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flo-compbio/goparser | goparser/parser.py | GOParser.clear_annotation_data | def clear_annotation_data(self):
"""Clear annotation data.
Parameters
----------
Returns
-------
None
"""
self.genes = set()
self.annotations = []
self.term_annotations = {}
self.gene_annotations = {} | python | def clear_annotation_data(self):
"""Clear annotation data.
Parameters
----------
Returns
-------
None
"""
self.genes = set()
self.annotations = []
self.term_annotations = {}
self.gene_annotations = {} | [
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flo-compbio/goparser | goparser/parser.py | GOParser.parse_ontology | def parse_ontology(self, fn, flatten=True, part_of_cc_only=False):
""" Parse an OBO file and store GO term information.
This function needs to be called before `parse_annotations`, in order
to read in the Gene Ontology terms and structure.
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fn: str
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flo-compbio/goparser | goparser/parser.py | GOParser._flatten_ancestors | def _flatten_ancestors(self, include_part_of=True):
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include_part_of: bool, optional
Whether to include ``part_of`` relations in determining
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include_part_of: bool, optional
Whether to include ``part_of`` relations in determining
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flo-compbio/goparser | goparser/parser.py | GOParser.parse_annotations | def parse_annotations(
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flo-compbio/goparser | goparser/parser.py | GOParser.get_gene_goterms | def get_gene_goterms(self, gene, ancestors=False):
"""Return all GO terms a particular gene is annotated with.
Parameters
----------
gene: str
The gene symbol of the gene.
ancestors: bool, optional
If set to True, also return all ancestor GO terms.
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gene: str
The gene symbol of the gene.
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flo-compbio/goparser | goparser/parser.py | GOParser.get_goterm_genes | def get_goterm_genes(self, id_, descendants=True):
"""Return all genes that are annotated with a particular GO term.
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----------
id_: str
GO term ID of the GO term.
descendants: bool, optional
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GO term ID of the GO term.
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flo-compbio/goparser | goparser/parser.py | GOParser.get_gene_sets | def get_gene_sets(self, min_genes=None, max_genes=None):
"""Return the set of annotated genes for each GO term.
Parameters
----------
min_genes: int, optional
Exclude GO terms with fewer than this number of genes.
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openmeteo/pd2hts | pd2hts/__init__.py | _ReadFile.read_meta | def read_meta(self, f):
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majerteam/sqla_inspect | sqla_inspect/export.py | format_value | def format_value(column_dict, value, key=None):
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._is_excluded | def _is_excluded(self, prop, info_dict):
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._get_title | def _get_title(self, prop, main_infos, info_dict):
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._get_prop_infos | def _get_prop_infos(self, prop):
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._collect_headers | def _collect_headers(self):
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._collect_relationship | def _collect_relationship(self, main_infos, prop, result):
"""
collect a relationship header:
* One To many : if {'export': {'reletad_key': 'remote_attr'}} is
provided, we take all the related objects and join their remote
attr's value with commas
If an index... | python | def _collect_relationship(self, main_infos, prop, result):
"""
collect a relationship header:
* One To many : if {'export': {'reletad_key': 'remote_attr'}} is
provided, we take all the related objects and join their remote
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._merge_many_to_one_field | def _merge_many_to_one_field(self, main_infos, prop, result):
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* Find the foreignkey associated to the current relationship
* Get its title
* Remove this fkey field from the export
:param dict main_infos: The datas collected about the relationship
:param obj prop: The... | python | def _merge_many_to_one_field(self, main_infos, prop, result):
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* Get its title
* Remove this fkey field from the export
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._merge_many_to_one_field_from_fkey | def _merge_many_to_one_field_from_fkey(self, main_infos, prop, result):
"""
Find the relationship associated with this fkey and set the title
:param dict main_infos: The already collected datas about this column
:param obj prop: The property mapper of the relationship
:param lis... | python | def _merge_many_to_one_field_from_fkey(self, main_infos, prop, result):
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Find the relationship associated with this fkey and set the title
:param dict main_infos: The already collected datas about this column
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter.add_row | def add_row(self, obj):
"""
fill a new row with the given obj
obj
instance of the exporter's model
"""
row = {}
for column in self.headers:
value = ''
if '__col__' in column:
if isinstance(column['__col__'], C... | python | def add_row(self, obj):
"""
fill a new row with the given obj
obj
instance of the exporter's model
"""
row = {}
for column in self.headers:
value = ''
if '__col__' in column:
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._get_formatted_val | def _get_formatted_val(self, obj, name, column):
"""
Format the value of the attribute 'name' from the given object
"""
attr_path = name.split('.')
val = None
tmp_val = obj
for attr in attr_path:
tmp_val = getattr(tmp_val, attr, None)
if tm... | python | def _get_formatted_val(self, obj, name, column):
"""
Format the value of the attribute 'name' from the given object
"""
attr_path = name.split('.')
val = None
tmp_val = obj
for attr in attr_path:
tmp_val = getattr(tmp_val, attr, None)
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._get_relationship_cell_val | def _get_relationship_cell_val(self, obj, column):
"""
Return the value to insert in a relationship cell
"""
val = ""
key = column['key']
related_key = column.get('related_key', None)
related_obj = getattr(obj, key, None)
if related_obj is None:
... | python | def _get_relationship_cell_val(self, obj, column):
"""
Return the value to insert in a relationship cell
"""
val = ""
key = column['key']
related_key = column.get('related_key', None)
related_obj = getattr(obj, key, None)
if related_obj is None:
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majerteam/sqla_inspect | sqla_inspect/export.py | SqlaExporter._get_column_cell_val | def _get_column_cell_val(self, obj, column):
"""
Return a value of a "column" cell
"""
name = column['name']
return self._get_formatted_val(obj, name, column) | python | def _get_column_cell_val(self, obj, column):
"""
Return a value of a "column" cell
"""
name = column['name']
return self._get_formatted_val(obj, name, column) | [
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thespacedoctor/tastic | tastic/workspace/workspace.py | workspace.sort | def sort(self):
"""
*sort the workspace or individual taskpaper document via the workflow tags found in the settings file*
**Usage:**
To sort all of the taskpaper documents in the workspace via the workflow tag set with the settings file, for example:
.. code-block:: y... | python | def sort(self):
"""
*sort the workspace or individual taskpaper document via the workflow tags found in the settings file*
**Usage:**
To sort all of the taskpaper documents in the workspace via the workflow tag set with the settings file, for example:
.. code-block:: y... | [
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**Usage:**
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.. code-block:: yaml
workflowTags: "... | [
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thespacedoctor/tastic | tastic/workspace/workspace.py | workspace.archive_done | def archive_done(
self):
"""*move done tasks from the document's 'Archive' project into an adjacent markdown tasklog file*
**Usage:**
To move the archived tasks within a workspace's taskpaper docs into ``-tasklog.md`` files use the ``archive_done()`` method:
.. cod... | python | def archive_done(
self):
"""*move done tasks from the document's 'Archive' project into an adjacent markdown tasklog file*
**Usage:**
To move the archived tasks within a workspace's taskpaper docs into ``-tasklog.md`` files use the ``archive_done()`` method:
.. cod... | [
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.. code-block:: python
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thespacedoctor/tastic | tastic/workspace/workspace.py | workspace._get_all_taskpaper_files | def _get_all_taskpaper_files(
self):
"""*get a list of all the taskpaper filepaths in the workspace*
**Return:**
- ``taskpaperFiles`` -- a list of paths to all the taskpaper files within the workspace
"""
self.log.info('starting the ``_get_all_taskpaper_files`` m... | python | def _get_all_taskpaper_files(
self):
"""*get a list of all the taskpaper filepaths in the workspace*
**Return:**
- ``taskpaperFiles`` -- a list of paths to all the taskpaper files within the workspace
"""
self.log.info('starting the ``_get_all_taskpaper_files`` m... | [
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thespacedoctor/tastic | tastic/workspace/workspace.py | workspace._sort_tp_file | def _sort_tp_file(
self,
taskpaperPath):
"""*sort individual taskpaper documents*
**Key Arguments:**
- ``taskpaperPath`` -- path to a taskpaper file
**Return:**
- None
"""
self.log.info('starting the ``_sort_tp_file`` method')
... | python | def _sort_tp_file(
self,
taskpaperPath):
"""*sort individual taskpaper documents*
**Key Arguments:**
- ``taskpaperPath`` -- path to a taskpaper file
**Return:**
- None
"""
self.log.info('starting the ``_sort_tp_file`` method')
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thespacedoctor/tastic | tastic/workspace/workspace.py | workspace._archive_tp_file_done_tasks | def _archive_tp_file_done_tasks(
self,
taskpaperPath):
"""* archive tp file done tasks*
**Key Arguments:**
- ``taskpaperPath`` -- path to a taskpaper file
**Return:**
- None
"""
self.log.info('starting the ``_archive_tp_file_done_... | python | def _archive_tp_file_done_tasks(
self,
taskpaperPath):
"""* archive tp file done tasks*
**Key Arguments:**
- ``taskpaperPath`` -- path to a taskpaper file
**Return:**
- None
"""
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thespacedoctor/astrocalc | astrocalc/times/conversions.py | conversions.get | def get(self):
"""
*get the conversions object*
**Return:**
- ``conversions``
.. todo::
- @review: when complete, clean get method
- @review: when complete add logging
"""
self.log.info('starting the ``get`` method')
convers... | python | def get(self):
"""
*get the conversions object*
**Return:**
- ``conversions``
.. todo::
- @review: when complete, clean get method
- @review: when complete add logging
"""
self.log.info('starting the ``get`` method')
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thespacedoctor/astrocalc | astrocalc/times/conversions.py | conversions.ut_datetime_to_mjd | def ut_datetime_to_mjd(
self,
utDatetime):
"""*ut datetime to mjd*
If the date given has no time associated with it (e.g. ``20160426``), then the datetime assumed is ``20160426 00:00:00.0``.
Precision should be respected.
**Key Arguments:**
- ``utD... | python | def ut_datetime_to_mjd(
self,
utDatetime):
"""*ut datetime to mjd*
If the date given has no time associated with it (e.g. ``20160426``), then the datetime assumed is ``20160426 00:00:00.0``.
Precision should be respected.
**Key Arguments:**
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thespacedoctor/astrocalc | astrocalc/times/conversions.py | conversions.mjd_to_ut_datetime | def mjd_to_ut_datetime(
self,
mjd,
sqlDate=False,
datetimeObject=False):
"""*mjd to ut datetime*
Precision should be respected.
**Key Arguments:**
- ``mjd`` -- time in MJD.
- ``sqlDate`` -- add a 'T' between date and time... | python | def mjd_to_ut_datetime(
self,
mjd,
sqlDate=False,
datetimeObject=False):
"""*mjd to ut datetime*
Precision should be respected.
**Key Arguments:**
- ``mjd`` -- time in MJD.
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thespacedoctor/astrocalc | astrocalc/times/conversions.py | conversions.decimal_day_to_day_hour_min_sec | def decimal_day_to_day_hour_min_sec(
self,
daysFloat):
"""*Convert a day from decimal format to hours mins and sec*
Precision should be respected.
**Key Arguments:**
- ``daysFloat`` -- the day as a decimal.
**Return:**
- ``daysInt`` -- ... | python | def decimal_day_to_day_hour_min_sec(
self,
daysFloat):
"""*Convert a day from decimal format to hours mins and sec*
Precision should be respected.
**Key Arguments:**
- ``daysFloat`` -- the day as a decimal.
**Return:**
- ``daysInt`` -- ... | [
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PlatformStories/geojsontools | geojsontools/geojsontools.py | join | def join(input_files, output_file):
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Join geojsons into one. The spatial reference system of the output file is the same
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Args:
input_files (list): List of file name strings.
output_file (str): Output file name.
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PlatformStories/geojsontools | geojsontools/geojsontools.py | get_from | def get_from(input_file, property_names):
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Args:
input_file (str): File name.
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property_name (str): Property name.
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Find unique values of a given property in a geojson file.
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PlatformStories/geojsontools | geojsontools/geojsontools.py | filter_by_property | def filter_by_property(input_file, output_file, property_name, values):
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input_file (str): File name.
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PlatformStories/geojsontools | geojsontools/geojsontools.py | create_balanced_geojson | def create_balanced_geojson(input_file, classes, output_file='balanced.geojson',
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Create a geojson comprised of balanced classes from the class_name property in
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JukeboxPipeline/jukebox-core | src/jukeboxcore/launcher.py | Launcher.setup_manage_parser | def setup_manage_parser(self, parser):
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:type parser: :class:`argparse.ArgumentParser`
:returns: None
:rtype: None
:raises: None
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JukeboxPipeline/jukebox-core | src/jukeboxcore/launcher.py | Launcher.setup_compile_ui_parser | def setup_compile_ui_parser(self, parser):
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JukeboxPipeline/jukebox-core | src/jukeboxcore/launcher.py | Launcher.compile_ui | def compile_ui(self, namespace, unknown):
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JukeboxPipeline/jukebox-core | src/jukeboxcore/launcher.py | Launcher.setup_compile_rcc_parser | def setup_compile_rcc_parser(self, parser):
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lcgong/redbean | redbean/logs.py | setup_logging | def setup_logging(
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env_key='LOG_CFG'
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"""
path = config
value = os.getenv(env_key, None)
if value:
path = value
if path.exists():
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pip-services3-python/pip-services3-commons-python | pip_services3_commons/convert/ArrayConverter.py | ArrayConverter.to_nullable_array | def to_nullable_array(value):
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sbarham/dsrt | dsrt/data/transform/Vectorizer.py | Vectorizer.init_encoders | def init_encoders(self, config=DataConfig()):
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"""
self.log('info', 'Initializing the encoders ...')
# create the integer encoder and fit it to our corpus' vocab
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sbarham/dsrt | dsrt/data/transform/Vectorizer.py | Vectorizer.vectorize_dialogue | def vectorize_dialogue(self, dialogue, safe=True):
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theSage21/lanchat | lanchat/utils.py | get_server_sock | def get_server_sock():
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theSage21/lanchat | lanchat/utils.py | get_beacon | def get_beacon():
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endeepak/pungi | pungi/matchers.py | Base.message | def message(self):
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realestate-com-au/dashmat | dashmat/core_modules/splunk/splunk-sdk-1.3.0/splunklib/searchcommands/search_command.py | SearchCommand.options | def options(self):
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realestate-com-au/dashmat | dashmat/core_modules/splunk/splunk-sdk-1.3.0/splunklib/searchcommands/search_command.py | SearchCommand.search_results_info | def search_results_info(self):
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realestate-com-au/dashmat | dashmat/core_modules/splunk/splunk-sdk-1.3.0/splunklib/searchcommands/search_command.py | SearchCommand.service | def service(self):
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realestate-com-au/dashmat | dashmat/core_modules/splunk/splunk-sdk-1.3.0/splunklib/searchcommands/search_command.py | SearchCommand.process | def process(self, args=argv, input_file=stdin, output_file=stdout):
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gisce/heman | heman/auth/__init__.py | check_contract_allowed | def check_contract_allowed(func):
"""Check if Contract is allowed by token
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majerteam/sqla_inspect | sqla_inspect/py3o.py | SqlaContext.make_doc | def make_doc(self):
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majerteam/sqla_inspect | sqla_inspect/py3o.py | SqlaContext._get_to_many_relationship_value | def _get_to_many_relationship_value(self, obj, column):
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adsabs/adsutils | adsutils/sourcematchers.py | TrigdictSourceMatcher._addPub | def _addPub(self, stem, source):
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ringly/django-postgres-dbdefaults | setup.py | long_description | def long_description():
"""
Build the long description from a README file located in the same directory
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"""
base_path = os.path.dirname(os.path.realpath(__file__))
with io.open(os.path.join(base_path, 'README.md'), encoding='utf-8') as f:
return f.read() | python | def long_description():
"""
Build the long description from a README file located in the same directory
as this module.
"""
base_path = os.path.dirname(os.path.realpath(__file__))
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toumorokoshi/jenks | jenks/subcommand/build.py | get_build_info | def get_build_info(api_instance, build_id=None,
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output = ""
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""" print build info about a job """
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racker/python-twisted-service-registry-client | utils/dist.py | _filter_names | def _filter_names(names):
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racker/python-twisted-service-registry-client | utils/dist.py | relative_to | def relative_to(base, relativee):
"""
Gets 'relativee' relative to 'basepath'.
i.e.,
>>> relative_to('/home/', '/home/radix/')
'radix'
>>> relative_to('.', '/home/radix/Projects/Twisted') # curdir is /home/radix
'Projects/Twisted'
The 'relativee' must be a child of 'basepath'.
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"""
Gets 'relativee' relative to 'basepath'.
i.e.,
>>> relative_to('/home/', '/home/radix/')
'radix'
>>> relative_to('.', '/home/radix/Projects/Twisted') # curdir is /home/radix
'Projects/Twisted'
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Get all packages which are under dname. This is necessary for
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"""
Get all packages which are under dname. This is necessary for
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler._open | def _open(self, mode=None):
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Open the current base file with the (original) mode and encoding.
Return the resulting stream.
Note: Copied from stdlib. Added option to override 'mode'
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler.acquire | def acquire(self):
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# handle thread lock
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""" Acquire thread and file locks. Re-opening log for 'degraded' mode.
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler.release | def release(self):
""" Release file and thread locks. If in 'degraded' mode, close the
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if self._rotateFailed:
self._close()
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""" Release file and thread locks. If in 'degraded' mode, close the
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler.close | def close(self):
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Close log stream and stream_lock. """
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler._degrade | def _degrade(self, degrade, msg, *args):
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cltrudeau/wrench | wrench/logtools/srothandler.py | SizeRotatingFileHandler._degrade_debug | def _degrade_debug(self, degrade, msg, *args):
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roboogle/gtkmvc3 | gtkmvco/examples/custom_widget/htmltextview.py | _parse_css_color | def _parse_css_color(color):
'''_parse_css_color(css_color) -> gtk.gdk.Color'''
if color.startswith("rgb(") and color.endswith(')'):
r, g, b = [int(c)*257 for c in color[4:-1].split(',')]
return gtk.gdk.Color(r, g, b)
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return gtk.gdk.color_parse(color) | python | def _parse_css_color(color):
'''_parse_css_color(css_color) -> gtk.gdk.Color'''
if color.startswith("rgb(") and color.endswith(')'):
r, g, b = [int(c)*257 for c in color[4:-1].split(',')]
return gtk.gdk.Color(r, g, b)
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return gtk.gdk.color_parse(color) | [
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gevious/flask_slither | flask_slither/decorators.py | endpoint | def endpoint(f):
"""This decorator marks this method as an endpoint. It is responsible for
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def check_authentication(self, **kwargs):
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mikicz/arca | arca/_arca.py | Arca.get_backend_instance | def get_backend_instance(self, backend: BackendDefinitionType) -> BaseBackend:
""" Returns a backend instance, either from the argument or from the settings.
:raise ArcaMisconfigured: If the instance is not a subclass of :class:`BaseBackend`
"""
if backend is NOT_SET:
backen... | python | def get_backend_instance(self, backend: BackendDefinitionType) -> BaseBackend:
""" Returns a backend instance, either from the argument or from the settings.
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mikicz/arca | arca/_arca.py | Arca.make_region | def make_region(self) -> CacheRegion:
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mikicz/arca | arca/_arca.py | Arca.validate_repo_url | def validate_repo_url(self, repo: str):
""" Validates repo URL - if it's a valid git URL and if Arca can handle that type of repo URL
:raise ValueError: If the URL is not valid
"""
# that should match valid git repos
if not isinstance(repo, str) or not re.match(r"^(https?|file):... | python | def validate_repo_url(self, repo: str):
""" Validates repo URL - if it's a valid git URL and if Arca can handle that type of repo URL
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"""
# that should match valid git repos
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