def uninstall_skirt_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling SKIRT locally ...")
# Check installation
skirt_root_path = introspection.skirt_root_dir
if not fs.is_directory(skirt_root_path):
log.warning("SKIRT was not found locally")
return
# Debugging
log.debug("Removing the SKIRT directory ...")
# Remove the entire directory
fs.remove_directory(skirt_root_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For SKIRT and FitSKIRT, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
def uninstall_conda_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling the Conda python distribution locally ...")
# Check installation
installation_path = fs.join(fs.home(), "miniconda")
if not fs.is_directory(installation_path):
log.warning("Conda was not found locally")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
fs.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
terminal.remove_from_path_variable_containing("miniconda/bin")
def uninstall_conda_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling the Conda python distribution locally ...")
# Check installation
installation_path = fs.join(fs.home, "miniconda")
if not fs.is_directory(installation_path):
log.warning("Conda was not found locally")
return
# Debugging
log.debug("Removing the Conda directory ...")
# Remove the directory
fs.remove_directory(installation_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For Conda, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
terminal.remove_from_path_variable_containing("miniconda/bin")
def check_reference_data(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Checking the reference data ...")
# Determine simulation directory
if self.config.reference_path is not None:
data_path = self.config.reference_path
elif self.config.reference_test is not None:
data_path = fs.join(introspection.pts_tests_dir,
self.config.reference_test, "data")
else:
raise ValueError(
"Reference path and reference test settings are None")
# Check whether directory exist and not empty
if not fs.is_directory(data_path):
raise ValueError("Directory does not exist: " + data_path)
if fs.is_empty(data_path):
raise ValueError("Empty directory: " + data_path)
# Remove data directory for this test
fs.remove_directory(self.data_path)
# Set data path
self.data_path = data_path
def uninstall_skirt_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling SKIRT locally ...")
# Check installation
skirt_root_path = introspection.skirt_root_dir
if not fs.is_directory(skirt_root_path):
log.warning("SKIRT was not found locally")
return
# Debugging
log.debug("Removing the SKIRT directory ...")
# Remove the entire directory
fs.remove_directory(skirt_root_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For SKIRT, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
def uninstall_pts_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling PTS locally ...")
# Check installation
pts_root_path = introspection.pts_root_dir
if not fs.is_directory(pts_root_path):
log.warning("PTS could not be found locally (which is certainly weird) ...")
return
# Debugging
log.debug("Removing the PTS directory ...")
# Remove the entire directory
fs.remove_directory(pts_root_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For PTS, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
def uninstall_pts_local(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Uninstalling PTS locally ...")
# Check installation
pts_root_path = introspection.pts_root_dir
if not fs.is_directory(pts_root_path):
log.warning(
"PTS could not be found locally (which is certainly weird) ..."
)
return
# Debugging
log.debug("Removing the PTS directory ...")
# Remove the entire directory
fs.remove_directory(pts_root_path)
# Debugging
log.debug("Removing lines from shell configuration ...")
# Remove lines from shell configuration file
comment = "For PTS, added by PTS (Python Toolkit for SKIRT)"
terminal.remove_aliases_and_variables_with_comment(comment)
def load_reference(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the reference simulation ...")
# Determine simulation directory
if self.config.reference_path is not None:
simulation_path = self.config.reference_path
elif self.config.reference_test is not None:
simulation_path = fs.join(introspection.pts_tests_dir,
self.config.reference_test, "ref")
else:
raise ValueError(
"Reference path and reference test settings are None")
# Check whether present
if not fs.is_directory(simulation_path):
raise ValueError(
"The reference simulation path could not be found")
# Look for simulation
prefix, ski_path, in_path, out_path = find_one_simulation_in_path(
simulation_path)
# Load the ski file
self.ski = LabeledSkiFile(ski_path)
# Other paths
extr_path = fs.join(simulation_path, "extr")
plot_path = fs.join(simulation_path, "plot")
misc_path = fs.join(simulation_path, "misc")
# Check existence
if not fs.is_directory(extr_path):
raise IOError("Extraction directory not found")
if not fs.is_directory(plot_path):
raise IOError("Plotting directory not found")
if not fs.is_directory(misc_path):
raise IOError("Misc directory not found")
# Copy
self.copy_reference(ski_path, in_path, out_path, extr_path, plot_path,
misc_path)
def has_best(self):
"""
This function ...
:return:
"""
return fs.is_directory(self.restore_best_path)
def has_generation(self, generation_name):
"""
This function ...
:param generation_name:
:return:
"""
return fs.is_directory(self.get_generation_restore_path(generation_name))
def restore_path(self):
"""
This function ...
:return:
"""
path = fs.join(self.fitting_run.refitting_path, self.config.name)
if not fs.is_directory(path): raise ValueError("'" + self.config.name + "' is not a backup of a fit")
return path
def load_reference(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Loading the reference simulation ...")
# Determine simulation directory
if self.config.reference_path is not None: simulation_path = self.config.reference_path
elif self.config.reference_test is not None: simulation_path = fs.join(introspection.pts_tests_dir, self.config.reference_test, "ref")
else: raise ValueError("Reference path and reference test settings are None")
# Check whether present
if not fs.is_directory(simulation_path): raise ValueError("The reference simulation path could not be found")
# Look for simulation
prefix, ski_path, in_path, out_path = find_one_simulation_in_path(simulation_path)
# Load the ski file
self.ski = SkiFile(ski_path)
# Other paths
extr_path = fs.join(simulation_path, "extr")
plot_path = fs.join(simulation_path, "plot")
misc_path = fs.join(simulation_path, "misc")
# Check existence
if not fs.is_directory(extr_path): raise IOError("Extraction directory not found")
if not fs.is_directory(plot_path): raise IOError("Plotting directory not found")
if not fs.is_directory(misc_path): raise IOError("Misc directory not found")
# Copy
self.copy_reference(ski_path, in_path, out_path, extr_path, plot_path, misc_path)
def check_reference_data(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Checking the reference data ...")
# Determine simulation directory
if self.config.reference_path is not None: data_path = self.config.reference_path
elif self.config.reference_test is not None: data_path = fs.join(introspection.pts_tests_dir, self.config.reference_test, "data")
else: raise ValueError("Reference path and reference test settings are None")
# Check whether directory exist and not empty
if not fs.is_directory(data_path): raise ValueError("Directory does not exist: " + data_path)
if fs.is_empty(data_path): raise ValueError("Empty directory: " + data_path)
# Remove data directory for this test
fs.remove_directory(self.data_path)
# Set data path
self.data_path = data_path
def setup(self, **kwargs):
"""
This function ...
:param kwargs:
:return:
"""
# CAll the setup function of the base class
super(NGC4013Test, self).setup(**kwargs)
# Check the data
if fs.is_directory(norm_path): self.data_path = norm_path
else:
# Create the data directory and get the data
self.data_path = fs.create_directory_in(self.path, "data")
self.get_data()
# Create the reference directory and subdirectories
self.reference_path = fs.create_directory_in(self.path, "ref")
self.reference_output_path = fs.create_directory_in(
self.reference_path, "out")
self.reference_ski_path = fs.join(self.reference_path, "NGC4013.ski")
self.reference_fski_path = fs.join(self.reference_path, "NGC4013.fski")
# Loop over the remote hosts
for host_id in config.remotes:
# Check whether the remote is available
if config.full:
remote = Remote()
if not remote.setup(host_id):
log.warning("The remote host '" + host_id + "' is not available: skipping ...")
continue
else: remote = None
# Determine the path to the run directory for the specified remote host
host_run_path = fs.join(introspection.skirt_run_dir, host_id)
# Check if there are simulations
if not fs.is_directory(host_run_path):
log.debug("No run directory for host '" + host_id + "'")
continue
if fs.is_empty(host_run_path): log.debug("No simulations for host '" + host_id + "'")
# Loop over the simulation files in the run directory
for path, name in fs.files_in_path(host_run_path, extension="sim", returns=["path", "name"], sort=int):
# Skip
if config.ids is not None and int(name) not in config.ids: continue
# Inform the user
log.info("Removing simulation " + name + " ...")
# Fully clear
if config.full:
# Interpolation method
parser.add_argument("--method", type=str, help="the interpolation method to use", default="biharmonic")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# If an input directory is given
if arguments.input is not None:
# Determine the full path to the input directory
input_path = fs.absolute(arguments.input)
# Give an error if the input directory does not exist
if not fs.is_directory(input_path): raise argparse.ArgumentError(input_path, "The input directory does not exist")
# If no input directory is given, assume the input is placed in the current working directory
else: input_path = fs.cwd()
# -----------------------------------------------------------------
# If an output directory is given
if arguments.output is not None:
# Determine the full path to the output directory
output_path = fs.absolute(arguments.output)
# Create the directory if it does not yet exist
if not fs.is_directory(output_path): fs.create_directory(output_path)
galaxy_name = galactic_catalog["Name"][i]
break
# If the galaxy name is still None, something is wrong with the galaxy catalog (principal not defined)
if galaxy_name is None:
raise RuntimeError(
"The galactic catalog is invalid: principal galaxy not defined")
# Determine the path to the user catalogs directory
catalogs_user_path = fs.join(introspection.pts_user_dir, "magic", "catalogs")
# Determint the path to the directory to contain the catalogs for this galaxy
galaxy_user_path = fs.join(catalogs_user_path, galaxy_name)
# Cache the galaxy and stellar catalog
if fs.is_directory(galaxy_user_path):
old_galactic_catalog_path = fs.join(galaxy_user_path, "galaxies.dat")
old_stellar_catalog_path = fs.join(galaxy_user_path, "stars.dat")
if fs.is_file(old_galactic_catalog_path):
# Open the 'old' galaxy catalog
old_galaxy_catalog = tables.from_file(old_galactic_catalog_path)
# Create merged galaxy catalog
galaxy_catalog = catalogs.merge_galactic_catalogs(
galactic_catalog, old_galaxy_catalog)
# Save the merged catalog
path = fs.join(galaxy_user_path, "galaxies.dat")
# Show the fitting filters
print("")
print("FITTING FILTERS:")
print("")
for fltr in fitting_run.fitting_filters: print(" - " + tostr(fltr))
print("")
# -----------------------------------------------------------------
# Determine the path to the wavelength grids directory
grids_path = fitting_run.wavelength_grids_path
# -----------------------------------------------------------------
# Check whether there are already wavelength grids
if fs.is_directory(grids_path) and not fs.is_empty(grids_path):
if config.backup: fs.backup_directory(grids_path)
fs.clear_directory(grids_path)
# -----------------------------------------------------------------
# Create a wavelength grids table
table = WavelengthGridsTable()
# -----------------------------------------------------------------
# Get fixed wavelengths
fixed_wavelengths = fitting_run.normalization_wavelengths
# -----------------------------------------------------------------
# Loop over the remotes, look for match
for host_id in simulation_paths:
if simulation_name in simulation_paths[host_id]:
the_host_id = host_id
break
# Simulation file not found
if the_host_id is None:
if config.ignore_missing: continue
else: raise ValueError("Cannot find simulation file for simulation '" + simulation_name + "'")
# Determine the output path
if config.per_host:
new_path = fs.join(output_path, the_host_id)
if not fs.is_directory(new_path): fs.create_directory(new_path)
else: new_path = output_path
# Get the original simulation file path
filepath = simulation_paths[the_host_id][simulation_name]
# Debugging
log.debug("Moving the '" + simulation_name + "' simulation ...")
# Move the file
if config.rename: new_name = simulation_name + ".sim"
else: new_name = None
fs.move_file(filepath, new_path, new_name=new_name)
# -----------------------------------------------------------------
# Determine the preparation name
if frame.filter is not None: prep_name = str(frame.filter)
else: prep_name = image_name
# Set the row entries
names_column.append(image_name)
paths_column.append(image_path)
prep_names_column.append(prep_name)
# Create the table
data = [names_column, paths_column, prep_names_column]
table = tables.new(data, names)
# Check whether the preparation directory exists
prep_path = fs.join(config.path, "prep")
if not fs.is_directory(prep_path): fs.create_directory(prep_path)
# Save the table
prep_info_table_path = fs.join(prep_path, "prep_info.dat")
tables.write(table, prep_info_table_path, format="ascii.ecsv")
# -----------------------------------------------------------------
# Create a PreparationInitializer instance
initializer = PreparationInitializer(config)
# Run the data initializer
initializer.run()
# -----------------------------------------------------------------
# -----------------------------------------------------------------
# Set figsize
if config.small:
figsize = "8,6"
figsize_timelines = "8,8"
else:
figsize = "12,9"
figsize_timelines = "12,12"
# -----------------------------------------------------------------
# Locate the scaling test suite directory
suite_path = fs.join(fs.cwd(), config.suite_name)
if not fs.is_directory(suite_path):
raise ValueError("The directory '" + suite_path + "' does not exist")
# -----------------------------------------------------------------
# Make directory for output
output_path = fs.create_directory_in(fs.cwd(),
time.unique_name("scaling_plots"))
# Make subdirectories
single_node_path = fs.create_directory_in(output_path,
"Single-node comparison")
multi_node_path = fs.create_directory_in(
output_path, "Load balancing and multi-node scaling")
communication_path = fs.create_directory_in(output_path, "Communication")
hybridization_path = fs.create_directory_in(output_path, "Hybridization")
parser.add_argument("--special", type=str, help="the name of the file specifying regions with objects needing special attention (in sky coordinates!)")
parser.add_argument("--bad", type=str, help="the name of the file specifying regions that have to be added to the mask of bad pixels")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# If an input directory is given
if arguments.input is not None:
# Determine the full path to the input directory
input_path = fs.absolute(arguments.input)
# Give an error if the input directory does not exist
if not fs.is_directory(input_path):
raise argparse.ArgumentError(input_path, "The input directory does not exist")
# If no input directory is given, assume the input is placed in the current working directory
else: input_path = fs.cwd()
# -----------------------------------------------------------------
# If an output directory is given
if arguments.output is not None:
# Determine the full path to the output directory
output_path = fs.absolute(arguments.output)
# Create the directory if it does not yet exist
if not fs.is_directory(output_path): fs.create_directory(output_path)
# Determine the preparation name
if frame.filter is not None: prep_name = str(frame.filter)
else: prep_name = image_name
# Set the row entries
names_column.append(image_name)
paths_column.append(image_path)
prep_names_column.append(prep_name)
# Create the table
data = [names_column, paths_column, prep_names_column]
table = tables.new(data, names)
# Check whether the preparation directory exists
prep_path = fs.join(config.path, "prep")
if not fs.is_directory(prep_path): fs.create_directory(prep_path)
# Save the table
prep_info_table_path = fs.join(prep_path, "prep_info.dat")
tables.write(table, prep_info_table_path, format="ascii.ecsv")
# -----------------------------------------------------------------
# Create a PreparationInitializer instance
initializer = PreparationInitializer(config)
# Run the data initializer
initializer.run()
# -----------------------------------------------------------------
def run_configurable(table_matches, args, tables):
"""
This function ...
:param table_matches:
:param args:
:param tables:
:return:
"""
# Determine the configuration method
configuration_method = None
if args.interactive: configuration_method = "interactive"
elif args.arguments: configuration_method = "arguments"
elif args.configfile is not None: configuration_method = "file:" + args.configfile
elif args.rerun: configuration_method = "last"
# Regenerate the configuration method option
if args.interactive: configuration_method_argument = "--interactive"
elif args.arguments: configuration_method_argument = "--arguments"
elif args.configfile is not None: configuration_method_argument = "--configfile '" + args.configfile + "'"
elif args.rerun: configuration_method_argument = "--rerun"
else: configuration_method_argument = ""
# Resolve
subproject, index = table_matches[0]
resolved = introspection.resolve_from_match(subproject, tables[subproject], index)
# Get properties
title = resolved.title
command_name = resolved.command_name
hidden = resolved.hidden
description = resolved.description
module_path = resolved.module_path
class_name = resolved.class_name
configuration_method_table = resolved.configuration_method
configuration_module_path = resolved.configuration_module_path
subproject_path = introspection.pts_subproject_dir(subproject)
# Set
sys.argv[0] = fs.join(introspection.pts_root_dir, module_path.replace(".", "/") + ".py") # this is actually not necessary (and not really correct, it's not like we are calling the module where the class is..)
del sys.argv[1] # but this is important
# Get a list of the leftover arguments
leftover_arguments = sys.argv[1:]
# Welcome message
if subproject == "modeling": welcome_modeling()
elif subproject == "magic": welcome_magic()
elif subproject == "dustpedia": welcome_dustpedia()
elif subproject == "evolve": welcome_evolve()
# Special
if subproject == "modeling": check_modeling_cwd(command_name, fs.cwd())
# Get the configuration definition
definition = introspection.get_configuration_definition_pts_not_yet_in_pythonpath(configuration_module_path)
# If not specified on the command line (before the command name), then use the default specified in the commands.dat file
if configuration_method is None: configuration_method = configuration_method_table
# Check whether arguments are passed and the configuration method is interactive
if configuration_method == "interactive" and len(leftover_arguments) > 0: raise ValueError("Arguments on the command-line are not supported by default for this command. Run with pts --arguments to change this behaviour.")
# Create the configuration
config = create_configuration(definition, command_name, description, configuration_method)
## SAVE THE CONFIG if requested
if config.write_config:
config_filepath = config.config_file_path(command_name)
config.saveto(config_filepath)
else: config_filepath = None
# If this is not a re-run
if not args.rerun:
if not fs.is_directory(introspection.pts_user_config_dir): fs.create_directory(introspection.pts_user_config_dir)
# CACHE THE CONFIG
config_cache_path = fs.join(introspection.pts_user_config_dir, command_name + ".cfg")
config.saveto(config_cache_path)
# Setup function
if subproject == "modeling": setup_modeling(command_name, fs.cwd(), configuration_method_argument)
elif subproject == "magic": setup_magic(command_name, fs.cwd())
elif subproject == "dustpedia": setup_dustpedia(command_name, fs.cwd())
elif subproject == "evolve": setup_evolve(command_name, fs.cwd())
# Initialize the logger
log = initialize_pts(config, remote=args.remote, command_name=command_name)
# Exact command name
exact_command_name = subproject + "/" + command_name
# If the PTS command has to be executed remotely
if args.remote is not None: run_remotely(exact_command_name, config, args.keep, args.remote, log)
# The PTS command has to be executed locally
else: run_locally(exact_command_name, module_path, class_name, config, args.input_files, args.output_files, args.output, log)
# Finish function
if subproject == "modeling": finish_modeling(command_name, fs.cwd(), config_path=config_filepath)
elif subproject == "magic": finish_magic(command_name, fs.cwd())
elif subproject == "dustpedia": finish_dustpedia(command_name, fs.cwd())
elif subproject == "evolve": finish_evolve(command_name, fs.cwd())
# Visualization
parser.add_argument("--visualise", action="store_true", help="make visualisations")
# Parse the command line arguments
arguments = parser.parse_args()
# -----------------------------------------------------------------
# If an input directory is given
if arguments.input is not None:
# Determine the full path to the input directory
input_path = fs.absolute(arguments.input)
# Give an error if the input directory does not exist
if not fs.is_directory(input_path): raise argparse.ArgumentError(input_path, "The input directory does not exist")
# If no input directory is given, assume the input is placed in the current working directory
else: input_path = fs.cwd()
# -----------------------------------------------------------------
# If an output directory is given
if arguments.output is not None:
# Determine the full path to the output directory
output_path = fs.absolute(arguments.output)
# Create the directory if it does not yet exist
if not fs.is_directory(output_path): fs.create_directory(output_path)
# No input?
if len(sys.argv) == 1: no_input(parser, scripts, tables)
# -----------------------------------------------------------------
# Parse the command-line arguments
args = parser.parse_args()
# -----------------------------------------------------------------
if args.version: show_version()
# -----------------------------------------------------------------
# Check input and output options, should be directories
if args.input is not None and not fs.is_directory(args.input): raise ValueError("Input path should be an existing directory")
if args.output is not None and not fs.is_directory(args.output): raise ValueError("Output path should be an existing directory")
# -----------------------------------------------------------------
# Get the name of the do script
script_name = args.do_command
# Construct clean arguments list
sys.argv = ["pts", args.do_command] + args.options
# -----------------------------------------------------------------
# Find matches
matches = introspection.find_matches_scripts(script_name, scripts)
table_matches = introspection.find_matches_tables(script_name, tables)
# Check whether the remote is available
if config.full:
remote = Remote()
if not remote.setup(host_id):
log.warning("The remote host '" + host_id +
"' is not available: skipping ...")
continue
else:
remote = None
# Determine the path to the run directory for the specified remote host
host_run_path = fs.join(introspection.skirt_run_dir, host_id)
# Check if there are simulations
if not fs.is_directory(host_run_path):
log.debug("No run directory for host '" + host_id + "'")
continue
if fs.is_empty(host_run_path):
log.debug("No simulations for host '" + host_id + "'")
# Loop over the simulation files in the run directory
for path, name in fs.files_in_path(host_run_path,
extension="sim",
returns=["path", "name"],
sort=int):
# Skip
if config.ids is not None and int(name) not in config.ids: continue
# Inform the user
# No input?
if len(sys.argv) == 1: no_input(parser, scripts, tables)
# -----------------------------------------------------------------
# Parse the command-line arguments
args = parser.parse_args()
# -----------------------------------------------------------------
if args.version: show_version()
# -----------------------------------------------------------------
# Check input and output options, should be directories
if args.input is not None and not fs.is_directory(args.input):
raise ValueError("Input path should be an existing directory")
if args.output is not None and not fs.is_directory(args.output):
raise ValueError("Output path should be an existing directory")
# -----------------------------------------------------------------
# Get the name of the do script
script_name = args.do_command
# Construct clean arguments list
sys.argv = ["pts", args.do_command] + args.options
# -----------------------------------------------------------------
# Find matches
if galactic_catalog["Principal"][i]:
galaxy_name = galactic_catalog["Name"][i]
break
# If the galaxy name is still None, something is wrong with the galaxy catalog (principal not defined)
if galaxy_name is None: raise RuntimeError("The galactic catalog is invalid: principal galaxy not defined")
# Determine the path to the user catalogs directory
catalogs_user_path = fs.join(introspection.pts_user_dir, "magic", "catalogs")
# Determint the path to the directory to contain the catalogs for this galaxy
galaxy_user_path = fs.join(catalogs_user_path, galaxy_name)
# Cache the galaxy and stellar catalog
if fs.is_directory(galaxy_user_path):
old_galactic_catalog_path = fs.join(galaxy_user_path, "galaxies.dat")
old_stellar_catalog_path = fs.join(galaxy_user_path, "stars.dat")
if fs.is_file(old_galactic_catalog_path):
# Open the 'old' galaxy catalog
old_galaxy_catalog = tables.from_file(old_galactic_catalog_path)
# Create merged galaxy catalog
galaxy_catalog = catalogs.merge_galactic_catalogs(galactic_catalog, old_galaxy_catalog)
# Save the merged catalog
path = fs.join(galaxy_user_path, "galaxies.dat")
tables.write(galaxy_catalog, path)
def run_configurable(table_matches, args, tables):
"""
This function ...
:param table_matches:
:param args:
:param tables:
:return:
"""
# Determine the configuration method
configuration_method = None
if args.interactive: configuration_method = "interactive"
elif args.arguments: configuration_method = "arguments"
elif args.configfile is not None:
configuration_method = "file:" + args.configfile
elif args.rerun:
configuration_method = "last"
# Resolve
subproject, index = table_matches[0]
resolved = introspection.resolve_from_match(subproject, tables[subproject],
index)
# Get properties
title = resolved.title
command_name = resolved.command_name
hidden = resolved.hidden
description = resolved.description
module_path = resolved.module_path
class_name = resolved.class_name
configuration_method_table = resolved.configuration_method
configuration_module_path = resolved.configuration_module_path
subproject_path = introspection.pts_subproject_dir(subproject)
# Set
sys.argv[0] = fs.join(
introspection.pts_root_dir,
module_path.replace(".", "/") + ".py"
) # this is actually not necessary (and not really correct, it's not like we are calling the module where the class is..)
del sys.argv[1] # but this is important
# Get a list of the leftover arguments
leftover_arguments = sys.argv[1:]
# Welcome message
if subproject == "modeling": welcome_modeling()
elif subproject == "magic": welcome_magic()
elif subproject == "dustpedia": welcome_dustpedia()
elif subproject == "evolve": welcome_evolve()
# Get the configuration definition
definition = introspection.get_configuration_definition_pts_not_yet_in_pythonpath(
configuration_module_path)
# If not specified on the command line (before the command name), then use the default specified in the commands.dat file
if configuration_method is None:
configuration_method = configuration_method_table
# Check whether arguments are passed and the configuration method is interactive
if configuration_method == "interactive" and len(leftover_arguments) > 0:
raise ValueError(
"Arguments on the command-line are not supported by default for this command. Run with pts --arguments to change this behaviour."
)
# Create the configuration
config = create_configuration(definition, command_name, description,
configuration_method)
## SAVE THE CONFIG if requested
if config.write_config:
config.saveto(config.config_file_path(command_name))
# If this is not a re-run
if not args.rerun:
if not fs.is_directory(introspection.pts_user_config_dir):
fs.create_directory(introspection.pts_user_config_dir)
# CACHE THE CONFIG
config_cache_path = fs.join(introspection.pts_user_config_dir,
command_name + ".cfg")
config.saveto(config_cache_path)
# Setup function
if subproject == "modeling": setup_modeling(command_name, fs.cwd())
elif subproject == "magic": setup_magic(command_name, fs.cwd())
elif subproject == "dustpedia": setup_dustpedia(command_name, fs.cwd())
elif subproject == "evolve": setup_evolve(command_name, fs.cwd())
# Initialize the logger
log = initialize_pts(config, remote=args.remote, command_name=command_name)
# Exact command name
exact_command_name = subproject + "/" + command_name
# If the PTS command has to be executed remotely
if args.remote is not None:
run_remotely(exact_command_name, config, args.keep, args.remote, log)
# The PTS command has to be executed locally
else:
run_locally(exact_command_name, module_path, class_name, config,
args.input_files, args.output_files, args.output, log)
# Finish function
if subproject == "modeling": finish_modeling(command_name, fs.cwd())
elif subproject == "magic": finish_magic(command_name, fs.cwd())
elif subproject == "dustpedia": finish_dustpedia(command_name, fs.cwd())
elif subproject == "evolve": finish_evolve(command_name, fs.cwd())
# -----------------------------------------------------------------
# Set figsize
if config.small:
figsize = "8,6"
figsize_timelines = "8,8"
else:
figsize = "12,9"
figsize_timelines = "12,12"
# -----------------------------------------------------------------
# Locate the scaling test suite directory
suite_path = fs.join(fs.cwd(), config.suite_name)
if not fs.is_directory(suite_path): raise ValueError("The directory '" + suite_path + "' does not exist")
# -----------------------------------------------------------------
# Make directory for output
output_path = fs.create_directory_in(fs.cwd(), time.unique_name("scaling_plots"))
# Make subdirectories
single_node_path = fs.create_directory_in(output_path, "Single-node comparison")
multi_node_path = fs.create_directory_in(output_path, "Load balancing and multi-node scaling")
communication_path = fs.create_directory_in(output_path, "Communication")
hybridization_path = fs.create_directory_in(output_path, "Hybridization")
photon_packages_path = fs.create_directory_in(output_path, "Increased number of photon packages")
memory_path = fs.create_directory_in(output_path, "Memory scaling")
# -----------------------------------------------------------------
