repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
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OpenHydrology/floodestimation | floodestimation/parsers.py | FehFileParser.parse | def parse(self, file_name):
"""
Parse entire file and return relevant object.
:param file_name: File path
:type file_name: str
:return: Parsed object
"""
self.object = self.parsed_class()
with open(file_name, encoding='utf-8') as f:
self.parse... | python | def parse(self, file_name):
"""
Parse entire file and return relevant object.
:param file_name: File path
:type file_name: str
:return: Parsed object
"""
self.object = self.parsed_class()
with open(file_name, encoding='utf-8') as f:
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staticdev/django-pagination-bootstrap | pagination_bootstrap/paginator.py | FinitePage.has_next | def has_next(self):
"""
Checks for one more item than last on this page.
"""
try:
next_item = self.paginator.object_list[self.paginator.per_page]
except IndexError:
return False
return True | python | def has_next(self):
"""
Checks for one more item than last on this page.
"""
try:
next_item = self.paginator.object_list[self.paginator.per_page]
except IndexError:
return False
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acutesoftware/AIKIF | scripts/examples/puzzle_missions_canninballs.py | parse_miss_cann | def parse_miss_cann(node, m, c):
"""
extracts names from the node to get
counts of miss + cann on both sides
"""
if node[2]:
m1 = node[0]
m2 = m-node[0]
c1 = node[1]
c2 = c-node[1]
else:
m1=m-node[0]
m2=node[0]
c1=c-node[1]
c2=node... | python | def parse_miss_cann(node, m, c):
"""
extracts names from the node to get
counts of miss + cann on both sides
"""
if node[2]:
m1 = node[0]
m2 = m-node[0]
c1 = node[1]
c2 = c-node[1]
else:
m1=m-node[0]
m2=node[0]
c1=c-node[1]
c2=node... | [
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acutesoftware/AIKIF | scripts/examples/puzzle_missions_canninballs.py | solve | def solve(m,c):
"""
run the algorithm to find the path list
"""
G={ (m,c,1):[] }
frontier=[ (m,c,1) ] # 1 as boat starts on left bank
while len(frontier) > 0:
hold=list(frontier)
for node in hold:
newnode=[]
frontier.remove(node)
newnode.exte... | python | def solve(m,c):
"""
run the algorithm to find the path list
"""
G={ (m,c,1):[] }
frontier=[ (m,c,1) ] # 1 as boat starts on left bank
while len(frontier) > 0:
hold=list(frontier)
for node in hold:
newnode=[]
frontier.remove(node)
newnode.exte... | [
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acutesoftware/AIKIF | aikif/dataTools/cls_sql_code_generator.py | SQLCodeGenerator.create_script_fact | def create_script_fact(self):
"""
appends the CREATE TABLE, index etc to self.ddl_text
"""
self.ddl_text += '---------------------------------------------\n'
self.ddl_text += '-- CREATE Fact Table - ' + self.fact_table + '\n'
self.ddl_text += '----------------------------... | python | def create_script_fact(self):
"""
appends the CREATE TABLE, index etc to self.ddl_text
"""
self.ddl_text += '---------------------------------------------\n'
self.ddl_text += '-- CREATE Fact Table - ' + self.fact_table + '\n'
self.ddl_text += '----------------------------... | [
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acutesoftware/AIKIF | aikif/dataTools/cls_sql_code_generator.py | SQLCodeGenerator.create_script_staging_table | def create_script_staging_table(self, output_table, col_list):
"""
appends the CREATE TABLE, index etc to another table
"""
self.ddl_text += '---------------------------------------------\n'
self.ddl_text += '-- CREATE Staging Table - ' + output_table + '\n'
self.ddl_text... | python | def create_script_staging_table(self, output_table, col_list):
"""
appends the CREATE TABLE, index etc to another table
"""
self.ddl_text += '---------------------------------------------\n'
self.ddl_text += '-- CREATE Staging Table - ' + output_table + '\n'
self.ddl_text... | [
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acutesoftware/AIKIF | scripts/examples/table_compare.py | distinct_values | def distinct_values(t_old, t_new):
"""
for all columns, check which values are not in
the other table
"""
res = []
res.append([' -- NOT IN check -- '])
for new_col in t_new.header:
dist_new = t_new.get_distinct_values_from_cols([new_col])
#print('NEW Distinct values for '... | python | def distinct_values(t_old, t_new):
"""
for all columns, check which values are not in
the other table
"""
res = []
res.append([' -- NOT IN check -- '])
for new_col in t_new.header:
dist_new = t_new.get_distinct_values_from_cols([new_col])
#print('NEW Distinct values for '... | [
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acutesoftware/AIKIF | aikif/web_app/web_aikif.py | aikif_web_menu | def aikif_web_menu(cur=''):
""" returns the web page header containing standard AIKIF top level web menu """
pgeHdg = ''
pgeBlurb = ''
if cur == '':
cur = 'Home'
txt = get_header(cur) #"<div id=top_menu>"
txt += '<div id = "container">\n'
txt += ' <div id = "header">\n'
txt +=... | python | def aikif_web_menu(cur=''):
""" returns the web page header containing standard AIKIF top level web menu """
pgeHdg = ''
pgeBlurb = ''
if cur == '':
cur = 'Home'
txt = get_header(cur) #"<div id=top_menu>"
txt += '<div id = "container">\n'
txt += ' <div id = "header">\n'
txt +=... | [
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acutesoftware/AIKIF | scripts/res_core_data_NOTES.py | main | def main():
"""
This generates the research document based on the results of
the various programs and includes RST imports for introduction
and summary
"""
print("Generating research notes...")
if os.path.exists(fname):
os.remove(fname)
append_rst('===============================... | python | def main():
"""
This generates the research document based on the results of
the various programs and includes RST imports for introduction
and summary
"""
print("Generating research notes...")
if os.path.exists(fname):
os.remove(fname)
append_rst('===============================... | [
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acutesoftware/AIKIF | aikif/knowledge.py | RawData.find | def find(self, txt):
"""
returns a list of records containing text
"""
result = []
for d in self.data:
if txt in d:
result.append(d)
return result | python | def find(self, txt):
"""
returns a list of records containing text
"""
result = []
for d in self.data:
if txt in d:
result.append(d)
return result | [
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Nachtfeuer/pipeline | spline/tools/report/collector.py | CollectorUpdate.schema_complete | def schema_complete():
"""Schema for data in CollectorUpdate."""
return Schema({
'stage': And(str, len),
'timestamp': int,
'status': And(str, lambda s: s in ['started', 'succeeded', 'failed']),
# optional matrix
Optional('matrix', default='defa... | python | def schema_complete():
"""Schema for data in CollectorUpdate."""
return Schema({
'stage': And(str, len),
'timestamp': int,
'status': And(str, lambda s: s in ['started', 'succeeded', 'failed']),
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Nachtfeuer/pipeline | spline/tools/report/collector.py | CollectorStage.schema_event_items | def schema_event_items():
"""Schema for event items."""
return {
'timestamp': And(int, lambda n: n > 0),
Optional('information', default={}): {
Optional(Regex(r'([a-z][_a-z]*)')): object
}
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"""Schema for event items."""
return {
'timestamp': And(int, lambda n: n > 0),
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Optional(Regex(r'([a-z][_a-z]*)')): object
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Nachtfeuer/pipeline | spline/tools/report/collector.py | CollectorStage.schema_complete | def schema_complete():
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"""Schema for data in CollectorStage."""
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Nachtfeuer/pipeline | spline/tools/report/collector.py | CollectorStage.add | def add(self, timestamp, information):
"""
Add event information.
Args:
timestamp (int): event timestamp.
information (dict): event information.
Raises:
RuntimeError: when validation of parameters has failed.
"""
try:
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"""
Add event information.
Args:
timestamp (int): event timestamp.
information (dict): event information.
Raises:
RuntimeError: when validation of parameters has failed.
"""
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Nachtfeuer/pipeline | spline/tools/report/collector.py | CollectorStage.duration | def duration(self):
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Returns:
float: (current) duration of the stage
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last = datetime.fromtime... | python | def duration(self):
"""
Calculate how long the stage took.
Returns:
float: (current) duration of the stage
"""
duration = 0.0
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Nachtfeuer/pipeline | spline/tools/report/collector.py | Store.count_stages | def count_stages(self, matrix_name):
"""
Number of registered stages for given matrix name.
Parameters:
matrix_name (str): name of the matrix
Returns:
int: number of reported stages for given matrix name.
"""
return len(self.data[matrix_name]) if... | python | def count_stages(self, matrix_name):
"""
Number of registered stages for given matrix name.
Parameters:
matrix_name (str): name of the matrix
Returns:
int: number of reported stages for given matrix name.
"""
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matrix_name (str): name of the matrix
stage_name (str): name of the stage.
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CollectorStage: when stage has been found or None.
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matrix_name (str): name of the matrix
stage_name (str): name of the stage.
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Nachtfeuer/pipeline | spline/tools/report/collector.py | Store.get_duration | def get_duration(self, matrix_name):
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Get duration for a concrete matrix.
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matrix_name (str): name of the Matrix.
Returns:
float: duration of concrete matrix in seconds.
"""
duration = 0.0
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Get duration for a concrete matrix.
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matrix_name (str): name of the Matrix.
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float: duration of concrete matrix in seconds.
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Args:
item (CollectorUpdate): event data like stage, timestampe and status.
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Nachtfeuer/pipeline | spline/tools/report/collector.py | Collector.run | def run(self):
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break
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while True:
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acutesoftware/AIKIF | scripts/examples/gui_view_world.py | read_map | def read_map(fname):
"""
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lst.append(line)
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acutesoftware/AIKIF | scripts/examples/gui_view_world.py | gui_view_tk.show_grid_from_file | def show_grid_from_file(self, fname):
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reads a saved grid file and paints it on the canvas
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acutesoftware/AIKIF | scripts/examples/gui_view_world.py | gui_view_tk.draw_cell | def draw_cell(self, row, col, val):
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acutesoftware/AIKIF | scripts/examples/gui_view_world.py | gui_view_tk.paint_agent_trail | def paint_agent_trail(self, y, x, val):
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"""
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paint an agent trail as ONE pixel to allow for multiple agent
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"""
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acutesoftware/AIKIF | scripts/examples/gui_view_world.py | gui_view_tk.agent_color | def agent_color(self, val):
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gets a colour for agent 0 - 9
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colour = 'blue'
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gets a colour for agent 0 - 9
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acutesoftware/AIKIF | scripts/examples/happiness_solver.py | create_random_population | def create_random_population(num=100):
"""
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"""
people = []
for _ in range(num):
nme = 'blah'
tax_min = random.randint(1,40)/100
tax_max = tax_min + random.randint(1,40)/100
tradition = random.randint(1,10... | python | def create_random_population(num=100):
"""
create a list of people with randomly generated names and stats
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people = []
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Nachtfeuer/pipeline | spline/pipeline.py | Pipeline.cleanup | def cleanup(self):
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env = self.data.env_list[0].copy()
env.update({'PIPELINE_RESULT': 'SUCCESS', 'PIPELINE_SHELL_EXIT_CODE': '0'})
config = ShellConfi... | python | def cleanup(self):
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Nachtfeuer/pipeline | spline/pipeline.py | Pipeline.process | def process(self, pipeline):
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output = []
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# an environment block can be repeated
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self.data.env_list[0].update(entry[key])
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output = []
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acutesoftware/AIKIF | scripts/AI_CLI.py | AICLI.process | def process(self, txt, mode):
"""
Top level function to process the command, mainly
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This should work by using the function name defined
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"""
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"""
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acutesoftware/AIKIF | scripts/AI_CLI.py | AICLI.cmd_add | def cmd_add(self, txt):
"""
Enter add mode - all text entered now will be
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"""
self.show_output('Adding ', txt)
self.raw.add(txt)
print(self.raw)
return 'Added ' + txt | python | def cmd_add(self, txt):
"""
Enter add mode - all text entered now will be
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acutesoftware/AIKIF | scripts/AI_CLI.py | AICLI.cmd_query | def cmd_query(self, txt):
"""
search and query the AIKIF
"""
self.show_output('Searching for ', txt)
res = self.raw.find(txt)
for d in res:
self.show_output(d)
return str(len(res)) + ' results for ' + txt | python | def cmd_query(self, txt):
"""
search and query the AIKIF
"""
self.show_output('Searching for ', txt)
res = self.raw.find(txt)
for d in res:
self.show_output(d)
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.verify_integrity | def verify_integrity(self):
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raise Exception('U2F_APPID was not defined! Please define it in configuration file.')
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"""Verifies that all required functions been injected."""
if not self.__integrity_check:
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.devices | def devices(self):
"""Manages users enrolled u2f devices"""
self.verify_integrity()
if session.get('u2f_device_management_authorized', False):
if request.method == 'GET':
return jsonify(self.get_devices()), 200
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... | python | def devices(self):
"""Manages users enrolled u2f devices"""
self.verify_integrity()
if session.get('u2f_device_management_authorized', False):
if request.method == 'GET':
return jsonify(self.get_devices()), 200
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.facets | def facets(self):
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"""Provides facets support. REQUIRES VALID HTTPS!"""
self.verify_integrity()
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.get_enroll | def get_enroll(self):
"""Returns new enroll seed"""
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enroll = start_register(self.__appid, devices)
enroll['status'] = 'ok'
session['_u2f_enroll_'] = enroll.json
return enroll | python | def get_enroll(self):
"""Returns new enroll seed"""
devices = [DeviceRegistration.wrap(device) for device in self.__get_u2f_devices()]
enroll = start_register(self.__appid, devices)
enroll['status'] = 'ok'
session['_u2f_enroll_'] = enroll.json
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.verify_enroll | def verify_enroll(self, response):
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"""Verifies and saves U2F enroll"""
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.get_signature_challenge | def get_signature_challenge(self):
"""Returns new signature challenge"""
devices = [DeviceRegistration.wrap(device) for device in self.__get_u2f_devices()]
if devices == []:
return {
'status' : 'failed',
'error' : 'No devices been associated with t... | python | def get_signature_challenge(self):
"""Returns new signature challenge"""
devices = [DeviceRegistration.wrap(device) for device in self.__get_u2f_devices()]
if devices == []:
return {
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.remove_device | def remove_device(self, request):
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for i in range(len(devices)):
if devices[i]['keyHandle'] == request['id']:
del devices[i]
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... | python | def remove_device(self, request):
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devices = self.__get_u2f_devices()
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herrjemand/flask-fido-u2f | flask_fido_u2f.py | U2F.verify_counter | def verify_counter(self, signature, counter):
""" Verifies that counter value is greater than previous signature"""
devices = self.__get_u2f_devices()
for device in devices:
# Searching for specific keyhandle
if device['keyHandle'] == signature['keyHandle']:
... | python | def verify_counter(self, signature, counter):
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Nachtfeuer/pipeline | spline/validation.py | Validator.validate | def validate(data):
"""
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Args:
data(dict): data structure to validate.
Returns:
dict: data as provided and defaults where defined in schema.
"""
try:
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... | python | def validate(data):
"""
Validate data against the schema.
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data(dict): data structure to validate.
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dict: data as provided and defaults where defined in schema.
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Nachtfeuer/pipeline | spline/tools/loader.py | Loader.include | def include(self, node):
"""Include the defined yaml file."""
result = None
if isinstance(node, ScalarNode):
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else:
raise RuntimeError("Not supported !include on type %s" % type(node))
return result | python | def include(self, node):
"""Include the defined yaml file."""
result = None
if isinstance(node, ScalarNode):
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acutesoftware/AIKIF | aikif/transpose.py | Transpose.pivot | def pivot(self):
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acutesoftware/AIKIF | aikif/transpose.py | Transpose.key_value_pairs | def key_value_pairs(self):
"""
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ID COLNUM VAL... | python | def key_value_pairs(self):
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acutesoftware/AIKIF | aikif/transpose.py | Transpose.links_to_data | def links_to_data(self, col_name_col_num, col_val_col_num, id_a_col_num, id_b_col_num):
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This is the reverse of data_to_links and takes a links table and
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acutesoftware/AIKIF | aikif/lib/cls_goal_friendly.py | GoalFriendly.find_best_plan | def find_best_plan(self):
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self.run_plan(plan, strat) | python | def find_best_plan(self):
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try each strategy with different amounts
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acutesoftware/AIKIF | aikif/ontology/read_opencyc.py | load_data | def load_data(fname):
""" loads previously exported CSV file to redis database """
print('Loading ' + fname + ' to redis')
r = redis.StrictRedis(host = '127.0.0.1', port = 6379, db = 0);
with open(fname, 'r') as f:
for line_num, row in enumerate(f):
if row.strip('') != '':
... | python | def load_data(fname):
""" loads previously exported CSV file to redis database """
print('Loading ' + fname + ' to redis')
r = redis.StrictRedis(host = '127.0.0.1', port = 6379, db = 0);
with open(fname, 'r') as f:
for line_num, row in enumerate(f):
if row.strip('') != '':
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acutesoftware/AIKIF | aikif/ontology/read_opencyc.py | parse_n3 | def parse_n3(row, src='csv'):
"""
takes a row from an n3 file and returns the triple
NOTE - currently parses a CSV line already split via
cyc_extract.py
"""
if row.strip() == '':
return '',''
l_root = 'opencyc'
key = ''
val = ''
if src == 'csv':
cols = row.split... | python | def parse_n3(row, src='csv'):
"""
takes a row from an n3 file and returns the triple
NOTE - currently parses a CSV line already split via
cyc_extract.py
"""
if row.strip() == '':
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acutesoftware/AIKIF | aikif/ontology/read_opencyc.py | summarise_file_as_html | def summarise_file_as_html(fname):
"""
takes a large data file and produces a HTML summary as html
"""
txt = '<H1>' + fname + '</H1>'
num_lines = 0
print('Reading OpenCyc file - ', fname)
with open(ip_folder + os.sep + fname, 'r') as f:
txt += '<PRE>'
for line in f:
... | python | def summarise_file_as_html(fname):
"""
takes a large data file and produces a HTML summary as html
"""
txt = '<H1>' + fname + '</H1>'
num_lines = 0
print('Reading OpenCyc file - ', fname)
with open(ip_folder + os.sep + fname, 'r') as f:
txt += '<PRE>'
for line in f:
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acutesoftware/AIKIF | scripts/examples/game_of_life_console.py | main | def main():
"""
Example to show AIKIF logging of results.
Generates a sequence of random grids and runs the
Game of Life, saving results
"""
iterations = 9 # how many simulations to run
years = 3 # how many times to run each simulation
width = 22 # grid height
... | python | def main():
"""
Example to show AIKIF logging of results.
Generates a sequence of random grids and runs the
Game of Life, saving results
"""
iterations = 9 # how many simulations to run
years = 3 # how many times to run each simulation
width = 22 # grid height
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acutesoftware/AIKIF | scripts/examples/game_of_life_console.py | run_game_of_life | def run_game_of_life(years, width, height, time_delay, silent="N"):
"""
run a single game of life for 'years' and log start and
end living cells to aikif
"""
lfe = mod_grid.GameOfLife(width, height, ['.', 'x'], 1)
set_random_starting_grid(lfe)
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"""
run a single game of life for 'years' and log start and
end living cells to aikif
"""
lfe = mod_grid.GameOfLife(width, height, ['.', 'x'], 1)
set_random_starting_grid(lfe)
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acutesoftware/AIKIF | scripts/examples/game_of_life_console.py | print_there | def print_there(x, y, text):
""""
allows display of a game of life on a console via
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for testing but not production quality.
"""
sys.stdout.write("\x1b7\x1b[%d;%df%s\x1b8" % (x, y, text))
sys.stdout.flush() | python | def print_there(x, y, text):
""""
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"""
sys.stdout.write("\x1b7\x1b[%d;%df%s\x1b8" % (x, y, text))
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acutesoftware/AIKIF | aikif/toolbox/text_tools.py | identify_col_pos | def identify_col_pos(txt):
"""
assume no delimiter in this file, so guess the best
fixed column widths to split by
"""
res = []
#res.append(0)
lines = txt.split('\n')
prev_ch = ''
for col_pos, ch in enumerate(lines[0]):
if _is_white_space(ch) is False and _is_white_space(prev_ch) is True:
res.a... | python | def identify_col_pos(txt):
"""
assume no delimiter in this file, so guess the best
fixed column widths to split by
"""
res = []
#res.append(0)
lines = txt.split('\n')
prev_ch = ''
for col_pos, ch in enumerate(lines[0]):
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acutesoftware/AIKIF | aikif/toolbox/text_tools.py | load_tbl_from_csv | def load_tbl_from_csv(fname):
"""
read a CSV file to list without worrying about odd characters
"""
import csv
rows_to_load = []
with open(fname, 'r', encoding='cp1252', errors='ignore') as csvfile:
csvreader = csv.reader(csvfile, delimiter = ',' )
reader = csv.reader(csvfile)
rows_to_load ... | python | def load_tbl_from_csv(fname):
"""
read a CSV file to list without worrying about odd characters
"""
import csv
rows_to_load = []
with open(fname, 'r', encoding='cp1252', errors='ignore') as csvfile:
csvreader = csv.reader(csvfile, delimiter = ',' )
reader = csv.reader(csvfile)
rows_to_load ... | [
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acutesoftware/AIKIF | aikif/toolbox/text_tools.py | _get_dict_char_count | def _get_dict_char_count(txt):
"""
reads the characters in txt and returns a dictionary
of all letters
"""
dct = {}
for letter in txt:
if letter in dct:
dct[letter] += 1
else:
dct[letter] = 1
return dct | python | def _get_dict_char_count(txt):
"""
reads the characters in txt and returns a dictionary
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"""
dct = {}
for letter in txt:
if letter in dct:
dct[letter] += 1
else:
dct[letter] = 1
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Nachtfeuer/pipeline | spline/components/docker.py | Container.creator | def creator(entry, config):
"""Creator function for creating an instance of a Bash."""
template_file = os.path.join(os.path.dirname(__file__), 'templates/docker-container.sh.j2')
with open(template_file) as handle:
template = handle.read()
# all fields are re-rendered vi... | python | def creator(entry, config):
"""Creator function for creating an instance of a Bash."""
template_file = os.path.join(os.path.dirname(__file__), 'templates/docker-container.sh.j2')
with open(template_file) as handle:
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Nachtfeuer/pipeline | spline/components/docker.py | Image.creator | def creator(entry, config):
"""Creator function for creating an instance of a Docker image script."""
# writing Dockerfile
dockerfile = render(config.script, model=config.model, env=config.env,
variables=config.variables, item=config.item)
filename = "dockerfi... | python | def creator(entry, config):
"""Creator function for creating an instance of a Docker image script."""
# writing Dockerfile
dockerfile = render(config.script, model=config.model, env=config.env,
variables=config.variables, item=config.item)
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Nachtfeuer/pipeline | spline/tools/stream.py | stdout_redirector | def stdout_redirector():
"""
Simplify redirect of stdout.
Taken from here: https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/
"""
old_stdout = sys.stdout
sys.stdout = Stream()
try:
yield sys.stdout
finally:
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sys.stdout... | python | def stdout_redirector():
"""
Simplify redirect of stdout.
Taken from here: https://eli.thegreenplace.net/2015/redirecting-all-kinds-of-stdout-in-python/
"""
old_stdout = sys.stdout
sys.stdout = Stream()
try:
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Nachtfeuer/pipeline | spline/tools/stream.py | write_temporary_file | def write_temporary_file(content, prefix='', suffix=''):
"""
Generating a temporary file with content.
Args:
content (str): file content (usually a script, Dockerfile, playbook or config file)
prefix (str): the filename starts with this prefix (default: no prefix)
suffix (str): the ... | python | def write_temporary_file(content, prefix='', suffix=''):
"""
Generating a temporary file with content.
Args:
content (str): file content (usually a script, Dockerfile, playbook or config file)
prefix (str): the filename starts with this prefix (default: no prefix)
suffix (str): the ... | [
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aartur/mschematool | mschematool/cli.py | print_new | def print_new(ctx, name, migration_type):
"""Prints filename of a new migration"""
click.echo(ctx.obj.repository.generate_migration_name(name, migration_type)) | python | def print_new(ctx, name, migration_type):
"""Prints filename of a new migration"""
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acutesoftware/AIKIF | aikif/agents/agent.py | Agent.start | def start(self):
"""
Starts an agent with standard logging
"""
self.running = True
self.status = 'RUNNING'
self.mylog.record_process('agent', self.name + ' - starting') | python | def start(self):
"""
Starts an agent with standard logging
"""
self.running = True
self.status = 'RUNNING'
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acutesoftware/AIKIF | aikif/agents/agent.py | Agent.set_coords | def set_coords(self, x=0, y=0, z=0, t=0):
"""
set coords of agent in an arbitrary world
"""
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self.coords['x'] = x
self.coords['y'] = y
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self.coords['t'] = t | python | def set_coords(self, x=0, y=0, z=0, t=0):
"""
set coords of agent in an arbitrary world
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self.coords = {}
self.coords['x'] = x
self.coords['y'] = y
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self.coords['t'] = t | [
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OpenHydrology/floodestimation | floodestimation/loaders.py | from_file | def from_file(file_path, incl_pot=True):
"""
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If there is also a corresponding ``.AM`` file (annual maximum flow data) or
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"""
Load catchment object from a ``.CD3`` or ``.xml`` file.
If there is also a corresponding ``.AM`` file (annual maximum flow data) or
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OpenHydrology/floodestimation | floodestimation/loaders.py | to_db | def to_db(catchment, session, method='create', autocommit=False):
"""
Load catchment object into the database.
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"""
Load catchment object into the database.
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OpenHydrology/floodestimation | floodestimation/loaders.py | userdata_to_db | def userdata_to_db(session, method='update', autocommit=False):
"""
Add catchments from a user folder to the database.
The user folder is specified in the ``config.ini`` file like this::
[import]
folder = path/to/import/folder
If this configuration key does not exist this will be sile... | python | def userdata_to_db(session, method='update', autocommit=False):
"""
Add catchments from a user folder to the database.
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folder = path/to/import/folder
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acutesoftware/AIKIF | aikif/toolbox/interface_windows_tools.py | send_text | def send_text(hwnd, txt):
"""
sends the text 'txt' to the window handle hwnd using SendMessage
"""
try:
for c in txt:
if c == '\n':
win32api.SendMessage(hwnd, win32con.WM_KEYDOWN, win32con.VK_RETURN, 0)
win32api.SendMessage(hwnd, win32con.WM_KEYUP, win... | python | def send_text(hwnd, txt):
"""
sends the text 'txt' to the window handle hwnd using SendMessage
"""
try:
for c in txt:
if c == '\n':
win32api.SendMessage(hwnd, win32con.WM_KEYDOWN, win32con.VK_RETURN, 0)
win32api.SendMessage(hwnd, win32con.WM_KEYUP, win... | [
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acutesoftware/AIKIF | aikif/toolbox/interface_windows_tools.py | launch_app | def launch_app(app_path, params=[], time_before_kill_app=15):
"""
start an app
"""
import subprocess
try:
res = subprocess.call([app_path, params], timeout=time_before_kill_app, shell=True)
print('res = ', res)
if res == 0:
return True
else:
re... | python | def launch_app(app_path, params=[], time_before_kill_app=15):
"""
start an app
"""
import subprocess
try:
res = subprocess.call([app_path, params], timeout=time_before_kill_app, shell=True)
print('res = ', res)
if res == 0:
return True
else:
re... | [
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acutesoftware/AIKIF | aikif/toolbox/interface_windows_tools.py | app_activate | def app_activate(caption):
"""
use shell to bring the application with caption to front
"""
try:
shell = win32com.client.Dispatch("WScript.Shell")
shell.AppActivate(caption)
except Exception as ex:
print('error calling win32com.client.Dispatch (AppActivate)') | python | def app_activate(caption):
"""
use shell to bring the application with caption to front
"""
try:
shell = win32com.client.Dispatch("WScript.Shell")
shell.AppActivate(caption)
except Exception as ex:
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OpenHydrology/floodestimation | floodestimation/collections.py | CatchmentCollections.most_similar_catchments | def most_similar_catchments(self, subject_catchment, similarity_dist_function, records_limit=500,
include_subject_catchment='auto'):
"""
Return a list of catchments sorted by hydrological similarity defined by `similarity_distance_function`
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"""
Return a list of catchments sorted by hydrological similarity defined by `similarity_distance_function`
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mpg-age-bioinformatics/AGEpy | AGEpy/sam.py | readSAM | def readSAM(SAMfile,header=False):
"""
Reads and parses a sam file.
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:param header: logical, if True, reads the header information
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"""
Reads and parses a sam file.
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mpg-age-bioinformatics/AGEpy | AGEpy/sam.py | SAMflags | def SAMflags(x):
"""
Explains a SAM flag.
:param x: flag
:returns: complete SAM flag explanaition
"""
flags=[]
if x & 1:
l="1: Read paired"
else:
l="0: Read unpaired"
flags.append(l)
if x & 2 :
l="1: Read mapped in proper pair"
else:
l="0: ... | python | def SAMflags(x):
"""
Explains a SAM flag.
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:returns: complete SAM flag explanaition
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l="1: Read paired"
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acutesoftware/AIKIF | aikif/bias.py | Bias.get_bias_details | def get_bias_details(self):
"""
returns a string representation of the bias details
"""
res = 'Bias File Details\n'
for b in self.bias_details:
if len(b) > 2:
res += b[0].ljust(35)
res += b[1].ljust(35)
res += b[2].ljust... | python | def get_bias_details(self):
"""
returns a string representation of the bias details
"""
res = 'Bias File Details\n'
for b in self.bias_details:
if len(b) > 2:
res += b[0].ljust(35)
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acutesoftware/AIKIF | aikif/bias.py | Bias._read_bias_rating | def _read_bias_rating(self, short_filename):
"""
read the bias file based on the short_filename
and return as a dictionary
"""
res = {}
full_name = os.path.join(root_fldr, 'aikif', 'data', 'ref', short_filename)
lg.record_process('bias.py','reading ' + full_name)
... | python | def _read_bias_rating(self, short_filename):
"""
read the bias file based on the short_filename
and return as a dictionary
"""
res = {}
full_name = os.path.join(root_fldr, 'aikif', 'data', 'ref', short_filename)
lg.record_process('bias.py','reading ' + full_name)
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acutesoftware/AIKIF | aikif/config.py | get_root_folder | def get_root_folder():
"""
returns the home folder and program root depending on OS
"""
locations = {
'linux':{'hme':'/home/duncan/', 'core_folder':'/home/duncan/dev/src/python/AIKIF'},
'win32':{'hme':'T:\\user\\', 'core_folder':'T:\\user\\dev\\src\\python\\AIKIF'},
'cygwin':{'hme':os.... | python | def get_root_folder():
"""
returns the home folder and program root depending on OS
"""
locations = {
'linux':{'hme':'/home/duncan/', 'core_folder':'/home/duncan/dev/src/python/AIKIF'},
'win32':{'hme':'T:\\user\\', 'core_folder':'T:\\user\\dev\\src\\python\\AIKIF'},
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acutesoftware/AIKIF | aikif/config.py | read_credentials | def read_credentials(fname):
"""
read a simple text file from a private location to get
username and password
"""
with open(fname, 'r') as f:
username = f.readline().strip('\n')
password = f.readline().strip('\n')
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:param outFile: MEME file to be written
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Selectes motifs from a meme file based on the number of sites.
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# Empty and refill the config object
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"""
Restore the default configuration and remove the user's config file.
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Write data to user config file.
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self.write(f) | python | def save(self):
"""
Write data to user config file.
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with open(self._user_config_file, 'w', encoding='utf-8') as f:
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cdgriffith/puremagic | puremagic/main.py | _magic_data | def _magic_data(filename=os.path.join(here, 'magic_data.json')):
""" Read the magic file"""
with open(filename) as f:
data = json.load(f)
headers = [_create_puremagic(x) for x in data['headers']]
footers = [_create_puremagic(x) for x in data['footers']]
return headers, footers | python | def _magic_data(filename=os.path.join(here, 'magic_data.json')):
""" Read the magic file"""
with open(filename) as f:
data = json.load(f)
headers = [_create_puremagic(x) for x in data['headers']]
footers = [_create_puremagic(x) for x in data['footers']]
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cdgriffith/puremagic | puremagic/main.py | _max_lengths | def _max_lengths():
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max_footer_length = max([len(x.byte_match) + abs(x.offset)
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cdgriffith/puremagic | puremagic/main.py | _confidence | def _confidence(matches, ext=None):
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""" Rough confidence based on string length and file extension"""
results = []
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cdgriffith/puremagic | puremagic/main.py | _identify_all | def _identify_all(header, footer, ext=None):
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""" Attempt to identify 'data' by its magic numbers"""
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cdgriffith/puremagic | puremagic/main.py | _magic | def _magic(header, footer, mime, ext=None):
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cdgriffith/puremagic | puremagic/main.py | ext_from_filename | def ext_from_filename(filename):
""" Scan a filename for it's extension.
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"""
try:
base, ext = filename.lower().rsplit(".", 1)
except ValueError:
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""" Scan a filename for it's extension.
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"""
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cdgriffith/puremagic | puremagic/main.py | from_string | def from_string(string, mime=False, filename=None):
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If mime is True it will return the mime type instead.
If filename is provided it will be used in the computation.
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | retrieve_GTF_field | def retrieve_GTF_field(field,gtf):
"""
Returns a field of choice from the attribute column of the GTF
:param field: field to be retrieved
:returns: a Pandas dataframe with one columns containing the field of choice
"""
inGTF=gtf.copy()
def splits(x):
l=x.split(";")
l=[ s.sp... | python | def retrieve_GTF_field(field,gtf):
"""
Returns a field of choice from the attribute column of the GTF
:param field: field to be retrieved
:returns: a Pandas dataframe with one columns containing the field of choice
"""
inGTF=gtf.copy()
def splits(x):
l=x.split(";")
l=[ s.sp... | [
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | attributesGTF | def attributesGTF(inGTF):
"""
List the type of attributes in a the attribute section of a GTF file
:param inGTF: GTF dataframe to be analysed
:returns: a list of attributes present in the attribute section
"""
df=pd.DataFrame(inGTF['attribute'].str.split(";").tolist())
desc=[]
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"""
List the type of attributes in a the attribute section of a GTF file
:param inGTF: GTF dataframe to be analysed
:returns: a list of attributes present in the attribute section
"""
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | parseGTF | def parseGTF(inGTF):
"""
Reads an extracts all attributes in the attributes section of a GTF and constructs a new dataframe wiht one collumn per attribute instead of the attributes column
:param inGTF: GTF dataframe to be parsed
:returns: a dataframe of the orignal input GTF with attributes parsed.
... | python | def parseGTF(inGTF):
"""
Reads an extracts all attributes in the attributes section of a GTF and constructs a new dataframe wiht one collumn per attribute instead of the attributes column
:param inGTF: GTF dataframe to be parsed
:returns: a dataframe of the orignal input GTF with attributes parsed.
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | writeGTF | def writeGTF(inGTF,file_path):
"""
Write a GTF dataframe into a file
:param inGTF: GTF dataframe to be written. It should either have 9 columns with the last one being the "attributes" section or more than 9 columns where all columns after the 8th will be colapsed into one.
:param file_path: path/to/th... | python | def writeGTF(inGTF,file_path):
"""
Write a GTF dataframe into a file
:param inGTF: GTF dataframe to be written. It should either have 9 columns with the last one being the "attributes" section or more than 9 columns where all columns after the 8th will be colapsed into one.
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | GTFtoBED | def GTFtoBED(inGTF,name):
"""
Transform a GTF dataframe into a bed dataframe
:param inGTF: GTF dataframe for transformation
:param name: field of the GTF data frame to be use for the bed 'name' positon
returns: a bed dataframe with the corresponding bed fiels: 'chrom','chromStart','chromEnd','name... | python | def GTFtoBED(inGTF,name):
"""
Transform a GTF dataframe into a bed dataframe
:param inGTF: GTF dataframe for transformation
:param name: field of the GTF data frame to be use for the bed 'name' positon
returns: a bed dataframe with the corresponding bed fiels: 'chrom','chromStart','chromEnd','name... | [
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | MAPGenoToTrans | def MAPGenoToTrans(parsedGTF,feature):
"""
Gets all positions of all bases in an exon
:param df: a Pandas dataframe with 'start','end', and 'strand' information for each entry.
df must contain 'seqname','feature','start','end','strand','frame','gene_id',
'transcript_id','exo... | python | def MAPGenoToTrans(parsedGTF,feature):
"""
Gets all positions of all bases in an exon
:param df: a Pandas dataframe with 'start','end', and 'strand' information for each entry.
df must contain 'seqname','feature','start','end','strand','frame','gene_id',
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mpg-age-bioinformatics/AGEpy | AGEpy/gtf.py | GetTransPosition | def GetTransPosition(df,field,dic,refCol="transcript_id"):
"""
Maps a genome position to transcript positon"
:param df: a Pandas dataframe
:param field: the head of the column containing the genomic position
:param dic: a dictionary containing for each transcript the respective bases eg. {ENST23923... | python | def GetTransPosition(df,field,dic,refCol="transcript_id"):
"""
Maps a genome position to transcript positon"
:param df: a Pandas dataframe
:param field: the head of the column containing the genomic position
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acutesoftware/AIKIF | aikif/toolbox/network_tools.py | get_protected_page | def get_protected_page(url, user, pwd, filename):
"""
having problems with urllib on a specific site so trying requests
"""
import requests
r = requests.get(url, auth=(user, pwd))
print(r.status_code)
if r.status_code == 200:
print('success')
with open(filename, 'wb') as fd:
... | python | def get_protected_page(url, user, pwd, filename):
"""
having problems with urllib on a specific site so trying requests
"""
import requests
r = requests.get(url, auth=(user, pwd))
print(r.status_code)
if r.status_code == 200:
print('success')
with open(filename, 'wb') as fd:
... | [
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cox-labs/perseuspy | perseuspy/io/maxquant.py | read_rawFilesTable | def read_rawFilesTable(filename):
"""parse the 'rawFilesTable.txt' file into a pandas dataframe"""
exp = pd.read_table(filename)
expected_columns = {'File', 'Exists', 'Size', 'Data format', 'Parameter group', 'Experiment', 'Fraction'}
found_columns = set(exp.columns)
if len(expected_columns - found_... | python | def read_rawFilesTable(filename):
"""parse the 'rawFilesTable.txt' file into a pandas dataframe"""
exp = pd.read_table(filename)
expected_columns = {'File', 'Exists', 'Size', 'Data format', 'Parameter group', 'Experiment', 'Fraction'}
found_columns = set(exp.columns)
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nocarryr/python-dispatch | pydispatch/utils.py | WeakMethodContainer.add_method | def add_method(self, m, **kwargs):
"""Add an instance method or function
Args:
m: The instance method or function to store
"""
if isinstance(m, types.FunctionType):
self['function', id(m)] = m
else:
f, obj = get_method_vars(m)
wrke... | python | def add_method(self, m, **kwargs):
"""Add an instance method or function
Args:
m: The instance method or function to store
"""
if isinstance(m, types.FunctionType):
self['function', id(m)] = m
else:
f, obj = get_method_vars(m)
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nocarryr/python-dispatch | pydispatch/utils.py | WeakMethodContainer.del_method | def del_method(self, m):
"""Remove an instance method or function if it exists
Args:
m: The instance method or function to remove
"""
if isinstance(m, types.FunctionType) and not iscoroutinefunction(m):
wrkey = ('function', id(m))
else:
f, obj... | python | def del_method(self, m):
"""Remove an instance method or function if it exists
Args:
m: The instance method or function to remove
"""
if isinstance(m, types.FunctionType) and not iscoroutinefunction(m):
wrkey = ('function', id(m))
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