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Ruff format code (#199)
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* Apply Ruff to cp2k parser

* Update metainfo

* Ruff autoformat all parser

---------

Co-authored-by: [email protected] <[email protected]>
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@ndaelman-hu
ndaelman-hu and [email protected] authored Feb 19, 2024
1 parent 402b0e1 commit f74c5d5
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Showing 129 changed files with 73,226 additions and 49,274 deletions.
548 changes: 318 additions & 230 deletions electronicparsers/abacus/metainfo/abacus.py
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2,018 changes: 1,140 additions & 878 deletions electronicparsers/abacus/parser.py
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557 changes: 328 additions & 229 deletions electronicparsers/abinit/metainfo/abinit.py
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5,439 changes: 3,092 additions & 2,347 deletions electronicparsers/abinit/metainfo/abinit_autogenerated.py
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1,318 changes: 842 additions & 476 deletions electronicparsers/abinit/parser.py
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523 changes: 313 additions & 210 deletions electronicparsers/ams/metainfo/ams.py
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2,204 changes: 1,319 additions & 885 deletions electronicparsers/ams/parser.py
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155 changes: 101 additions & 54 deletions electronicparsers/ams/rkf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,13 @@

logger = get_logger(__name__)

__all__ = ['KFFile', 'KFReader', 'KFHistory']
__all__ = ["KFFile", "KFReader", "KFHistory"]


def rkf_to_dict(rkffile):
'''
"""
return a python dictionary of an rkf file
'''
"""
data = KFFile(rkffile)
json_data = {}
all_sections = data.sections()
Expand Down Expand Up @@ -47,17 +47,17 @@ class KFReader:
"""

_sizes = {'s': 1, 'i': 4, 'd': 8, 'q': 8}
_sizes = {"s": 1, "i": 4, "d": 8, "q": 8}

def __init__(self, path, blocksize=4096, autodetect=True):
if os.path.isfile(path):
self.path = os.path.abspath(path)
else:
logger.warning('File {} not present'.format(path))
logger.warning("File {} not present".format(path))

self._blocksize = blocksize
self.endian = '<' # endian: '<' = little, '>' = big
self.word = 'i' # length of int: 'i' = 4 bits, 'q' = 8 bits
self.endian = "<" # endian: '<' = little, '>' = big
self.word = "i" # length of int: 'i' = 4 bits, 'q' = 8 bits
self._sections = None
if autodetect:
self._autodetect()
Expand All @@ -76,18 +76,22 @@ def read(self, section, variable):
try:
tmp = self._sections[section]
except KeyError:
raise KeyError('Section {} not present in {}'.format(section, self.path))
raise KeyError("Section {} not present in {}".format(section, self.path))
try:
vtype, vlb, vstart, vlen = tmp[variable]
except KeyError:
raise KeyError('Variable {} not present in section {} of {}'.format(variable, section, self.path))
raise KeyError(
"Variable {} not present in section {} of {}".format(
variable, section, self.path
)
)

ret = []
first = True
with open(self.path, 'rb') as f:
with open(self.path, "rb") as f:
for i in KFReader._datablocks(self._data[section], vlb):
if first:
ret = self._get_data(self._read_block(f, i), vtype)[vstart - 1:]
ret = self._get_data(self._read_block(f, i), vtype)[vstart - 1 :]
first = False
else:
ret += self._get_data(self._read_block(f, i), vtype)
Expand Down Expand Up @@ -116,24 +120,24 @@ def _autodetect(self):
Try to automatically detect the format (int size and endian) of
this KF file.
"""
with open(self.path, 'rb') as f:
with open(self.path, "rb") as f:
b = f.read(128)

blocksize = struct.unpack(b'i', b[28:32])[0]
blocksize = struct.unpack(b"i", b[28:32])[0]
self._blocksize = 4096 if blocksize == 538976288 else blocksize

one = b[80:84]

if struct.unpack(b'32s', b[48:80])[0] == b'SUPERINDEX ':
self.word = 'i'
elif struct.unpack(b'32s', b[64:96])[0] == b'SUPERINDEX ':
self.word = 'q'
if struct.unpack(b"32s", b[48:80])[0] == b"SUPERINDEX ":
self.word = "i"
elif struct.unpack(b"32s", b[64:96])[0] == b"SUPERINDEX ":
self.word = "q"
one = b[96:104]
else:
pass
return

for e in ['<', '>']:
for e in ["<", ">"]:
if struct.unpack(str(e + self.word), one)[0] == 1:
self.endian = e
# d = {'q': '8 bytes', 'i': '4 bytes', '<': 'little endian', '>': 'big endian'}
Expand All @@ -143,7 +147,7 @@ def _read_block(self, f, pos):
f.seek((pos - 1) * self._blocksize)
return f.read(self._blocksize)

def _parse(self, block, format): # format = [(32,'s'),(4,'i'),(2,'d')]
def _parse(self, block, format): # format = [(32,'s'),(4,'i'),(2,'d')]
"""
Translate a *block* of binary data into list of values in specified *format*.
*format* should be a list of pairs *(a,t)* where *t* is one of the following
Expand Down Expand Up @@ -174,19 +178,23 @@ def _get_data(self, datablock, vtype):
"""
hlen = 4 * self._sizes[self.word]
i, d, s, b = self._parse(datablock[:hlen], [(4, self.word)])[0]
contents = self._parse(datablock[hlen:], zip((i, d, s, b), (self.word, 'd', 's', self.word)))
contents = self._parse(
datablock[hlen:], zip((i, d, s, b), (self.word, "d", "s", self.word))
)
if contents:
contents = contents[0] # there won't be more than one chunk of data in any data block
contents = contents[
0
] # there won't be more than one chunk of data in any data block
if vtype == 1:
return list(contents[:i])
elif vtype == 2:
return list(contents[i:i + d])
return list(contents[i : i + d])
elif vtype == 3:
return contents[i + d]
elif vtype == 4:
return list(map(bool, contents[i + d + 1:]))
return list(map(bool, contents[i + d + 1 :]))
else:
raise KeyError('Unknown vtype')
raise KeyError("Unknown vtype")
else:
return []

Expand All @@ -210,43 +218,53 @@ def _create_index(self):
this information with mapping stored in ``_data`` allows to extract each single variable.
"""

hlen = 32 + 7 * self._sizes[self.word] # length of index block header
hlen = 32 + 7 * self._sizes[self.word] # length of index block header

with open(self.path, 'rb') as f:
superlist = self._parse(self._read_block(f, 1), [(32, 's'), (4, self.word)])
with open(self.path, "rb") as f:
superlist = self._parse(self._read_block(f, 1), [(32, "s"), (4, self.word)])
nextsuper = superlist[0][4]
while nextsuper != 1:
nsl = self._parse(self._read_block(f, nextsuper), [(32, 's'), (4, self.word)])
nsl = self._parse(
self._read_block(f, nextsuper), [(32, "s"), (4, self.word)]
)
nextsuper = nsl[0][4]
superlist += nsl

self._data = {} # list of triples to convert logical to physical block numbers
self._data = {} # list of triples to convert logical to physical block numbers
self._sections = {}
for key, pb, lb, le, ty in superlist: # pb=physical block, lb=logical block, le=length, ty=type (3 for index, 4 for data)
for (
key,
pb,
lb,
le,
ty,
) in superlist: # pb=physical block, lb=logical block, le=length, ty=type (3 for index, 4 for data)
try:
key = key.decode()
except UnicodeDecodeError:
key = key.decode("Latin-1")
key = key.rstrip(' ')
if key in ['SUPERINDEX', 'EMPTY']:
key = key.rstrip(" ")
if key in ["SUPERINDEX", "EMPTY"]:
continue
if ty == 4: # data block
if ty == 4: # data block
if key not in self._data:
self._data[key] = []
self._data[key].append((lb, pb, pb + le))
elif ty == 3: # index block
elif ty == 3: # index block
if key not in self._sections:
self._sections[key] = {}
for i in range(le):
indexblock = self._read_block(f, pb + i)
body = self._parse(indexblock[hlen:], [(32, 's'), (6, self.word)])
body = self._parse(
indexblock[hlen:], [(32, "s"), (6, self.word)]
)
for var, vlb, vstart, _, _, vused, vtype in body:
try:
var = var.decode()
except UnicodeDecodeError:
var = var.decode("Latin-1")
var = var.rstrip(' ')
if var == 'EMPTY':
var = var.rstrip(" ")
if var == "EMPTY":
continue
self._sections[key][var] = (vtype, vlb, vstart, vused)

Expand Down Expand Up @@ -315,11 +333,12 @@ class KFFile:
mykf.write('Geometry','xyz', somevariable)
"""

_types = {
int: (1, 8, lambda x: '%10i' % x),
float: (2, 3, lambda x: '%26.16e' % x),
int: (1, 8, lambda x: "%10i" % x),
float: (2, 3, lambda x: "%26.16e" % x),
str: (3, 80, lambda x: x),
bool: (4, 80, lambda x: 'T' if x else 'F')
bool: (4, 80, lambda x: "T" if x else "F"),
}

def __init__(self, path, autosave=True):
Expand Down Expand Up @@ -349,14 +368,18 @@ def write(self, section, variable, value):
"""Write a *variable* with a *value* in a *section* . If such a variable already
exists in this section, the old value is overwritten."""
if not isinstance(value, (int, bool, float, str, list)):
raise ValueError('Trying to store improper value in KFFile')
raise ValueError("Trying to store improper value in KFFile")
if isinstance(value, list):
if len(value) == 0:
raise ValueError('Cannot store empty lists in KFFile')
raise ValueError("Cannot store empty lists in KFFile")
if any(not isinstance(i, type(value[0])) for i in value):
raise ValueError('Lists stored in KFFile must have all elements of the same type')
raise ValueError(
"Lists stored in KFFile must have all elements of the same type"
)
if not isinstance(value[0], (int, bool, float, str)):
raise ValueError('Only lists of int, float, str or bool can be stored in KFFile')
raise ValueError(
"Only lists of int, float, str or bool can be stored in KFFile"
)

if section not in self.tmpdata:
self.tmpdata[section] = OrderedDict()
Expand Down Expand Up @@ -392,7 +415,11 @@ def read_section(self, section):
ret[var] = self.read(sec, var)
if len(ret) == 0:
logger.warning(
"WARNING: Section '{}' not present in {} or present, but empty. Returning empty dictionary".format(section, self.path), 1)
"WARNING: Section '{}' not present in {} or present, but empty. Returning empty dictionary".format(
section, self.path
),
1,
)
return ret

def get_skeleton(self):
Expand Down Expand Up @@ -439,13 +466,20 @@ def __contains__(self, arg):
with a section name or a pair of strings (section, variable)."""
if isinstance(arg, str):
return arg in self.sections()
if isinstance(arg, tuple) and len(arg) == 2 and isinstance(arg[0], str) and isinstance(arg[1], str):
if (
isinstance(arg, tuple)
and len(arg) == 2
and isinstance(arg[0], str)
and isinstance(arg[1], str)
):
try:
self.read(*arg)
return True
except KeyError:
return False
raise TypeError("'in <KFFile>' requires string of a pair of strings as left operand")
raise TypeError(
"'in <KFFile>' requires string of a pair of strings as left operand"
)

@staticmethod
def _split(name):
Expand All @@ -454,10 +488,10 @@ def _split(name):
if isinstance(name, tuple) and len(name) == 2:
return name[0], name[1]
if isinstance(name, str):
s = name.split('%')
s = name.split("%")
if len(s) == 2:
return s[0], s[1]
raise ValueError('Improper key used in KFFile dictionary-like notation')
raise ValueError("Improper key used in KFFile dictionary-like notation")

@staticmethod
def _str(val):
Expand All @@ -467,16 +501,17 @@ def _str(val):
valtype = type(val[0])
t, step, f = KFFile._types[valtype]
nl = len(val)
if (valtype == str and isinstance(val, list)):
if valtype == str and isinstance(val, list):
# udmpkf reads 160 characters per variable, split over max. 80 per line, to make a string array
nl = nl * 160
step = 1
splitstrings = [[s[0:80], s[80:160]] for s in val]
val = [item for sublist in splitstrings for item in sublist]

ret = '%10i%10i%10i' % (nl, nl, t)
ret = "%10i%10i%10i" % (nl, nl, t)
for i, el in enumerate(val):
if i % step == 0: ret += '\n'
if i % step == 0:
ret += "\n"
ret += f(el)
return ret

Expand Down Expand Up @@ -525,9 +560,21 @@ def read_all(self, name):
if name not in self.shapes:
self._init_shape(name)
if name in self.blocked:
return numpy.concatenate([numpy.atleast_1d(self.kf.read(self.section, "{}({})".format(name, i))) for i in range(1, self.nblocks + 1)])
return numpy.concatenate(
[
numpy.atleast_1d(
self.kf.read(self.section, "{}({})".format(name, i))
)
for i in range(1, self.nblocks + 1)
]
)
else:
return numpy.asarray([self.kf.read(self.section, "{}({})".format(name, i)) for i in range(1, self.nsteps + 1)])
return numpy.asarray(
[
self.kf.read(self.section, "{}({})".format(name, i))
for i in range(1, self.nsteps + 1)
]
)

def iter(self, name):
"""Iterate over the values of history item *name*."""
Expand Down
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