def get_pseudos(options):
"""
Find pseudos in paths, return :class:`DojoTable` object sorted by atomic number Z.
Accepts filepaths or directory.
"""
exts = ("psp8",)
paths = options.pseudos
if len(paths) == 1 and os.path.isdir(paths[0]):
top = os.path.abspath(paths[0])
# print("top", top)
paths = find_exts(top, exts, exclude_dirs="_*")
# table = DojoTable.from_dir(paths[0])
pseudos = []
for p in paths:
try:
pseudos.append(Pseudo.from_file(p))
except Exception as exc:
warn("Error in %s:\n%s. This pseudo will be ignored" % (p, exc))
table = DojoTable(pseudos)
# Here we select a subset of pseudos according to family or rows
if options.rows:
table = table.select_rows(options.rows)
elif options.family:
table = table.select_families(options.family)
if options.symbols:
table = table.select_symbols(options.symbols)
return table.sort_by_z()
def get_pseudos(options):
"""
Find pseudos in paths, return :class:`DojoTable` object sorted by atomic number Z.
Accepts filepaths or directory.
"""
exts = ("psp8", "xml")
paths = options.pseudos
if len(paths) == 1:
# Handle directory argument
if os.path.isdir(paths[0]):
top = os.path.abspath(paths[0])
paths = find_exts(top, exts, exclude_dirs="_*")
# Handle glob syntax e.g. "./*.psp8"
elif "*" in paths[0]:
paths = glob.glob(paths[0])
if options.verbose > 1: print("Will read pseudo from: %s" % paths)
pseudos = []
for p in paths:
try:
pseudo = dojopseudo_from_file(p)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % p, "red")
continue
pseudos.append(pseudo)
except Exception as exc:
cprint("[%s] Python exception. This pseudo will be ignored" % p, "red")
if options.verbose: print(exc)
table = DojoTable(pseudos)
# Here we select a subset of pseudos according to family or rows
if options.rows:
table = table.select_rows(options.rows)
elif options.family:
table = table.select_families(options.family)
# here we select chemical symbols.
if options.symbols:
table = table.select_symbols(options.symbols)
return table.sort_by_z()
def get_pseudos(options):
"""
Find pseudos in paths, return :class:`DojoTable` object sorted by atomic number Z.
Accepts filepaths or directory.
"""
exts = ("psp8", "xml")
paths = options.pseudos
if len(paths) == 1:
# Handle directory argument
if os.path.isdir(paths[0]):
top = os.path.abspath(paths[0])
paths = find_exts(top, exts, exclude_dirs="_*")
# Handle glob syntax e.g. "./*.psp8"
elif "*" in paths[0]:
paths = glob.glob(paths[0])
if options.verbose > 1: print("Will read pseudo from: %s" % paths)
pseudos = []
for p in paths:
try:
pseudo = dojopseudo_from_file(p)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % p, "red")
continue
pseudos.append(pseudo)
except Exception as exc:
cprint("[%s] Python exception. This pseudo will be ignored" % p, "red")
if options.verbose: print(exc)
table = DojoTable(pseudos)
# Here we select a subset of pseudos according to family or rows
if options.rows:
table = table.select_rows(options.rows)
elif options.family:
table = table.select_families(options.family)
# here we select chemical symbols.
if options.symbols:
table = table.select_symbols(options.symbols)
return table.sort_by_z()
