def test_database(self):
"""Testing database of ABINIT variables."""
varscode = get_codevars()
assert varscode is get_codevars()
database = varscode["abinit"]
# The text of this variable contaings greek symbols in HTML.
var = database["cd_frqim_method"]
repr(var)
str(var)
# Print all variables in the database.
for name, var in database.items():
#print("testing variable: ", name)
assert var.name == name
repr(var)
str(var)
str(var.info)
# FIXME
#str(var._repr_html_())
# Database methods.
database.apropos("ecut")
# FIXME
#assert len(database.json_dumps_varnames())
for setname in [
"basic", "rlx", "gstate", "eph", "ffield", "paral", "gw",
"dfpt", "geo", "bse", "dev", "paw", "dmft", "files",
"internal", "w90"
]:
assert database.vars_with_varset(setname)
for section in database.my_varset_list:
assert len(database.vars_with_varset(section))
for charact in database.my_characteristics:
print("character:", charact)
assert len(database.vars_with_char(charact))
name2varset = database.name2varset
assert name2varset["ecut"] == "basic" and name2varset["ionmov"] == "rlx"
assert database.group_by_varset("ecut") == {'basic': ['ecut']}
natom_var = database["natom"]
ecut_var = database["ecut"]
assert ecut_var.name == "ecut"
assert not ecut_var.isarray
assert not ecut_var.depends_on_dimension("natom")
assert not ecut_var.depends_on_dimension(natom_var)
# FIXME
#assert ecut_var.url
#assert ecut_var.html_link() and ecut_var.html_link(label="foo")
spinat_var = database["spinat"]
assert spinat_var.isarray
assert spinat_var.depends_on_dimension("natom")
assert spinat_var.depends_on_dimension(natom_var)
assert not spinat_var.depends_on_dimension("ntypat")
def docvar(varname, executable="abinit"):
"""Return the `Variable` object associated to this name."""
from abipy.abio.abivar_database.variables import get_codevars
return get_codevars()[executable][varname]
def get_abinit_variables():
"""Returns the database with the description of the ABINIT variables."""
from abipy.abio.abivar_database.variables import get_codevars
return get_codevars()["abinit"]
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 get_abinit_variables():
"""Returns the database with the description of the ABINIT variables."""
from abipy.abio.abivar_database.variables import get_codevars
return get_codevars()["abinit"]
def is_abivar(varname):
"""True if s is an ABINIT variable."""
# Add include statement
# FIXME: These variables should be added to the database.
extra = ["include", "xyzfile"]
return varname in get_codevars()["abinit"] or varname in extra
def is_anaddb_var(varname):
"""True if varname is a valid Anaddb variable."""
return varname in get_codevars()["anaddb"]
def docvar(varname, executable="abinit"):
"""Return the `Variable` object associated to this name."""
from abipy.abio.abivar_database.variables import get_codevars
return get_codevars()[executable][varname]
def is_abivar(varname):
"""True if s is an ABINIT variable."""
# Add include statement
# FIXME: These variables should be added to the database.
extra = ["include", "xyzfile"]
return varname in get_codevars()["abinit"] or varname in extra
def is_anaddb_var(varname):
"""True if varname is a valid Anaddb variable."""
return varname in get_codevars()["anaddb"]