/tests/pytests/conftest.py

@@ -199,11 +199,13 @@ def make_nc(tmp_path, lon, lat, z, data, variable='Temp', file_name='fake.nc'):
 def get_test_data_dir():
     """!Get path to directory containing test data.
     """
-    def get_test_data_path(subdir):
+    def get_test_data_path(subdir=None):
         internal_tests_dir = os.path.abspath(
-            os.path.join(os.path.dirname(__file__), os.pardir)
+            os.path.join(os.path.dirname(__file__), os.pardir, 'data')
         )
-        return os.path.join(internal_tests_dir, 'data', subdir)
+        if subdir:
+            internal_tests_dir = os.path.join(internal_tests_dir, subdir)
+        return internal_tests_dir
 
     return get_test_data_path