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inspirehep/refextract | refextract/references/text.py | strip_footer | def strip_footer(ref_lines, section_title):
"""Remove footer title from references lines"""
pattern = ur'\(?\[?\d{0,4}\]?\)?\.?\s*%s\s*$' % re.escape(section_title)
re_footer = re.compile(pattern, re.UNICODE)
return [l for l in ref_lines if not re_footer.match(l)] | python | def strip_footer(ref_lines, section_title):
"""Remove footer title from references lines"""
pattern = ur'\(?\[?\d{0,4}\]?\)?\.?\s*%s\s*$' % re.escape(section_title)
re_footer = re.compile(pattern, re.UNICODE)
return [l for l in ref_lines if not re_footer.match(l)] | [
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inspirehep/refextract | refextract/references/api.py | extract_references_from_url | def extract_references_from_url(url, headers=None, chunk_size=1024, **kwargs):
"""Extract references from the pdf specified in the url.
The first parameter is the URL of the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the URL gives a 404,
UnknownDocumentTyp... | python | def extract_references_from_url(url, headers=None, chunk_size=1024, **kwargs):
"""Extract references from the pdf specified in the url.
The first parameter is the URL of the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the URL gives a 404,
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inspirehep/refextract | refextract/references/api.py | extract_references_from_file | def extract_references_from_file(path,
recid=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a lo... | python | def extract_references_from_file(path,
recid=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a lo... | [
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inspirehep/refextract | refextract/references/api.py | extract_references_from_string | def extract_references_from_string(source,
is_only_references=True,
recid=None,
reference_format="{title} {volume} ({year}) {page}",
linker_callback=None,
... | python | def extract_references_from_string(source,
is_only_references=True,
recid=None,
reference_format="{title} {volume} ({year}) {page}",
linker_callback=None,
... | [
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inspirehep/refextract | refextract/references/api.py | extract_journal_reference | def extract_journal_reference(line, override_kbs_files=None):
"""Extract the journal reference from string.
Extracts the journal reference from string and parses for specific
journal information.
"""
kbs = get_kbs(custom_kbs_files=override_kbs_files)
references, dummy_m, dummy_c, dummy_co = par... | python | def extract_journal_reference(line, override_kbs_files=None):
"""Extract the journal reference from string.
Extracts the journal reference from string and parses for specific
journal information.
"""
kbs = get_kbs(custom_kbs_files=override_kbs_files)
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inspirehep/refextract | refextract/references/record.py | build_references | def build_references(citations, reference_format=False):
"""Build list of reference dictionaries from a references list
"""
# Now, run the method which will take as input:
# 1. A list of lists of dictionaries, where each dictionary is a piece
# of citation information corresponding to a tag in the c... | python | def build_references(citations, reference_format=False):
"""Build list of reference dictionaries from a references list
"""
# Now, run the method which will take as input:
# 1. A list of lists of dictionaries, where each dictionary is a piece
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inspirehep/refextract | refextract/references/record.py | build_reference_fields | def build_reference_fields(citation_elements, line_marker, raw_ref,
reference_format):
"""Create the final representation of the reference information.
@param citation_elements: (list) an ordered list of dictionary elements,
with each element correspondi... | python | def build_reference_fields(citation_elements, line_marker, raw_ref,
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inspirehep/refextract | refextract/references/pdf.py | extract_texkeys_from_pdf | def extract_texkeys_from_pdf(pdf_file):
"""
Extract the texkeys from the given PDF file
This is done by looking up the named destinations in the PDF
@param pdf_file: path to a PDF
@return: list of all texkeys found in the PDF
"""
with open(pdf_file, 'rb') as pdf_stream:
try:
... | python | def extract_texkeys_from_pdf(pdf_file):
"""
Extract the texkeys from the given PDF file
This is done by looking up the named destinations in the PDF
@param pdf_file: path to a PDF
@return: list of all texkeys found in the PDF
"""
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inspirehep/refextract | refextract/references/regexs.py | get_reference_line_numeration_marker_patterns | def get_reference_line_numeration_marker_patterns(prefix=u''):
"""Return a list of compiled regex patterns used to search for the marker
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@param prefix: (string) the possible prefix to a reference line
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"... | python | def get_reference_line_numeration_marker_patterns(prefix=u''):
"""Return a list of compiled regex patterns used to search for the marker
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@param prefix: (string) the possible prefix to a reference line
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inspirehep/refextract | refextract/references/regexs.py | get_post_reference_section_title_patterns | def get_post_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title
of the section after the reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
thead = ur'^\s*([\{\(\<\[]?\s... | python | def get_post_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title
of the section after the reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
thead = ur'^\s*([\{\(\<\[]?\s... | [
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inspirehep/refextract | refextract/references/regexs.py | get_post_reference_section_keyword_patterns | def get_post_reference_section_keyword_patterns():
"""Return a list of compiled regex patterns used to search for various
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@return: (list) of compiled regex patterns.
"""
... | python | def get_post_reference_section_keyword_patterns():
"""Return a list of compiled regex patterns used to search for various
keywords that can often be found after, and therefore suggest the end of,
a reference section in a full-text document.
@return: (list) of compiled regex patterns.
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inspirehep/refextract | refextract/references/regexs.py | regex_match_list | def regex_match_list(line, patterns):
"""Given a list of COMPILED regex patters, perform the "re.match" operation
on the line for every pattern.
Break from searching at the first match, returning the match object.
In the case that no patterns match, the None type will be returned.
@param... | python | def regex_match_list(line, patterns):
"""Given a list of COMPILED regex patters, perform the "re.match" operation
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Break from searching at the first match, returning the match object.
In the case that no patterns match, the None type will be returned.
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inspirehep/refextract | refextract/documents/text.py | get_url_repair_patterns | def get_url_repair_patterns():
"""Initialise and return a list of precompiled regexp patterns that
are used to try to re-assemble URLs that have been broken during
a document's conversion to plain-text.
@return: (list) of compiled re regexp patterns used for finding
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"""Initialise and return a list of precompiled regexp patterns that
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@return: (list) of compiled re regexp patterns used for finding
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inspirehep/refextract | refextract/documents/text.py | join_lines | def join_lines(line1, line2):
"""Join 2 lines of text
>>> join_lines('abc', 'de')
'abcde'
>>> join_lines('a-', 'b')
'ab'
"""
if line1 == u"":
pass
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# hyphenated word at the end of the
# line - don't add in a space and remove hyphen
... | python | def join_lines(line1, line2):
"""Join 2 lines of text
>>> join_lines('abc', 'de')
'abcde'
>>> join_lines('a-', 'b')
'ab'
"""
if line1 == u"":
pass
elif line1[-1] == u'-':
# hyphenated word at the end of the
# line - don't add in a space and remove hyphen
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inspirehep/refextract | refextract/documents/text.py | repair_broken_urls | def repair_broken_urls(line):
"""Attempt to repair broken URLs in a line of text.
E.g.: remove spaces from the middle of a URL; something like that.
@param line: (string) the line in which to check for broken URLs.
@return: (string) the line after any broken URLs have been repaired.
"""
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"""Attempt to repair broken URLs in a line of text.
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inspirehep/refextract | refextract/documents/text.py | strip_headers_footers_pagebreaks | def strip_headers_footers_pagebreaks(docbody,
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inspirehep/refextract | refextract/documents/text.py | check_boundary_lines_similar | def check_boundary_lines_similar(l_1, l_2):
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@param l_2: (list) of strings.
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inspirehep/refextract | refextract/references/kbs.py | make_cache_key | def make_cache_key(custom_kbs_files=None):
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inspirehep/refextract | refextract/references/kbs.py | create_institute_numeration_group_regexp_pattern | def create_institute_numeration_group_regexp_pattern(patterns):
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inspirehep/refextract | refextract/references/kbs.py | _cmp_bystrlen_reverse | def _cmp_bystrlen_reverse(a, b):
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inspirehep/refextract | refextract/references/kbs.py | build_special_journals_kb | def build_special_journals_kb(fpath):
"""Load special journals database from file
Special journals are journals that have a volume which is not unique
among different years. To keep the volume unique we are adding the year
before the volume.
"""
journals = set()
with file_resolving(fpath) a... | python | def build_special_journals_kb(fpath):
"""Load special journals database from file
Special journals are journals that have a volume which is not unique
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before the volume.
"""
journals = set()
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brettcannon/gidgethub | gidgethub/sansio.py | _parse_content_type | def _parse_content_type(content_type: Optional[str]) -> Tuple[Optional[str], str]:
"""Tease out the content-type and character encoding.
A default character encoding of UTF-8 is used, so the content-type
must be used to determine if any decoding is necessary to begin
with.
"""
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brettcannon/gidgethub | gidgethub/sansio.py | _decode_body | def _decode_body(content_type: Optional[str], body: bytes,
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"""Decode an HTTP body based on the specified content type.
If 'strict' is true, then raise ValueError if the content type
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brettcannon/gidgethub | gidgethub/sansio.py | validate_event | def validate_event(payload: bytes, *, signature: str, secret: str) -> None:
"""Validate the signature of a webhook event."""
# https://developer.github.com/webhooks/securing/#validating-payloads-from-github
signature_prefix = "sha1="
if not signature.startswith(signature_prefix):
raise Validatio... | python | def validate_event(payload: bytes, *, signature: str, secret: str) -> None:
"""Validate the signature of a webhook event."""
# https://developer.github.com/webhooks/securing/#validating-payloads-from-github
signature_prefix = "sha1="
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brettcannon/gidgethub | gidgethub/sansio.py | accept_format | def accept_format(*, version: str = "v3", media: Optional[str] = None,
json: bool = True) -> str:
"""Construct the specification of the format that a request should return.
The version argument defaults to v3 of the GitHub API and is applicable to
all requests. The media argument along wi... | python | def accept_format(*, version: str = "v3", media: Optional[str] = None,
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brettcannon/gidgethub | gidgethub/sansio.py | create_headers | def create_headers(requester: str, *, accept: str = accept_format(),
oauth_token: Optional[str] = None,
jwt: Optional[str] = None) -> Dict[str, str]:
"""Create a dict representing GitHub-specific header fields.
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oauth_token: Optional[str] = None,
jwt: Optional[str] = None) -> Dict[str, str]:
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brettcannon/gidgethub | gidgethub/sansio.py | decipher_response | def decipher_response(status_code: int, headers: Mapping[str, str],
body: bytes) -> Tuple[Any, Optional[RateLimit], Optional[str]]:
"""Decipher an HTTP response for a GitHub API request.
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brettcannon/gidgethub | gidgethub/sansio.py | format_url | def format_url(url: str, url_vars: Mapping[str, Any]) -> str:
"""Construct a URL for the GitHub API.
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domain will be added. This is to help when copying the relative URL directly
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brettcannon/gidgethub | gidgethub/sansio.py | Event.from_http | def from_http(cls, headers: Mapping[str, str], body: bytes,
*, secret: Optional[str] = None) -> "Event":
"""Construct an event from HTTP headers and JSON body data.
The mapping providing the headers is expected to support lowercase keys.
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brettcannon/gidgethub | gidgethub/sansio.py | RateLimit.from_http | def from_http(cls, headers: Mapping[str, str]) -> Optional["RateLimit"]:
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brettcannon/gidgethub | gidgethub/routing.py | Router.add | def add(self, func: AsyncCallback, event_type: str, **data_detail: Any) -> None:
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brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI._make_request | async def _make_request(self, method: str, url: str, url_vars: Dict[str, str],
data: Any, accept: str,
jwt: Opt[str] = None,
oauth_token: Opt[str] = None,
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brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI.getitem | async def getitem(self, url: str, url_vars: Dict[str, str] = {},
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jwt: Opt[str] = None,
oauth_token: Opt[str] = None
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brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI.getiter | async def getiter(self, url: str, url_vars: Dict[str, str] = {},
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jwt: Opt[str] = None,
oauth_token: Opt[str] = None
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rkargon/pixelsorter | pixelsorter/images2gif.py | NeuQuant.quantize | def quantize(self, image):
""" Use a kdtree to quickly find the closest palette colors for the pixels """
if get_cKDTree():
return self.quantize_with_scipy(image)
else:
print('Scipy not available, falling back to slower version.')
return self.quantize_without_... | python | def quantize(self, image):
""" Use a kdtree to quickly find the closest palette colors for the pixels """
if get_cKDTree():
return self.quantize_with_scipy(image)
else:
print('Scipy not available, falling back to slower version.')
return self.quantize_without_... | [
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rkargon/pixelsorter | pixelsorter/images2gif.py | NeuQuant.inxsearch | def inxsearch(self, r, g, b):
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"""Search for BGR values 0..255 and return colour index"""
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European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | gen_filename | def gen_filename(endpoint):
"""Generate a filename from endpoint with timestamp.
return: str
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"""
now = datetime.now().strftime('%Y%m%d_%H%M%S%f')[:-4]
base = endpoint.split('://', 1)[1]
if base.startswith('localhost:'):
base = gethost... | python | def gen_filename(endpoint):
"""Generate a filename from endpoint with timestamp.
return: str
hostname_port_YearMonthDay_HourMinSecFrac.h5
"""
now = datetime.now().strftime('%Y%m%d_%H%M%S%f')[:-4]
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European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | dict_to_hdf5 | def dict_to_hdf5(dic, endpoint):
"""Dump a dict to an HDF5 file.
"""
filename = gen_filename(endpoint)
with h5py.File(filename, 'w') as handler:
walk_dict_to_hdf5(dic, handler)
print('dumped to', filename) | python | def dict_to_hdf5(dic, endpoint):
"""Dump a dict to an HDF5 file.
"""
filename = gen_filename(endpoint)
with h5py.File(filename, 'w') as handler:
walk_dict_to_hdf5(dic, handler)
print('dumped to', filename) | [
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European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | hdf5_to_dict | def hdf5_to_dict(filepath, group='/'):
"""load the content of an hdf5 file to a dict.
# TODO: how to split domain_type_dev : parameter : value ?
"""
if not h5py.is_hdf5(filepath):
raise RuntimeError(filepath, 'is not a valid HDF5 file.')
with h5py.File(filepath, 'r') as handler:
di... | python | def hdf5_to_dict(filepath, group='/'):
"""load the content of an hdf5 file to a dict.
# TODO: how to split domain_type_dev : parameter : value ?
"""
if not h5py.is_hdf5(filepath):
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European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | print_one_train | def print_one_train(client, verbosity=0):
"""Retrieve data for one train and print it.
Returns the (data, metadata) dicts from the client.
This is used by the -glimpse and -monitor command line tools.
"""
ts_before = time()
data, meta = client.next()
ts_after = time()
if not data:
... | python | def print_one_train(client, verbosity=0):
"""Retrieve data for one train and print it.
Returns the (data, metadata) dicts from the client.
This is used by the -glimpse and -monitor command line tools.
"""
ts_before = time()
data, meta = client.next()
ts_after = time()
if not data:
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European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | pretty_print | def pretty_print(d, ind='', verbosity=0):
"""Pretty print a data dictionary from the bridge client
"""
assert isinstance(d, dict)
for k, v in sorted(d.items()):
str_base = '{} - [{}] {}'.format(ind, type(v).__name__, k)
if isinstance(v, dict):
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"""Pretty print a data dictionary from the bridge client
"""
assert isinstance(d, dict)
for k, v in sorted(d.items()):
str_base = '{} - [{}] {}'.format(ind, type(v).__name__, k)
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European-XFEL/karabo-bridge-py | karabo_bridge/simulation.py | start_gen | def start_gen(port, ser='msgpack', version='2.2', detector='AGIPD',
raw=False, nsources=1, datagen='random', *,
debug=True):
""""Karabo bridge server simulation.
Simulate a Karabo Bridge server and send random data from a detector,
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Parameters
------... | python | def start_gen(port, ser='msgpack', version='2.2', detector='AGIPD',
raw=False, nsources=1, datagen='random', *,
debug=True):
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Simulate a Karabo Bridge server and send random data from a detector,
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European-XFEL/karabo-bridge-py | karabo_bridge/client.py | Client.next | def next(self):
"""Request next data container.
This function call is blocking.
Returns
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data : dict
The data for this train, keyed by source name.
meta : dict
The metadata for this train, keyed by source name.
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This function call is blocking.
Returns
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data : dict
The data for this train, keyed by source name.
meta : dict
The metadata for this train, keyed by source name.
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materialsvirtuallab/monty | monty/io.py | zopen | def zopen(filename, *args, **kwargs):
"""
This function wraps around the bz2, gzip and standard python's open
function to deal intelligently with bzipped, gzipped or standard text
files.
Args:
filename (str/Path): filename or pathlib.Path.
\*args: Standard args for python open(..). ... | python | def zopen(filename, *args, **kwargs):
"""
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function to deal intelligently with bzipped, gzipped or standard text
files.
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filename (str/Path): filename or pathlib.Path.
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materialsvirtuallab/monty | monty/io.py | reverse_readline | def reverse_readline(m_file, blk_size=4096, max_mem=4000000):
"""
Generator method to read a file line-by-line, but backwards. This allows
one to efficiently get data at the end of a file.
Based on code by Peter Astrand <astrand@cendio.se>, using modifications by
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"""
Generator method to read a file line-by-line, but backwards. This allows
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materialsvirtuallab/monty | monty/io.py | get_open_fds | def get_open_fds():
"""
Return the number of open file descriptors for current process
.. warning: will only work on UNIX-like OS-es.
"""
pid = os.getpid()
procs = subprocess.check_output(["lsof", '-w', '-Ff', "-p", str(pid)])
procs = procs.decode("utf-8")
return len([s for s in procs.... | python | def get_open_fds():
"""
Return the number of open file descriptors for current process
.. warning: will only work on UNIX-like OS-es.
"""
pid = os.getpid()
procs = subprocess.check_output(["lsof", '-w', '-Ff', "-p", str(pid)])
procs = procs.decode("utf-8")
return len([s for s in procs.... | [
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materialsvirtuallab/monty | monty/io.py | FileLock.acquire | def acquire(self):
"""
Acquire the lock, if possible. If the lock is in use, it check again
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exceeds `timeout` number of seconds, in which case it throws
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"""
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"""
Acquire the lock, if possible. If the lock is in use, it check again
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materialsvirtuallab/monty | monty/io.py | FileLock.release | def release(self):
""" Get rid of the lock by deleting the lockfile.
When working in a `with` statement, this gets automatically
called at the end.
"""
if self.is_locked:
os.close(self.fd)
os.unlink(self.lockfile)
self.is_locked = False | python | def release(self):
""" Get rid of the lock by deleting the lockfile.
When working in a `with` statement, this gets automatically
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"""
if self.is_locked:
os.close(self.fd)
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materialsvirtuallab/monty | monty/fnmatch.py | WildCard.filter | def filter(self, names):
"""
Returns a list with the names matching the pattern.
"""
names = list_strings(names)
fnames = []
for f in names:
for pat in self.pats:
if fnmatch.fnmatch(f, pat):
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return... | python | def filter(self, names):
"""
Returns a list with the names matching the pattern.
"""
names = list_strings(names)
fnames = []
for f in names:
for pat in self.pats:
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materialsvirtuallab/monty | monty/fnmatch.py | WildCard.match | def match(self, name):
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materialsvirtuallab/monty | monty/dev.py | deprecated | def deprecated(replacement=None, message=None):
"""
Decorator to mark classes or functions as deprecated,
with a possible replacement.
Args:
replacement (callable): A replacement class or method.
message (str): A warning message to be displayed.
Returns:
Original function, ... | python | def deprecated(replacement=None, message=None):
"""
Decorator to mark classes or functions as deprecated,
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Args:
replacement (callable): A replacement class or method.
message (str): A warning message to be displayed.
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materialsvirtuallab/monty | monty/dev.py | install_excepthook | def install_excepthook(hook_type="color", **kwargs):
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materialsvirtuallab/monty | monty/re.py | regrep | def regrep(filename, patterns, reverse=False, terminate_on_match=False,
postprocess=str):
"""
A powerful regular expression version of grep.
Args:
filename (str): Filename to grep.
patterns (dict): A dict of patterns, e.g.,
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postprocess=str):
"""
A powerful regular expression version of grep.
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filename (str): Filename to grep.
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materialsvirtuallab/monty | monty/design_patterns.py | cached_class | def cached_class(klass):
"""
Decorator to cache class instances by constructor arguments.
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set of constructor arguments, ensuring efficiency.
Note that this should be used for *immutable classes only*. Having
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"""
Decorator to cache class instances by constructor arguments.
This results in a class that behaves like a singleton for each
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materialsvirtuallab/monty | monty/operator.py | operator_from_str | def operator_from_str(op):
"""
Return the operator associated to the given string `op`.
raises:
`KeyError` if invalid string.
>>> assert operator_from_str("==")(1, 1) and operator_from_str("+")(1,1) == 2
"""
d = {"==": operator.eq,
"!=": operator.ne,
">": operator.gt,... | python | def operator_from_str(op):
"""
Return the operator associated to the given string `op`.
raises:
`KeyError` if invalid string.
>>> assert operator_from_str("==")(1, 1) and operator_from_str("+")(1,1) == 2
"""
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materialsvirtuallab/monty | monty/subprocess.py | Command.run | def run(self, timeout=None, **kwargs):
"""
Run a command in a separated thread and wait timeout seconds.
kwargs are keyword arguments passed to Popen.
Return: self
"""
from subprocess import Popen, PIPE
def target(**kw):
try:
# print(... | python | def run(self, timeout=None, **kwargs):
"""
Run a command in a separated thread and wait timeout seconds.
kwargs are keyword arguments passed to Popen.
Return: self
"""
from subprocess import Popen, PIPE
def target(**kw):
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materialsvirtuallab/monty | monty/string.py | marquee | def marquee(text="", width=78, mark='*'):
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Return the input string centered in a 'marquee'.
Args:
text (str): Input string
width (int): Width of final output string.
mark (str): Character used to fill string.
:Examples:
>>> marquee('A test', width=40)
'*************... | python | def marquee(text="", width=78, mark='*'):
"""
Return the input string centered in a 'marquee'.
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text (str): Input string
width (int): Width of final output string.
mark (str): Character used to fill string.
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materialsvirtuallab/monty | monty/string.py | boxed | def boxed(msg, ch="=", pad=5):
"""
Returns a string in a box
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msg: Input string.
ch: Character used to form the box.
pad: Number of characters ch added before and after msg.
>>> print(boxed("hello", ch="*", pad=2))
***********
** hello **
***********
"""
... | python | def boxed(msg, ch="=", pad=5):
"""
Returns a string in a box
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msg: Input string.
ch: Character used to form the box.
pad: Number of characters ch added before and after msg.
>>> print(boxed("hello", ch="*", pad=2))
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** hello **
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materialsvirtuallab/monty | monty/string.py | indent | def indent(lines, amount, ch=' '):
"""Indent the lines in a string by padding each one with proper number of pad characters"""
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materialsvirtuallab/monty | monty/functools.py | prof_main | def prof_main(main):
"""
Decorator for profiling main programs.
Profiling is activated by prepending the command line options
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Example:
$ script.py arg --foo=1
becomes
$ script.py prof arg --foo=1
The decorat... | python | def prof_main(main):
"""
Decorator for profiling main programs.
Profiling is activated by prepending the command line options
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materialsvirtuallab/monty | monty/functools.py | lazy_property.invalidate | def invalidate(cls, inst, name):
"""Invalidate a lazy attribute.
This obviously violates the lazy contract. A subclass of lazy
may however have a contract where invalidation is appropriate.
"""
inst_cls = inst.__class__
if not hasattr(inst, '__dict__'):
rais... | python | def invalidate(cls, inst, name):
"""Invalidate a lazy attribute.
This obviously violates the lazy contract. A subclass of lazy
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"""
inst_cls = inst.__class__
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materialsvirtuallab/monty | monty/collections.py | as_set | def as_set(obj):
"""
Convert obj into a set, returns None if obj is None.
>>> assert as_set(None) is None and as_set(1) == set([1]) and as_set(range(1,3)) == set([1, 2])
"""
if obj is None or isinstance(obj, collections.Set):
return obj
if not isinstance(obj, collections.Iterable):
... | python | def as_set(obj):
"""
Convert obj into a set, returns None if obj is None.
>>> assert as_set(None) is None and as_set(1) == set([1]) and as_set(range(1,3)) == set([1, 2])
"""
if obj is None or isinstance(obj, collections.Set):
return obj
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materialsvirtuallab/monty | monty/logging.py | logged | def logged(level=logging.DEBUG):
"""
Useful logging decorator. If a method is logged, the beginning and end of
the method call will be logged at a pre-specified level.
Args:
level: Level to log method at. Defaults to DEBUG.
"""
def wrap(f):
_logger = logging.getLogger("{}.{}".fo... | python | def logged(level=logging.DEBUG):
"""
Useful logging decorator. If a method is logged, the beginning and end of
the method call will be logged at a pre-specified level.
Args:
level: Level to log method at. Defaults to DEBUG.
"""
def wrap(f):
_logger = logging.getLogger("{}.{}".fo... | [
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materialsvirtuallab/monty | monty/logging.py | enable_logging | def enable_logging(main):
"""
This decorator is used to decorate main functions.
It adds the initialization of the logger and an argument parser that allows
one to select the loglevel.
Useful if we are writing simple main functions that call libraries where
the logging module is used
Args:
... | python | def enable_logging(main):
"""
This decorator is used to decorate main functions.
It adds the initialization of the logger and an argument parser that allows
one to select the loglevel.
Useful if we are writing simple main functions that call libraries where
the logging module is used
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materialsvirtuallab/monty | monty/os/path.py | which | def which(cmd):
"""
Returns full path to a executable.
Args:
cmd (str): Executable command to search for.
Returns:
(str) Full path to command. None if it is not found.
Example::
full_path_to_python = which("python")
"""
def is_exe(fp):
return os.path.isfil... | python | def which(cmd):
"""
Returns full path to a executable.
Args:
cmd (str): Executable command to search for.
Returns:
(str) Full path to command. None if it is not found.
Example::
full_path_to_python = which("python")
"""
def is_exe(fp):
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materialsvirtuallab/monty | monty/inspect.py | all_subclasses | def all_subclasses(cls):
"""
Given a class `cls`, this recursive function returns a list with
all subclasses, subclasses of subclasses, and so on.
"""
subclasses = cls.__subclasses__()
return subclasses + [g for s in subclasses for g in all_subclasses(s)] | python | def all_subclasses(cls):
"""
Given a class `cls`, this recursive function returns a list with
all subclasses, subclasses of subclasses, and so on.
"""
subclasses = cls.__subclasses__()
return subclasses + [g for s in subclasses for g in all_subclasses(s)] | [
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materialsvirtuallab/monty | monty/inspect.py | find_top_pyfile | def find_top_pyfile():
"""
This function inspects the Cpython frame to find the path of the script.
"""
import os
frame = currentframe()
while True:
if frame.f_back is None:
finfo = getframeinfo(frame)
#print(getframeinfo(frame))
return os.path.abspath... | python | def find_top_pyfile():
"""
This function inspects the Cpython frame to find the path of the script.
"""
import os
frame = currentframe()
while True:
if frame.f_back is None:
finfo = getframeinfo(frame)
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materialsvirtuallab/monty | monty/pprint.py | pprint_table | def pprint_table(table, out=sys.stdout, rstrip=False):
"""
Prints out a table of data, padded for alignment
Each row must have the same number of columns.
Args:
table: The table to print. A list of lists.
out: Output stream (file-like object)
rstrip: if True, trailing withespace... | python | def pprint_table(table, out=sys.stdout, rstrip=False):
"""
Prints out a table of data, padded for alignment
Each row must have the same number of columns.
Args:
table: The table to print. A list of lists.
out: Output stream (file-like object)
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materialsvirtuallab/monty | monty/fractions.py | gcd | def gcd(*numbers):
"""
Returns the greatest common divisor for a sequence of numbers.
Args:
\*numbers: Sequence of numbers.
Returns:
(int) Greatest common divisor of numbers.
"""
n = numbers[0]
for i in numbers:
n = pygcd(n, i)
return n | python | def gcd(*numbers):
"""
Returns the greatest common divisor for a sequence of numbers.
Args:
\*numbers: Sequence of numbers.
Returns:
(int) Greatest common divisor of numbers.
"""
n = numbers[0]
for i in numbers:
n = pygcd(n, i)
return n | [
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materialsvirtuallab/monty | monty/fractions.py | lcm | def lcm(*numbers):
"""
Return lowest common multiple of a sequence of numbers.
Args:
\*numbers: Sequence of numbers.
Returns:
(int) Lowest common multiple of numbers.
"""
n = 1
for i in numbers:
n = (i * n) // gcd(i, n)
return n | python | def lcm(*numbers):
"""
Return lowest common multiple of a sequence of numbers.
Args:
\*numbers: Sequence of numbers.
Returns:
(int) Lowest common multiple of numbers.
"""
n = 1
for i in numbers:
n = (i * n) // gcd(i, n)
return n | [
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materialsvirtuallab/monty | monty/fractions.py | gcd_float | def gcd_float(numbers, tol=1e-8):
"""
Returns the greatest common divisor for a sequence of numbers.
Uses a numerical tolerance, so can be used on floats
Args:
numbers: Sequence of numbers.
tol: Numerical tolerance
Returns:
(int) Greatest common divisor of numbers.
"""
... | python | def gcd_float(numbers, tol=1e-8):
"""
Returns the greatest common divisor for a sequence of numbers.
Uses a numerical tolerance, so can be used on floats
Args:
numbers: Sequence of numbers.
tol: Numerical tolerance
Returns:
(int) Greatest common divisor of numbers.
"""
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materialsvirtuallab/monty | monty/itertools.py | chunks | def chunks(items, n):
"""
Yield successive n-sized chunks from a list-like object.
>>> import pprint
>>> pprint.pprint(list(chunks(range(1, 25), 10)))
[(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
(11, 12, 13, 14, 15, 16, 17, 18, 19, 20),
(21, 22, 23, 24)]
"""
it = iter(items)
chunk = tup... | python | def chunks(items, n):
"""
Yield successive n-sized chunks from a list-like object.
>>> import pprint
>>> pprint.pprint(list(chunks(range(1, 25), 10)))
[(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
(11, 12, 13, 14, 15, 16, 17, 18, 19, 20),
(21, 22, 23, 24)]
"""
it = iter(items)
chunk = tup... | [
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materialsvirtuallab/monty | monty/itertools.py | iterator_from_slice | def iterator_from_slice(s):
"""
Constructs an iterator given a slice object s.
.. note::
The function returns an infinite iterator if s.stop is None
"""
import numpy as np
start = s.start if s.start is not None else 0
step = s.step if s.step is not None else 1
if s.stop is Non... | python | def iterator_from_slice(s):
"""
Constructs an iterator given a slice object s.
.. note::
The function returns an infinite iterator if s.stop is None
"""
import numpy as np
start = s.start if s.start is not None else 0
step = s.step if s.step is not None else 1
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materialsvirtuallab/monty | monty/termcolor.py | colored_map | def colored_map(text, cmap):
"""
Return colorized text. cmap is a dict mapping tokens to color options.
.. Example:
colored_key("foo bar", {bar: "green"})
colored_key("foo bar", {bar: {"color": "green", "on_color": "on_red"}})
"""
if not __ISON: return text
for key, v in cmap.i... | python | def colored_map(text, cmap):
"""
Return colorized text. cmap is a dict mapping tokens to color options.
.. Example:
colored_key("foo bar", {bar: "green"})
colored_key("foo bar", {bar: {"color": "green", "on_color": "on_red"}})
"""
if not __ISON: return text
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materialsvirtuallab/monty | monty/termcolor.py | cprint_map | def cprint_map(text, cmap, **kwargs):
"""
Print colorize text.
cmap is a dict mapping keys to color options.
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Example:
cprint_map("Hello world", {"Hello": "red"})
"""
try:
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... | python | def cprint_map(text, cmap, **kwargs):
"""
Print colorize text.
cmap is a dict mapping keys to color options.
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Example:
cprint_map("Hello world", {"Hello": "red"})
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try:
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except TypeError:
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materialsvirtuallab/monty | monty/json.py | MSONable.as_dict | def as_dict(self):
"""
A JSON serializable dict representation of an object.
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__}
try:
parent_module = self.__class__.__module__.split('.')[0]
module_version = impor... | python | def as_dict(self):
"""
A JSON serializable dict representation of an object.
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__}
try:
parent_module = self.__class__.__module__.split('.')[0]
module_version = impor... | [
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materialsvirtuallab/monty | monty/json.py | MontyDecoder.process_decoded | def process_decoded(self, d):
"""
Recursive method to support decoding dicts and lists containing
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"""
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modname = d["@module"]
classname = d["@class"]
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"""
if isinstance(d, dict):
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modname = d["@module"]
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materialsvirtuallab/monty | monty/math.py | nCr | def nCr(n, r):
"""
Calculates nCr.
Args:
n (int): total number of items.
r (int): items to choose
Returns:
nCr.
"""
f = math.factorial
return int(f(n) / f(r) / f(n-r)) | python | def nCr(n, r):
"""
Calculates nCr.
Args:
n (int): total number of items.
r (int): items to choose
Returns:
nCr.
"""
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materialsvirtuallab/monty | monty/math.py | nPr | def nPr(n, r):
"""
Calculates nPr.
Args:
n (int): total number of items.
r (int): items to permute
Returns:
nPr.
"""
f = math.factorial
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"""
Calculates nPr.
Args:
n (int): total number of items.
r (int): items to permute
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nPr.
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materialsvirtuallab/monty | monty/shutil.py | copy_r | def copy_r(src, dst):
"""
Implements a recursive copy function similar to Unix's "cp -r" command.
Surprisingly, python does not have a real equivalent. shutil.copytree
only works if the destination directory is not present.
Args:
src (str): Source folder to copy.
dst (str): Destinat... | python | def copy_r(src, dst):
"""
Implements a recursive copy function similar to Unix's "cp -r" command.
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src (str): Source folder to copy.
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materialsvirtuallab/monty | monty/shutil.py | gzip_dir | def gzip_dir(path, compresslevel=6):
"""
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Args:
... | python | def gzip_dir(path, compresslevel=6):
"""
Gzips all files in a directory. Note that this is different from
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is to create gzipped files that can still be read using common Unix-style
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materialsvirtuallab/monty | monty/shutil.py | compress_file | def compress_file(filepath, compression="gz"):
"""
Compresses a file with the correct extension. Functions like standard
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uncompressed files are not retained.
Args:
filepath (str): Path to file.
compression (str): A comp... | python | def compress_file(filepath, compression="gz"):
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Compresses a file with the correct extension. Functions like standard
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materialsvirtuallab/monty | monty/shutil.py | compress_dir | def compress_dir(path, compression="gz"):
"""
Recursively compresses all files in a directory. Note that this
compresses all files singly, i.e., it does not create a tar archive. For
that, just use Python tarfile class.
Args:
path (str): Path to parent directory.
compression (str): ... | python | def compress_dir(path, compression="gz"):
"""
Recursively compresses all files in a directory. Note that this
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materialsvirtuallab/monty | monty/shutil.py | decompress_file | def decompress_file(filepath):
"""
Decompresses a file with the correct extension. Automatically detects
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Args:
filepath (str): Path to file.
compression (str): A compression mode. Valid options are "gz" or
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"""
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"""
Decompresses a file with the correct extension. Automatically detects
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filepath (str): Path to file.
compression (str): A compression mode. Valid options are "gz" or
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materialsvirtuallab/monty | monty/shutil.py | decompress_dir | def decompress_dir(path):
"""
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path (str): Path to parent directory.
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"""
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path (str): Path to parent directory.
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materialsvirtuallab/monty | monty/shutil.py | remove | def remove(path, follow_symlink=False):
"""
Implements an remove function that will delete files, folder trees and symlink trees
1.) Remove a file
2.) Remove a symlink and follow into with a recursive rm if follow_symlink
3.) Remove directory with rmtree
Args:
path (str): path to remov... | python | def remove(path, follow_symlink=False):
"""
Implements an remove function that will delete files, folder trees and symlink trees
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fair-research/bdbag | bdbag/bdbag_utils.py | compute_hashes | def compute_hashes(obj, hashes=frozenset(['md5'])):
"""
Digests input data read from file-like object fd or passed directly as bytes-like object.
Compute hashes for multiple algorithms. Default is MD5.
Returns a tuple of a hex-encoded digest string and a base64-encoded value suitable for an HTT... | python | def compute_hashes(obj, hashes=frozenset(['md5'])):
"""
Digests input data read from file-like object fd or passed directly as bytes-like object.
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fair-research/bdbag | bdbag/bdbag_utils.py | compute_file_hashes | def compute_file_hashes(file_path, hashes=frozenset(['md5'])):
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Digests data read from file denoted by file_path.
"""
if not os.path.exists(file_path):
logging.warning("%s does not exist" % file_path)
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logging.debug("Computing [%s] hashes for file [%s]" % ('... | python | def compute_file_hashes(file_path, hashes=frozenset(['md5'])):
"""
Digests data read from file denoted by file_path.
"""
if not os.path.exists(file_path):
logging.warning("%s does not exist" % file_path)
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fair-research/bdbag | bdbag/bdbagit.py | BDBag.validate | def validate(self, processes=1, fast=False, completeness_only=False, callback=None):
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be used to check that the payload files are present and accounted for,
instead of... | python | def validate(self, processes=1, fast=False, completeness_only=False, callback=None):
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If you supply the parameter fast=True the Payload-Oxum (if present) will
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instead of re-calculating fixities and comparing them against the
manifest. By default validate() ... | [
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] | 795229d1fb77721d0a2d024b34645319d15502cf | https://github.com/fair-research/bdbag/blob/795229d1fb77721d0a2d024b34645319d15502cf/bdbag/bdbagit.py#L473-L489 | train |
fair-research/bdbag | bdbag/bdbagit.py | BDBag._validate_fetch | def _validate_fetch(self):
"""Validate the fetch.txt file
Raises `BagError` for errors and otherwise returns no value
"""
for url, file_size, filename in self.fetch_entries():
# fetch_entries will raise a BagError for unsafe filenames
# so at this point we will c... | python | def _validate_fetch(self):
"""Validate the fetch.txt file
Raises `BagError` for errors and otherwise returns no value
"""
for url, file_size, filename in self.fetch_entries():
# fetch_entries will raise a BagError for unsafe filenames
# so at this point we will c... | [
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fair-research/bdbag | bdbag/bdbagit.py | BDBag._validate_completeness | def _validate_completeness(self):
"""
Verify that the actual file manifests match the files in the data directory
"""
errors = list()
# First we'll make sure there's no mismatch between the filesystem
# and the list of files in the manifest(s)
only_in_manifests, ... | python | def _validate_completeness(self):
"""
Verify that the actual file manifests match the files in the data directory
"""
errors = list()
# First we'll make sure there's no mismatch between the filesystem
# and the list of files in the manifest(s)
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alertot/detectem | detectem/cli.py | get_detection_results | def get_detection_results(url, timeout, metadata=False, save_har=False):
""" Return results from detector.
This function prepares the environment loading the plugins,
getting the response and passing it to the detector.
In case of errors, it raises exceptions to be handled externally.
"""
plu... | python | def get_detection_results(url, timeout, metadata=False, save_har=False):
""" Return results from detector.
This function prepares the environment loading the plugins,
getting the response and passing it to the detector.
In case of errors, it raises exceptions to be handled externally.
"""
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This function prepares the environment loading the plugins,
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alertot/detectem | detectem/cli.py | get_plugins | def get_plugins(metadata):
""" Return the registered plugins.
Load and return all registered plugins.
"""
plugins = load_plugins()
if not plugins:
raise NoPluginsError('No plugins found')
results = []
for p in sorted(plugins.get_all(), key=attrgetter('name')):
if metadata:
... | python | def get_plugins(metadata):
""" Return the registered plugins.
Load and return all registered plugins.
"""
plugins = load_plugins()
if not plugins:
raise NoPluginsError('No plugins found')
results = []
for p in sorted(plugins.get_all(), key=attrgetter('name')):
if metadata:
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