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Nexus: replace optparse in __init__.py with argparse #6211

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Nexus: replace optparse in __init__.py with argparse #6211

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296 changes: 185 additions & 111 deletions nexus/nexus/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@

from .nexus_version import nexus_version
from .generic import generic_settings
from .developer import obj, log, NexusError
from .developer import obj, log, NexusError, warn
from .debug import ci
from .utilities import path_string

Expand Down Expand Up @@ -358,123 +358,197 @@ def __call__(self,**kwargs):
# process quantum package settings
QuantumPackage.restore_default_settings()
QuantumPackage.settings(**qm_pkg_kw)

return
#end def __call__


def process_command_line_settings(self,script_settings):
from optparse import OptionParser
usage = '''usage: %prog [options]'''
version = '{}.{}.{}'.format(*nexus_version)
parser = OptionParser(usage=usage,add_help_option=True,version='%prog '+version)

parser.add_option('--status_only',dest='status_only',
action='store_true',default=False,
help='Report status of all simulations and then exit.'
)
parser.add_option('--status',dest='status',
default='none',
help="Controls displayed simulation status information. May be set to one of 'standard', 'active', 'failed', or 'ready'."
)
parser.add_option('--generate_only',dest='generate_only',
action='store_true',default=False,
help='Write inputs to all simulations and then exit. Note that no dependencies are processed, e.g. if one simulation depends on another for an orbital file location or for a relaxed structure, this information will not be present in the generated input file for that simulation since no simulations are actually run with this option.'
)
parser.add_option('--graph_sims',dest='graph_sims',
action='store_true',default=False,
help='Display a graph of simulation workflows, then exit.'
)
parser.add_option('--progress_tty',dest='progress_tty',
action='store_true',default=False,
help='Print abbreviated polling messages.'
)
parser.add_option('--sleep',dest='sleep',
default='none',
help=f'Number of seconds between polls. At each poll, simulations are actually run provided all simulations they depend on have successfully completed (default={nexus_core_defaults.sleep}).'
)
parser.add_option('--timeout',dest='timeout',
default='none',
help=f'Number of seconds to wait for output and error files after a job exits the queue before marking the simulation as failed (default={nexus_core_defaults.timeout}).'
)
parser.add_option('--machine',dest='machine',
default='none',
help="(Required) Name of the machine the simulations will be run on. Workstations with between 1 and 128 cores may be specified by 'ws1' to 'ws128' (works for any machine where only mpirun is used). For a complete listing of currently available machines (including those at HPC centers) please see the manual."
)
parser.add_option('--account',dest='account',
default='none',
help='Account name required to submit jobs at some HPC centers.'
)
parser.add_option('--runs',dest='runs',
default='none',
help=f'Directory to perform all runs in. Simulation paths are appended to this directory (default={nexus_core_defaults.runs}).'
)
parser.add_option('--results',dest='results',
default='none',
help=f"Directory to copy out lightweight results data. If set to '', results will not be stored outside of the runs directory (default={nexus_core_defaults.results})."
)
parser.add_option('--local_directory',dest='local_directory',
default='none',
help=f'Base path where runs and results directories will be created (default={nexus_core_defaults.local_directory}).'
)
parser.add_option('--pseudo_dir',dest='pseudo_dir',
default='none',
help='Path to directory containing pseudopotential files (required if running with pseudopotentials).'
)
parser.add_option('--basis_dir',dest='basis_dir',
default='none',
help='Path to directory containing basis set files (useful if running gaussian based QMC workflows).'
)
parser.add_option('--ericfmt',dest='ericfmt',
default='none',
help='Path to the ericfmt file used with GAMESS (required if running GAMESS).'
)
parser.add_option('--mcppath',dest='mcppath',
default='none',
help='Path to the mcpdata file used with GAMESS (optional for most workflows)'
)
parser.add_option('--vdw_table',dest='vdw_table',
default='none',
help='Path to the vdw_table file used with Quantum Espresso (required only if running Quantum Espresso with van der Waals functionals).'
)
parser.add_option('--qprc',dest='qprc',
default='none',
help='Path to the quantum_package.rc file used with Quantum Package.'
)

# parse the command line inputs
options,files_in = parser.parse_args()
opt = obj(**options.__dict__)
def process_command_line_settings(self, script_settings: obj):
import argparse
from argparse import ArgumentParser

# check that all options are allowed (developer check)
invalid = set(opt.keys())-Settings.allowed_vars
if len(invalid)>0:
msg = f'invalid command line settings encountered\ninvalid settings: {sorted(invalid)}\nthis is a developer error'
raise NexusError(msg)
#end if
parser = ArgumentParser(prog="Nexus")
parser.add_argument(
"--version",
action="version",
version="Nexus {}.{}.{}".format(*nexus_version)
)
parser.add_argument(
"--status-only",
"--status_only",
action="store_true",
default=argparse.SUPPRESS,
help=(
"Report status of all simulations and then exit. "
f"(default: {nexus_core_defaults.status_only})"
)
)
parser.add_argument(
"--status",
default=argparse.SUPPRESS,
choices=("standard", "active", "failed", "ready"),
help=(
"Controls displayed simulation status information. "
f"(default: {nexus_core_defaults.status})"
)
)
parser.add_argument(
"--generate-only",
"--generate_only",
action="store_true",
default=argparse.SUPPRESS,
help=(
"Write inputs to all simulations and then exit. "
"Note that no dependencies are processed, "
"e.g. if one simulation depends on another for an "
"orbital file location or for a relaxed structure, "
"this information will not be present in the generated "
"input file for that simulation since no simulations are "
"actually run with this option. "
f"(default: {nexus_core_defaults.generate_only})"
)
)
parser.add_argument(
"--graph-sims",
"--graph_sims",
action="store_true",
default=argparse.SUPPRESS,
help=(
"Display a graph of simulation workflows, then exit. "
f"(default: {nexus_core_defaults.graph_sims})"
)
)
parser.add_argument(
"--progress-tty",
"--progress_tty",
action="store_true",
default=argparse.SUPPRESS,
help=(
"Print abbreviated polling messages. "
"(default: {nexus_core_defaults.progress_tty})"
)
)
parser.add_argument(
"--sleep",
type=float,
default=argparse.SUPPRESS,
help=(
"Number of seconds between polls. "
"At each poll, simulations are actually run provided all "
"simulations they depend on have successfully completed "
f"(default: {nexus_core_defaults.sleep})."
)
)
parser.add_argument(
"--timeout",
type=float,
default=argparse.SUPPRESS,
help=(
"Number of seconds to wait for output and error files after "
"a job exits the queue before marking the simulation as failed "
f"(default: {nexus_core_defaults.timeout})."
)
)
parser.add_argument(
"--machine",
choices=("ws", *Machine.machines),
default=argparse.SUPPRESS,
help=(
"Name of the machine the simulations will be run on. "
"Workstations may be specified by 'ws', which will "
"automatically detect the number of cores "
"(works for any machine where only mpirun is used). "
"For a complete listing of currently available machines "
"(including those at HPC centers) please see the manual."
)
)
parser.add_argument(
"--account",
default=argparse.SUPPRESS,
help="Account name required to submit jobs at some HPC centers."
)
parser.add_argument(
"--runs",
default=argparse.SUPPRESS,
help=(
"Directory to perform all runs in. "
"Simulation paths are appended to this directory "
f"(default: {nexus_core_defaults.runs})."
)
)
parser.add_argument(
"--results",
default=argparse.SUPPRESS,
help=(
"Directory to copy out lightweight results data. "
"If set to '', results will not be stored outside of the runs "
f"directory (default: {nexus_core_defaults.results})."
)
)
parser.add_argument(
"--local-directory",
"--local_directory",
default=argparse.SUPPRESS,
help=(
"Base path where runs and results directories will be created "
f"(default={nexus_core_defaults.local_directory})."
)
)
parser.add_argument(
"--pseudo-dir",
"--pseudo_dir",
default=argparse.SUPPRESS,
help=(
"Path to directory containing pseudopotential files "
"(required if running with pseudopotentials)."
)
)
parser.add_argument(
"--basis-dir",
"--basis_dir",
default=argparse.SUPPRESS,
help=(
"Path to directory containing basis set files "
"(useful if running gaussian based QMC workflows)."
)
)
parser.add_argument(
"--ericfmt",
default=argparse.SUPPRESS,
help=(
"Path to the ericfmt file used with GAMESS "
"(required if running GAMESS)."
)
)
parser.add_argument(
"--mcppath",
default=argparse.SUPPRESS,
help=(
"Path to the mcpdata file used with GAMESS "
"(optional for most workflows)"
)
)
parser.add_argument(
"--vdw-table",
"--vdw_table",
default=argparse.SUPPRESS,
help=(
"Path to the vdw_table file used with Quantum ESPRESSO "
"(required only if running QE with van der Waals functionals)."
)
)
parser.add_argument(
"--qprc",
default=argparse.SUPPRESS,
help="Path to the quantum_package.rc file used with Quantum Package."
)

# pre-process options, full processing occurs upon return
boolean_options = set(['status_only','generate_only','progress_tty'])
real_options = {'sleep', 'timeout'}
for ropt in real_options:
if opt[ropt]!='none':
try:
opt[ropt] = float(opt[ropt])
except:
msg = f"command line option '{ropt}' must be a real value\nyou provided: {opt[ropt]}\nplease try again"
raise ValueError(msg)
#end try
#end if
#end for
# parse the command line inputs
args = vars(parser.parse_args())

# override script settings with command line settings
for name,value in opt.items():
bool_name = name in boolean_options
if (bool_name and value) or (not bool_name and value!='none'):
script_settings[name] = value
#end if
#end for

for name,value in args.items():
if name in script_settings:
warn(f"Overriding setting {name} with value from command line.")
script_settings[name] = value
#end def process_command_line_settings


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