Update develop-ref after dtcenter/MET#2820

.github/workflows/testing.yml

@@ -238,7 +238,6 @@ jobs:
     needs: use_case_tests
     if: ${{ always() && needs.use_case_tests.result == 'failure' }}
     steps:
-      - uses: actions/checkout@v4
       - name: Check for error logs
         id: check-for-error-logs
         run: |

docs/Users_Guide/release-notes.rst

@@ -30,6 +30,48 @@ When applicable, release notes are followed by the
 `GitHub issue <https://github.com/dtcenter/METplus/issues>`__ number which
 describes the bugfix, enhancement, or new feature.
 
+METplus Version 6.0.0 Beta 3 Release Notes (2024-02-08)
+-------------------------------------------------------
+
+  .. dropdown:: Enhancements
+
+     * Add support for MET land-mask settings in Point-Stat
+       (`#2334 <https://github.com/dtcenter/METplus/issues/2334>`_)
+     * Enhance the TC-Pairs wrapper to support the new diag_required and diag_min_req configuration options
+       (`#2430 <https://github.com/dtcenter/METplus/issues/2430>`_)
+     * Enhance the TC-Diag wrapper to support new configuration options added in MET-12.0.0-beta2
+       (`#2432 <https://github.com/dtcenter/METplus/issues/2432>`_)
+     * Prevent error if some input files are missing
+       (`#2460 <https://github.com/dtcenter/METplus/issues/2460>`_)
+
+  .. dropdown:: Bugfix
+
+     NONE
+
+  .. dropdown:: New Wrappers
+
+     NONE
+
+  .. dropdown:: New Use Cases
+
+     * Verify Total Column Ozone against NASA's OMI dataset
+       (`#1989 <https://github.com/dtcenter/METplus/issues/1989>`_)
+     * RRFS reformatting, aggregating, and plotting use case
+       (`#2406 <https://github.com/dtcenter/METplus/issues/2406>`_)
+     * Satellite Altimetry data
+       (`#2383 <https://github.com/dtcenter/METplus/issues/2383>`_)
+
+  .. dropdown:: Documentation
+
+     * Create video to demonstrate how to update use cases that use deprecated environment variables
+       (`#2371 <https://github.com/dtcenter/METplus/issues/2371>`_)
+
+  .. dropdown:: Internal
+
+     * Update Documentation Overview and Conventions
+       (`#2454 <https://github.com/dtcenter/METplus/issues/2454>`_)
+
+
 METplus Version 6.0.0 Beta 2 Release Notes (2023-11-14)
 -------------------------------------------------------
 

internal/tests/pytests/conftest.py

@@ -113,6 +113,14 @@ def test_example(metplus_config):
                 if len(msg.args) != 0]
         print("Tests raised the following errors:")
         print("\n".join(err_msgs))
+    if config.logger.warning.call_args_list:
+        warn_msgs = [
+                str(msg.args[0])
+                for msg
+                in config.logger.warning.call_args_list
+                if len(msg.args) != 0]
+        print("\nTests raised the following warnings:")
+        print("\n".join(warn_msgs))
     config.logger = old_logger
     # don't remove output base if test fails
     if request.node.rep_call.failed:
@@ -185,3 +193,16 @@ def make_nc(tmp_path, lon, lat, z, data, variable='Temp', file_name='fake.nc'):
         temp[0, :, :, :] = data
 
     return file_name
+
+
+@pytest.fixture(scope="function")
+def get_test_data_dir():
+    """!Get path to directory containing test data.
+    """
+    def get_test_data_path(subdir):
+        internal_tests_dir = os.path.abspath(
+            os.path.join(os.path.dirname(__file__), os.pardir)
+        )
+        return os.path.join(internal_tests_dir, 'data', subdir)
+
+    return get_test_data_path

internal/tests/pytests/util/run_util/test_run_util.py

@@ -48,6 +48,8 @@
     'METPLUS_BASE',
     'PARM_BASE',
     'METPLUS_VERSION',
+    'ALLOW_MISSING_INPUTS',
+    'INPUT_THRESH',
 ]
 
 

internal/tests/pytests/wrappers/ascii2nc/test_ascii2nc_wrapper.py

@@ -17,8 +17,8 @@ def ascii2nc_wrapper(metplus_config, config_overrides=None):
         'LOOP_BY': 'VALID',
         'VALID_TIME_FMT': '%Y%m%d%H',
         'VALID_BEG': '2010010112',
-        'VALID_END': '2010010112',
-        'VALID_INCREMENT': '1M',
+        'VALID_END': '2010010118',
+        'VALID_INCREMENT': '6H',
         'ASCII2NC_INPUT_TEMPLATE': '{INPUT_BASE}/met_test/data/sample_obs/ascii/precip24_{valid?fmt=%Y%m%d%H}.ascii',
         'ASCII2NC_OUTPUT_TEMPLATE': '{OUTPUT_BASE}/ascii2nc/precip24_{valid?fmt=%Y%m%d%H}.nc',
         'ASCII2NC_CONFIG_FILE': '{PARM_BASE}/met_config/Ascii2NcConfig_wrapped',
@@ -47,6 +47,36 @@ def ascii2nc_wrapper(metplus_config, config_overrides=None):
     return ASCII2NCWrapper(config, instance=instance)
 
 
+@pytest.mark.parametrize(
+    'missing, run, thresh, errors, allow_missing', [
+        (1, 3, 0.5, 0, True),
+        (1, 3, 0.8, 1, True),
+        (1, 3, 0.5, 1, False),
+    ]
+)
+@pytest.mark.wrapper
+def test_ascii2nc_missing_inputs(metplus_config, get_test_data_dir,
+                                 missing, run, thresh, errors, allow_missing):
+    config_overrides = {
+        'INPUT_MUST_EXIST': True,
+        'ASCII2NC_ALLOW_MISSING_INPUTS': allow_missing,
+        'ASCII2NC_INPUT_THRESH': thresh,
+        'ASCII2NC_INPUT_TEMPLATE': os.path.join(get_test_data_dir('ascii'), 'precip24_{valid?fmt=%Y%m%d%H}.ascii'),
+        'VALID_END': '2010010200',
+    }
+    wrapper = ascii2nc_wrapper(metplus_config, config_overrides)
+    assert wrapper.isOK
+
+    all_cmds = wrapper.run_all_times()
+    for cmd, _ in all_cmds:
+        print(cmd)
+
+    print(f'missing: {wrapper.missing_input_count} / {wrapper.run_count}, errors: {wrapper.errors}')
+    assert wrapper.missing_input_count == missing
+    assert wrapper.run_count == run
+    assert wrapper.errors == errors
+
+
 @pytest.mark.parametrize(
     'config_overrides, env_var_values', [
         ({},
@@ -163,11 +193,13 @@ def test_ascii2nc_wrapper(metplus_config, config_overrides,
 
     input_path = wrapper.config.getraw('config', 'ASCII2NC_INPUT_TEMPLATE')
     input_dir = os.path.dirname(input_path)
-    input_file = 'precip24_2010010112.ascii'
+    input_file1 = 'precip24_2010010112.ascii'
+    input_file2 = 'precip24_2010010118.ascii'
 
     output_path = wrapper.config.getraw('config', 'ASCII2NC_OUTPUT_TEMPLATE')
     output_dir = os.path.dirname(output_path)
-    output_file = 'precip24_2010010112.nc'
+    output_file1 = 'precip24_2010010112.nc'
+    output_file2 = 'precip24_2010010118.nc'
 
     all_commands = wrapper.run_all_times()
     print(f"ALL COMMANDS: {all_commands}")
@@ -177,13 +209,17 @@ def test_ascii2nc_wrapper(metplus_config, config_overrides,
     verbosity = f"-v {wrapper.c_dict['VERBOSITY']}"
     config_file = wrapper.c_dict.get('CONFIG_FILE')
 
-    expected_cmd = (f"{app_path} "
-                    f"{input_dir}/{input_file} "
-                    f"{output_dir}/{output_file} "
-                    f"-config {config_file} "
-                    f"{verbosity}")
+    expected_cmds = [
+        (f"{app_path} {input_dir}/{input_file1} {output_dir}/{output_file1} "
+         f"-config {config_file} {verbosity}"),
+        (f"{app_path} {input_dir}/{input_file2} {output_dir}/{output_file2} "
+         f"-config {config_file} {verbosity}"),
+    ]
 
-    assert all_commands[0][0] == expected_cmd
+    assert len(all_commands) == len(expected_cmds)
+    for (cmd, _), expected_cmd in zip(all_commands, expected_cmds):
+        # ensure commands are generated as expected
+        assert cmd == expected_cmd
 
     env_vars = all_commands[0][1]
 

internal/tests/pytests/wrappers/command_builder/test_command_builder.py

@@ -1199,17 +1199,20 @@ def test_errors_and_defaults(metplus_config):
     assert actual == False
     assert _in_last_err('Could not generate command', cb.logger)
 
-    # test python embedding error
+    # test python embedding check
     with mock.patch.object(cb_wrapper, 'is_python_script', return_value=True):
         actual = cb.check_for_python_embedding('FCST',{'fcst_name':'pyEmbed'})
-    assert actual == None
-    assert _in_last_err('must be set to a valid Python Embedding type', cb.logger)
+    assert actual == 'python_embedding'
 
-    cb.c_dict['FCST_INPUT_DATATYPE'] = 'PYTHON_XARRAY'
+    cb.env_var_dict['METPLUS_FCST_FILE_TYPE'] = "PYTHON_NUMPY"
     with mock.patch.object(cb_wrapper, 'is_python_script', return_value=True):
         actual = cb.check_for_python_embedding('FCST',{'fcst_name':'pyEmbed'})
     assert actual == 'python_embedding'
 
+    with mock.patch.object(cb_wrapper, 'is_python_script', return_value=False):
+        actual = cb.check_for_python_embedding('FCST',{'fcst_name':'pyEmbed'})
+    assert actual == 'pyEmbed'
+
     # test field_info not set
     cb.c_dict['CURRENT_VAR_INFO'] = None
     actual = cb.set_current_field_config()

internal/tests/pytests/wrappers/ensemble_stat/test_ensemble_stat_wrapper.py

@@ -4,9 +4,6 @@
 
 import os
 
-from datetime import datetime
-
-
 from metplus.wrappers.ensemble_stat_wrapper import EnsembleStatWrapper
 
 fcst_dir = '/some/path/fcst'
@@ -27,7 +24,7 @@
 run_times = ['2005080700', '2005080712']
 
 
-def set_minimum_config_settings(config, set_fields=True):
+def set_minimum_config_settings(config, set_fields=True, set_obs=True):
     # set config variables to prevent command from running and bypass check
     # if input files actually exist
     config.set('config', 'DO_NOT_RUN_EXE', True)
@@ -46,11 +43,12 @@ def set_minimum_config_settings(config, set_fields=True):
     config.set('config', 'ENSEMBLE_STAT_CONFIG_FILE',
                '{PARM_BASE}/met_config/EnsembleStatConfig_wrapped')
     config.set('config', 'FCST_ENSEMBLE_STAT_INPUT_DIR', fcst_dir)
-    config.set('config', 'OBS_ENSEMBLE_STAT_GRID_INPUT_DIR', obs_dir)
     config.set('config', 'FCST_ENSEMBLE_STAT_INPUT_TEMPLATE',
                '{init?fmt=%Y%m%d%H}/fcst_file_F{lead?fmt=%3H}')
-    config.set('config', 'OBS_ENSEMBLE_STAT_GRID_INPUT_TEMPLATE',
-               '{valid?fmt=%Y%m%d%H}/obs_file')
+    if set_obs:
+        config.set('config', 'OBS_ENSEMBLE_STAT_GRID_INPUT_DIR', obs_dir)
+        config.set('config', 'OBS_ENSEMBLE_STAT_GRID_INPUT_TEMPLATE',
+                   '{valid?fmt=%Y%m%d%H}/obs_file')
     config.set('config', 'ENSEMBLE_STAT_OUTPUT_DIR',
                '{OUTPUT_BASE}/EnsembleStat/output')
     config.set('config', 'ENSEMBLE_STAT_OUTPUT_TEMPLATE', '{valid?fmt=%Y%m%d%H}')
@@ -62,6 +60,74 @@ def set_minimum_config_settings(config, set_fields=True):
         config.set('config', 'OBS_VAR1_LEVELS', obs_level)
 
 
+@pytest.mark.parametrize(
+    'allow_missing, optional_input, missing, run, thresh, errors', [
+        (True, None, 3, 8, 0.4, 0),
+        (True, None, 3, 8, 0.7, 1),
+        (False, None, 3, 8, 0.7, 3),
+        (True, 'obs_grid', 4, 8, 0.4, 0),
+        (True, 'obs_grid', 4, 8, 0.7, 1),
+        (False, 'obs_grid', 4, 8, 0.7, 4),
+        (True, 'point_grid', 4, 8, 0.4, 0),
+        (True, 'point_grid', 4, 8, 0.7, 1),
+        (False, 'point_grid', 4, 8, 0.7, 4),
+        (True, 'ens_mean', 4, 8, 0.4, 0),
+        (True, 'ens_mean', 4, 8, 0.7, 1),
+        (False, 'ens_mean', 4, 8, 0.7, 4),
+        (True, 'ctrl', 4, 8, 0.4, 0),
+        (True, 'ctrl', 4, 8, 0.7, 1),
+        (False, 'ctrl', 4, 8, 0.7, 4),
+        # still errors if more members than n_members found
+        (True, 'low_n_member', 8, 8, 0.7, 6),
+        (False, 'low_n_member', 8, 8, 0.7, 8),
+    ]
+)
+@pytest.mark.wrapper_b
+def test_ensemble_stat_missing_inputs(metplus_config, get_test_data_dir, allow_missing,
+                                      optional_input, missing, run, thresh, errors):
+    config = metplus_config
+    set_minimum_config_settings(config, set_obs=False)
+    config.set('config', 'INPUT_MUST_EXIST', True)
+    config.set('config', 'ENSEMBLE_STAT_ALLOW_MISSING_INPUTS', allow_missing)
+    config.set('config', 'ENSEMBLE_STAT_INPUT_THRESH', thresh)
+    n_members = 4 if optional_input == 'low_n_member' else 6
+    config.set('config', 'ENSEMBLE_STAT_N_MEMBERS', n_members)
+    config.set('config', 'INIT_BEG', '2009123106')
+    config.set('config', 'INIT_END', '2010010100')
+    config.set('config', 'INIT_INCREMENT', '6H')
+    config.set('config', 'LEAD_SEQ', '24H, 48H')
+    config.set('config', 'FCST_ENSEMBLE_STAT_INPUT_DIR', get_test_data_dir('ens'))
+    config.set('config', 'FCST_ENSEMBLE_STAT_INPUT_TEMPLATE',
+               '{init?fmt=%Y%m%d%H}/arw-*-gep?/d01_{init?fmt=%Y%m%d%H}_{lead?fmt=%3H}00.grib')
+
+    if optional_input == 'obs_grid':
+        prefix = 'OBS_ENSEMBLE_STAT_GRID'
+    elif optional_input == 'point_grid':
+        prefix = 'OBS_ENSEMBLE_STAT_POINT'
+    elif optional_input == 'ens_mean':
+        prefix = 'ENSEMBLE_STAT_ENS_MEAN'
+    elif optional_input == 'ctrl':
+        prefix = 'ENSEMBLE_STAT_CTRL'
+    else:
+        prefix = None
+
+    if prefix:
+        config.set('config', f'{prefix}_INPUT_DIR', get_test_data_dir('obs'))
+        config.set('config', f'{prefix}_INPUT_TEMPLATE', '{valid?fmt=%Y%m%d%H}_obs_file')
+
+    wrapper = EnsembleStatWrapper(config)
+    assert wrapper.isOK
+
+    all_cmds = wrapper.run_all_times()
+    for cmd, _ in all_cmds:
+        print(cmd)
+
+    print(f'missing: {wrapper.missing_input_count} / {wrapper.run_count}, errors: {wrapper.errors}')
+    assert wrapper.missing_input_count == missing
+    assert wrapper.run_count == run
+    assert wrapper.errors == errors
+
+
 @pytest.mark.parametrize(
     'config_overrides, expected_filename', [
         # 0 - set forecast level

internal/tests/pytests/wrappers/extract_tiles/test_extract_tiles.py

@@ -7,6 +7,7 @@
 
 from metplus.wrappers.extract_tiles_wrapper import ExtractTilesWrapper
 
+
 def extract_tiles_wrapper(metplus_config):
     config = metplus_config
     config.set('config', 'PROCESS_LIST', 'ExtractTiles')
@@ -22,10 +23,6 @@ def extract_tiles_wrapper(metplus_config):
     config.set('config', 'EXTRACT_TILES_LAT_ADJ', '15')
     config.set('config', 'EXTRACT_TILES_LON_ADJ', '15')
     config.set('config', 'EXTRACT_TILES_FILTER_OPTS', '-basin ML')
-    config.set('config', 'FCST_EXTRACT_TILES_INPUT_TEMPLATE',
-               'gfs_4_{init?fmt=%Y%m%d}_{init?fmt=%H}00_{lead?fmt=%HHH}.grb2')
-    config.set('config', 'OBS_EXTRACT_TILES_INPUT_TEMPLATE',
-               'gfs_4_{valid?fmt=%Y%m%d}_{valid?fmt=%H}00_000.grb2')
     config.set('config', 'EXTRACT_TILES_GRID_INPUT_DIR',
                '{INPUT_BASE}/cyclone_track_feature/reduced_model_data')
     config.set('config', 'EXTRACT_TILES_PAIRS_INPUT_DIR',