per #2578, added documentation and tests for setting -input_thresh an…

…d -vld_thresh

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/wrappers/pcp_combine/test_pcp_combine_wrapper.py

@@ -706,7 +706,7 @@ def test_get_extra_fields(metplus_config, names, levels, expected_args):
 
     wrapper = PCPCombineWrapper(config)
 
-    wrapper._handle_extra_field_arguments(data_src)
+    wrapper.set_command_line_arguments(data_src)
     wrapper._handle_name_argument('', data_src)
     for index, expected_arg in enumerate(expected_args):
         assert wrapper.args[index] == expected_arg
@@ -858,42 +858,66 @@ def test_subtract_method_zero_accum(metplus_config):
 
 
 @pytest.mark.parametrize(
-    'thresh, success', [
-        (None, False),
-        (0.6, True),
-        (1.0, False),
+    'input_thresh, vld_thresh, success', [
+        (None, None, False),
+        (0.6, None, True),
+        (1.0, None, False),
+        (None, 0.2, False),
+        (0.6, 0.2, True),
+        (1.0, 0.2, False),
     ]
 )
 @pytest.mark.wrapper
-def test_add_method_missing_input(metplus_config, thresh, success):
+def test_add_method_missing_input(metplus_config, get_test_data_dir, input_thresh, vld_thresh, success):
     data_src = "OBS"
-    lookback = 6 * 3600
-    task_info = {
-        'valid': datetime.strptime("2016090415", '%Y%m%d%H')
-    }
-    time_info = ti_calculate(task_info)
+    input_dir = get_test_data_dir('accum')
 
     config = metplus_config
     set_minimum_config_settings(config, data_src)
-    if thresh is not None:
-        config.set('config', f'{data_src}_PCP_COMBINE_INPUT_THRESH', thresh)
+    config.set('config', 'LOOP_BY', "VALID")
+    config.set('config', 'VALID_TIME_FMT', "%Y%m%d%H")
+    config.set('config', 'VALID_BEG', "2016090415")
+    config.set('config', 'VALID_END', "2016090415")
+    config.set('config', 'VALID_INCREMENT', "1d")
+    config.set('config', f'{data_src}_PCP_COMBINE_INPUT_DIR', input_dir)
+    config.set('config', f'{data_src}_PCP_COMBINE_OUTPUT_ACCUM', '6H')
+    config.set('config', f'{data_src}_PCP_COMBINE_INPUT_ACCUMS', '1H')
+    if input_thresh is not None:
+        config.set('config', f'{data_src}_PCP_COMBINE_INPUT_THRESH', input_thresh)
+    if vld_thresh is not None:
+        config.set('config', f'{data_src}_PCP_COMBINE_VLD_THRESH', vld_thresh)
     wrapper = PCPCombineWrapper(config)
 
-    input_dir = get_test_data_dir(wrapper.config, subdir='accum')
-    files_found = wrapper.setup_add_method(time_info, lookback, data_src)
+    assert wrapper.isOK
+
+    all_cmds = wrapper.run_all_times()
     if not success:
-        assert not files_found
+        assert len(all_cmds) == 0
         return
 
-    assert files_found
+    field_name = wrapper.config.get('config', f'{data_src}_PCP_COMBINE_INPUT_NAMES')
+    field_info = f"'name=\"{field_name}\";'"
 
-    in_files = [item[0] for item in files_found]
-    print(f"Input files: {in_files}")
-    assert (len(in_files) == 6 and
-            f"{input_dir}/20160904/file.2016090415.01h" in in_files and
-            f"{input_dir}/20160904/file.2016090414.01h" in in_files and
-            f"{input_dir}/20160904/file.2016090413.01h" in in_files and
-            f"{input_dir}/20160904/file.2016090412.01h" in in_files and
-            f"MISSING{input_dir}/20160904/file.2016090411.01h" in in_files and
-            f"MISSING{input_dir}/20160904/file.2016090410.01h" in in_files
-            )
+    app_path = os.path.join(config.getdir('MET_BIN_DIR'), wrapper.app_name)
+    verbosity = f"-v {wrapper.c_dict['VERBOSITY']}"
+    out_dir = wrapper.c_dict.get(f'{data_src}_OUTPUT_DIR')
+    extra_args = ''
+    if input_thresh:
+        extra_args += f' -input_thresh {input_thresh}'
+    if vld_thresh:
+        extra_args += f' -vld_thresh {vld_thresh}'
+    expected_cmds = [
+        f"{app_path} {verbosity} -add"
+        f" {input_dir}/20160904/file.2016090415.01h {field_info}"
+        f" {input_dir}/20160904/file.2016090414.01h {field_info}"
+        f" {input_dir}/20160904/file.2016090413.01h {field_info}"
+        f" {input_dir}/20160904/file.2016090412.01h {field_info}"
+        f" MISSING{input_dir}/20160904/file.2016090411.01h {field_info}"
+        f" MISSING{input_dir}/20160904/file.2016090410.01h {field_info}"
+        f"{extra_args} {out_dir}/20160904/outfile.2016090415_A06h"
+    ]
+    assert len(all_cmds) == len(expected_cmds)
+
+    for (cmd, env_vars), expected_cmd in zip(all_cmds, expected_cmds):
+        # ensure commands are generated as expected
+        assert cmd == expected_cmd

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_add.conf

@@ -70,3 +70,6 @@ FCST_PCP_COMBINE_INPUT_LEVELS = Surface
 
 FCST_PCP_COMBINE_OUTPUT_ACCUM = 15M
 FCST_PCP_COMBINE_OUTPUT_NAME = A001500
+
+#FCST_PCP_COMBINE_INPUT_THRESH =
+#FCST_PCP_COMBINE_VLD_THRESH =

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_bucket.conf

@@ -66,3 +66,6 @@ FCST_PCP_COMBINE_INPUT_ACCUMS = {lead}
 
 FCST_PCP_COMBINE_OUTPUT_ACCUM = 15H
 FCST_PCP_COMBINE_OUTPUT_NAME = APCP
+
+#FCST_PCP_COMBINE_INPUT_THRESH =
+#FCST_PCP_COMBINE_VLD_THRESH =

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_derive.conf

@@ -79,3 +79,6 @@ FCST_PCP_COMBINE_OUTPUT_NAME =
 #FCST_PCP_COMBINE_EXTRA_NAMES =
 #FCST_PCP_COMBINE_EXTRA_LEVELS =
 #FCST_PCP_COMBINE_EXTRA_OUTPUT_NAMES =
+
+#FCST_PCP_COMBINE_INPUT_THRESH =
+#FCST_PCP_COMBINE_VLD_THRESH =

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_loop_custom.conf

@@ -70,3 +70,6 @@ FCST_PCP_COMBINE_INPUT_ACCUMS = 24H
 
 FCST_PCP_COMBINE_OUTPUT_ACCUM = 24H
 FCST_PCP_COMBINE_OUTPUT_NAME = APCP
+
+#FCST_PCP_COMBINE_INPUT_THRESH =
+#FCST_PCP_COMBINE_VLD_THRESH =

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_python_embedding.conf

@@ -64,6 +64,9 @@ OBS_PCP_COMBINE_INPUT_DATATYPE = PYTHON_NUMPY
 OBS_PCP_COMBINE_INPUT_ACCUMS = 6
 OBS_PCP_COMBINE_INPUT_NAMES = {PARM_BASE}/use_cases/met_tool_wrapper/PCPCombine/sum_IMERG_V06_HDF5.py {OBS_PCP_COMBINE_INPUT_DIR} IRprecipitation {valid?fmt=%Y%m%d%H} 02
 
+#OBS_PCP_COMBINE_INPUT_THRESH =
+#OBS_PCP_COMBINE_VLD_THRESH =
+
 [user_env_vars]
 # uncomment and change this to the path of a version of python that has the h5py package installed
 #MET_PYTHON_EXE = /path/to/python/with/h5-py/and/numpy/packages/bin/python

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_subtract.conf

@@ -69,3 +69,5 @@ FCST_PCP_COMBINE_OUTPUT_ACCUM = 3H
 FCST_PCP_COMBINE_OUTPUT_NAME = APCP_03
 
 FCST_PCP_COMBINE_USE_ZERO_ACCUM = False
+
+#FCST_PCP_COMBINE_VLD_THRESH =

parm/use_cases/met_tool_wrapper/PCPCombine/PCPCombine_sum.conf

@@ -66,3 +66,6 @@ FCST_PCP_COMBINE_INPUT_LEVELS = Surface
 
 FCST_PCP_COMBINE_OUTPUT_ACCUM = 15M
 FCST_PCP_COMBINE_OUTPUT_NAME = A001500
+
+#FCST_PCP_COMBINE_INPUT_THRESH =
+#FCST_PCP_COMBINE_VLD_THRESH =