Merge pull request #67 from noaa-ocs-modeling/develop

add entry points to initialize and generate configuration

client/generate_adcirc.py

@@ -0,0 +1,39 @@
+from argparse import ArgumentParser
+from pathlib import Path
+
+from coupledmodeldriver.generate import (
+    generate_adcirc_configuration,
+    generate_nems_adcirc_configuration,
+)
+from coupledmodeldriver.utilities import convert_value
+
+
+def main():
+    argument_parser = ArgumentParser()
+
+    argument_parser.add_argument('--configuration-directory', default=Path().cwd(),
+                                 help='path containing JSON configuration files')
+    argument_parser.add_argument('--output-directory', default=None, help='path to store generated configuration files')
+    argument_parser.add_argument('--verbose', action='store_true', help='show more verbose log messages')
+
+    arguments = argument_parser.parse_args()
+
+    configuration_directory = convert_value(arguments.configuration_directory, Path)
+    output_directory = convert_value(arguments.output_directory, Path)
+
+    if output_directory is None:
+        output_directory = configuration_directory
+
+    if 'configure_nems.json' in [
+        filename.lower() for filename in configuration_directory.listdir()
+    ]:
+        generate = generate_nems_adcirc_configuration
+    else:
+        generate = generate_adcirc_configuration
+
+    generate(
+        configuration_directory=configuration_directory,
+        output_directory=output_directory,
+        overwrite=True,
+        verbose=arguments.verbose,
+    )

client/initialize_adcirc.py

@@ -0,0 +1,138 @@
+from argparse import ArgumentParser
+from datetime import datetime, timedelta
+from pathlib import Path
+
+from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
+
+from coupledmodeldriver import Platform
+from coupledmodeldriver.configure.forcings.base import FORCING_SOURCES
+from coupledmodeldriver.generate import (
+    ADCIRCGenerationScript,
+    ADCIRCRunConfiguration,
+    NEMSADCIRCGenerationScript,
+    NEMSADCIRCRunConfiguration,
+)
+from coupledmodeldriver.utilities import convert_value
+
+
+def main():
+    argument_parser = ArgumentParser()
+
+    argument_parser.add_argument('--platform', required=True, help='HPC platform for which to configure')
+    argument_parser.add_argument('--mesh-directory', required=True, help='path to input mesh (`fort.13`, `fort.14`)')
+    argument_parser.add_argument('--modeled-start-time', required=True, help='start time within the modeled system')
+    argument_parser.add_argument('--modeled-duration', required=True, help=' end time within the modeled system')
+    argument_parser.add_argument('--modeled-timestep', required=True, help='time interval within the modeled system')
+    argument_parser.add_argument('--nems-interval', default=None, help='main loop interval of NEMS run')
+    argument_parser.add_argument('--modulefile', required=True, help='path to module file to `source`')
+    argument_parser.add_argument('--tidal-spinup-duration', default=None, help='spinup time for ADCIRC tidal coldstart')
+    argument_parser.add_argument('--tidal-forcing-source', default='TPXO',
+                                 help=f'source of tidal forcing (can be one of `{list(TidalSource)}`)')
+    argument_parser.add_argument('--tidal-forcing-path', default=None, help='file path to tidal forcing resource')
+    argument_parser.add_argument('--additional-forcings', default=[],
+                                 help='comma-separated list of additional forcings to configure')
+    argument_parser.add_argument('--adcirc-executable', default='adcirc', help='filename of compiled `adcirc` or `NEMS.x`')
+    argument_parser.add_argument('--adcprep-executable', default='adcprep', help='filename of compiled `adcprep`')
+    argument_parser.add_argument('--adcirc-processors', default=11, help='numbers of processors to assign for ADCIRC')
+    argument_parser.add_argument('--job-duration', default='06:00:00', help='wall clock time for job')
+    argument_parser.add_argument('--configuration-directory', default=Path().cwd(),
+                                 help='directory to which to write configuration files')
+    argument_parser.add_argument('--generate-script', action='store_true', help='write a Python script to load configuration')
+
+    arguments = argument_parser.parse_args()
+
+    platform = convert_value(arguments.platform, Platform)
+    mesh_directory = convert_value(arguments.mesh_directory, Path)
+
+    modeled_start_time = convert_value(arguments.modeled_start_time, datetime)
+    modeled_duration = convert_value(arguments.modeled_duration, timedelta)
+    modeled_timestep = convert_value(arguments.modeled_timestep, timedelta)
+    nems_interval = convert_value(arguments.nems_interval, timedelta)
+
+    adcirc_processors = convert_value(arguments.adcirc_processors, int)
+
+    modulefile = convert_value(arguments.modulefile, Path)
+
+    tidal_spinup_duration = convert_value(arguments.tidal_spinup_duration, timedelta)
+    tidal_source = convert_value(arguments.tidal_forcing_source, TidalSource)
+    tidal_forcing_path = convert_value(arguments.tidal_forcing_path, Path)
+    additional_forcings = arguments.additional_forcings
+    if additional_forcings is not None:
+        additional_forcings = [forcing.strip() for forcing in additional_forcings.split(',')]
+    else:
+        additional_forcings = []
+
+    adcirc_executable = convert_value(arguments.adcirc_executable, Path)
+    adcprep_executable = convert_value(arguments.adcprep_executable, Path)
+
+    job_duration = convert_value(arguments.job_duration, timedelta)
+    configuration_directory = convert_value(arguments.configuration_directory, timedelta)
+
+    # initialize `adcircpy` forcing objects
+    forcings = []
+
+    tidal_forcing = Tides(tidal_source=tidal_source, resource=tidal_forcing_path)
+    tidal_forcing.use_all()
+    forcings.append(tidal_forcing)
+
+    for forcing in additional_forcings:
+        if forcing.upper() in FORCING_SOURCES:
+            forcing = FORCING_SOURCES[forcing.upper()](filename=None)
+            forcings.append(forcing)
+        else:
+            raise NotImplementedError(
+                f'unrecognized forcing "{forcing}"; must be one of {list(FORCING_SOURCES)}'
+            )
+
+    if nems_interval is not None:
+        configuration = NEMSADCIRCRunConfiguration(
+            fort13=mesh_directory / 'fort.13',
+            fort14=mesh_directory / 'fort.14',
+            modeled_start_time=modeled_start_time,
+            modeled_end_time=modeled_start_time + modeled_duration,
+            modeled_timestep=modeled_timestep,
+            nems_interval=nems_interval,
+            nems_connections=None,
+            nems_mediations=None,
+            nems_sequence=None,
+            tidal_spinup_duration=tidal_spinup_duration,
+            platform=platform,
+            runs=None,
+            forcings=forcings,
+            adcirc_processors=adcirc_processors,
+            slurm_partition=None,
+            slurm_job_duration=job_duration,
+            slurm_email_address=None,
+            nems_executable=adcirc_executable,
+            adcprep_executable=adcprep_executable,
+            source_filename=modulefile,
+        )
+        generation_script = NEMSADCIRCGenerationScript()
+    else:
+        configuration = ADCIRCRunConfiguration(
+            fort13=mesh_directory / 'fort.13',
+            fort14=mesh_directory / 'fort.14',
+            modeled_start_time=modeled_start_time,
+            modeled_end_time=modeled_start_time + modeled_duration,
+            modeled_timestep=modeled_timestep,
+            tidal_spinup_duration=tidal_spinup_duration,
+            platform=platform,
+            runs=None,
+            forcings=forcings,
+            adcirc_processors=adcirc_processors,
+            slurm_partition=None,
+            slurm_job_duration=job_duration,
+            slurm_email_address=None,
+            adcirc_executable=adcirc_executable,
+            adcprep_executable=adcprep_executable,
+            source_filename=modulefile,
+        )
+        generation_script = ADCIRCGenerationScript()
+
+    configuration.write_directory(directory=configuration_directory, overwrite=True)
+
+    if arguments.create_script:
+        generation_script.write(
+            filename=configuration_directory / 'generate_adcirc.py', overwrite=True,
+        )

coupledmodeldriver/configure/forcings/base.py

@@ -292,3 +292,12 @@ def nemspy_entry(self) -> WaveMeshEntry:
         return WaveMeshEntry(
             filename=self['resource'], processors=self['processors'], **self['nems_parameters']
         )
+
+
+FORCING_SOURCES = {
+    'Tides': TidalForcingJSON,
+    'AtmosphericMeshForcing': ATMESHForcingJSON,
+    'BestTrackForcing': BestTrackForcingJSON,
+    'OwiForcing': OWIForcingJSON,
+    'WaveWatch3DataForcing': WW3DATAForcingJSON,
+}

coupledmodeldriver/generate/adcirc/configure.py

@@ -2,16 +2,16 @@
 from os import PathLike
 from pathlib import Path
 
-from adcircpy import AdcircMesh, AdcircRun, Tides
+from adcircpy import AdcircMesh, AdcircRun
 from adcircpy.forcing.base import Forcing
-from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
-from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
 
-from ...configure.base import ModelDriverJSON, NEMSJSON, SlurmJSON
+from ...configure.base import ModelDriverJSON, NEMSCapJSON, NEMSJSON, \
+    SlurmJSON
 from ...configure.configure import RunConfiguration
 from ...configure.forcings.base import (
     ATMESHForcingJSON,
+    FORCING_SOURCES,
     ForcingJSON,
     TidalForcingJSON,
     WW3DATAForcingJSON,
@@ -59,9 +59,9 @@ def __init__(
         :param modeled_start_time: start time within the modeled system
         :param modeled_end_time: end time within the modeled system
         :param modeled_timestep: time interval within the modeled system
-        :param adcirc_processors: numbers of processors to use for Slurm job
+        :param adcirc_processors: numbers of processors to assign for ADCIRC
         :param platform: HPC platform for which to configure
-        :param tidal_spinup_duration: spinup time for ADCIRC coldstart
+        :param tidal_spinup_duration: spinup time for ADCIRC tidal coldstart
         :param runs: dictionary of run name to run value and mesh attribute name
         :param slurm_job_duration: wall clock time of job
         :param slurm_partition: Slurm partition
@@ -113,12 +113,9 @@ def __init__(
 
     def add_forcing(self, forcing: ForcingJSON):
         if not isinstance(forcing, ForcingJSON):
-            if isinstance(forcing, AtmosphericMeshForcing):
-                forcing = ATMESHForcingJSON.from_adcircpy(forcing)
-            elif isinstance(forcing, WaveWatch3DataForcing):
-                forcing = WW3DATAForcingJSON.from_adcircpy(forcing)
-            elif isinstance(forcing, Tides):
-                forcing = TidalForcingJSON.from_adcircpy(forcing)
+            class_name = forcing.__class__.__name__
+            if class_name in FORCING_SOURCES:
+                forcing = FORCING_SOURCES[class_name].from_adcircpy(forcing)
             else:
                 raise NotImplementedError(f'unable to parse object of type {type(forcing)}')
 
@@ -259,16 +256,13 @@ def nemspy_modeling_system(self) -> ModelingSystem:
 
     def add_forcing(self, forcing: Forcing):
         if not isinstance(forcing, ForcingJSON):
-            if isinstance(forcing, AtmosphericMeshForcing):
-                forcing = ATMESHForcingJSON.from_adcircpy(forcing)
-                self['nems']['models'].append(forcing.nemspy_entry)
-            elif isinstance(forcing, WaveWatch3DataForcing):
-                forcing = WW3DATAForcingJSON.from_adcircpy(forcing)
-                self['nems']['models'].append(forcing.nemspy_entry)
-            elif isinstance(forcing, Tides):
-                forcing = TidalForcingJSON.from_adcircpy(forcing)
+            class_name = forcing.__class__.__name__
+            if class_name in FORCING_SOURCES:
+                forcing = FORCING_SOURCES[class_name].from_adcircpy(forcing)
             else:
                 raise NotImplementedError(f'unable to parse object of type {type(forcing)}')
+            if isinstance(forcing, NEMSCapJSON):
+                self['nems']['models'].append(forcing.nemspy_entry)
 
         if forcing not in self:
             self[forcing.name] = forcing

coupledmodeldriver/generate/adcirc/generate.py

@@ -14,30 +14,30 @@
 
 
 def generate_adcirc_configuration(
-    output_directory: PathLike,
-    configuration_directory: PathLike = None,
+    configuration_directory: PathLike,
+    output_directory: PathLike = None,
     overwrite: bool = False,
     verbose: bool = False,
 ):
     """
     Generate ADCIRC run configuration for given variable values.
 
-    :param output_directory: path to store generated configuration files
     :param configuration_directory: path containing JSON configuration files
+    :param output_directory: path to store generated configuration files
     :param overwrite: whether to overwrite existing files
     :param verbose: whether to show more verbose log messages
     """
 
     get_logger(LOGGER.name, console_level=logging.DEBUG if verbose else logging.INFO)
 
-    if not isinstance(output_directory, Path):
-        output_directory = Path(output_directory)
-
-    if configuration_directory is None:
-        configuration_directory = output_directory
-    elif not isinstance(configuration_directory, Path):
+    if not isinstance(configuration_directory, Path):
         configuration_directory = Path(configuration_directory)
 
+    if output_directory is None:
+        output_directory = configuration_directory
+    elif not isinstance(output_directory, Path):
+        output_directory = Path(output_directory)
+
     if not output_directory.exists():
         os.makedirs(output_directory, exist_ok=True)
 
@@ -263,30 +263,30 @@ def generate_adcirc_configuration(
 
 
 def generate_nems_adcirc_configuration(
-    output_directory: PathLike,
-    configuration_directory: PathLike = None,
+    configuration_directory: PathLike,
+    output_directory: PathLike = None,
     overwrite: bool = False,
     verbose: bool = False,
 ):
     """
     Generate ADCIRC run configuration for given variable values.
 
-    :param output_directory: path to store generated configuration files
     :param configuration_directory: path containing JSON configuration files
+    :param output_directory: path to store generated configuration files
     :param overwrite: whether to overwrite existing files
     :param verbose: whether to show more verbose log messages
     """
 
     get_logger(LOGGER.name, console_level=logging.DEBUG if verbose else logging.INFO)
 
-    if not isinstance(output_directory, Path):
-        output_directory = Path(output_directory)
-
-    if configuration_directory is None:
-        configuration_directory = output_directory
-    elif not isinstance(configuration_directory, Path):
+    if not isinstance(configuration_directory, Path):
         configuration_directory = Path(configuration_directory)
 
+    if output_directory is None:
+        output_directory = configuration_directory
+    elif not isinstance(output_directory, Path):
+        output_directory = Path(output_directory)
+
     if not output_directory.exists():
         os.makedirs(output_directory, exist_ok=True)
 

coupledmodeldriver/script.py

@@ -257,7 +257,7 @@ def __str__(self) -> str:
             '# run every hotstart configuration',
             bash_for_loop(
                 'for hotstart in ${DIRECTORY}/runs/*/',
-                ['pushd ${hotstart} >/dev/null 2>&1', self.hotstart, 'popd >/dev/null 2>&1', ],
+                ['pushd ${hotstart} >/dev/null 2>&1', self.hotstart, 'popd >/dev/null 2>&1'],
             ),
             *(str(command) for command in self.commands),
         ]

coupledmodeldriver/utilities.py

@@ -50,6 +50,7 @@ def get_logger(
             logger.setLevel(logging.DEBUG)
             if console_level != logging.NOTSET:
                 if console_level <= logging.INFO:
+
                     class LoggingOutputFilter(logging.Filter):
                         def filter(self, rec):
                             return rec.levelno in (logging.DEBUG, logging.INFO)
@@ -180,7 +181,12 @@ def convert_value(value: Any, to_type: type) -> Any:
             try:
                 value = to_type[value]
             except (KeyError, ValueError):
-                value = to_type(value)
+                try:
+                    value = to_type(value)
+                except (KeyError, ValueError):
+                    raise ValueError(
+                        f'unrecognized entry "{value}"; must be one of {list(to_type)}'
+                    )
     elif not isinstance(value, to_type) and value is not None:
         if isinstance(value, timedelta):
             if issubclass(to_type, str):

setup.py

@@ -83,4 +83,10 @@
         'testing': ['flake8', 'pytest', 'pytest-cov', 'wget'],
         'development': ['oitnb'],
     },
+    entry_points={
+        'console_scripts': [
+            'initialize_adcirc=client.initialize_adcirc:main',
+            'generate_adcirc=client.generate_adcirc:main',
+        ],
+    },
 )