def print_vlist(vlist, options):
for v in vlist:
print(repr(v))
if options.verbose:
for v in vlist: abilab.abinit_help(v)
else:
print("\nUse -v for more info")
def print_vlist(vlist, options):
for v in vlist:
print(repr(v))
if options.verbose:
for v in vlist: abinit_help(v)
else:
print("\nUse -v for more info")
def main():
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(get_epilog())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = get_parser(with_epilog=True)
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
# Get the dabase of variables for codename.
from abipy.abio.abivar_database.variables import get_codevars
vdb = get_codevars()[options.codename]
if options.command == "man":
abilab.abinit_help(options.varname)
elif options.command == "browse":
return vdb[options.varname].browse()
elif options.command == "graphviz":
if options.varname in vdb.my_varset_list:
graph = vdb.get_graphviz(varset=options.varname,
vartype=None,
engine=options.engine)
else:
graph = vdb.get_graphviz_varname(varname=options.varname,
engine=options.engine)
import tempfile
directory = tempfile.mkdtemp()
print("Producing source files in:", directory)
graph.view(directory=directory, cleanup=False)
elif options.command == "apropos":
vlist = vdb.apropos(options.varname)
print_vlist(vlist, options)
elif options.command == "find":
vlist = [v for v in vdb.values() if options.varname in v.name]
print("Find results:\n")
print_vlist(vlist, options)
elif options.command == "list":
if options.mode == "a":
# Alphabetical
for i, var in enumerate(vdb.values()):
print(i, repr(var))
elif options.mode == "s":
# Grouped by varset
for section in vdb.my_varset_list:
print(30 * "#" + " Section: " + section + " " + 30 * "#")
print_vlist(vdb.vars_with_section(section), options)
elif options.mode == "c":
# Grouped by characteristics.
for char in vdb.my_characteristics:
print(30 * "#" + " Characteristic: " + char + 30 * "#")
print_vlist(vdb.vars_with_char(char), options)
else:
raise ValueError("Wrong mode %s" % options.mode)
elif options.command == "withdim":
for var in vdb.values():
if var.depends_on_dimension(options.dimname):
cprint(repr(var), "yellow")
print("dimensions:", str(var.dimensions), "\n")
elif options.command == "scheduler":
print("Options that can be specified in scheduler.yml:")
print(flowtk.PyFlowScheduler.autodoc())
return 0
elif options.command == "manager":
# Document TaskManager options and qparams.
qtype = options.qtype
if qtype == "script":
manager = flowtk.TaskManager.from_user_config()
script = manager.qadapter.get_script_str(
job_name="job_name",
launch_dir="workdir",
executable="executable",
qout_path="qout_file.path",
qerr_path="qerr_file.path",
stdin="stdin",
stdout="stdout",
stderr="stderr")
print(script)
else:
print(flowtk.TaskManager.autodoc())
print("qtype supported: %s" % flowtk.all_qtypes())
print(
"Use `abidoc.py manager slurm` to have the list of qparams for slurm.\n"
)
if qtype is not None:
print("QPARAMS for %s" % qtype)
flowtk.show_qparams(qtype)
elif options.command == "abibuild":
abinit_build = flowtk.AbinitBuild()
print()
print(abinit_build)
print()
if not options.verbose:
print("Use --verbose for additional info")
else:
print(abinit_build.info)
else:
raise ValueError("Don't know how to handle command %s" %
options.command)
return 0
def main():
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(get_epilog())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = get_parser(with_epilog=True)
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
# Get the dabase of variables for codename.
from abipy.abio.abivar_database.variables import get_codevars
vdb = get_codevars()[options.codename]
if options.command == "man":
abilab.abinit_help(options.varname)
elif options.command == "browse":
return vdb[options.varname].browse()
elif options.command == "graphviz":
if options.varname in vdb.my_varset_list:
graph = vdb.get_graphviz(varset=options.varname, vartype=None, engine=options.engine)
else:
graph = vdb.get_graphviz_varname(varname=options.varname, engine=options.engine)
import tempfile
directory = tempfile.mkdtemp()
print("Producing source files in:", directory)
graph.view(directory=directory, cleanup=False)
elif options.command == "apropos":
vlist = vdb.apropos(options.varname)
print_vlist(vlist, options)
elif options.command == "find":
vlist = [v for v in vdb.values() if options.varname in v.name]
print("Find results:\n")
print_vlist(vlist, options)
elif options.command == "list":
if options.mode == "a":
# Alphabetical
for i, var in enumerate(vdb.values()):
print(i, repr(var))
elif options.mode == "s":
# Grouped by varset
for section in vdb.my_varset_list:
print(30*"#" + " Section: " + section + " " + 30*"#")
print_vlist(vdb.vars_with_section(section), options)
elif options.mode == "c":
# Grouped by characteristics.
for char in vdb.my_characteristics:
print(30*"#" + " Characteristic: " + char + 30*"#")
print_vlist(vdb.vars_with_char(char), options)
else:
raise ValueError("Wrong mode %s" % options.mode)
elif options.command == "withdim":
for var in vdb.values():
if var.depends_on_dimension(options.dimname):
cprint(repr(var), "yellow")
print("dimensions:", str(var.dimensions), "\n")
elif options.command == "scheduler":
print("Options that can be specified in scheduler.yml:")
print(flowtk.PyFlowScheduler.autodoc())
return 0
elif options.command == "manager":
# Document TaskManager options and qparams.
qtype = options.qtype
if qtype == "script":
manager = flowtk.TaskManager.from_user_config()
script = manager.qadapter.get_script_str(
job_name="job_name", launch_dir="workdir", executable="executable",
qout_path="qout_file.path", qerr_path="qerr_file.path",
stdin="stdin", stdout="stdout", stderr="stderr")
print(script)
else:
print(flowtk.TaskManager.autodoc())
print("qtype supported: %s" % flowtk.all_qtypes())
print("Use `abidoc.py manager slurm` to have the list of qparams for slurm.\n")
if qtype is not None:
print("QPARAMS for %s" % qtype)
flowtk.show_qparams(qtype)
elif options.command == "abibuild":
abinit_build = flowtk.AbinitBuild()
print()
print(abinit_build)
print()
if not options.verbose:
print("Use --verbose for additional info")
else:
print(abinit_build.info)
else:
raise ValueError("Don't know how to handle command %s" % options.command)
return 0
def main():
def str_examples():
examples = """\
Usage example:
abidoc.py man ecut --> Show documentation for ecut input variable.
abidoc.py apropos ecut --> To search in the database for the variables related to ecut.
abidoc.py find paw --> To search in the database for the variables whose name contains paw
abidoc.py list --> Print full list of variables
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Build the main parser.
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-V', '--version', action='version', version="%(prog)s version " + __version__)
# Parent parser for common options.
copts_parser = argparse.ArgumentParser(add_help=False)
copts_parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
copts_parser.add_argument('--loglevel', default="ERROR", type=str,
help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
var_parser = argparse.ArgumentParser(add_help=False)
var_parser.add_argument('varname', help="ABINIT variable")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for man.
p_man = subparsers.add_parser('man', parents=[copts_parser, var_parser], help="Show documentation for varname.")
# Subparser for apropos.
p_apropos = subparsers.add_parser('apropos', parents=[copts_parser, var_parser], help="Find variables related to varname.")
# Subparser for find.
p_find = subparsers.add_parser('find', parents=[copts_parser, var_parser],
help="Find all variables whose name contains varname.")
# Subparser for require.
#p_require = subparsers.add_parser('require', parents=[copts_parser], help="Find all variables required by varname.")
# Subparser for list.
p_list = subparsers.add_parser('list', parents=[copts_parser], help="List all variables.")
p_list.add_argument('--mode', default="a",
help="Sorte mode, `a` for alphabethical, `s` for sections, `c` for characteristics.")
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
database = get_abinit_variables()
if options.command == "man":
abinit_help(options.varname)
elif options.command == "apropos":
vlist = database.apropos(options.varname)
print_vlist(vlist, options)
elif options.command == "find":
vlist = [v for v in database.values() if options.varname in v.varname]
print("find results:\n")
print_vlist(vlist, options)
elif options.command == "list":
if options.mode == "a":
# Alphabetical
for i, var in enumerate(database.values()):
print(i, repr(var))
elif options.mode == "s":
# Grouped by sections.
for section in database.sections:
header = 30*"#" + " Section: " + section + " " + 30*"#"
print(header)
print_vlist(database.vars_with_section(section), options)
elif options.mode == "c":
# Grouped by characteristics.
for char in database.characteristics:
header = 30*"#" + " Characteristic: " + char + 30*"#"
print(header)
print_vlist(database.vars_with_char(char), options)
else:
raise ValueError("Wrong mode %s" % options.mode)
else:
raise ValueError("Don't know how to handle command %s" % options.command)
def main():
def str_examples():
examples = """\
Usage example:
abidoc.py man ecut --> Show documentation for ecut input variable.
abidoc.py apropos ecut --> To search in the database for the variables related to ecut.
abidoc.py find paw --> To search in the database for the variables whose name contains paw
abidoc.py list --> Print full list of variables
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Build the main parser.
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
base_parser = argparse.ArgumentParser(add_help=False)
base_parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
var_parser = argparse.ArgumentParser(add_help=False)
var_parser.add_argument('varname', help="ABINIT variable")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for man.
p_man = subparsers.add_parser('man', parents=[base_parser, var_parser], help="Show documentation for varname.")
# Subparser for apropos.
p_apropos = subparsers.add_parser('apropos', parents=[base_parser, var_parser], help="Find variables related to varname.")
# Subparser for find.
p_find = subparsers.add_parser('find', parents=[base_parser, var_parser], help="Find all variables whose name contains varname.")
# Subparser for require.
#p_require = subparsers.add_parser('require', parents=[base_parser], help="Find all variables required by varname.")
# Subparser for list.
p_list = subparsers.add_parser('list', parents=[base_parser], help="List all variables.")
p_list.add_argument('--mode', default="a", help="Sorte mode, `a` for alphabethical, `s` for sections, `c` for characteristics.")
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
database = get_abinit_variables()
if options.command == "man":
abinit_help(options.varname)
elif options.command == "apropos":
vlist = database.apropos(options.varname)
print("apropos results:\n")
print_vlist(vlist, options)
elif options.command == "find":
vlist = [v for v in database.values() if options.varname in v.varname]
print("find results:\n")
print_vlist(vlist, options)
elif options.command == "list":
if options.mode == "a":
# Alphabetical
for i, var in enumerate(database.values()):
print(i, repr(var))
elif options.mode == "s":
# Grouped by sections.
for section in database.sections:
header = 30*"#" + " Section: " + section + " " + 30*"#"
print(header)
print_vlist(database.vars_with_section(section), options)
elif options.mode == "c":
# Grouped by characteristics.
for char in database.characteristics:
header = 30*"#" + " Characteristic: " + char + 30*"#"
print(header)
print_vlist(database.vars_with_char(char), options)
else:
raise ValueError("Wrong mode %s" % options.mode)
else:
raise ValueError("Don't know how to handle command %s" % options.command)
def main():
def str_examples():
examples = """\
Usage example:
abidoc.py man ecut --> Show documentation for ecut input variable.
abidoc.py apropos ecut --> To search in the database for the variables related to ecut.
abidoc.py find paw --> To search in the database for the variables whose name contains paw
abidoc.py list --> Print full list of variables
abidoc.py withdim natom --> Print arrays depending on natom.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Build the main parser.
parser = argparse.ArgumentParser(
epilog=str_examples(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-V',
'--version',
action='version',
version="%(prog)s version " + __version__)
# Parent parser for common options.
copts_parser = argparse.ArgumentParser(add_help=False)
copts_parser.add_argument(
'-v',
'--verbose',
default=0,
action='count', # -vv --> verbose=2
help='verbose, can be supplied multiple times to increase verbosity')
copts_parser.add_argument(
'--loglevel',
default="ERROR",
type=str,
help=
"set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG"
)
var_parser = argparse.ArgumentParser(add_help=False)
var_parser.add_argument('varname', help="ABINIT variable")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command',
help='sub-command help',
description="Valid subcommands")
# Subparser for man.
p_man = subparsers.add_parser('man',
parents=[copts_parser, var_parser],
help="Show documentation for varname.")
# Subparser for apropos.
p_apropos = subparsers.add_parser(
'apropos',
parents=[copts_parser, var_parser],
help="Find variables related to varname.")
# Subparser for find.
p_find = subparsers.add_parser(
'find',
parents=[copts_parser, var_parser],
help="Find all variables whose name contains varname.")
# Subparser for require.
#p_require = subparsers.add_parser('require', parents=[copts_parser], help="Find all variables required by varname.")
# Subparser for withdim.
p_withdim = subparsers.add_parser(
'withdim',
parents=[copts_parser],
help="Find all arrays depending on the given dimension.")
p_withdim.add_argument("dimname", help="Dimension name")
# Subparser for list.
p_list = subparsers.add_parser('list',
parents=[copts_parser],
help="List all variables.")
p_list.add_argument(
'--mode',
default="a",
help=
"Sorte mode, `a` for alphabethical, `s` for sections, `c` for characteristics."
)
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
database = get_abinit_variables()
if options.command == "man":
abinit_help(options.varname)
elif options.command == "apropos":
vlist = database.apropos(options.varname)
print_vlist(vlist, options)
elif options.command == "find":
vlist = [v for v in database.values() if options.varname in v.varname]
print("find results:\n")
print_vlist(vlist, options)
elif options.command == "list":
if options.mode == "a":
# Alphabetical
for i, var in enumerate(database.values()):
print(i, repr(var))
elif options.mode == "s":
# Grouped by sections.
for section in database.sections:
header = 30 * "#" + " Section: " + section + " " + 30 * "#"
print(header)
print_vlist(database.vars_with_section(section), options)
elif options.mode == "c":
# Grouped by characteristics.
for char in database.characteristics:
header = 30 * "#" + " Characteristic: " + char + 30 * "#"
print(header)
print_vlist(database.vars_with_char(char), options)
else:
raise ValueError("Wrong mode %s" % options.mode)
elif options.command == "withdim":
for var in database.values():
if var.isarray and options.dimname in str(var.dimensions):
print(repr(var), "\n", str(var.dimensions),
"\n") # type(var.dimensions)
else:
raise ValueError("Don't know how to handle command %s" %
options.command)
