def test_abilab(self):
"""Testing abilab"""
abilab.abiopen_ext2class_table()
assert abilab.abifile_subclass_from_filename("GSR.nc") is not None
assert len(abilab.dir2abifiles(top=abidata.dirpath))
assert len(abilab.dir2abifiles(top=abidata.dirpath, recurse=False)) == 1
with self.assertRaises(ValueError):
abilab.abifile_subclass_from_filename("foobar")
assert abilab.isabifile("foo_GSR.nc")
assert not abilab.isabifile("foobar")
import pandas
df = pandas.DataFrame({"a": [1, 2], "b": [3, 4]})
abilab.print_dataframe(df, title="foo")
d = abilab.software_stack()
assert d
assert not abilab.abicheck(verbose=1)
abilab.abipy_logo1()
abilab.abipy_logo2()
abilab.abipy_logo3()
assert not abilab.in_notebook()
abilab.enable_notebook(with_seaborn=True)
assert abilab.in_notebook()
abilab.disable_notebook()
assert not abilab.in_notebook()
def test_abilab(self):
"""Testing abilab"""
abilab.abiopen_ext2class_table()
assert abilab.abifile_subclass_from_filename("GSR.nc") is not None
assert len(abilab.dir2abifiles(top=abidata.dirpath))
assert len(abilab.dir2abifiles(top=abidata.dirpath, recurse=False)) == 1
with self.assertRaises(ValueError):
abilab.abifile_subclass_from_filename("foobar")
assert abilab.isabifile("foo_GSR.nc")
assert not abilab.isabifile("foobar")
import pandas
df = pandas.DataFrame({"a": [1, 2], "b": [3, 4]})
abilab.print_dataframe(df, title="foo")
d = abilab.software_stack()
assert d
assert not abilab.abicheck(verbose=1)
abilab.abipy_logo1()
abilab.abipy_logo2()
abilab.abipy_logo3()
assert not abilab.in_notebook()
abilab.enable_notebook(with_seaborn=True)
assert abilab.in_notebook()
abilab.disable_notebook()
assert not abilab.in_notebook()
def from_filename(filename):
"""
Static factory function that instanciates the appropriate subclass of `NcFilePopupMenu`
Returns None if the extesion of filename is not supported.
"""
# Find the AbinitNcFile subclass associated to files.
try:
file_class = abifile_subclass_from_filename(filename)
except KeyError:
if filename.endswith(".nc"): NcFilePopupMenu()
return None
# Check whether a subclass handles this file..
# Fallback to a simple PopupMenu if no match.
def allsubclasses(cls):
"""Returns the set of subclasses of cls."""
children = [cls]
for sc in cls.__subclasses__():
if sc.__subclasses__():
for k in sc.__subclasses__():
children.extend(allsubclasses(k))
else:
children.append(sc)
return set(children)
for cls in allsubclasses(PopupMenu):
if cls.handle_file_class(file_class):
return cls()
else:
if filename.endswith(".nc"): NcFilePopupMenu()
return PopupMenu()
def from_filename(filename):
"""
Static factory function that instanciates the appropriate subclass of `NcFilePopupMenu`
Returns None if the extesion of filename is not supported.
"""
# Find the AbinitNcFile subclass associated to files.
try:
file_class = abifile_subclass_from_filename(filename)
except KeyError:
if filename.endswith(".nc"):
NcFilePopupMenu()
return None
# Check whether a subclass handles this file..
# Fallback to a simple PopupMenu if no match.
def allsubclasses(cls):
"""Returns the set of subclasses of cls."""
children = [cls]
for sc in cls.__subclasses__():
if sc.__subclasses__():
for k in sc.__subclasses__():
children.extend(allsubclasses(k))
else:
children.append(sc)
return set(children)
for cls in allsubclasses(PopupMenu):
if cls.handle_file_class(file_class):
return cls()
else:
if filename.endswith(".nc"):
NcFilePopupMenu()
return PopupMenu()
def test_abilab(self):
"""Testing abilab"""
abilab.abiopen_ext2class_table()
assert abilab.abifile_subclass_from_filename("GSR.nc") is not None
assert len(abilab.dir2abifiles(top=abidata.dirpath))
assert len(abilab.dir2abifiles(top=abidata.dirpath,
recurse=False)) == 1
with self.assertRaises(ValueError):
abilab.abifile_subclass_from_filename("foobar")
assert abilab.isabifile("foo_GSR.nc")
assert not abilab.isabifile("foobar")
import pandas
df = pandas.DataFrame({"a": [1, 2], "b": [3, 4]})
abilab.print_dataframe(df, title="foo")
d = abilab.software_stack()
assert d
filepath = self.get_tmpname(text=True, suffix=".json")
data = {"foo": "bar"}
abilab.mjson_write(data, filepath, indent=4)
data = abilab.mjson_load(filepath)
assert data["foo"] == "bar"
same_data = abilab.mjson_loads(json.dumps(data))
assert len(same_data) == len(data)
assert same_data["foo"] == data["foo"]
assert not abilab.abicheck(verbose=1)
abilab.abipy_logo1()
abilab.abipy_logo2()
abilab.abipy_logo3()
assert not abilab.in_notebook()
abilab.enable_notebook(with_seaborn=True)
assert abilab.in_notebook()
abilab.disable_notebook()
assert not abilab.in_notebook()
assert abilab.install_config_files(workdir=self.mkdtemp()) == 0
def test_abilab(self):
"""Testing abilab"""
abilab.abiopen_ext2class_table()
assert abilab.abifile_subclass_from_filename("GSR.nc") is not None
assert len(abilab.dir2abifiles(top=abidata.dirpath))
with self.assertRaises(ValueError):
abilab.abifile_subclass_from_filename("foobar")
assert abilab.isabifile("foo_GSR.nc")
assert not abilab.isabifile("foobar")
d = abilab.software_stack()
assert d
assert not abilab.abicheck(verbose=1)
abilab.abipy_logo1()
abilab.abipy_logo2()
abilab.abipy_logo3()
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)
# Parse the command line.
try:
options = parser.parse_args()
except Exception:
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)
if options.verbose > 2:
print(options)
if not os.path.exists(options.filepath):
raise RuntimeError("%s: no such file" % options.filepath)
if not options.notebook:
# Start ipython shell with namespace
abifile = abilab.abiopen(options.filepath)
if options.print:
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
return 0
import IPython
# Use embed because I don't know how to show a header with start_ipython.
IPython.embed(
header=
"The Abinit file is bound to the `abifile` variable.\nTry `print(abifile)`"
)
else:
# Call specialized method if the object is a NotebookWriter
# else generate simple notebook by calling `make_and_open_notebook`
cls = abilab.abifile_subclass_from_filename(options.filepath)
if hasattr(cls, "make_and_open_notebook"):
if hasattr(cls, "__exit__"):
with abilab.abiopen(options.filepath) as abifile:
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
abifile = abilab.abiopen(options.filepath)
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
return make_and_open_notebook(options)
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)
# Parse the command line.
try:
options = parser.parse_args()
except Exception:
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)
if options.verbose > 2:
print(options)
if options.mpl_backend is not None:
# Set matplotlib backend
import matplotlib
matplotlib.use(options.mpl_backend)
if options.seaborn:
# Use seaborn settings.
import seaborn as sns
sns.set(context=options.seaborn, style='darkgrid', palette='deep',
font='sans-serif', font_scale=1, color_codes=False, rc=None)
if not os.path.exists(options.filepath):
raise RuntimeError("%s: no such file" % options.filepath)
if not options.notebook:
abifile = abilab.abiopen(options.filepath)
if options.print:
# Print object to terminal.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
return 0
elif options.expose:
# Generate matplotlib plots automatically.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
if not hasattr(abifile, "expose"):
raise TypeError("Object of type `%s` does not implement expose method" % type(abifile))
abifile.expose(slide_mode=options.slide_mode, slide_timeout=options.slide_timeout,
verbose=options.verbose)
return 0
# Start ipython shell with namespace
# Use embed because I don't know how to show a header with start_ipython.
import IPython
IPython.embed(header="The Abinit file is bound to the `abifile` variable.\nTry `print(abifile)`")
else:
# Call specialized method if the object is a NotebookWriter
# else generate simple notebook by calling `make_and_open_notebook`
cls = abilab.abifile_subclass_from_filename(options.filepath)
if hasattr(cls, "make_and_open_notebook"):
if hasattr(cls, "__exit__"):
with abilab.abiopen(options.filepath) as abifile:
return abifile.make_and_open_notebook(foreground=options.foreground)
else:
abifile = abilab.abiopen(options.filepath)
return abifile.make_and_open_notebook(foreground=options.foreground)
else:
return make_and_open_notebook(options)
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)
# Parse the command line.
try:
options = parser.parse_args()
except Exception:
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)
if options.verbose > 2:
print(options)
if options.mpl_backend is not None:
# Set matplotlib backend
import matplotlib
matplotlib.use(options.mpl_backend)
if options.seaborn:
# Use seaborn settings.
import seaborn as sns
sns.set(context=options.seaborn,
style='darkgrid',
palette='deep',
font='sans-serif',
font_scale=1,
color_codes=False,
rc=None)
if not os.path.exists(options.filepath):
raise RuntimeError("%s: no such file" % options.filepath)
if not options.notebook:
abifile = abilab.abiopen(options.filepath)
if options.print:
# Print object to terminal.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
return 0
elif options.expose:
# Generate matplotlib plots automatically.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
if hasattr(abifile, "expose"):
abifile.expose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout,
verbose=options.verbose)
else:
if not hasattr(abifile, "yield_figs"):
raise TypeError(
"Object of type `%s` does not implement (expose or yield_figs methods"
% type(abifile))
from abipy.tools.plotting import MplExpose
with MplExpose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout,
verbose=options.verbose) as e:
e(abifile.yield_figs())
return 0
# Start ipython shell with namespace
# Use embed because I don't know how to show a header with start_ipython.
import IPython
IPython.embed(
header=
"The Abinit file is bound to the `abifile` variable.\nTry `print(abifile)`"
)
else:
# Call specialized method if the object is a NotebookWriter
# else generate simple notebook by calling `make_and_open_notebook`
cls = abilab.abifile_subclass_from_filename(options.filepath)
if hasattr(cls, "make_and_open_notebook"):
if hasattr(cls, "__exit__"):
with abilab.abiopen(options.filepath) as abifile:
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
abifile = abilab.abiopen(options.filepath)
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
return make_and_open_notebook(options)
return 0
def main():
def str_examples():
s = """\
Usage example:
abiopen.py out_GSR.nc
abiopen.py out_DDB -nb # To generate jupyter notebook
File extensions supported:
"""
return s + abilab.abiopen_ext2class_table()
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)
parser = argparse.ArgumentParser(
epilog=str_examples(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--loglevel',
default="ERROR",
type=str,
help=
"Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG"
)
parser.add_argument('-V',
'--version',
action='version',
version="%(prog)s version " + abilab.__version__)
#parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
# help='verbose, can be supplied multiple times to increase verbosity')
parser.add_argument('-nb',
'--notebook',
action='store_true',
default=False,
help="Open file in jupyter notebook")
parser.add_argument('--foreground',
action='store_true',
default=False,
help="Run jupyter notebook in the foreground.")
parser.add_argument('-p',
'--print',
action='store_true',
default=False,
help="Print python object and return.")
parser.add_argument(
"filepath",
help=
"File to open. See table below for the list of supported extensions.")
# Parse the command line.
try:
options = parser.parse_args()
except Exception:
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)
options.filepath = os.path.abspath(options.filepath)
if not os.path.exists(options.filepath):
raise RuntimeError("%s: no such file" % options.filepath)
if not options.notebook:
# Start ipython shell with namespace
abifile = abilab.abiopen(options.filepath)
if options.print:
print(abifile)
return 0
import IPython
# Use embed because I don't know how to show a header with start_ipython.
IPython.embed(
header=
"The Abinit file is bound to the `abifile` variable.\nTry `print(abifile)`"
)
#IPython.start_ipython(argv=options.argv,
# user_ns={"abifile": abifile},
# banner="hello",
# banner1="hello1",
# header="hello_header",
# )
#
else:
# Call specialized method if the object is a NotebookWriter
# else generate simple notebook by calling `make_and_open_notebook`
cls = abilab.abifile_subclass_from_filename(options.filepath)
if hasattr(cls, "make_and_open_notebook"):
if hasattr(cls, "__exit__"):
with abilab.abiopen(options.filepath) as abifile:
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
abifile = abilab.abiopen(options.filepath)
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
return make_and_open_notebook(options)
return 0
