Cleanup, adding unit tests for ccpp_track_variables.py, activate "chunked data" CI test, add missing MPI target in src/CMakeLists.txt

.github/workflows/prebuild.yaml

@@ -55,3 +55,12 @@ jobs:
         cmake ..
         make
         ./test_blocked_data.x
+    - name: ccpp-prebuild chunked data tests
+      run: |
+        cd test_prebuild/test_chunked_data
+        python3 ../../scripts/ccpp_prebuild.py --config=ccpp_prebuild_config.py --builddir=build
+        cd build
+        cmake ..
+        make
+        ./test_chunked_data.x
+

scripts/ccpp_prebuild.py

@@ -70,7 +70,7 @@ def import_config(configfile, builddir):
     if not os.path.isfile(configfile):
         logging.error("Configuration file {0} not found".format(configfile))
         success = False
-        return
+        return(success, config)
 
     # Import the host-model specific CCPP prebuild config;
     # split into path and module name for import

scripts/ccpp_track_variables.py

@@ -57,7 +57,6 @@ def parse_suite(sdf, run_env):
        the ordered list of schemes for the suite specified by the provided sdf"""
     run_env.logger.info(f'Reading sdf {sdf} and populating Suite object')
     suite = Suite(sdf_name=sdf)
-    run_env.logger.info(f'Reading sdf {sdf} and populating Suite object')
     success = suite.parse(make_call_tree=True)
     if not success:
         raise Exception(f'Parsing suite definition file {sdf} failed.')
@@ -100,9 +99,6 @@ def create_var_graph(suite, var, config, metapath, run_env):
     run_env.logger.debug(f"reading .meta files in path:\n {metapath}")
     metadata_dict=create_metadata_filename_dict(metapath)
 
-    run_env.logger.debug(f"reading metadata files for schemes defined in config file: "
-                  f"{config['scheme_files']}")
-
     # Loop through call tree, find matching filename for scheme via dictionary schemes_in_files,
     # then parse that metadata file to find variable info
     partial_matches = {}
@@ -170,20 +166,29 @@ def create_var_graph(suite, var, config, metapath, run_env):
 
     return (success,var_graph)
 
-def main():
+def track_variables(sdf,metadata_path,config,variable,debug):
     """Main routine that traverses a CCPP suite and outputs the list of schemes that use given
-       variable, broken down by group"""
+       variable, broken down by group
 
-    args = parse_arguments()
+    Args:
+        sdf           (str) : The full path of the suite definition file to parse
+        metadata_path (str) : path to CCPP scheme metadata files
+        config        (str) : path to CCPP prebuild configuration file
+        variable      (str) : variable to track through CCPP suite
+        debug        (bool) : Enable extra output for debugging
+
+    Returns:
+        None
+"""
 
-    logger = setup_logging(args.debug)
+    logger = setup_logging(debug)
 
     #Use new capgen class CCPPFrameworkEnv
     run_env = CCPPFrameworkEnv(logger, host_files="", scheme_files="", suites="")
 
-    suite = parse_suite(args.sdf,run_env)
+    suite = parse_suite(sdf,run_env)
 
-    (success, config) = import_config(args.config, None)
+    (success, config) = import_config(config, None)
     if not success:
         raise Exception('Call to import_config failed.')
 
@@ -194,10 +199,10 @@ def main():
     if not success:
         raise Exception('Call to gather_variable_definitions failed.')
 
-    (success, var_graph) = create_var_graph(suite, args.variable, config, args.metadata_path, run_env)
+    (success, var_graph) = create_var_graph(suite, variable, config, metadata_path, run_env)
     if success:
         print(f"For suite {suite.sdf_name}, the following schemes (in order for each group) "
-              f"use the variable {args.variable}:")
+              f"use the variable {variable}:")
         for group in var_graph:
             if var_graph[group]:
                 print(f"In group {group}")
@@ -206,4 +211,7 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+
+    args = parse_arguments()
+
+    track_variables(args.sdf,args.metadata_path,args.config,args.variable,args.debug)

test_prebuild/test_track_variables.py

@@ -0,0 +1,130 @@
+#! /usr/bin/env python3
+"""
+-----------------------------------------------------------------------
+ Description:  Contains unit tests for ccpp_track_variables.py script
+
+ Assumptions:  Assumes user has correct environment for running ccpp_track_variables.py script.
+               This script should not be run directly, but rather invoked with pytest.
+
+ Command line arguments: none
+
+ Usage: pytest test_track_variables.py         # run the unit tests
+-----------------------------------------------------------------------
+"""
+import sys
+import os
+import pytest
+
+TEST_DIR = os.path.dirname(os.path.abspath(__file__))
+SCRIPTS_DIR = os.path.abspath(os.path.join(TEST_DIR, os.pardir, "scripts"))
+SAMPLE_FILES_DIR = "test_track_variables"
+SUITE_FILE = f'{SAMPLE_FILES_DIR}/suite_TEST_SUITE.xml'
+SMALL_SUITE_FILE = f'{SAMPLE_FILES_DIR}/suite_small_suite.xml'
+CONFIG_FILE = f'{SAMPLE_FILES_DIR}/ccpp_prebuild_config.py'
+if not os.path.exists(SCRIPTS_DIR):
+    raise ImportError(f"Cannot find scripts directory {SCRIPTS_DIR}")
+
+sys.path.append(SCRIPTS_DIR)
+
+from ccpp_track_variables import track_variables
+
+def test_successful_match(capsys):
+    """Tests whether test_track_variables.py produces expected output from sample suite and
+       metadata files for a case with a successful match (user provided a variable that exists
+       within the schemes specified by the test suite)"""
+    expected_output = """For suite test_track_variables/suite_small_suite.xml, the following schemes (in order for each group) use the variable air_pressure:
+In group group1
+  scheme_1_run (intent in)
+  scheme_1_run (intent in)"""
+    track_variables(SMALL_SUITE_FILE,SAMPLE_FILES_DIR,CONFIG_FILE,'air_pressure',False)
+    streams = capsys.readouterr()
+    expected_output_list = expected_output.splitlines()
+    streams_err_list = streams.err.splitlines()
+    for (err, expected) in zip(streams_err_list, expected_output_list):
+        assert err.strip() == expected.strip()
+
+def test_successful_match_with_subcycles(capsys):
+    """Tests whether test_track_variables.py produces expected output from sample suite and
+       metadata files for a case with a successful match (user provided a variable that exists
+       within the schemes specified by the test suite). In this case, the test suite file
+       contains subcycles, so the output should reflect this."""
+
+    expected_output = """For suite test_track_variables/suite_TEST_SUITE.xml, the following schemes (in order for each group) use the variable surface_air_pressure:
+In group group1
+  scheme_3_run (intent inout)
+  scheme_3_timestep_finalize (intent inout)
+  scheme_3_timestep_finalize (intent out)
+  scheme_4_run (intent in)
+  scheme_3_run (intent inout)
+  scheme_3_timestep_finalize (intent inout)
+  scheme_3_timestep_finalize (intent out)
+  scheme_4_run (intent in)
+In group group2
+  scheme_4_run (intent in)
+  scheme_4_run (intent in)
+  scheme_4_run (intent in)"""
+    track_variables(SUITE_FILE,SAMPLE_FILES_DIR,CONFIG_FILE,'surface_air_pressure',False)
+    streams = capsys.readouterr()
+    expected_output_list = expected_output.splitlines()
+    streams_err_list = streams.err.splitlines()
+    for (err, expected) in zip(streams_err_list, expected_output_list):
+        assert err.strip() == expected.strip()
+
+
+def test_partial_match(capsys):
+    """Tests whether test_track_variables.py produces expected output from sample suite and
+       metadata files for a case with a partial match: user provided a variable that does not
+       exist in the test suite, but is a substring of one or more other variables that do
+       exist."""
+
+    expected_output = """Variable surface not found in any suites for sdf test_track_variables/suite_TEST_SUITE.xml
+
+ERROR:ccpp_track_variables:Variable surface not found in any suites for sdf test_track_variables/suite_TEST_SUITE.xml
+
+Did find partial matches that may be of interest:
+
+In scheme_2_init found variable(s) ['surface_emissivity_data_file']
+In scheme_2_run found variable(s) ['surface_roughness_length', 'surface_ground_temperature_for_radiation', 'surface_air_temperature_for_radiation', 'surface_skin_temperature_over_ice', 'baseline_surface_longwave_emissivity', 'surface_longwave_emissivity', 'surface_albedo_components', 'surface_albedo_for_diffused_shortwave_on_radiation_timestep']
+In scheme_3_init found variable(s) ['flag_for_mellor_yamada_nakanishi_niino_surface_layer_scheme']
+In scheme_3_timestep_init found variable(s) ['flag_for_mellor_yamada_nakanishi_niino_surface_layer_scheme']
+In scheme_3_run found variable(s) ['do_compute_surface_scalar_fluxes', 'do_compute_surface_diagnostics', 'surface_air_pressure', 'reference_air_pressure_normalized_by_surface_air_pressure']
+In scheme_3_timestep_finalize found variable(s) ['surface_air_pressure']
+In scheme_4_run found variable(s) ['surface_air_pressure']
+In scheme_B_run found variable(s) ['flag_nonzero_wet_surface_fraction', 'sea_surface_temperature', 'surface_skin_temperature_after_iteration_over_water']
+"""
+    track_variables(SUITE_FILE,SAMPLE_FILES_DIR,CONFIG_FILE,'surface',False)
+    streams = capsys.readouterr()
+    expected_output_list = expected_output.splitlines()
+    streams_err_list = streams.err.splitlines()
+    for (err, expected) in zip(streams_err_list, expected_output_list):
+        assert err.strip() == expected.strip()
+
+
+def test_no_match(capsys):
+    """Tests whether test_track_variables.py produces expected output from sample suite and
+       metadata files for a case with no match (user provided a variable that does not exist
+       within the schemes specified by the test suite)"""
+
+    expected_output = """Variable abc not found in any suites for sdf test_track_variables/suite_TEST_SUITE.xml
+
+ERROR:ccpp_track_variables:Variable abc not found in any suites for sdf test_track_variables/suite_TEST_SUITE.xml"""
+    track_variables(SUITE_FILE,SAMPLE_FILES_DIR,CONFIG_FILE,'abc',False)
+    streams = capsys.readouterr()
+    expected_output_list = expected_output.splitlines()
+    streams_err_list = streams.err.splitlines()
+    for (err, expected) in zip(streams_err_list, expected_output_list):
+        assert err.strip() == expected.strip()
+
+
+def test_bad_config(capsys):
+    """Tests whether test_track_variables.py fails gracefully when provided a config file that does
+       not exist."""
+    with pytest.raises(Exception) as excinfo:
+        track_variables(SUITE_FILE,SAMPLE_FILES_DIR,f'{SAMPLE_FILES_DIR}/nofile','abc',False)
+    assert str(excinfo.value) == "Call to import_config failed."
+
+
+if __name__ == "__main__":
+    print("This test file is designed to be run with pytest; can not be run directly")
+    sys.exit(1)
+

test_prebuild/test_track_variables/ccpp_prebuild_config.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+
+# CCPP prebuild config for CCPP track variables tool test
+
+
+###############################################################################
+# Definitions                                                                 #
+###############################################################################
+
+HOST_MODEL_IDENTIFIER = "TEST"
+
+# Add all files with metadata tables on the host model side and in CCPP,
+# relative to basedir = top-level directory of host model. This includes
+# kind and type definitions used in CCPP physics. Also add any internal
+# dependencies of these files to the list.
+VARIABLE_DEFINITION_FILES = [
+    # actual variable definition files
+    '../src/ccpp_types.F90',
+    ]
+
+# Add all physics scheme files relative to basedir
+SCHEME_FILES = [ ]
+
+# Default build dir, relative to current working directory,
+# if not specified as command-line argument
+DEFAULT_BUILD_DIR = 'build'
+
+# Auto-generated makefile/cmakefile snippets that contain all type definitions
+TYPEDEFS_MAKEFILE   = '{build_dir}/CCPP_TYPEDEFS.mk'
+TYPEDEFS_CMAKEFILE  = '{build_dir}/CCPP_TYPEDEFS.cmake'
+TYPEDEFS_SOURCEFILE = '{build_dir}/CCPP_TYPEDEFS.sh'
+
+# Auto-generated makefile/cmakefile snippets that contain all schemes
+SCHEMES_MAKEFILE   = '{build_dir}/CCPP_SCHEMES.mk'
+SCHEMES_CMAKEFILE  = '{build_dir}/CCPP_SCHEMES.cmake'
+SCHEMES_SOURCEFILE = '{build_dir}/CCPP_SCHEMES.sh'
+
+# Auto-generated makefile/cmakefile snippets that contain all caps
+CAPS_MAKEFILE   = '{build_dir}/CCPP_CAPS.mk'
+CAPS_CMAKEFILE  = '{build_dir}/CCPP_CAPS.cmake'
+CAPS_SOURCEFILE = '{build_dir}/CCPP_CAPS.sh'
+
+# Directory where to put all auto-generated physics caps
+CAPS_DIR = '{build_dir}'
+
+# Directory where the suite definition files are stored
+SUITES_DIR = '.'
+
+# Optional arguments - only required for schemes that use
+# optional arguments. ccpp_prebuild.py will throw an exception
+# if it encounters a scheme subroutine with optional arguments
+# if no entry is made here. Possible values are: 'all', 'none',
+# or a list of standard_names: [ 'var1', 'var3' ].
+OPTIONAL_ARGUMENTS = {}
+
+# Directory where to write static API to
+STATIC_API_DIR = '{build_dir}'
+STATIC_API_CMAKEFILE  = '{build_dir}/CCPP_API.cmake'
+STATIC_API_SOURCEFILE = '{build_dir}/CCPP_API.sh'
+
+# Directory for writing HTML pages generated from metadata files
+METADATA_HTML_OUTPUT_DIR = '{build_dir}'
+
+# HTML document containing the model-defined CCPP variables
+HTML_VARTABLE_FILE = '{build_dir}/CCPP_VARIABLES_BLOCKED_DATA.html'
+
+# LaTeX document containing the provided vs requested CCPP variables
+LATEX_VARTABLE_FILE = '{build_dir}/CCPP_VARIABLES_BLOCKED_DATA.tex'
+

test_prebuild/test_track_variables/scheme_1.meta

@@ -0,0 +1,25 @@
+[ccpp-table-properties]
+  name = scheme_1
+  type = scheme
+  dependencies = ../../hooks/machine.F
+
+########################################################################
+[ccpp-arg-table]
+  name = scheme_1_run
+  type = scheme
+[p_lay]
+  standard_name = air_pressure
+  long_name = mean layer pressure
+  units = Pa
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
+  type = real
+  kind = kind_phys
+  intent = in
+[p_lev]
+  standard_name = air_pressure_at_interface
+  long_name = air pressure at model layer interfaces
+  units = Pa
+  dimensions = (horizontal_loop_extent,vertical_interface_dimension)
+  type = real
+  kind = kind_phys
+  intent = in