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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | DBBenchmarkRun.get_experimental_ddg_values | def get_experimental_ddg_values(self, record, dataframe_record):
'''Adds the mean experimental value associated with each analysis set to the dataframe row.'''
new_idxs = []
for analysis_set in self.get_analysis_sets(record):
ddg_details = record['DDG'][analysis_set]
exp_... | python | def get_experimental_ddg_values(self, record, dataframe_record):
'''Adds the mean experimental value associated with each analysis set to the dataframe row.'''
new_idxs = []
for analysis_set in self.get_analysis_sets(record):
ddg_details = record['DDG'][analysis_set]
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | DBBenchmarkRun.compute_stability_classification | def compute_stability_classification(self, predicted_data, record, dataframe_record):
'''Calculate the stability classification for the analysis cases. Must be called after get_experimental_ddg_values.'''
new_idxs = []
stability_classication_x_cutoff, stability_classication_y_cutoff = self.stab... | python | def compute_stability_classification(self, predicted_data, record, dataframe_record):
'''Calculate the stability classification for the analysis cases. Must be called after get_experimental_ddg_values.'''
new_idxs = []
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Kortemme-Lab/klab | klab/benchmarking/analysis/ddg_monomeric_stability_analysis.py | DBBenchmarkRun.compute_absolute_error | def compute_absolute_error(self, predicted_data, record, dataframe_record):
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new_idxs = []
for analysis_set in self.get_analysis_sets(record):
ddg_details = record['DDG'][anal... | python | def compute_absolute_error(self, predicted_data, record, dataframe_record):
'''Calculate the absolute error for the analysis cases. Must be called after get_experimental_ddg_values.'''
new_idxs = []
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brunato/lograptor | lograptor/application.py | AppRule.add_result | def add_result(self, values):
"""
Add a tuple or increment the value of an existing one
in the rule results dictionary.
"""
idx = [values['host']]
for gid in self.key_gids[1:]:
idx.append(values[gid])
idx = tuple(idx)
try:
... | python | def add_result(self, values):
"""
Add a tuple or increment the value of an existing one
in the rule results dictionary.
"""
idx = [values['host']]
for gid in self.key_gids[1:]:
idx.append(values[gid])
idx = tuple(idx)
try:
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brunato/lograptor | lograptor/application.py | AppRule.increase_last | def increase_last(self, k):
"""
Increase the last result by k.
"""
idx = self._last_idx
if idx is not None:
self.results[idx] += k | python | def increase_last(self, k):
"""
Increase the last result by k.
"""
idx = self._last_idx
if idx is not None:
self.results[idx] += k | [
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brunato/lograptor | lograptor/application.py | AppLogParser.parse_rules | def parse_rules(self):
"""
Add a set of rules to the app, dividing between filter and other rule set
"""
# Load patterns: an app is removed when has no defined patterns.
try:
rule_options = self.config.items('rules')
except configparser.NoSectionError:
... | python | def parse_rules(self):
"""
Add a set of rules to the app, dividing between filter and other rule set
"""
# Load patterns: an app is removed when has no defined patterns.
try:
rule_options = self.config.items('rules')
except configparser.NoSectionError:
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brunato/lograptor | lograptor/application.py | AppLogParser.increase_last | def increase_last(self, k):
"""
Increase the counter of the last matched rule by k.
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rule = self._last_rule
if rule is not None:
rule.increase_last(k) | python | def increase_last(self, k):
"""
Increase the counter of the last matched rule by k.
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_sections_by_delegate_and_term | def get_sections_by_delegate_and_term(person,
term,
future_terms=0,
include_secondaries=True,
transcriptable_course='yes',
delete_... | python | def get_sections_by_delegate_and_term(person,
term,
future_terms=0,
include_secondaries=True,
transcriptable_course='yes',
delete_... | [
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_sections_by_curriculum_and_term | def get_sections_by_curriculum_and_term(curriculum, term):
"""
Returns a list of uw_sws.models.SectionReference objects
for the passed curriculum and term.
"""
url = "{}?{}".format(
section_res_url_prefix,
urlencode([("curriculum_abbreviation", curriculum.label,),
... | python | def get_sections_by_curriculum_and_term(curriculum, term):
"""
Returns a list of uw_sws.models.SectionReference objects
for the passed curriculum and term.
"""
url = "{}?{}".format(
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urlencode([("curriculum_abbreviation", curriculum.label,),
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_sections_by_building_and_term | def get_sections_by_building_and_term(building, term):
"""
Returns a list of uw_sws.models.SectionReference objects
for the passed building and term.
"""
url = "{}?{}".format(
section_res_url_prefix,
urlencode([("quarter", term.quarter.lower(),),
("facility_code", ... | python | def get_sections_by_building_and_term(building, term):
"""
Returns a list of uw_sws.models.SectionReference objects
for the passed building and term.
"""
url = "{}?{}".format(
section_res_url_prefix,
urlencode([("quarter", term.quarter.lower(),),
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | _json_to_sectionref | def _json_to_sectionref(data):
"""
Returns a list of SectionReference object created from
the passed json data.
"""
section_term = None
sections = []
for section_data in data.get("Sections", []):
if (section_term is None or
section_data["Year"] != section_term.year or... | python | def _json_to_sectionref(data):
"""
Returns a list of SectionReference object created from
the passed json data.
"""
section_term = None
sections = []
for section_data in data.get("Sections", []):
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_section_by_url | def get_section_by_url(url,
include_instructor_not_on_time_schedule=True):
"""
Returns a uw_sws.models.Section object
for the passed section url.
"""
if not course_url_pattern.match(url):
raise InvalidSectionURL(url)
return _json_to_section(
get_resource(u... | python | def get_section_by_url(url,
include_instructor_not_on_time_schedule=True):
"""
Returns a uw_sws.models.Section object
for the passed section url.
"""
if not course_url_pattern.match(url):
raise InvalidSectionURL(url)
return _json_to_section(
get_resource(u... | [
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_section_by_label | def get_section_by_label(label,
include_instructor_not_on_time_schedule=True):
"""
Returns a uw_sws.models.Section object for
the passed section label.
"""
validate_section_label(label)
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encod... | python | def get_section_by_label(label,
include_instructor_not_on_time_schedule=True):
"""
Returns a uw_sws.models.Section object for
the passed section label.
"""
validate_section_label(label)
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_linked_sections | def get_linked_sections(section,
include_instructor_not_on_time_schedule=True):
"""
Returns a list of uw_sws.models.Section objects,
representing linked sections for the passed section.
"""
linked_sections = []
for url in section.linked_section_urls:
section = ge... | python | def get_linked_sections(section,
include_instructor_not_on_time_schedule=True):
"""
Returns a list of uw_sws.models.Section objects,
representing linked sections for the passed section.
"""
linked_sections = []
for url in section.linked_section_urls:
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uw-it-aca/uw-restclients-sws | uw_sws/section.py | get_joint_sections | def get_joint_sections(section,
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"""
Returns a list of uw_sws.models.Section objects,
representing joint sections for the passed section.
"""
joint_sections = []
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section = get_sec... | python | def get_joint_sections(section,
include_instructor_not_on_time_schedule=True):
"""
Returns a list of uw_sws.models.Section objects,
representing joint sections for the passed section.
"""
joint_sections = []
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Kortemme-Lab/klab | klab/bio/scop.py | SCOPeDatabase.get_chain_details_by_related_pdb_chains | def get_chain_details_by_related_pdb_chains(self, pdb_id, chain_id, pfam_accs):
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TUNE-Archive/freight_forwarder | freight_forwarder/container_ship.py | ContainerShip.recall_service | def recall_service(self, service):
"""
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This method should be extended later to be more useful.
"""
if not isinstance(service, Service):
raise TypeError("service mus... | python | def recall_service(self, service):
"""
This method assumes that its a roll back during a deployment. If not used during a deployment session
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"""
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TUNE-Archive/freight_forwarder | freight_forwarder/container_ship.py | ContainerShip.clean_up_dangling_images | def clean_up_dangling_images(self):
"""
Clean up all dangling images.
"""
cargoes = Image.all(client=self._client_session, filters={'dangling': True})
for id, cargo in six.iteritems(cargoes):
logger.info("Removing dangling image: {0}".format(id))
cargo.del... | python | def clean_up_dangling_images(self):
"""
Clean up all dangling images.
"""
cargoes = Image.all(client=self._client_session, filters={'dangling': True})
for id, cargo in six.iteritems(cargoes):
logger.info("Removing dangling image: {0}".format(id))
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TUNE-Archive/freight_forwarder | freight_forwarder/container_ship.py | ContainerShip.offload_all_service_containers | def offload_all_service_containers(self, service):
"""Deletes all containers related to the service.
"""
def anonymous(anonymous_service):
if not isinstance(anonymous_service, Service):
raise TypeError("service must be an instance of Service.")
containers... | python | def offload_all_service_containers(self, service):
"""Deletes all containers related to the service.
"""
def anonymous(anonymous_service):
if not isinstance(anonymous_service, Service):
raise TypeError("service must be an instance of Service.")
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TUNE-Archive/freight_forwarder | freight_forwarder/container_ship.py | ContainerShip._container_registration | def _container_registration(self, alias):
"""
Check for an available name and return that to the caller.
"""
containers = Container.find_by_name(self._client_session, alias)
def validate_name(name):
valid = True
if name in containers:
vali... | python | def _container_registration(self, alias):
"""
Check for an available name and return that to the caller.
"""
containers = Container.find_by_name(self._client_session, alias)
def validate_name(name):
valid = True
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jpulec/django-protractor | protractor/management/commands/protractor.py | Command.teardown_databases | def teardown_databases(self, old_config, options):
"""
Destroys all the non-mirror databases.
"""
if len(old_config) > 1:
old_names, mirrors = old_config
else:
old_names = old_config
for connection, old_name, destroy in old_names:
if de... | python | def teardown_databases(self, old_config, options):
"""
Destroys all the non-mirror databases.
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if len(old_config) > 1:
old_names, mirrors = old_config
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mardix/Mocha | mocha/extras/jinja_helpers.py | oembed | def oembed(url, class_=""):
"""
Create OEmbed link
{{ url | oembed }}
:param url:
:param class_:
:return:
"""
o = "<a href=\"{url}\" class=\"oembed {class_}\" ></a>".format(url=url,
class_=class_)
return Markup(o) | python | def oembed(url, class_=""):
"""
Create OEmbed link
{{ url | oembed }}
:param url:
:param class_:
:return:
"""
o = "<a href=\"{url}\" class=\"oembed {class_}\" ></a>".format(url=url,
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mardix/Mocha | mocha/extras/jinja_helpers.py | img_src | def img_src(url, class_="", responsive=False, lazy_load=False, id_=""):
"""
Create an image src
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:param url:
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"""
Create an image src
{{ xyz.jpg | img_src }}
:param url:
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assamite/creamas | creamas/examples/spiro/spiro.py | give_dots_yield | def give_dots_yield(R, r, r_, resolution=2*PI/1000, spins=50):
'''Generate Spirograph dots without numpy using yield.
'''
def x(theta):
return (R-r) * math.cos(theta) + r_*math.cos((R-r) / r * theta)
def y(theta):
return (R-r) * math.sin(theta) - r_*math.sin((R-r) / r * theta)
thet... | python | def give_dots_yield(R, r, r_, resolution=2*PI/1000, spins=50):
'''Generate Spirograph dots without numpy using yield.
'''
def x(theta):
return (R-r) * math.cos(theta) + r_*math.cos((R-r) / r * theta)
def y(theta):
return (R-r) * math.sin(theta) - r_*math.sin((R-r) / r * theta)
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assamite/creamas | creamas/examples/spiro/spiro.py | give_dots | def give_dots(R, r, r_, resolution=2*PI/1000, spins=50):
'''Generate Spirograph dots with numpy.
'''
thetas = np.arange(0, 2*PI*spins, resolution)
Rr = R - r
x = Rr * np.cos(thetas) + r_*np.cos(Rr / r * thetas)
y = Rr * np.sin(thetas) - r_*np.sin(Rr / r * thetas)
return x, y | python | def give_dots(R, r, r_, resolution=2*PI/1000, spins=50):
'''Generate Spirograph dots with numpy.
'''
thetas = np.arange(0, 2*PI*spins, resolution)
Rr = R - r
x = Rr * np.cos(thetas) + r_*np.cos(Rr / r * thetas)
y = Rr * np.sin(thetas) - r_*np.sin(Rr / r * thetas)
return x, y | [
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assamite/creamas | creamas/examples/spiro/spiro.py | spiro_image | def spiro_image(R, r, r_, resolution=2*PI/1000, spins=50, size=[32, 32]):
'''Create image with given Spirograph parameters using numpy and scipy.
'''
x, y = give_dots(200, r, r_, spins=20)
xy = np.array([x, y]).T
xy = np.array(np.around(xy), dtype=np.int64)
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'''Create image with given Spirograph parameters using numpy and scipy.
'''
x, y = give_dots(200, r, r_, spins=20)
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mardix/Mocha | mocha/extras/md.py | html | def html(text, lazy_images=False):
"""
To render a markdown format text into HTML.
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add the tags: [TOC]
It will include a <ul><li>...</ul> of all <h*>
:param text:
:param lazy_images: bool - If true, it will activate the ... | python | def html(text, lazy_images=False):
"""
To render a markdown format text into HTML.
- If you want to also build a Table of Content inside of the markdow,
add the tags: [TOC]
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mardix/Mocha | mocha/extras/md.py | ExtractImagesTreeprocessor.run | def run(self, root):
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for image in root.getiterator("img"):
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jaraco/jaraco.collections | jaraco/collections.py | dict_map | def dict_map(function, dictionary):
"""
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>>> d = dict_map(lambda x:x+1, dict(a=1, b=2))
>>> d == dict(a=2,b=3)
Tr... | python | def dict_map(function, dictionary):
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>>> d = dict_map(lambda x:x+1, dict(a=1, b=2))
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jaraco/jaraco.collections | jaraco/collections.py | sorted_items | def sorted_items(d, key=__identity, reverse=False):
"""
Return the items of the dictionary sorted by the keys
>>> sample = dict(foo=20, bar=42, baz=10)
>>> tuple(sorted_items(sample))
(('bar', 42), ('baz', 10), ('foo', 20))
>>> reverse_string = lambda s: ''.join(reversed(s))
>>> tuple(sorted_items(sample, key=... | python | def sorted_items(d, key=__identity, reverse=False):
"""
Return the items of the dictionary sorted by the keys
>>> sample = dict(foo=20, bar=42, baz=10)
>>> tuple(sorted_items(sample))
(('bar', 42), ('baz', 10), ('foo', 20))
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jaraco/jaraco.collections | jaraco/collections.py | invert_map | def invert_map(map):
"""
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>>> numbers = dict(a=1, b=2, c=3)
>>> letters = invert_map(numbers)
>>> letters[1]
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>>> numbers['d'] = 3
>>> invert_map(numbers)
Traceba... | python | def invert_map(map):
"""
Given a dictionary, return another dictionary with keys and values
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>>> numbers = dict(a=1, b=2, c=3)
>>> letters = invert_map(numbers)
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jaraco/jaraco.collections | jaraco/collections.py | KeyTransformingDict.matching_key_for | def matching_key_for(self, key):
"""
Given a key, return the actual key stored in self that matches.
Raise KeyError if the key isn't found.
"""
try:
return next(e_key for e_key in self.keys() if e_key == key)
except StopIteration:
raise KeyError(key) | python | def matching_key_for(self, key):
"""
Given a key, return the actual key stored in self that matches.
Raise KeyError if the key isn't found.
"""
try:
return next(e_key for e_key in self.keys() if e_key == key)
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cozy/python_cozy_management | cozy_management/backup.py | backup | def backup(backup_filename=None):
'''
Backup a Cozy
'''
timestamp = time.strftime("%Y-%m-%d-%H-%M-%S", time.gmtime())
if not backup_filename:
if not os.path.isdir(BACKUPS_PATH):
print 'Need to create {}'.format(BACKUPS_PATH)
os.makedirs(BACKUPS_PATH, 0700)
... | python | def backup(backup_filename=None):
'''
Backup a Cozy
'''
timestamp = time.strftime("%Y-%m-%d-%H-%M-%S", time.gmtime())
if not backup_filename:
if not os.path.isdir(BACKUPS_PATH):
print 'Need to create {}'.format(BACKUPS_PATH)
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projectshift/shift-boiler | boiler/cli/db.py | get_config | def get_config():
"""
Prepare and return alembic config
These configurations used to live in alembic config initialiser, but that
just tight coupling. Ideally we should move that to userspace and find a
way to pass these into alembic commands.
@todo: think about it
"""
from boiler.migra... | python | def get_config():
"""
Prepare and return alembic config
These configurations used to live in alembic config initialiser, but that
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projectshift/shift-boiler | boiler/cli/db.py | init | def init():
""" Initialize new migrations directory """
try:
config = get_config()
print(config.dir)
alembic_command.init(config, config.dir, 'project')
except CommandError as e:
click.echo(red(str(e))) | python | def init():
""" Initialize new migrations directory """
try:
config = get_config()
print(config.dir)
alembic_command.init(config, config.dir, 'project')
except CommandError as e:
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projectshift/shift-boiler | boiler/cli/db.py | revision | def revision(revision, path, branch_label, splice, head, sql, autogenerate, message):
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config=get_config(),
rev_id=revision,
version_path=path,
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""" Create new revision file """
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projectshift/shift-boiler | boiler/cli/db.py | merge | def merge(revision, branch_label, message, list_revisions=''):
""" Merge two revision together, create new revision file """
alembic_command.merge(
config=get_config(),
revisions=list_revisions,
message=message,
branch_label=branch_label,
rev_id=revision
) | python | def merge(revision, branch_label, message, list_revisions=''):
""" Merge two revision together, create new revision file """
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revisions=list_revisions,
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projectshift/shift-boiler | boiler/cli/db.py | up | def up(tag, sql, revision):
""" Upgrade to revision """
alembic_command.upgrade(
config=get_config(),
revision=revision,
sql=sql,
tag=tag
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projectshift/shift-boiler | boiler/cli/db.py | down | def down(tag, sql, revision):
""" Downgrade to revision """
alembic_command.downgrade(
config=get_config(),
revision=revision,
sql=sql,
tag=tag
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""" Downgrade to revision """
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projectshift/shift-boiler | boiler/cli/db.py | history | def history(verbose, range):
""" List revision changesets chronologically """
alembic_command.history(
config=get_config(),
rev_range=range,
verbose=verbose
) | python | def history(verbose, range):
""" List revision changesets chronologically """
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projectshift/shift-boiler | boiler/cli/db.py | heads | def heads(resolve, verbose):
""" Show available heads """
alembic_command.heads(
config=get_config(),
verbose=verbose,
resolve_dependencies=resolve
) | python | def heads(resolve, verbose):
""" Show available heads """
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config=get_config(),
verbose=verbose,
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projectshift/shift-boiler | boiler/cli/db.py | stamp | def stamp(revision, sql, tag):
""" Stamp db to given revision without migrating """
alembic_command.stamp(
config=get_config(),
revision=revision,
sql=sql,
tag=tag
) | python | def stamp(revision, sql, tag):
""" Stamp db to given revision without migrating """
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sql=sql,
tag=tag
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Kortemme-Lab/klab | klab/db/sqlalchemy_interface.py | get_or_create_in_transaction | def get_or_create_in_transaction(tsession, model, values, missing_columns = [], variable_columns = [], updatable_columns = [], only_use_supplied_columns = False, read_only = False):
'''
Uses the SQLAlchemy model to retrieve an existing record based on the supplied field values or, if there is no
existing re... | python | def get_or_create_in_transaction(tsession, model, values, missing_columns = [], variable_columns = [], updatable_columns = [], only_use_supplied_columns = False, read_only = False):
'''
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Kortemme-Lab/klab | klab/db/sqlalchemy_interface.py | get_or_create_in_transaction_wrapper | def get_or_create_in_transaction_wrapper(tsession, model, values, missing_columns = [], variable_columns = [], updatable_columns = [], only_use_supplied_columns = False, read_only = False):
'''This function can be used to determine which calling method is spending time in get_or_create_in_transaction when profiling... | python | def get_or_create_in_transaction_wrapper(tsession, model, values, missing_columns = [], variable_columns = [], updatable_columns = [], only_use_supplied_columns = False, read_only = False):
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assamite/creamas | creamas/rules/agent.py | RuleAgent.get_weight | def get_weight(self, rule):
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If rule is not in :attr:`R`, returns ``None``.
"""
if not issubclass(rule.__class__, (Rule, RuleLeaf)):
raise TypeError("Rule to get weight ({}) is not subclass "
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"""Get weight for rule.
If rule is not in :attr:`R`, returns ``None``.
"""
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assamite/creamas | creamas/rules/agent.py | RuleAgent.evaluate | def evaluate(self, artifact):
r"""Evaluate artifact with agent's current rules and weights.
:param artifact:
:class:`~creamas.core.artifact.Artifact` to be evaluated
:type artifact:
:py:class:`~creamas.core.artifact.Artifact`
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r"""Evaluate artifact with agent's current rules and weights.
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TheGhouls/oct | oct/results/report.py | ReportResults._init_dates | def _init_dates(self):
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TheGhouls/oct | oct/results/report.py | ReportResults._init_dataframes | def _init_dataframes(self):
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"""
df = pd.read_sql_query("SELECT elapsed, epoch, scriptrun_time, custom_timers FROM result ORDER BY epoch ASC",
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"""Initialise the main dataframe for the results and the custom timers dataframes
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TheGhouls/oct | oct/results/report.py | ReportResults._get_processed_dataframe | def _get_processed_dataframe(self, dataframe):
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:rtype: dict
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TheGhouls/oct | oct/results/report.py | ReportResults._init_turrets | def _init_turrets(self):
"""Setup data from database
"""
for turret in Turret.select():
self.turrets.append(turret.to_dict()) | python | def _init_turrets(self):
"""Setup data from database
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TheGhouls/oct | oct/results/report.py | ReportResults.compile_results | def compile_results(self):
"""Compile all results for the current test
"""
self._init_dataframes()
self.total_transactions = len(self.main_results['raw'])
self._init_dates() | python | def compile_results(self):
"""Compile all results for the current test
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self._init_dataframes()
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Kortemme-Lab/klab | klab/bio/kabsch.py | centroid | def centroid(X):
"""
Calculate the centroid from a matrix X
"""
C = np.sum(X, axis=0) / len(X)
return C | python | def centroid(X):
"""
Calculate the centroid from a matrix X
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C = np.sum(X, axis=0) / len(X)
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eventbrite/rebar | src/rebar/validators.py | StateValidator.is_valid | def is_valid(self, instance):
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instance can be a dict (ie, form.cleaned_data), a form, or a
model instance. If instance is a form, full_clean() will be
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"""
errors = self.errors(instance)
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eventbrite/rebar | src/rebar/validators.py | StateValidator._validate | def _validate(self, data):
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errors = {}
# if the validator is not enabled, return the empty error dict
if not self._enabled:
return errors
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peergradeio/flask-mongo-profiler | flask_mongo_profiler/contrib/flask_admin/formatters/relational.py | queryset_formatter | def queryset_formatter(queryset):
"""
This is used for custom detail fields returning a QuerySet of
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"""
return Markup(
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"""
This is used for custom detail fields returning a QuerySet of
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peergradeio/flask-mongo-profiler | flask_mongo_profiler/contrib/flask_admin/formatters/relational.py | qs_field | def qs_field(
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Show computed fields based on QuerySet's.
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Kortemme-Lab/klab | klab/bio/pdbtm.py | PDBTM._get_pdb_id | def _get_pdb_id(self, elem, **kwargs):
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id = elem.attrib['ID']
if self.restrict_to_transmembrane_proteins:
tmp = elem.attrib['TMP']
... | python | def _get_pdb_id(self, elem, **kwargs):
'''If self.restrict_to_transmembrane_proteins is False then this adds all ids to self.ids. Otherwise, only transmembrane protein ids are added.'''
id = elem.attrib['ID']
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Kortemme-Lab/klab | klab/bio/pdbtm.py | PDBTM.get_xml | def get_xml(self, pdb_id):
''' Returns the XML for pdb_id if the tag exists.'''
self.tmp_string = None
context = etree.iterparse(io.BytesIO(self.xml_contents), events=('end',), tag=self.PDBTM_entry_tag_type)
try:
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... | python | def get_xml(self, pdb_id):
''' Returns the XML for pdb_id if the tag exists.'''
self.tmp_string = None
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uogbuji/versa | tools/py/driver/mongo.py | connection.multimatch | def multimatch(self, origin=None, rel=None, target=None, attrs=None, include_ids=False):
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uogbuji/versa | tools/py/driver/mongo.py | connection.add | def add(self, origin, rel, target, attrs=None):
'''
Add one relationship to the model
origin - origin of the relationship (similar to an RDF subject)
rel - type IRI of the relationship (similar to an RDF predicate)
target - target of the relationship (similar to an RDF object), ... | python | def add(self, origin, rel, target, attrs=None):
'''
Add one relationship to the model
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rel - type IRI of the relationship (similar to an RDF predicate)
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uogbuji/versa | tools/py/driver/mongo.py | connection.remove | def remove(self, index):
'''
Delete one or more relationship, by index, from the extent
index - either a single index or a list of indices
'''
raise NotImplementedError
if hasattr(index, '__iter__'):
ind = set(index)
else:
ind = [index]
... | python | def remove(self, index):
'''
Delete one or more relationship, by index, from the extent
index - either a single index or a list of indices
'''
raise NotImplementedError
if hasattr(index, '__iter__'):
ind = set(index)
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ind = [index]
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assamite/creamas | creamas/examples/spiro/spiro_agent.py | SpiroAgent.act | async def act(self):
'''Agent's main method to create new spirographs.
See Simulation and CreativeAgent documentation for details.
'''
# Learn from domain artifacts.
self.age += 1
self.added_last = False
self.learn_from_domain(method=self.env_learning_method,
... | python | async def act(self):
'''Agent's main method to create new spirographs.
See Simulation and CreativeAgent documentation for details.
'''
# Learn from domain artifacts.
self.age += 1
self.added_last = False
self.learn_from_domain(method=self.env_learning_method,
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assamite/creamas | creamas/examples/spiro/spiro_agent.py | SpiroAgent.learn_from_domain | def learn_from_domain(self, method='random', amount=10):
'''Learn SOM from artifacts introduced to the environment.
:param str method:
learning method, should be either 'random' or 'closest', where
'random' chooses **amount** random artifacts, and 'closest' samples
c... | python | def learn_from_domain(self, method='random', amount=10):
'''Learn SOM from artifacts introduced to the environment.
:param str method:
learning method, should be either 'random' or 'closest', where
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assamite/creamas | creamas/examples/spiro/spiro_agent.py | SpiroAgent.plot_distances | def plot_distances(self, mean_dist, distances, indeces):
'''Plot distances of the generated spirographs w.r.t. the previously
generated spirogaphs.
'''
from matplotlib import pyplot as plt
x = np.arange(len(distances))
y = [mean_dist for i in x]
fig, ax = plt.subp... | python | def plot_distances(self, mean_dist, distances, indeces):
'''Plot distances of the generated spirographs w.r.t. the previously
generated spirogaphs.
'''
from matplotlib import pyplot as plt
x = np.arange(len(distances))
y = [mean_dist for i in x]
fig, ax = plt.subp... | [
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PBR/MQ2 | MQ2/plugins/mapqtl_plugin.py | get_qtls_from_mapqtl_data | def get_qtls_from_mapqtl_data(matrix, threshold, inputfile):
"""Extract the QTLs found by MapQTL reading its file.
This assume that there is only one QTL per linkage group.
:arg matrix, the MapQTL file read in memory
:arg threshold, threshold used to determine if a given LOD value is
reflective... | python | def get_qtls_from_mapqtl_data(matrix, threshold, inputfile):
"""Extract the QTLs found by MapQTL reading its file.
This assume that there is only one QTL per linkage group.
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PBR/MQ2 | MQ2/plugins/mapqtl_plugin.py | MapQTLPlugin.get_files | def get_files(cls, folder, session_id=''):
""" Retrieve the list of files the plugin can work on.
Find this list based on the files name, files extension or even
actually by reading in the file.
If a session identifier is specified it will restrict the list
of files returned to t... | python | def get_files(cls, folder, session_id=''):
""" Retrieve the list of files the plugin can work on.
Find this list based on the files name, files extension or even
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If a session identifier is specified it will restrict the list
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PBR/MQ2 | MQ2/plugins/mapqtl_plugin.py | MapQTLPlugin.get_session_identifiers | def get_session_identifiers(cls, folder=None, inputfile=None):
""" Retrieve the list of session identifiers contained in the
data on the folder.
:kwarg folder: the path to the folder containing the files to
check. This folder may contain sub-folders.
:kwarg inputfile: the pa... | python | def get_session_identifiers(cls, folder=None, inputfile=None):
""" Retrieve the list of session identifiers contained in the
data on the folder.
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Kortemme-Lab/klab | klab/general/strutil.py | parse_range | def parse_range(s, range_separator = '-'):
''' Parses the string s which contains indices and ranges and returns the explicit list of integers defined by s.
Written by Laurens Kraal 2014.
'''
return reduce(lambda x,y: x+y, (map(lambda r: (range(int(r.split(range_separator)[0]), int(r.split(range_sep... | python | def parse_range(s, range_separator = '-'):
''' Parses the string s which contains indices and ranges and returns the explicit list of integers defined by s.
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'''
return reduce(lambda x,y: x+y, (map(lambda r: (range(int(r.split(range_separator)[0]), int(r.split(range_sep... | [
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Kortemme-Lab/klab | klab/general/strutil.py | merge_range_pairs | def merge_range_pairs(prs):
'''Takes in a list of pairs specifying ranges and returns a sorted list of merged, sorted ranges.'''
new_prs = []
sprs = [sorted(p) for p in prs]
sprs = sorted(sprs)
merged = False
x = 0
while x < len(sprs):
newx = x + 1
new_pair = list(sprs[x])
... | python | def merge_range_pairs(prs):
'''Takes in a list of pairs specifying ranges and returns a sorted list of merged, sorted ranges.'''
new_prs = []
sprs = [sorted(p) for p in prs]
sprs = sorted(sprs)
merged = False
x = 0
while x < len(sprs):
newx = x + 1
new_pair = list(sprs[x])
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Kortemme-Lab/klab | klab/general/strutil.py | split_pdb_residue | def split_pdb_residue(s):
'''Splits a PDB residue into the numeric and insertion code components.'''
if s.isdigit():
return (int(s), ' ')
else:
assert(s[:-1].isdigit())
return ((s[:-1], s[-1])) | python | def split_pdb_residue(s):
'''Splits a PDB residue into the numeric and insertion code components.'''
if s.isdigit():
return (int(s), ' ')
else:
assert(s[:-1].isdigit())
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brunato/lograptor | lograptor/utils.py | do_chunked_gzip | def do_chunked_gzip(infh, outfh, filename):
"""
A memory-friendly way of compressing the data.
"""
import gzip
gzfh = gzip.GzipFile('rawlogs', mode='wb', fileobj=outfh)
if infh.closed:
infh = open(infh.name, 'r')
else:
infh.seek(0)
readsize = 0
sys.stdout.w... | python | def do_chunked_gzip(infh, outfh, filename):
"""
A memory-friendly way of compressing the data.
"""
import gzip
gzfh = gzip.GzipFile('rawlogs', mode='wb', fileobj=outfh)
if infh.closed:
infh = open(infh.name, 'r')
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infh.seek(0)
readsize = 0
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brunato/lograptor | lograptor/utils.py | mail_message | def mail_message(smtp_server, message, from_address, rcpt_addresses):
"""
Send mail using smtp.
"""
if smtp_server[0] == '/':
# Sending the message with local sendmail
p = os.popen(smtp_server, 'w')
p.write(message)
p.close()
else:
# Sending the message using ... | python | def mail_message(smtp_server, message, from_address, rcpt_addresses):
"""
Send mail using smtp.
"""
if smtp_server[0] == '/':
# Sending the message with local sendmail
p = os.popen(smtp_server, 'w')
p.write(message)
p.close()
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brunato/lograptor | lograptor/utils.py | get_value_unit | def get_value_unit(value, unit, prefix):
"""
Return a human-readable value with unit specification. Try to
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transform to higher prefix apply nearest integer round.
"""
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"""
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brunato/lograptor | lograptor/utils.py | get_fmt_results | def get_fmt_results(results, limit=5, sep='::', fmt=None):
"""
Return a list of formatted strings representation on a result dictionary.
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appended after the key between parentheses. Apply a format transformation
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Return a list of formatted strings representation on a result dictionary.
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brunato/lograptor | lograptor/utils.py | safe_expand | def safe_expand(template, mapping):
"""
Safe string template expansion. Raises an error if the provided substitution mapping has circularities.
"""
for _ in range(len(mapping) + 1):
_template = template
template = string.Template(template).safe_substitute(mapping)
if template == ... | python | def safe_expand(template, mapping):
"""
Safe string template expansion. Raises an error if the provided substitution mapping has circularities.
"""
for _ in range(len(mapping) + 1):
_template = template
template = string.Template(template).safe_substitute(mapping)
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brunato/lograptor | lograptor/utils.py | protected_property | def protected_property(func):
"""
Class method decorator that creates a property that returns the protected attribute
or the value returned by the wrapped method, if the protected attribute is not defined.
"""
if func.__name__.startswith('_'):
raise ValueError("%r: Cannot decorate a protecte... | python | def protected_property(func):
"""
Class method decorator that creates a property that returns the protected attribute
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"""
if func.__name__.startswith('_'):
raise ValueError("%r: Cannot decorate a protecte... | [
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brunato/lograptor | lograptor/utils.py | open_resource | def open_resource(source):
"""
Opens a resource in binary reading mode. Wraps the resource with a
context manager when it doesn't have one.
:param source: a filepath or an URL.
"""
try:
return open(source, mode='rb')
except (IOError, OSError) as err:
try:
resourc... | python | def open_resource(source):
"""
Opens a resource in binary reading mode. Wraps the resource with a
context manager when it doesn't have one.
:param source: a filepath or an URL.
"""
try:
return open(source, mode='rb')
except (IOError, OSError) as err:
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DsixTools/python-smeftrunner | smeftrunner/io.py | load | def load(stream, fmt='lha'):
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if fmt == 'lha':
return pylha.load(stream)
elif fmt == 'json':
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return json.loads(stream)
else:
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"""Load a parameter file in DSixTools SLHA-like format or its JSON or
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DsixTools/python-smeftrunner | smeftrunner/io.py | sm_lha2dict | def sm_lha2dict(lha):
"""Convert a dictionary returned by pylha from a DSixTools SM input file
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d = OrderedDict()
v = dict(lha['BLOCK']['GAUGE']['values'])
d['g'] = v[1]
d['gp'] = v[2]
d['gs'] = v[3]
v = dict(lha['BLOCK']['SCALAR']['values'])
d['Lamb... | python | def sm_lha2dict(lha):
"""Convert a dictionary returned by pylha from a DSixTools SM input file
into a dictionary of SM values."""
d = OrderedDict()
v = dict(lha['BLOCK']['GAUGE']['values'])
d['g'] = v[1]
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d['gs'] = v[3]
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DsixTools/python-smeftrunner | smeftrunner/io.py | sm_dict2lha | def sm_dict2lha(d):
"""Convert a a dictionary of SM parameters into
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blocks = OrderedDict([
('GAUGE', {'values': [[1, d['g'].real], [2, d['gp'].real], [3, d['gs'].real]]}),
('SCALAR', {'values': [[1, d['Lambda'].real], [2... | python | def sm_dict2lha(d):
"""Convert a a dictionary of SM parameters into
a dictionary that pylha can convert into a DSixTools SM output file."""
blocks = OrderedDict([
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DsixTools/python-smeftrunner | smeftrunner/io.py | wc_lha2dict | def wc_lha2dict(lha):
"""Convert a dictionary returned by pylha from a DSixTools WC input file
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C = OrderedDict()
# try to read all WCs with 0, 2, or 4 fermions; if not found, set to zero
for k, (block, i) in WC_dict_0f.items():
try:
C[... | python | def wc_lha2dict(lha):
"""Convert a dictionary returned by pylha from a DSixTools WC input file
into a dictionary of Wilson coefficients."""
C = OrderedDict()
# try to read all WCs with 0, 2, or 4 fermions; if not found, set to zero
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Kortemme-Lab/klab | klab/pymath/cartesian/rmsd.py | compute_rmsd_by_matrix | def compute_rmsd_by_matrix(dataframe_1, dataframe_2, use_assertion = False):
'''Computes the RMSD of two pandas dataframes. The dataframes are expected to be of equal dimensions and use_assertion
can be set to assert that the row indices match. '''
if use_assertion: assert([i for i in dataframe_1.index] ... | python | def compute_rmsd_by_matrix(dataframe_1, dataframe_2, use_assertion = False):
'''Computes the RMSD of two pandas dataframes. The dataframes are expected to be of equal dimensions and use_assertion
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projectshift/shift-boiler | boiler/feature/jinja_extensions.py | jinja_extensions_feature | def jinja_extensions_feature(app):
""" Enables custom templating extensions """
# register jinja filters
app.jinja_env.globals['momentjs'] = MomentJsFilters
app.jinja_env.filters.update(MomentJsFilters().get_filters())
app.jinja_env.filters.update(DateFilters().get_filters())
app.jinja_env.filt... | python | def jinja_extensions_feature(app):
""" Enables custom templating extensions """
# register jinja filters
app.jinja_env.globals['momentjs'] = MomentJsFilters
app.jinja_env.filters.update(MomentJsFilters().get_filters())
app.jinja_env.filters.update(DateFilters().get_filters())
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ethan92429/onshapepy | onshapepy/core/utils.py | log | def log(msg, level=0):
'''
Logs a message to the console, with optional level paramater
Args:
- msg (str): message to send to console
- level (int): log level; 0 for info, 1 for error (default = 0)
'''
red = '\033[91m'
endc = '\033[0m'
# configure the logging module
cf... | python | def log(msg, level=0):
'''
Logs a message to the console, with optional level paramater
Args:
- msg (str): message to send to console
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ethan92429/onshapepy | onshapepy/assembly.py | Assembly.insert | def insert(self, part):
""" Insert a part into this assembly.
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- part (onshapepy.part.Part) A Part instance that will be inserted.
Returns:
- requests.Response: Onshape response data
"""
params = {k: str(v) for k,v in part.params.items()}
r... | python | def insert(self, part):
""" Insert a part into this assembly.
Args:
- part (onshapepy.part.Part) A Part instance that will be inserted.
Returns:
- requests.Response: Onshape response data
"""
params = {k: str(v) for k,v in part.params.items()}
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TUNE-Archive/freight_forwarder | freight_forwarder/utils/utils.py | parse_http_scheme | def parse_http_scheme(uri):
"""
match on http scheme if no match is found will assume http
"""
regex = re.compile(
r'^(?:http)s?://',
flags=re.IGNORECASE
)
match = regex.match(uri)
return match.group(0) if match else 'http://' | python | def parse_http_scheme(uri):
"""
match on http scheme if no match is found will assume http
"""
regex = re.compile(
r'^(?:http)s?://',
flags=re.IGNORECASE
)
match = regex.match(uri)
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TUNE-Archive/freight_forwarder | freight_forwarder/utils/utils.py | parse_stream | def parse_stream(response):
"""
take stream from docker-py lib and display it to the user.
this also builds a stream list and returns it.
"""
stream_data = []
stream = stdout
for data in response:
if data:
try:
data = data.decode('utf-8')
exc... | python | def parse_stream(response):
"""
take stream from docker-py lib and display it to the user.
this also builds a stream list and returns it.
"""
stream_data = []
stream = stdout
for data in response:
if data:
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data = data.decode('utf-8')
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TUNE-Archive/freight_forwarder | freight_forwarder/utils/utils.py | normalize_keys | def normalize_keys(suspect, snake_case=True):
"""
take a dict and turn all of its type string keys into snake_case
"""
if not isinstance(suspect, dict):
raise TypeError('you must pass a dict.')
for key in list(suspect):
if not isinstance(key, six.string_types):
continue
... | python | def normalize_keys(suspect, snake_case=True):
"""
take a dict and turn all of its type string keys into snake_case
"""
if not isinstance(suspect, dict):
raise TypeError('you must pass a dict.')
for key in list(suspect):
if not isinstance(key, six.string_types):
continue
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TUNE-Archive/freight_forwarder | freight_forwarder/utils/utils.py | _display_status | def _display_status(normalized_data, stream):
"""
print status message from docker-py stream.
"""
if 'Pull complete' in normalized_data['status'] or 'Download complete' in normalized_data['status']:
stream.write("\n")
if 'id' in normalized_data:
stream.write("%s - " % normalized_dat... | python | def _display_status(normalized_data, stream):
"""
print status message from docker-py stream.
"""
if 'Pull complete' in normalized_data['status'] or 'Download complete' in normalized_data['status']:
stream.write("\n")
if 'id' in normalized_data:
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TUNE-Archive/freight_forwarder | freight_forwarder/utils/utils.py | _display_stream | def _display_stream(normalized_data, stream):
"""
print stream message from docker-py stream.
"""
try:
stream.write(normalized_data['stream'])
except UnicodeEncodeError:
stream.write(normalized_data['stream'].encode("utf-8")) | python | def _display_stream(normalized_data, stream):
"""
print stream message from docker-py stream.
"""
try:
stream.write(normalized_data['stream'])
except UnicodeEncodeError:
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fjwCode/cerium | cerium/service.py | BaseService.version | def version(self) -> str:
'''Show the version number of Android Debug Bridge.'''
output, _ = self._execute('version')
return output.splitlines()[0].split()[-1] | python | def version(self) -> str:
'''Show the version number of Android Debug Bridge.'''
output, _ = self._execute('version')
return output.splitlines()[0].split()[-1] | [
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fjwCode/cerium | cerium/service.py | BaseService.get_state | def get_state(self) -> str:
'''offline | bootloader | device'''
output, error = self._execute('get-state')
if error:
raise DeviceConnectionException(error.split(':', 1)[-1].strip())
return output.strip() | python | def get_state(self) -> str:
'''offline | bootloader | device'''
output, error = self._execute('get-state')
if error:
raise DeviceConnectionException(error.split(':', 1)[-1].strip())
return output.strip() | [
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cozy/python_cozy_management | cozy_management/ssl.py | acme_init | def acme_init():
'''
Init acme key
'''
acme_private_key = ACME_PRIVATE_KEY
acme_intermediate_cert = ACME_INTERMEDIATE_CERT
acme_intermediate_cert_url = ACME_INTERMEDIATE_CERT_URL
if not os.path.isfile(acme_private_key):
print 'Create {}'.format(acme_private_key)
cmd = 'o... | python | def acme_init():
'''
Init acme key
'''
acme_private_key = ACME_PRIVATE_KEY
acme_intermediate_cert = ACME_INTERMEDIATE_CERT
acme_intermediate_cert_url = ACME_INTERMEDIATE_CERT_URL
if not os.path.isfile(acme_private_key):
print 'Create {}'.format(acme_private_key)
cmd = 'o... | [
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cozy/python_cozy_management | cozy_management/ssl.py | acme_sign_certificate | def acme_sign_certificate(common_name, size=DEFAULT_KEY_SIZE):
'''
Sign certificate with acme_tiny for let's encrypt
'''
private_key_path = '{}/{}.key'.format(CERTIFICATES_PATH, common_name)
certificate_path = '{}/{}.crt'.format(CERTIFICATES_PATH, common_name)
certificate_request_path = '{}/... | python | def acme_sign_certificate(common_name, size=DEFAULT_KEY_SIZE):
'''
Sign certificate with acme_tiny for let's encrypt
'''
private_key_path = '{}/{}.key'.format(CERTIFICATES_PATH, common_name)
certificate_path = '{}/{}.crt'.format(CERTIFICATES_PATH, common_name)
certificate_request_path = '{}/... | [
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cozy/python_cozy_management | cozy_management/ssl.py | acme_renew_certificates | def acme_renew_certificates():
'''
Renew certificates with acme_tiny for let's encrypt
'''
for csr in glob(os.path.join(CERTIFICATES_PATH, '*.csr')):
common_name = os.path.basename(csr)
common_name = os.path.splitext(common_name)[0]
certificate_path = "{}.crt".format(common... | python | def acme_renew_certificates():
'''
Renew certificates with acme_tiny for let's encrypt
'''
for csr in glob(os.path.join(CERTIFICATES_PATH, '*.csr')):
common_name = os.path.basename(csr)
common_name = os.path.splitext(common_name)[0]
certificate_path = "{}.crt".format(common... | [
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cozy/python_cozy_management | cozy_management/ssl.py | get_crt_common_name | def get_crt_common_name(certificate_path=OLD_CERTIFICATE_PATH):
'''
Get CN from certificate
'''
try:
certificate_file = open(certificate_path)
crt = OpenSSL.crypto.load_certificate(OpenSSL.crypto.FILETYPE_PEM,
certificate_file.read())
... | python | def get_crt_common_name(certificate_path=OLD_CERTIFICATE_PATH):
'''
Get CN from certificate
'''
try:
certificate_file = open(certificate_path)
crt = OpenSSL.crypto.load_certificate(OpenSSL.crypto.FILETYPE_PEM,
certificate_file.read())
... | [
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cozy/python_cozy_management | cozy_management/ssl.py | normalize_cert_dir | def normalize_cert_dir():
'''
Put old cerfificate form to new one
'''
current_cn = get_crt_common_name()
if not os.path.isdir(COZY_CONFIG_PATH):
print 'Need to create {}'.format(COZY_CONFIG_PATH)
os.mkdir(COZY_CONFIG_PATH, 0755)
if not os.path.isdir(CERTIFICATES_PATH):
... | python | def normalize_cert_dir():
'''
Put old cerfificate form to new one
'''
current_cn = get_crt_common_name()
if not os.path.isdir(COZY_CONFIG_PATH):
print 'Need to create {}'.format(COZY_CONFIG_PATH)
os.mkdir(COZY_CONFIG_PATH, 0755)
if not os.path.isdir(CERTIFICATES_PATH):
... | [
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cozy/python_cozy_management | cozy_management/ssl.py | clean_links | def clean_links():
'''
Clean symlink for nginx
'''
if os.path.isfile(CURRENT_CERTIFICATE_PATH):
print 'Delete symlink {}'.format(CURRENT_CERTIFICATE_PATH)
os.remove(CURRENT_CERTIFICATE_PATH)
if os.path.isfile(CURRENT_PRIVATE_KEY_PATH):
print 'Delete symlink {}'.format(CU... | python | def clean_links():
'''
Clean symlink for nginx
'''
if os.path.isfile(CURRENT_CERTIFICATE_PATH):
print 'Delete symlink {}'.format(CURRENT_CERTIFICATE_PATH)
os.remove(CURRENT_CERTIFICATE_PATH)
if os.path.isfile(CURRENT_PRIVATE_KEY_PATH):
print 'Delete symlink {}'.format(CU... | [
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