def info():
"""Show versions of GPAW and its dependencies."""
results = [('python-' + sys.version.split()[0], sys.executable)]
for name in ['gpaw', 'ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
results.append((name, False))
else:
results.append((name + '-' + module.__version__,
module.__file__.rsplit('/', 1)[0] + '/'))
module = import_module('_gpaw')
results.append(
('_gpaw', op.normpath(getattr(module, '__file__', 'built-in'))))
p = subprocess.Popen(['which', 'gpaw-python'], stdout=subprocess.PIPE)
results.append(('parallel', p.communicate()[0].strip().decode() or False))
results.append(('FFTW', fftw.FFTPlan is fftw.FFTWPlan))
results.append(('scalapack', compiled_with_sl()))
results.append(('libvdwxc', compiled_with_libvdwxc()))
paths = [
'{0}: {1}'.format(i + 1, path)
for i, path in enumerate(gpaw.setup_paths)
]
results.append(('PAW-datasets', '\n '.join(paths)))
for a, b in results:
if isinstance(b, bool):
b = ['no', 'yes'][b]
print('{0:16}{1}'.format(a, b))
def initialize(format):
"""Import read and write functions."""
if format in ioformats:
return # already done
_format = format.replace('-', '_')
module_name = format2modulename.get(format, _format)
try:
module = import_module('ase.io.' + module_name)
except ImportError as err:
raise ValueError('File format not recognized: %s. Error: %s' %
(format, err))
read = getattr(module, 'read_' + _format, None)
write = getattr(module, 'write_' + _format, None)
if read and not inspect.isgeneratorfunction(read):
read = functools.partial(wrap_read_function, read)
if not read and not write:
raise ValueError('File format not recognized: ' + format)
code = all_formats[format][1]
single = code[0] == '1'
acceptsfd = code[1] == 'F'
ioformats[format] = IOFormat(read, write, single, acceptsfd)
def initialize(format):
"""Import read and write functions."""
if format in ioformats:
return # already done
_format = format.replace('-', '_')
module_name = format2modulename.get(format, _format)
try:
module = import_module('ase.io.' + module_name)
except ImportError as err:
raise ValueError('File format not recognized: %s. Error: %s'
% (format, err))
read = getattr(module, 'read_' + _format, None)
write = getattr(module, 'write_' + _format, None)
if read and not inspect.isgeneratorfunction(read):
read = functools.partial(wrap_read_function, read)
if not read and not write:
raise ValueError('File format not recognized: ' + format)
code = all_formats[format][1]
single = code[0] == '1'
acceptsfd = code[1] == 'F'
ioformats[format] = IOFormat(read, write, single, acceptsfd)
def info():
"""Show versions of GPAW and its dependencies."""
results = [('python-' + sys.version.split()[0], sys.executable)]
for name in ['gpaw', 'ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
results.append((name, False))
else:
# Search for git hash
githash = search_current_git_hash(module)
if githash is None:
githash = ''
else:
githash = '-{:.10}'.format(githash)
results.append((name + '-' + module.__version__ + githash,
module.__file__.rsplit('/', 1)[0] + '/'))
results.append(('libxc-' + _gpaw.libxc_version, ''))
module = import_module('_gpaw')
if hasattr(module, 'githash'):
githash = '-{:.10}'.format(module.githash())
results.append(
('_gpaw' + githash, op.normpath(getattr(module, '__file__',
'built-in'))))
p = subprocess.Popen(['which', 'gpaw-python'], stdout=subprocess.PIPE)
results.append(('parallel', p.communicate()[0].strip().decode() or False))
results.append(('MPI enabled', have_mpi))
if have_mpi:
have_sl = compiled_with_sl()
have_elpa = LibElpa.have_elpa()
else:
have_sl = have_elpa = 'no (MPI unavailable)'
results.append(('scalapack', have_sl))
results.append(('Elpa', have_elpa))
results.append(('FFTW', fftw.FFTPlan is fftw.FFTWPlan))
results.append(('libvdwxc', compiled_with_libvdwxc()))
paths = [
'{0}: {1}'.format(i + 1, path)
for i, path in enumerate(gpaw.setup_paths)
]
results.append(('PAW-datasets', '\n{:25}'.format('').join(paths)))
if rank == 0:
for a, b in results:
if isinstance(b, bool):
b = ['no', 'yes'][b]
print('{0:25}{1}'.format(a, b))
def main(prog='ase', description='ASE command line tool',
version=__version__, commands=commands, hook=None):
parser = argparse.ArgumentParser(prog=prog, description=description)
parser.add_argument('--version', action='version',
version='%(prog)s-{}'.format(version))
parser.add_argument('-T', '--traceback', action='store_true')
subparsers = parser.add_subparsers(title='Sub-commands',
dest='command')
subparser = subparsers.add_parser('help',
description='Help',
help='Help for sub-command')
subparser.add_argument('helpcommand', nargs='?')
functions = {}
parsers = {}
for command, module_name in commands:
cmd = import_module(module_name).CLICommand
subparser = subparsers.add_parser(
command,
help=cmd.short_description,
description=getattr(cmd, 'description', cmd.short_description))
cmd.add_arguments(subparser)
functions[command] = cmd.run
parsers[command] = subparser
if hook:
args = hook(parser)
else:
args = parser.parse_args()
if args.command == 'help':
if args.helpcommand is None:
parser.print_help()
else:
parsers[args.helpcommand].print_help()
elif args.command is None:
parser.print_usage()
else:
f = functions[args.command]
try:
if f.__code__.co_argcount == 1:
f(args)
else:
f(args, parsers[args.command])
except KeyboardInterrupt:
pass
except Exception as x:
if args.traceback:
raise
else:
print('{}: {}'.format(x.__class__.__name__, x),
file=sys.stderr)
print('To get a full traceback, use: {} -T {} ...'
.format(prog, args.command), file=sys.stderr)
def main(prog='ase', description='ASE command line tool',
version=__version__, commands=commands, hook=None, args=None):
parser = argparse.ArgumentParser(prog=prog, description=description)
parser.add_argument('--version', action='version',
version='%(prog)s-{}'.format(version))
parser.add_argument('-T', '--traceback', action='store_true')
subparsers = parser.add_subparsers(title='Sub-commands',
dest='command')
subparser = subparsers.add_parser('help',
description='Help',
help='Help for sub-command')
subparser.add_argument('helpcommand', nargs='?')
functions = {}
parsers = {}
for command, module_name in commands:
cmd = import_module(module_name).CLICommand
subparser = subparsers.add_parser(
command,
help=cmd.short_description,
description=getattr(cmd, 'description', cmd.short_description))
cmd.add_arguments(subparser)
functions[command] = cmd.run
parsers[command] = subparser
if hook:
args = hook(parser, args)
else:
args = parser.parse_args(args)
if args.command == 'help':
if args.helpcommand is None:
parser.print_help()
else:
parsers[args.helpcommand].print_help()
elif args.command is None:
parser.print_usage()
else:
f = functions[args.command]
try:
if f.__code__.co_argcount == 1:
f(args)
else:
f(args, parsers[args.command])
except KeyboardInterrupt:
pass
except Exception as x:
if args.traceback:
raise
else:
print('{}: {}'.format(x.__class__.__name__, x),
file=sys.stderr)
print('To get a full traceback, use: {} -T {} ...'
.format(prog, args.command), file=sys.stderr)
def print_info():
versions = [('platform', platform.platform()),
('python-' + sys.version.split()[0], sys.executable)]
for name in ['ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
versions.append((name, 'no'))
else:
versions.append((name + '-' + module.__version__,
module.__file__.rsplit('/', 1)[0] + '/'))
for a, b in versions:
print('{:16}{}'.format(a, b))
def update(filename, commands):
"""Update commands dict.
Run this when ever options are changed::
python3 -m ase.cli.complete
"""
import textwrap
from ase.utils import import_module
dct = {} # Dict[str, List[str]]
class Subparser:
def __init__(self, command):
self.command = command
dct[command] = []
def add_argument(self, *args, **kwargs):
dct[command].extend(arg for arg in args if arg.startswith('-'))
def add_mutually_exclusive_group(self, required=False):
return self
for command, module_name in commands:
module = import_module(module_name)
module.CLICommand.add_arguments(Subparser(command))
txt = 'commands = {'
for command, opts in sorted(dct.items()):
txt += "\n '" + command + "':\n ["
if opts:
txt += '\n'.join(
textwrap.wrap("'" + "', '".join(opts) + "'],",
width=65,
break_on_hyphens=False,
subsequent_indent=' '))
else:
txt += '],'
txt = txt[:-1] + '}\n'
with open(filename) as fd:
lines = fd.readlines()
a = lines.index('# Beginning of computer generated data:\n')
b = lines.index('# End of computer generated data\n')
lines[a + 1:b] = [txt]
with open(filename + '.new', 'w') as fd:
print(''.join(lines), end='', file=fd)
os.rename(filename + '.new', filename)
os.chmod(filename, 0o775)
def print_info():
versions = [('platform', platform.platform()),
('python-' + sys.version.split()[0], sys.executable)]
for name in ['ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
versions.append((name, 'no'))
else:
versions.append((name + '-' + module.__version__,
module.__file__.rsplit('/', 1)[0] + '/'))
for a, b in versions:
print('{:16}{}'.format(a, b))
def update(filename, commands):
"""Update commands dict.
Run this when ever options are changed::
python3 -m ase.cli.complete
"""
import collections
import textwrap
from ase.utils import import_module
dct = collections.defaultdict(list)
class Subparser:
def __init__(self, command):
self.command = command
def add_argument(self, *args, **kwargs):
dct[command].extend(arg for arg in args
if arg.startswith('-'))
for command, module_name in commands:
module = import_module(module_name)
module.CLICommand.add_arguments(Subparser(command))
txt = 'commands = {'
for command, opts in sorted(dct.items()):
txt += "\n '" + command + "':\n ["
txt += '\n'.join(textwrap.wrap("'" + "', '".join(opts) + "'],",
width=65,
break_on_hyphens=False,
subsequent_indent=' '))
txt = txt[:-1] + '}\n'
with open(filename) as fd:
lines = fd.readlines()
a = lines.index('# Beginning of computer generated data:\n')
b = lines.index('# End of computer generated data\n')
lines[a + 1:b] = [txt]
with open(filename + '.new', 'w') as fd:
print(''.join(lines), end='', file=fd)
os.rename(filename + '.new', filename)
os.chmod(filename, 0o775)
def print_info():
versions = [('platform', platform.platform()),
('python-' + sys.version.split()[0], sys.executable)]
for name in ['ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
versions.append((name, 'no'))
else:
# Search for git hash
githash = search_current_git_hash(module)
if githash is None:
githash = ''
else:
githash = '-{:.10}'.format(githash)
versions.append((name + '-' + module.__version__ + githash,
module.__file__.rsplit(os.sep, 1)[0] + os.sep))
for a, b in versions:
print('{:25}{}'.format(a, b))
def main(prog='ase',
description='ASE command line tool.',
version=__version__,
commands=commands,
hook=None,
args=None):
parser = argparse.ArgumentParser(prog=prog,
description=description,
formatter_class=Formatter)
parser.add_argument('--version',
action='version',
version='%(prog)s-{}'.format(version))
parser.add_argument('-T', '--traceback', action='store_true')
subparsers = parser.add_subparsers(title='Sub-commands', dest='command')
subparser = subparsers.add_parser('help',
description='Help',
help='Help for sub-command.')
subparser.add_argument('helpcommand',
nargs='?',
metavar='sub-command',
help='Provide help for sub-command.')
functions = {}
parsers = {}
for command, module_name in commands:
cmd = import_module(module_name).CLICommand
docstring = cmd.__doc__
if docstring is None:
# Backwards compatibility with GPAW
short = cmd.short_description
long = getattr(cmd, 'description', short)
else:
parts = docstring.split('\n', 1)
if len(parts) == 1:
short = docstring
long = docstring
else:
short, body = parts
long = short + '\n' + textwrap.dedent(body)
subparser = subparsers.add_parser(command,
formatter_class=Formatter,
help=short,
description=long)
cmd.add_arguments(subparser)
functions[command] = cmd.run
parsers[command] = subparser
if hook:
args = hook(parser, args)
else:
args = parser.parse_args(args)
if args.command == 'help':
if args.helpcommand is None:
parser.print_help()
else:
parsers[args.helpcommand].print_help()
elif args.command is None:
parser.print_usage()
else:
f = functions[args.command]
try:
if f.__code__.co_argcount == 1:
f(args)
else:
f(args, parsers[args.command])
except KeyboardInterrupt:
pass
except CLIError as x:
parser.error(x)
except Exception as x:
if args.traceback:
raise
else:
l1 = '{}: {}\n'.format(x.__class__.__name__, x)
l2 = ('To get a full traceback, use: {} -T {} ...'.format(
prog, args.command))
parser.error(l1 + l2)
def test(verbosity=1, calculators=[],
testdir=None, display=True, stream=sys.stdout, files=None):
test_calculator_names.extend(calculators)
disable_calculators([name for name in calc_names
if name not in calculators])
ts = unittest.TestSuite()
if files:
files = [os.path.join(__path__[0], f) for f in files]
else:
files = glob(__path__[0] + '/*')
sdirtests = [] # tests from subdirectories: only one level assumed
tests = []
for f in files:
if os.path.isdir(f):
# add test subdirectories (like calculators)
sdirtests.extend(glob(f + '/*.py'))
else:
# add py files in testdir
if f.endswith('.py'):
tests.append(f)
tests.sort()
sdirtests.sort()
tests.extend(sdirtests) # run test subdirectories at the end
lasttest = None # is COCu111.py in the current set
for test in tests:
if test.endswith('__.py'):
continue
if test.endswith('COCu111.py'):
lasttest = test
continue
ts.addTest(ScriptTestCase(filename=os.path.abspath(test),
display=display))
if lasttest:
ts.addTest(ScriptTestCase(filename=os.path.abspath(lasttest),
display=display))
versions = [('platform', platform.platform()),
('python-' + sys.version.split()[0], sys.executable)]
for name in ['ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
versions.append((name, 'no'))
else:
versions.append((name + '-' + module.__version__,
module.__file__.rsplit('/', 1)[0] + '/'))
if verbosity:
for a, b in versions:
print('{0:16}{1}'.format(a, b))
sys.stdout = devnull
if verbosity == 0:
stream = devnull
ttr = unittest.TextTestRunner(verbosity=verbosity, stream=stream)
origcwd = os.getcwd()
if testdir is None:
testdir = tempfile.mkdtemp(prefix='ase-test-')
else:
if os.path.isdir(testdir):
shutil.rmtree(testdir) # clean before running tests!
os.mkdir(testdir)
os.chdir(testdir)
if verbosity:
print('test-dir ', testdir, '\n', file=sys.__stdout__)
try:
results = ttr.run(ts)
finally:
os.chdir(origcwd)
sys.stdout = sys.__stdout__
return results
def test(verbosity=1,
calculators=[],
testdir=None,
display=True,
stream=sys.stdout):
test_calculator_names.extend(calculators)
disable_calculators(
[name for name in calc_names if name not in calculators])
ts = unittest.TestSuite()
files = glob(__path__[0] + '/*')
sdirtests = [] # tests from subdirectories: only one level assumed
tests = []
for f in files:
if os.path.isdir(f):
# add test subdirectories (like calculators)
sdirtests.extend(glob(f + '/*.py'))
else:
# add py files in testdir
if f.endswith('.py'):
tests.append(f)
tests.sort()
sdirtests.sort()
tests.extend(sdirtests) # run test subdirectories at the end
lasttest = None # is COCu111.py in the current set
for test in tests:
if test.endswith('__.py'):
continue
if test.endswith('COCu111.py'):
lasttest = test
continue
ts.addTest(
ScriptTestCase(filename=os.path.abspath(test), display=display))
if lasttest:
ts.addTest(
ScriptTestCase(filename=os.path.abspath(lasttest),
display=display))
versions = [('platform', platform.platform()),
('python-' + sys.version.split()[0], sys.executable)]
for name in ['ase', 'numpy', 'scipy']:
try:
module = import_module(name)
except ImportError:
versions.append((name, 'no'))
else:
versions.append((name + '-' + module.__version__,
module.__file__.rsplit('/', 1)[0] + '/'))
for a, b in versions:
print('{0:16}{1}'.format(a, b))
sys.stdout = devnull
ttr = unittest.TextTestRunner(verbosity=verbosity, stream=stream)
origcwd = os.getcwd()
if testdir is None:
testdir = tempfile.mkdtemp(prefix='ase-test-')
else:
if os.path.isdir(testdir):
shutil.rmtree(testdir) # clean before running tests!
os.mkdir(testdir)
os.chdir(testdir)
print('test-dir ', testdir, '\n', file=sys.__stdout__)
try:
results = ttr.run(ts)
finally:
os.chdir(origcwd)
sys.stdout = sys.__stdout__
return results