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Semeru Lab 7

daskos/mentor

mentor/proxies/scheduler.py

SchedulerDriverProxy.acknowledge

def acknowledge(self, status): """Acknowledges the status update. This should only be called once the status update is processed durably by the scheduler. Not that explicit acknowledgements must be requested via the constructor argument, otherwise a call to this method will cause the driver to crash. """ logging.info('Acknowledges status update {}'.format(status)) return self.driver.acknowledgeStatusUpdate(encode(status))

python

def acknowledge(self, status): """Acknowledges the status update. This should only be called once the status update is processed durably by the scheduler. Not that explicit acknowledgements must be requested via the constructor argument, otherwise a call to this method will cause the driver to crash. """ logging.info('Acknowledges status update {}'.format(status)) return self.driver.acknowledgeStatusUpdate(encode(status))

Acknowledges the status update. This should only be called once the status update is processed durably by the scheduler. Not that explicit acknowledgements must be requested via the constructor argument, otherwise a call to this method will cause the driver to crash.

b5fd64e3a3192f5664fa5c03e8517cacb4e0590f

https://github.com/daskos/mentor/blob/b5fd64e3a3192f5664fa5c03e8517cacb4e0590f/mentor/proxies/scheduler.py#L221-L232

train

daskos/mentor

mentor/proxies/scheduler.py

SchedulerDriverProxy.message

def message(self, executor_id, slave_id, message): """Sends a message from the framework to one of its executors. These messages are best effort; do not expect a framework message to be retransmitted in any reliable fashion. """ logging.info('Sends message `{}` to executor `{}` on slave `{}`'.format( message, executor_id, slave_id)) return self.driver.sendFrameworkMessage(encode(executor_id), encode(slave_id), message)

python

def message(self, executor_id, slave_id, message): """Sends a message from the framework to one of its executors. These messages are best effort; do not expect a framework message to be retransmitted in any reliable fashion. """ logging.info('Sends message `{}` to executor `{}` on slave `{}`'.format( message, executor_id, slave_id)) return self.driver.sendFrameworkMessage(encode(executor_id), encode(slave_id), message)

Sends a message from the framework to one of its executors. These messages are best effort; do not expect a framework message to be retransmitted in any reliable fashion.

b5fd64e3a3192f5664fa5c03e8517cacb4e0590f

https://github.com/daskos/mentor/blob/b5fd64e3a3192f5664fa5c03e8517cacb4e0590f/mentor/proxies/scheduler.py#L234-L244

train

virtuald/pygi-composite-templates

gi_composites.py

_connect_func

def _connect_func(builder, obj, signal_name, handler_name, connect_object, flags, cls): '''Handles GtkBuilder signal connect events''' if connect_object is None: extra = () else: extra = (connect_object,) # The handler name refers to an attribute on the template instance, # so ask GtkBuilder for the template instance template_inst = builder.get_object(cls.__gtype_name__) if template_inst is None: # This should never happen errmsg = "Internal error: cannot find template instance! obj: %s; " \ "signal: %s; handler: %s; connect_obj: %s; class: %s" % \ (obj, signal_name, handler_name, connect_object, cls) warnings.warn(errmsg, GtkTemplateWarning) return handler = getattr(template_inst, handler_name) if flags == GObject.ConnectFlags.AFTER: obj.connect_after(signal_name, handler, *extra) else: obj.connect(signal_name, handler, *extra) template_inst.__connected_template_signals__.add(handler_name)

python

def _connect_func(builder, obj, signal_name, handler_name, connect_object, flags, cls): '''Handles GtkBuilder signal connect events''' if connect_object is None: extra = () else: extra = (connect_object,) # The handler name refers to an attribute on the template instance, # so ask GtkBuilder for the template instance template_inst = builder.get_object(cls.__gtype_name__) if template_inst is None: # This should never happen errmsg = "Internal error: cannot find template instance! obj: %s; " \ "signal: %s; handler: %s; connect_obj: %s; class: %s" % \ (obj, signal_name, handler_name, connect_object, cls) warnings.warn(errmsg, GtkTemplateWarning) return handler = getattr(template_inst, handler_name) if flags == GObject.ConnectFlags.AFTER: obj.connect_after(signal_name, handler, *extra) else: obj.connect(signal_name, handler, *extra) template_inst.__connected_template_signals__.add(handler_name)

Handles GtkBuilder signal connect events

a22be54ea95b8125b36deaa3ce7171e84158d486

https://github.com/virtuald/pygi-composite-templates/blob/a22be54ea95b8125b36deaa3ce7171e84158d486/gi_composites.py#L36-L63

train

virtuald/pygi-composite-templates

gi_composites.py

_register_template

def _register_template(cls, template_bytes): '''Registers the template for the widget and hooks init_template''' # This implementation won't work if there are nested templates, but # we can't do that anyways due to PyGObject limitations so it's ok if not hasattr(cls, 'set_template'): raise TypeError("Requires PyGObject 3.13.2 or greater") cls.set_template(template_bytes) bound_methods = set() bound_widgets = set() # Walk the class, find marked callbacks and child attributes for name in dir(cls): o = getattr(cls, name, None) if inspect.ismethod(o): if hasattr(o, '_gtk_callback'): bound_methods.add(name) # Don't need to call this, as connect_func always gets called #cls.bind_template_callback_full(name, o) elif isinstance(o, _Child): cls.bind_template_child_full(name, True, 0) bound_widgets.add(name) # Have to setup a special connect function to connect at template init # because the methods are not bound yet cls.set_connect_func(_connect_func, cls) cls.__gtemplate_methods__ = bound_methods cls.__gtemplate_widgets__ = bound_widgets base_init_template = cls.init_template cls.init_template = lambda s: _init_template(s, cls, base_init_template)

python

def _register_template(cls, template_bytes): '''Registers the template for the widget and hooks init_template''' # This implementation won't work if there are nested templates, but # we can't do that anyways due to PyGObject limitations so it's ok if not hasattr(cls, 'set_template'): raise TypeError("Requires PyGObject 3.13.2 or greater") cls.set_template(template_bytes) bound_methods = set() bound_widgets = set() # Walk the class, find marked callbacks and child attributes for name in dir(cls): o = getattr(cls, name, None) if inspect.ismethod(o): if hasattr(o, '_gtk_callback'): bound_methods.add(name) # Don't need to call this, as connect_func always gets called #cls.bind_template_callback_full(name, o) elif isinstance(o, _Child): cls.bind_template_child_full(name, True, 0) bound_widgets.add(name) # Have to setup a special connect function to connect at template init # because the methods are not bound yet cls.set_connect_func(_connect_func, cls) cls.__gtemplate_methods__ = bound_methods cls.__gtemplate_widgets__ = bound_widgets base_init_template = cls.init_template cls.init_template = lambda s: _init_template(s, cls, base_init_template)

Registers the template for the widget and hooks init_template

a22be54ea95b8125b36deaa3ce7171e84158d486

https://github.com/virtuald/pygi-composite-templates/blob/a22be54ea95b8125b36deaa3ce7171e84158d486/gi_composites.py#L66-L101

train

virtuald/pygi-composite-templates

gi_composites.py

_init_template

def _init_template(self, cls, base_init_template): '''This would be better as an override for Gtk.Widget''' # TODO: could disallow using a metaclass.. but this is good enough # .. if you disagree, feel free to fix it and issue a PR :) if self.__class__ is not cls: raise TypeError("Inheritance from classes with @GtkTemplate decorators " "is not allowed at this time") connected_signals = set() self.__connected_template_signals__ = connected_signals base_init_template(self) for name in self.__gtemplate_widgets__: widget = self.get_template_child(cls, name) self.__dict__[name] = widget if widget is None: # Bug: if you bind a template child, and one of them was # not present, then the whole template is broken (and # it's not currently possible for us to know which # one is broken either -- but the stderr should show # something useful with a Gtk-CRITICAL message) raise AttributeError("A missing child widget was set using " "GtkTemplate.Child and the entire " "template is now broken (widgets: %s)" % ', '.join(self.__gtemplate_widgets__)) for name in self.__gtemplate_methods__.difference(connected_signals): errmsg = ("Signal '%s' was declared with @GtkTemplate.Callback " + "but was not present in template") % name warnings.warn(errmsg, GtkTemplateWarning)

python

def _init_template(self, cls, base_init_template): '''This would be better as an override for Gtk.Widget''' # TODO: could disallow using a metaclass.. but this is good enough # .. if you disagree, feel free to fix it and issue a PR :) if self.__class__ is not cls: raise TypeError("Inheritance from classes with @GtkTemplate decorators " "is not allowed at this time") connected_signals = set() self.__connected_template_signals__ = connected_signals base_init_template(self) for name in self.__gtemplate_widgets__: widget = self.get_template_child(cls, name) self.__dict__[name] = widget if widget is None: # Bug: if you bind a template child, and one of them was # not present, then the whole template is broken (and # it's not currently possible for us to know which # one is broken either -- but the stderr should show # something useful with a Gtk-CRITICAL message) raise AttributeError("A missing child widget was set using " "GtkTemplate.Child and the entire " "template is now broken (widgets: %s)" % ', '.join(self.__gtemplate_widgets__)) for name in self.__gtemplate_methods__.difference(connected_signals): errmsg = ("Signal '%s' was declared with @GtkTemplate.Callback " + "but was not present in template") % name warnings.warn(errmsg, GtkTemplateWarning)

This would be better as an override for Gtk.Widget

a22be54ea95b8125b36deaa3ce7171e84158d486

https://github.com/virtuald/pygi-composite-templates/blob/a22be54ea95b8125b36deaa3ce7171e84158d486/gi_composites.py#L104-L136

train

mikeboers/PyHAML

haml/util.py

extract_haml

def extract_haml(fileobj, keywords, comment_tags, options): """ babel translation token extract function for haml files """ import haml from mako import lexer, parsetree from mako.ext.babelplugin import extract_nodes encoding = options.get('input_encoding', options.get('encoding', None)) template_node = lexer.Lexer(haml.preprocessor(fileobj.read()), input_encoding=encoding).parse() for extracted in extract_nodes(template_node.get_children(), keywords, comment_tags, options): yield extracted

python

def extract_haml(fileobj, keywords, comment_tags, options): """ babel translation token extract function for haml files """ import haml from mako import lexer, parsetree from mako.ext.babelplugin import extract_nodes encoding = options.get('input_encoding', options.get('encoding', None)) template_node = lexer.Lexer(haml.preprocessor(fileobj.read()), input_encoding=encoding).parse() for extracted in extract_nodes(template_node.get_children(), keywords, comment_tags, options): yield extracted

babel translation token extract function for haml files

9ecb7c85349948428474869aad5b8d1c7de8dbed

https://github.com/mikeboers/PyHAML/blob/9ecb7c85349948428474869aad5b8d1c7de8dbed/haml/util.py#L3-L13

train

openvax/isovar

isovar/read_helpers.py

get_single_allele_from_reads

def get_single_allele_from_reads(allele_reads): """ Given a sequence of AlleleRead objects, which are expected to all have the same allele, return that allele. """ allele_reads = list(allele_reads) if len(allele_reads) == 0: raise ValueError("Expected non-empty list of AlleleRead objects") seq = allele_reads[0].allele if any(read.allele != seq for read in allele_reads): raise ValueError("Expected all AlleleRead objects to have same allele '%s', got %s" % ( seq, allele_reads)) return seq

python

def get_single_allele_from_reads(allele_reads): """ Given a sequence of AlleleRead objects, which are expected to all have the same allele, return that allele. """ allele_reads = list(allele_reads) if len(allele_reads) == 0: raise ValueError("Expected non-empty list of AlleleRead objects") seq = allele_reads[0].allele if any(read.allele != seq for read in allele_reads): raise ValueError("Expected all AlleleRead objects to have same allele '%s', got %s" % ( seq, allele_reads)) return seq

Given a sequence of AlleleRead objects, which are expected to all have the same allele, return that allele.

b39b684920e3f6b344851d6598a1a1c67bce913b

https://github.com/openvax/isovar/blob/b39b684920e3f6b344851d6598a1a1c67bce913b/isovar/read_helpers.py#L25-L39

train

mikeboers/PyHAML

haml/nodes.py

Base.iter_all_children

def iter_all_children(self): '''Return an iterator that yields every node which is a child of this one. This includes inline children, and control structure `else` clauses. ''' if self.inline_child: yield self.inline_child for x in self.children: yield x

python

def iter_all_children(self): '''Return an iterator that yields every node which is a child of this one. This includes inline children, and control structure `else` clauses. ''' if self.inline_child: yield self.inline_child for x in self.children: yield x

Return an iterator that yields every node which is a child of this one. This includes inline children, and control structure `else` clauses.

9ecb7c85349948428474869aad5b8d1c7de8dbed

https://github.com/mikeboers/PyHAML/blob/9ecb7c85349948428474869aad5b8d1c7de8dbed/haml/nodes.py#L18-L27

train

pyviz/imagen

imagen/transferfn/__init__.py

TransferFn.initialize

def initialize(self, **kwargs): """ Transfer functions may need additional information before the supplied numpy array can be modified in place. For instance, transfer functions may have state which needs to be allocated in memory with a certain size. In other cases, the transfer function may need to know about the coordinate system associated with the input data. """ if not set(kwargs.keys()).issuperset(self.init_keys): raise Exception("TransferFn needs to be initialized with %s" % ','.join(repr(el) for el in self.init_keys))

python

def initialize(self, **kwargs): """ Transfer functions may need additional information before the supplied numpy array can be modified in place. For instance, transfer functions may have state which needs to be allocated in memory with a certain size. In other cases, the transfer function may need to know about the coordinate system associated with the input data. """ if not set(kwargs.keys()).issuperset(self.init_keys): raise Exception("TransferFn needs to be initialized with %s" % ','.join(repr(el) for el in self.init_keys))

Transfer functions may need additional information before the supplied numpy array can be modified in place. For instance, transfer functions may have state which needs to be allocated in memory with a certain size. In other cases, the transfer function may need to know about the coordinate system associated with the input data.

53c5685c880f54b42795964d8db50b02e8590e88

https://github.com/pyviz/imagen/blob/53c5685c880f54b42795964d8db50b02e8590e88/imagen/transferfn/__init__.py#L31-L42

train

pyviz/imagen

imagen/transferfn/__init__.py

TransferFnWithState.override_plasticity_state

def override_plasticity_state(self, new_plasticity_state): """ Temporarily disable plasticity of internal state. This function should be implemented by all subclasses so that after a call, the output should always be the same for any given input pattern, and no call should have any effect that persists after restore_plasticity_state() is called. By default, simply saves a copy of the 'plastic' parameter to an internal stack (so that it can be restored by restore_plasticity_state()), and then sets the plastic parameter to the given value (True or False). """ self._plasticity_setting_stack.append(self.plastic) self.plastic=new_plasticity_state

python

def override_plasticity_state(self, new_plasticity_state): """ Temporarily disable plasticity of internal state. This function should be implemented by all subclasses so that after a call, the output should always be the same for any given input pattern, and no call should have any effect that persists after restore_plasticity_state() is called. By default, simply saves a copy of the 'plastic' parameter to an internal stack (so that it can be restored by restore_plasticity_state()), and then sets the plastic parameter to the given value (True or False). """ self._plasticity_setting_stack.append(self.plastic) self.plastic=new_plasticity_state

Temporarily disable plasticity of internal state. This function should be implemented by all subclasses so that after a call, the output should always be the same for any given input pattern, and no call should have any effect that persists after restore_plasticity_state() is called. By default, simply saves a copy of the 'plastic' parameter to an internal stack (so that it can be restored by restore_plasticity_state()), and then sets the plastic parameter to the given value (True or False).

53c5685c880f54b42795964d8db50b02e8590e88

https://github.com/pyviz/imagen/blob/53c5685c880f54b42795964d8db50b02e8590e88/imagen/transferfn/__init__.py#L70-L85

train

pyblish/pyblish-houdini

pyblish_houdini/lib.py

register_host

def register_host(): """Register supported hosts""" pyblish.api.register_host("hython") pyblish.api.register_host("hpython") pyblish.api.register_host("houdini")

python

def register_host(): """Register supported hosts""" pyblish.api.register_host("hython") pyblish.api.register_host("hpython") pyblish.api.register_host("houdini")

Register supported hosts

661b08696f04b4c5d8b03aa0c75cba3ca72f1e8d

https://github.com/pyblish/pyblish-houdini/blob/661b08696f04b4c5d8b03aa0c75cba3ca72f1e8d/pyblish_houdini/lib.py#L80-L84

train

pyblish/pyblish-houdini

pyblish_houdini/lib.py

maintained_selection

def maintained_selection(): """Maintain selection during context Example: >>> with maintained_selection(): ... # Modify selection ... node.setSelected(on=False, clear_all_selected=True) >>> # Selection restored """ previous_selection = hou.selectedNodes() try: yield finally: if previous_selection: for node in previous_selection: node.setSelected(on=True) else: for node in previous_selection: node.setSelected(on=False)

python

def maintained_selection(): """Maintain selection during context Example: >>> with maintained_selection(): ... # Modify selection ... node.setSelected(on=False, clear_all_selected=True) >>> # Selection restored """ previous_selection = hou.selectedNodes() try: yield finally: if previous_selection: for node in previous_selection: node.setSelected(on=True) else: for node in previous_selection: node.setSelected(on=False)

Maintain selection during context Example: >>> with maintained_selection(): ... # Modify selection ... node.setSelected(on=False, clear_all_selected=True) >>> # Selection restored

661b08696f04b4c5d8b03aa0c75cba3ca72f1e8d

https://github.com/pyblish/pyblish-houdini/blob/661b08696f04b4c5d8b03aa0c75cba3ca72f1e8d/pyblish_houdini/lib.py#L104-L124

train

portfoliome/postpy

postpy/sql.py

execute_transaction

def execute_transaction(conn, statements: Iterable): """Execute several statements in single DB transaction.""" with conn: with conn.cursor() as cursor: for statement in statements: cursor.execute(statement) conn.commit()

python

def execute_transaction(conn, statements: Iterable): """Execute several statements in single DB transaction.""" with conn: with conn.cursor() as cursor: for statement in statements: cursor.execute(statement) conn.commit()

Execute several statements in single DB transaction.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L10-L17

train

portfoliome/postpy

postpy/sql.py

execute_transactions

def execute_transactions(conn, statements: Iterable): """Execute several statements each as a single DB transaction.""" with conn.cursor() as cursor: for statement in statements: try: cursor.execute(statement) conn.commit() except psycopg2.ProgrammingError: conn.rollback()

python

def execute_transactions(conn, statements: Iterable): """Execute several statements each as a single DB transaction.""" with conn.cursor() as cursor: for statement in statements: try: cursor.execute(statement) conn.commit() except psycopg2.ProgrammingError: conn.rollback()

Execute several statements each as a single DB transaction.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L20-L29

train

portfoliome/postpy

postpy/sql.py

execute_closing_transaction

def execute_closing_transaction(statements: Iterable): """Open a connection, commit a transaction, and close it.""" with closing(connect()) as conn: with conn.cursor() as cursor: for statement in statements: cursor.execute(statement)

python

def execute_closing_transaction(statements: Iterable): """Open a connection, commit a transaction, and close it.""" with closing(connect()) as conn: with conn.cursor() as cursor: for statement in statements: cursor.execute(statement)

Open a connection, commit a transaction, and close it.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L32-L38

train

portfoliome/postpy

postpy/sql.py

select

def select(conn, query: str, params=None, name=None, itersize=5000): """Return a select statement's results as a namedtuple. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server. """ with conn.cursor(name, cursor_factory=NamedTupleCursor) as cursor: cursor.itersize = itersize cursor.execute(query, params) for result in cursor: yield result

python

def select(conn, query: str, params=None, name=None, itersize=5000): """Return a select statement's results as a namedtuple. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server. """ with conn.cursor(name, cursor_factory=NamedTupleCursor) as cursor: cursor.itersize = itersize cursor.execute(query, params) for result in cursor: yield result

Return a select statement's results as a namedtuple. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L41-L58

train

portfoliome/postpy

postpy/sql.py

select_dict

def select_dict(conn, query: str, params=None, name=None, itersize=5000): """Return a select statement's results as dictionary. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server. """ with conn.cursor(name, cursor_factory=RealDictCursor) as cursor: cursor.itersize = itersize cursor.execute(query, params) for result in cursor: yield result

python

def select_dict(conn, query: str, params=None, name=None, itersize=5000): """Return a select statement's results as dictionary. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server. """ with conn.cursor(name, cursor_factory=RealDictCursor) as cursor: cursor.itersize = itersize cursor.execute(query, params) for result in cursor: yield result

Return a select statement's results as dictionary. Parameters ---------- conn : database connection query : select query string params : query parameters. name : server side cursor name. defaults to client side. itersize : number of records fetched by server.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L61-L78

train

portfoliome/postpy

postpy/sql.py

select_each

def select_each(conn, query: str, parameter_groups, name=None): """Run select query for each parameter set in single transaction.""" with conn: with conn.cursor(name=name) as cursor: for parameters in parameter_groups: cursor.execute(query, parameters) yield cursor.fetchone()

python

def select_each(conn, query: str, parameter_groups, name=None): """Run select query for each parameter set in single transaction.""" with conn: with conn.cursor(name=name) as cursor: for parameters in parameter_groups: cursor.execute(query, parameters) yield cursor.fetchone()

Run select query for each parameter set in single transaction.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L81-L88

train

portfoliome/postpy

postpy/sql.py

query_columns

def query_columns(conn, query, name=None): """Lightweight query to retrieve column list of select query. Notes ----- Strongly urged to specify a cursor name for performance. """ with conn.cursor(name) as cursor: cursor.itersize = 1 cursor.execute(query) cursor.fetchmany(0) column_names = [column.name for column in cursor.description] return column_names

python

def query_columns(conn, query, name=None): """Lightweight query to retrieve column list of select query. Notes ----- Strongly urged to specify a cursor name for performance. """ with conn.cursor(name) as cursor: cursor.itersize = 1 cursor.execute(query) cursor.fetchmany(0) column_names = [column.name for column in cursor.description] return column_names

Lightweight query to retrieve column list of select query. Notes ----- Strongly urged to specify a cursor name for performance.

fe26199131b15295fc5f669a0ad2a7f47bf490ee

https://github.com/portfoliome/postpy/blob/fe26199131b15295fc5f669a0ad2a7f47bf490ee/postpy/sql.py#L91-L105

train

openvax/isovar

isovar/reference_coding_sequence_key.py

ReferenceCodingSequenceKey.from_variant_and_transcript

def from_variant_and_transcript( cls, variant, transcript, context_size): """ Extracts the reference sequence around a variant locus on a particular transcript and determines the reading frame at the start of that sequence context. Parameters ---------- variant : varcode.Variant transcript : pyensembl.Transcript context_size : int Returns SequenceKeyWithReadingFrame object or None if Transcript lacks coding sequence, protein sequence or annotated start/stop codons. """ if not transcript.contains_start_codon: logger.info( "Expected transcript %s for variant %s to have start codon", transcript.name, variant) return None if not transcript.contains_stop_codon: logger.info( "Expected transcript %s for variant %s to have stop codon", transcript.name, variant) return None if not transcript.protein_sequence: logger.info( "Expected transript %s for variant %s to have protein sequence", transcript.name, variant) return None sequence_key = ReferenceSequenceKey.from_variant_and_transcript( variant=variant, transcript=transcript, context_size=context_size) if sequence_key is None: logger.info( "No sequence key for variant %s on transcript %s", variant, transcript.name) return None return cls.from_variant_and_transcript_and_sequence_key( variant=variant, transcript=transcript, sequence_key=sequence_key)

python

def from_variant_and_transcript( cls, variant, transcript, context_size): """ Extracts the reference sequence around a variant locus on a particular transcript and determines the reading frame at the start of that sequence context. Parameters ---------- variant : varcode.Variant transcript : pyensembl.Transcript context_size : int Returns SequenceKeyWithReadingFrame object or None if Transcript lacks coding sequence, protein sequence or annotated start/stop codons. """ if not transcript.contains_start_codon: logger.info( "Expected transcript %s for variant %s to have start codon", transcript.name, variant) return None if not transcript.contains_stop_codon: logger.info( "Expected transcript %s for variant %s to have stop codon", transcript.name, variant) return None if not transcript.protein_sequence: logger.info( "Expected transript %s for variant %s to have protein sequence", transcript.name, variant) return None sequence_key = ReferenceSequenceKey.from_variant_and_transcript( variant=variant, transcript=transcript, context_size=context_size) if sequence_key is None: logger.info( "No sequence key for variant %s on transcript %s", variant, transcript.name) return None return cls.from_variant_and_transcript_and_sequence_key( variant=variant, transcript=transcript, sequence_key=sequence_key)

Extracts the reference sequence around a variant locus on a particular transcript and determines the reading frame at the start of that sequence context. Parameters ---------- variant : varcode.Variant transcript : pyensembl.Transcript context_size : int Returns SequenceKeyWithReadingFrame object or None if Transcript lacks coding sequence, protein sequence or annotated start/stop codons.

b39b684920e3f6b344851d6598a1a1c67bce913b

https://github.com/openvax/isovar/blob/b39b684920e3f6b344851d6598a1a1c67bce913b/isovar/reference_coding_sequence_key.py#L150-L207

train

theno/fabsetup

setup.py

create_readme_with_long_description

def create_readme_with_long_description(): '''Try to convert content of README.md into rst format using pypandoc, write it into README and return it. If pypandoc cannot be imported write content of README.md unchanged into README and return it. ''' this_dir = os.path.abspath(os.path.dirname(__file__)) readme_md = os.path.join(this_dir, 'README.md') readme = os.path.join(this_dir, 'README') if os.path.exists(readme_md): # this is the case when running `python setup.py sdist` if os.path.exists(readme): os.remove(readme) try: import pypandoc long_description = pypandoc.convert(readme_md, 'rst', format='md') except(ImportError): with open(readme_md, encoding='utf-8') as in_: long_description = in_.read() with open(readme, 'w') as out: out.write(long_description) else: # this is in case of `pip install fabsetup-x.y.z.tar.gz` with open(readme, encoding='utf-8') as in_: long_description = in_.read() return long_description

python

def create_readme_with_long_description(): '''Try to convert content of README.md into rst format using pypandoc, write it into README and return it. If pypandoc cannot be imported write content of README.md unchanged into README and return it. ''' this_dir = os.path.abspath(os.path.dirname(__file__)) readme_md = os.path.join(this_dir, 'README.md') readme = os.path.join(this_dir, 'README') if os.path.exists(readme_md): # this is the case when running `python setup.py sdist` if os.path.exists(readme): os.remove(readme) try: import pypandoc long_description = pypandoc.convert(readme_md, 'rst', format='md') except(ImportError): with open(readme_md, encoding='utf-8') as in_: long_description = in_.read() with open(readme, 'w') as out: out.write(long_description) else: # this is in case of `pip install fabsetup-x.y.z.tar.gz` with open(readme, encoding='utf-8') as in_: long_description = in_.read() return long_description

Try to convert content of README.md into rst format using pypandoc, write it into README and return it. If pypandoc cannot be imported write content of README.md unchanged into README and return it.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/setup.py#L13-L44

train

sloria/pypi-cli

pypi_cli.py

stat

def stat(package, graph): """Print download statistics for a package. \b Example: pypi stat requests """ client = requests.Session() for name_or_url in package: package = get_package(name_or_url, client) if not package: secho(u'Invalid name or URL: "{name}"'.format(name=name_or_url), fg='red', file=sys.stderr) continue try: version_downloads = package.version_downloads except NotFoundError: secho(u'No versions found for "{0}". ' u'Skipping. . .'.format(package.name), fg='red', file=sys.stderr) continue echo(u"Fetching statistics for '{url}'. . .".format( url=package.package_url)) min_ver, min_downloads = package.min_version max_ver, max_downloads = package.max_version if min_ver is None or max_ver is None: raise click.ClickException('Package has no releases') avg_downloads = package.average_downloads total = package.downloads echo() header = u'Download statistics for {name}'.format(name=package.name) echo_header(header) if graph: echo() echo('Downloads by version') echo(package.chart()) echo() echo("Min downloads: {min_downloads:12,} ({min_ver})".format( **locals())) echo("Max downloads: {max_downloads:12,} ({max_ver})".format( **locals())) echo("Avg downloads: {avg_downloads:12,}".format(**locals())) echo("Total downloads: {total:12,}".format(**locals())) echo() echo_download_summary(package) echo()

python

def stat(package, graph): """Print download statistics for a package. \b Example: pypi stat requests """ client = requests.Session() for name_or_url in package: package = get_package(name_or_url, client) if not package: secho(u'Invalid name or URL: "{name}"'.format(name=name_or_url), fg='red', file=sys.stderr) continue try: version_downloads = package.version_downloads except NotFoundError: secho(u'No versions found for "{0}". ' u'Skipping. . .'.format(package.name), fg='red', file=sys.stderr) continue echo(u"Fetching statistics for '{url}'. . .".format( url=package.package_url)) min_ver, min_downloads = package.min_version max_ver, max_downloads = package.max_version if min_ver is None or max_ver is None: raise click.ClickException('Package has no releases') avg_downloads = package.average_downloads total = package.downloads echo() header = u'Download statistics for {name}'.format(name=package.name) echo_header(header) if graph: echo() echo('Downloads by version') echo(package.chart()) echo() echo("Min downloads: {min_downloads:12,} ({min_ver})".format( **locals())) echo("Max downloads: {max_downloads:12,} ({max_ver})".format( **locals())) echo("Avg downloads: {avg_downloads:12,}".format(**locals())) echo("Total downloads: {total:12,}".format(**locals())) echo() echo_download_summary(package) echo()

Print download statistics for a package. \b Example: pypi stat requests

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L97-L143

train

sloria/pypi-cli

pypi_cli.py

browse

def browse(package, homepage): """Browse to a package's PyPI or project homepage.""" p = Package(package) try: if homepage: secho(u'Opening homepage for "{0}"...'.format(package), bold=True) url = p.home_page else: secho(u'Opening PyPI page for "{0}"...'.format(package), bold=True) url = p.package_url except NotFoundError: abort_not_found(package) click.launch(url)

python

def browse(package, homepage): """Browse to a package's PyPI or project homepage.""" p = Package(package) try: if homepage: secho(u'Opening homepage for "{0}"...'.format(package), bold=True) url = p.home_page else: secho(u'Opening PyPI page for "{0}"...'.format(package), bold=True) url = p.package_url except NotFoundError: abort_not_found(package) click.launch(url)

Browse to a package's PyPI or project homepage.

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L157-L169

train

sloria/pypi-cli

pypi_cli.py

search

def search(query, n_results, web): """Search for a pypi package. \b Examples: \b pypi search requests pypi search 'requests oauth' pypi search requests -n 20 pypi search 'requests toolbelt' --web """ if web: secho(u'Opening search page for "{0}"...'.format(query), bold=True) url = SEARCH_URL.format(query=urlquote(query)) click.launch(url) else: searcher = Searcher() results = searcher.search(query, n=n_results) first_line = style(u'Search results for "{0}"\n'.format(query), bold=True) echo_via_pager( first_line + '\n'.join([format_result(result) for result in results]) )

python

def search(query, n_results, web): """Search for a pypi package. \b Examples: \b pypi search requests pypi search 'requests oauth' pypi search requests -n 20 pypi search 'requests toolbelt' --web """ if web: secho(u'Opening search page for "{0}"...'.format(query), bold=True) url = SEARCH_URL.format(query=urlquote(query)) click.launch(url) else: searcher = Searcher() results = searcher.search(query, n=n_results) first_line = style(u'Search results for "{0}"\n'.format(query), bold=True) echo_via_pager( first_line + '\n'.join([format_result(result) for result in results]) )

Search for a pypi package. \b Examples: \b pypi search requests pypi search 'requests oauth' pypi search requests -n 20 pypi search 'requests toolbelt' --web

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L192-L216

train

sloria/pypi-cli

pypi_cli.py

info

def info(package, long_description, classifiers, license): """Get info about a package or packages. """ client = requests.Session() for name_or_url in package: package = get_package(name_or_url, client) if not package: secho(u'Invalid name or URL: "{name}"'.format(name=name_or_url), fg='red', file=sys.stderr) continue # Name and summary try: info = package.data['info'] except NotFoundError: secho(u'No versions found for "{0}". ' u'Skipping. . .'.format(package.name), fg='red', file=sys.stderr) continue echo_header(name_or_url) if package.summary: echo(package.summary) # Version info echo() echo('Latest release: {version:12}'.format(version=info['version'])) # Long description if long_description: echo() echo(package.description) # Download info echo() echo_download_summary(package) # Author info echo() author, author_email = package.author, package.author_email if author: echo(u'Author: {author:12}'.format(**locals())) if author_email: echo(u'Author email: {author_email:12}'.format(**locals())) # Maintainer info maintainer, maintainer_email = (package.maintainer, package.maintainer_email) if maintainer or maintainer_email: echo() if maintainer: echo(u'Maintainer: {maintainer:12}'.format(**locals())) if maintainer_email: echo(u'Maintainer email: {maintainer_email:12}'.format(**locals())) # URLS echo() echo(u'PyPI URL: {pypi_url:12}'.format(pypi_url=package.package_url)) if package.home_page: echo(u'Home Page: {home_page:12}'.format( home_page=package.home_page)) if package.docs_url: echo(u'Documentation: {docs_url:12}'.format( docs_url=package.docs_url)) # Classifiers if classifiers: echo() echo(u'Classifiers: ') for each in info.get('classifiers', []): echo('\t' + each) if license and package.license: echo() echo(u'License: ', nl=False) # license may be just a name, e.g. 'BSD' or the full license text # If a new line is found in the text, print a new line if package.license.find('\n') >= 0 or len(package.license) > 80: echo() echo(package.license) echo()

python

def info(package, long_description, classifiers, license): """Get info about a package or packages. """ client = requests.Session() for name_or_url in package: package = get_package(name_or_url, client) if not package: secho(u'Invalid name or URL: "{name}"'.format(name=name_or_url), fg='red', file=sys.stderr) continue # Name and summary try: info = package.data['info'] except NotFoundError: secho(u'No versions found for "{0}". ' u'Skipping. . .'.format(package.name), fg='red', file=sys.stderr) continue echo_header(name_or_url) if package.summary: echo(package.summary) # Version info echo() echo('Latest release: {version:12}'.format(version=info['version'])) # Long description if long_description: echo() echo(package.description) # Download info echo() echo_download_summary(package) # Author info echo() author, author_email = package.author, package.author_email if author: echo(u'Author: {author:12}'.format(**locals())) if author_email: echo(u'Author email: {author_email:12}'.format(**locals())) # Maintainer info maintainer, maintainer_email = (package.maintainer, package.maintainer_email) if maintainer or maintainer_email: echo() if maintainer: echo(u'Maintainer: {maintainer:12}'.format(**locals())) if maintainer_email: echo(u'Maintainer email: {maintainer_email:12}'.format(**locals())) # URLS echo() echo(u'PyPI URL: {pypi_url:12}'.format(pypi_url=package.package_url)) if package.home_page: echo(u'Home Page: {home_page:12}'.format( home_page=package.home_page)) if package.docs_url: echo(u'Documentation: {docs_url:12}'.format( docs_url=package.docs_url)) # Classifiers if classifiers: echo() echo(u'Classifiers: ') for each in info.get('classifiers', []): echo('\t' + each) if license and package.license: echo() echo(u'License: ', nl=False) # license may be just a name, e.g. 'BSD' or the full license text # If a new line is found in the text, print a new line if package.license.find('\n') >= 0 or len(package.license) > 80: echo() echo(package.license) echo()

Get info about a package or packages.

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L227-L306

train

sloria/pypi-cli

pypi_cli.py

bargraph

def bargraph(data, max_key_width=30): """Return a bar graph as a string, given a dictionary of data.""" lines = [] max_length = min(max(len(key) for key in data.keys()), max_key_width) max_val = max(data.values()) max_val_length = max( len(_style_value(val)) for val in data.values()) term_width = get_terminal_size()[0] max_bar_width = term_width - MARGIN - (max_length + 3 + max_val_length + 3) template = u"{key:{key_width}} [ {value:{val_width}} ] {bar}" for key, value in data.items(): try: bar = int(math.ceil(max_bar_width * value / max_val)) * TICK except ZeroDivisionError: bar = '' line = template.format( key=key[:max_length], value=_style_value(value), bar=bar, key_width=max_length, val_width=max_val_length ) lines.append(line) return '\n'.join(lines)

python

def bargraph(data, max_key_width=30): """Return a bar graph as a string, given a dictionary of data.""" lines = [] max_length = min(max(len(key) for key in data.keys()), max_key_width) max_val = max(data.values()) max_val_length = max( len(_style_value(val)) for val in data.values()) term_width = get_terminal_size()[0] max_bar_width = term_width - MARGIN - (max_length + 3 + max_val_length + 3) template = u"{key:{key_width}} [ {value:{val_width}} ] {bar}" for key, value in data.items(): try: bar = int(math.ceil(max_bar_width * value / max_val)) * TICK except ZeroDivisionError: bar = '' line = template.format( key=key[:max_length], value=_style_value(value), bar=bar, key_width=max_length, val_width=max_val_length ) lines.append(line) return '\n'.join(lines)

Return a bar graph as a string, given a dictionary of data.

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L328-L352

train

sloria/pypi-cli

pypi_cli.py

Package.max_version

def max_version(self): """Version with the most downloads. :return: A tuple of the form (version, n_downloads) """ data = self.version_downloads if not data: return None, 0 return max(data.items(), key=lambda item: item[1])

python

def max_version(self): """Version with the most downloads. :return: A tuple of the form (version, n_downloads) """ data = self.version_downloads if not data: return None, 0 return max(data.items(), key=lambda item: item[1])

Version with the most downloads. :return: A tuple of the form (version, n_downloads)

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L440-L448

train

sloria/pypi-cli

pypi_cli.py

Package.min_version

def min_version(self): """Version with the fewest downloads.""" data = self.version_downloads if not data: return (None, 0) return min(data.items(), key=lambda item: item[1])

python

def min_version(self): """Version with the fewest downloads.""" data = self.version_downloads if not data: return (None, 0) return min(data.items(), key=lambda item: item[1])

Version with the fewest downloads.

beb007bf2bdd285209876ce2758982b5d8b54d5d

https://github.com/sloria/pypi-cli/blob/beb007bf2bdd285209876ce2758982b5d8b54d5d/pypi_cli.py#L451-L456

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

ripping_of_cds

def ripping_of_cds(): '''Install the tools ripit and burnit in order to rip and burn audio cds. More info: http://forums.debian.net/viewtopic.php?f=16&t=36826 ''' # install and configure ripit install_package('ripit') install_file_legacy(path='~/.ripit/config', username=env.user) # install burnit run('mkdir -p ~/bin') install_file_legacy('~/bin/burnit') run('chmod 755 ~/bin/burnit')

python

def ripping_of_cds(): '''Install the tools ripit and burnit in order to rip and burn audio cds. More info: http://forums.debian.net/viewtopic.php?f=16&t=36826 ''' # install and configure ripit install_package('ripit') install_file_legacy(path='~/.ripit/config', username=env.user) # install burnit run('mkdir -p ~/bin') install_file_legacy('~/bin/burnit') run('chmod 755 ~/bin/burnit')

Install the tools ripit and burnit in order to rip and burn audio cds. More info: http://forums.debian.net/viewtopic.php?f=16&t=36826

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L34-L45

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

i3

def i3(): '''Install and customize the tiling window manager i3.''' install_package('i3') install_file_legacy(path='~/.i3/config', username=env.user, repos_dir='repos') # setup: hide the mouse if not in use # in ~/.i3/config: 'exec /home/<USERNAME>/repos/hhpc/hhpc -i 10 &' install_packages(['make', 'pkg-config', 'gcc', 'libc6-dev', 'libx11-dev']) checkup_git_repo_legacy(url='https://github.com/aktau/hhpc.git') run('cd ~/repos/hhpc && make')

python

def i3(): '''Install and customize the tiling window manager i3.''' install_package('i3') install_file_legacy(path='~/.i3/config', username=env.user, repos_dir='repos') # setup: hide the mouse if not in use # in ~/.i3/config: 'exec /home/<USERNAME>/repos/hhpc/hhpc -i 10 &' install_packages(['make', 'pkg-config', 'gcc', 'libc6-dev', 'libx11-dev']) checkup_git_repo_legacy(url='https://github.com/aktau/hhpc.git') run('cd ~/repos/hhpc && make')

Install and customize the tiling window manager i3.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L78-L87

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

solarized

def solarized(): '''Set solarized colors in urxvt, tmux, and vim. More Infos: * Getting solarized colors right with urxvt, st, tmux and vim: https://bbs.archlinux.org/viewtopic.php?id=164108 * Creating ~/.Xresources: https://wiki.archlinux.org/index.php/Rxvt-unicode#Creating_.7E.2F.Xresources * Select a good font on Ubuntu: https://michaelheap.com/getting-solarized-working-on-ubuntu/ * tmux and 256 colors: http://unix.stackexchange.com/a/118903 ''' install_packages(['rxvt-unicode', 'tmux', 'vim']) install_file_legacy('~/.Xresources') if env.host_string == 'localhost': run('xrdb ~/.Xresources') # install and call term_colors run('mkdir -p ~/bin') install_file_legacy('~/bin/term_colors') run('chmod 755 ~/bin/term_colors') run('~/bin/term_colors')

python

def solarized(): '''Set solarized colors in urxvt, tmux, and vim. More Infos: * Getting solarized colors right with urxvt, st, tmux and vim: https://bbs.archlinux.org/viewtopic.php?id=164108 * Creating ~/.Xresources: https://wiki.archlinux.org/index.php/Rxvt-unicode#Creating_.7E.2F.Xresources * Select a good font on Ubuntu: https://michaelheap.com/getting-solarized-working-on-ubuntu/ * tmux and 256 colors: http://unix.stackexchange.com/a/118903 ''' install_packages(['rxvt-unicode', 'tmux', 'vim']) install_file_legacy('~/.Xresources') if env.host_string == 'localhost': run('xrdb ~/.Xresources') # install and call term_colors run('mkdir -p ~/bin') install_file_legacy('~/bin/term_colors') run('chmod 755 ~/bin/term_colors') run('~/bin/term_colors')

Set solarized colors in urxvt, tmux, and vim. More Infos: * Getting solarized colors right with urxvt, st, tmux and vim: https://bbs.archlinux.org/viewtopic.php?id=164108 * Creating ~/.Xresources: https://wiki.archlinux.org/index.php/Rxvt-unicode#Creating_.7E.2F.Xresources * Select a good font on Ubuntu: https://michaelheap.com/getting-solarized-working-on-ubuntu/ * tmux and 256 colors: http://unix.stackexchange.com/a/118903

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L92-L117

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

vim

def vim(): '''Customize vim, install package manager pathogen and some vim-packages. pathogen will be installed as a git repo at ~/repos/vim-pathogen and activated in vim by a symbolic link at ~/.vim/autoload/pathogen.vim A ~/.vimrc will be installed which loads the package manager within of vim. The vim packages vim-colors-solarized, nerdtree, and tagbar are installed as git repos placed at dir ~/.vim/bundle/ If you want to install more vim packages also place them at this dir, cf. https://logicalfriday.com/2011/07/18/using-vim-with-pathogen/ ''' install_package('vim') print_msg('## install ~/.vimrc\n') install_file_legacy('~/.vimrc') print_msg('\n## set up pathogen\n') run('mkdir -p ~/.vim/autoload ~/.vim/bundle') checkup_git_repo_legacy(url='https://github.com/tpope/vim-pathogen.git') run('ln -snf ~/repos/vim-pathogen/autoload/pathogen.vim ' '~/.vim/autoload/pathogen.vim') print_msg('\n## install vim packages\n') install_package('ctags') # required by package tagbar repos = [ { 'name': 'vim-colors-solarized', 'url': 'git://github.com/altercation/vim-colors-solarized.git', }, { 'name': 'nerdtree', 'url': 'https://github.com/scrooloose/nerdtree.git', }, { 'name': 'vim-nerdtree-tabs', 'url': 'https://github.com/jistr/vim-nerdtree-tabs.git', }, { 'name': 'tagbar', 'url': 'https://github.com/majutsushi/tagbar.git', }, ] checkup_git_repos_legacy(repos, base_dir='~/.vim/bundle')

python

def vim(): '''Customize vim, install package manager pathogen and some vim-packages. pathogen will be installed as a git repo at ~/repos/vim-pathogen and activated in vim by a symbolic link at ~/.vim/autoload/pathogen.vim A ~/.vimrc will be installed which loads the package manager within of vim. The vim packages vim-colors-solarized, nerdtree, and tagbar are installed as git repos placed at dir ~/.vim/bundle/ If you want to install more vim packages also place them at this dir, cf. https://logicalfriday.com/2011/07/18/using-vim-with-pathogen/ ''' install_package('vim') print_msg('## install ~/.vimrc\n') install_file_legacy('~/.vimrc') print_msg('\n## set up pathogen\n') run('mkdir -p ~/.vim/autoload ~/.vim/bundle') checkup_git_repo_legacy(url='https://github.com/tpope/vim-pathogen.git') run('ln -snf ~/repos/vim-pathogen/autoload/pathogen.vim ' '~/.vim/autoload/pathogen.vim') print_msg('\n## install vim packages\n') install_package('ctags') # required by package tagbar repos = [ { 'name': 'vim-colors-solarized', 'url': 'git://github.com/altercation/vim-colors-solarized.git', }, { 'name': 'nerdtree', 'url': 'https://github.com/scrooloose/nerdtree.git', }, { 'name': 'vim-nerdtree-tabs', 'url': 'https://github.com/jistr/vim-nerdtree-tabs.git', }, { 'name': 'tagbar', 'url': 'https://github.com/majutsushi/tagbar.git', }, ] checkup_git_repos_legacy(repos, base_dir='~/.vim/bundle')

Customize vim, install package manager pathogen and some vim-packages. pathogen will be installed as a git repo at ~/repos/vim-pathogen and activated in vim by a symbolic link at ~/.vim/autoload/pathogen.vim A ~/.vimrc will be installed which loads the package manager within of vim. The vim packages vim-colors-solarized, nerdtree, and tagbar are installed as git repos placed at dir ~/.vim/bundle/ If you want to install more vim packages also place them at this dir, cf. https://logicalfriday.com/2011/07/18/using-vim-with-pathogen/

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L122-L167

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

pyenv

def pyenv(): '''Install or update the pyenv python environment. Checkout or update the pyenv repo at ~/.pyenv and enable the pyenv. Pyenv wird also als Github-Repo "installiert" unter ~/.pyenv More info: * https://github.com/yyuu/pyenv * https://github.com/yyuu/pyenv/wiki/Common-build-problems#requirements Tutorial: * http://amaral-lab.org/resources/guides/pyenv-tutorial ''' install_packages([ 'make', 'build-essential', 'libssl-dev', 'zlib1g-dev', 'libbz2-dev', 'libreadline-dev', 'libsqlite3-dev', 'wget', 'curl', 'llvm', 'libncurses5-dev', 'libncursesw5-dev', ]) if exists('~/.pyenv'): run('cd ~/.pyenv && git pull') run('~/.pyenv/bin/pyenv update') else: run('curl -L https://raw.githubusercontent.com/yyuu/pyenv-installer/' 'master/bin/pyenv-installer | bash') # add pyenv to $PATH and set up pyenv init bash_snippet = '~/.bashrc_pyenv' install_file_legacy(path=bash_snippet) prefix = flo('if [ -f {bash_snippet} ]; ') enabler = flo('if [ -f {bash_snippet} ]; then source {bash_snippet}; fi') if env.host == 'localhost': # FIXME: next function currently only works for localhost uncomment_or_update_or_append_line(filename='~/.bashrc', prefix=prefix, new_line=enabler) else: print(cyan('\nappend to ~/.bashrc:\n\n ') + enabler)

python

def pyenv(): '''Install or update the pyenv python environment. Checkout or update the pyenv repo at ~/.pyenv and enable the pyenv. Pyenv wird also als Github-Repo "installiert" unter ~/.pyenv More info: * https://github.com/yyuu/pyenv * https://github.com/yyuu/pyenv/wiki/Common-build-problems#requirements Tutorial: * http://amaral-lab.org/resources/guides/pyenv-tutorial ''' install_packages([ 'make', 'build-essential', 'libssl-dev', 'zlib1g-dev', 'libbz2-dev', 'libreadline-dev', 'libsqlite3-dev', 'wget', 'curl', 'llvm', 'libncurses5-dev', 'libncursesw5-dev', ]) if exists('~/.pyenv'): run('cd ~/.pyenv && git pull') run('~/.pyenv/bin/pyenv update') else: run('curl -L https://raw.githubusercontent.com/yyuu/pyenv-installer/' 'master/bin/pyenv-installer | bash') # add pyenv to $PATH and set up pyenv init bash_snippet = '~/.bashrc_pyenv' install_file_legacy(path=bash_snippet) prefix = flo('if [ -f {bash_snippet} ]; ') enabler = flo('if [ -f {bash_snippet} ]; then source {bash_snippet}; fi') if env.host == 'localhost': # FIXME: next function currently only works for localhost uncomment_or_update_or_append_line(filename='~/.bashrc', prefix=prefix, new_line=enabler) else: print(cyan('\nappend to ~/.bashrc:\n\n ') + enabler)

Install or update the pyenv python environment. Checkout or update the pyenv repo at ~/.pyenv and enable the pyenv. Pyenv wird also als Github-Repo "installiert" unter ~/.pyenv More info: * https://github.com/yyuu/pyenv * https://github.com/yyuu/pyenv/wiki/Common-build-problems#requirements Tutorial: * http://amaral-lab.org/resources/guides/pyenv-tutorial

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L172-L215

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

virtualbox_host

def virtualbox_host(): '''Install a VirtualBox host system. More Infos: * overview: https://wiki.ubuntuusers.de/VirtualBox/ * installation: https://wiki.ubuntuusers.de/VirtualBox/Installation/ ''' if query_yes_no(question='Uninstall virtualbox-dkms?', default='yes'): run('sudo apt-get remove virtualbox-dkms') install_packages([ 'virtualbox', 'virtualbox-qt', 'virtualbox-dkms', 'virtualbox-guest-dkms', 'virtualbox-guest-additions-iso', ]) users = [env.user] for username in users: run(flo('sudo adduser {username} vboxusers'))

python

def virtualbox_host(): '''Install a VirtualBox host system. More Infos: * overview: https://wiki.ubuntuusers.de/VirtualBox/ * installation: https://wiki.ubuntuusers.de/VirtualBox/Installation/ ''' if query_yes_no(question='Uninstall virtualbox-dkms?', default='yes'): run('sudo apt-get remove virtualbox-dkms') install_packages([ 'virtualbox', 'virtualbox-qt', 'virtualbox-dkms', 'virtualbox-guest-dkms', 'virtualbox-guest-additions-iso', ]) users = [env.user] for username in users: run(flo('sudo adduser {username} vboxusers'))

Install a VirtualBox host system. More Infos: * overview: https://wiki.ubuntuusers.de/VirtualBox/ * installation: https://wiki.ubuntuusers.de/VirtualBox/Installation/

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L220-L238

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

pencil2

def pencil2(): '''Install or update latest Pencil version 2, a GUI prototyping tool. Tip: For svg exports displayed proper in other programs (eg. inkscape, okular, reveal.js presentations) only use the 'Common Shapes' and 'Desktop - Sketchy GUI' elements. More info: github repo (forked version 2): https://github.com/prikhi/pencil ''' repo_name = 'pencil2' repo_dir = flo('~/repos/{repo_name}') print_msg('## fetch latest pencil\n') checkup_git_repo_legacy(url='https://github.com/prikhi/pencil.git', name=repo_name) print_msg('\n## build properties\n') update_or_append_line(flo('{repo_dir}/build/properties.sh'), prefix='export MAX_VERSION=', new_line="export MAX_VERSION='100.*'") run(flo('cat {repo_dir}/build/properties.sh')) run(flo('cd {repo_dir}/build && ./build.sh linux'), msg='\n## build pencil\n') install_user_command_legacy('pencil2', pencil2_repodir=repo_dir) print_msg('\nNow You can start pencil version 2 with this command:\n\n' ' pencil2')

python

def pencil2(): '''Install or update latest Pencil version 2, a GUI prototyping tool. Tip: For svg exports displayed proper in other programs (eg. inkscape, okular, reveal.js presentations) only use the 'Common Shapes' and 'Desktop - Sketchy GUI' elements. More info: github repo (forked version 2): https://github.com/prikhi/pencil ''' repo_name = 'pencil2' repo_dir = flo('~/repos/{repo_name}') print_msg('## fetch latest pencil\n') checkup_git_repo_legacy(url='https://github.com/prikhi/pencil.git', name=repo_name) print_msg('\n## build properties\n') update_or_append_line(flo('{repo_dir}/build/properties.sh'), prefix='export MAX_VERSION=', new_line="export MAX_VERSION='100.*'") run(flo('cat {repo_dir}/build/properties.sh')) run(flo('cd {repo_dir}/build && ./build.sh linux'), msg='\n## build pencil\n') install_user_command_legacy('pencil2', pencil2_repodir=repo_dir) print_msg('\nNow You can start pencil version 2 with this command:\n\n' ' pencil2')

Install or update latest Pencil version 2, a GUI prototyping tool. Tip: For svg exports displayed proper in other programs (eg. inkscape, okular, reveal.js presentations) only use the 'Common Shapes' and 'Desktop - Sketchy GUI' elements. More info: github repo (forked version 2): https://github.com/prikhi/pencil

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L277-L304

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

pencil3

def pencil3(): '''Install or update latest Pencil version 3, a GUI prototyping tool. While it is the newer one and the GUI is more fancy, it is the "more beta" version of pencil. For exmaple, to display a svg export may fail from within a reveal.js presentation. More info: Homepage: http://pencil.evolus.vn/Next.html github repo: https://github.com/evolus/pencil ''' repo_name = 'pencil3' repo_dir = flo('~/repos/{repo_name}') print_msg('## fetch latest pencil\n') checkup_git_repo_legacy(url='https://github.com/evolus/pencil.git', name=repo_name) run(flo('cd {repo_dir} && npm install'), msg='\n## install npms\n') install_user_command_legacy('pencil3', pencil3_repodir=repo_dir) print_msg('\nNow You can start pencil version 3 with this command:\n\n' ' pencil3')

python

def pencil3(): '''Install or update latest Pencil version 3, a GUI prototyping tool. While it is the newer one and the GUI is more fancy, it is the "more beta" version of pencil. For exmaple, to display a svg export may fail from within a reveal.js presentation. More info: Homepage: http://pencil.evolus.vn/Next.html github repo: https://github.com/evolus/pencil ''' repo_name = 'pencil3' repo_dir = flo('~/repos/{repo_name}') print_msg('## fetch latest pencil\n') checkup_git_repo_legacy(url='https://github.com/evolus/pencil.git', name=repo_name) run(flo('cd {repo_dir} && npm install'), msg='\n## install npms\n') install_user_command_legacy('pencil3', pencil3_repodir=repo_dir) print_msg('\nNow You can start pencil version 3 with this command:\n\n' ' pencil3')

Install or update latest Pencil version 3, a GUI prototyping tool. While it is the newer one and the GUI is more fancy, it is the "more beta" version of pencil. For exmaple, to display a svg export may fail from within a reveal.js presentation. More info: Homepage: http://pencil.evolus.vn/Next.html github repo: https://github.com/evolus/pencil

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L309-L328

train

theno/fabsetup

fabsetup/fabfile/setup/__init__.py

powerline_shell

def powerline_shell(): '''Install and set up powerline-shell prompt. More infos: * https://github.com/banga/powerline-shell * https://github.com/ohnonot/powerline-shell * https://askubuntu.com/questions/283908/how-can-i-install-and-use-powerline-plugin ''' assert env.host == 'localhost', 'This task cannot run on a remote host' # set up fonts for powerline checkup_git_repo_legacy('https://github.com/powerline/fonts.git', name='powerline-fonts') run('cd ~/repos/powerline-fonts && ./install.sh') # run('fc-cache -vf ~/.local/share/fonts') prefix = 'URxvt*font: ' from config import fontlist line = prefix + fontlist update_or_append_line(filename='~/.Xresources', prefix=prefix, new_line=line) if env.host_string == 'localhost': run('xrdb ~/.Xresources') # set up powerline-shell checkup_git_repo_legacy('https://github.com/banga/powerline-shell.git') # checkup_git_repo_legacy('https://github.com/ohnonot/powerline-shell.git') install_file_legacy(path='~/repos/powerline-shell/config.py') run('cd ~/repos/powerline-shell && ./install.py') question = 'Use normal question mark (u003F) for untracked files instead '\ 'of fancy "black question mark ornament" (u2753, which may not work)?' if query_yes_no(question, default='yes'): filename = '~/repos/powerline-shell/powerline-shell.py' update_or_append_line(filename, keep_backup=False, prefix=" 'untracked': u'\u2753',", new_line=" 'untracked': u'\u003F',") run(flo('chmod u+x {filename}')) bash_snippet = '~/.bashrc_powerline_shell' install_file_legacy(path=bash_snippet) prefix = flo('if [ -f {bash_snippet} ]; ') enabler = flo('if [ -f {bash_snippet} ]; then source {bash_snippet}; fi') uncomment_or_update_or_append_line(filename='~/.bashrc', prefix=prefix, new_line=enabler)

python

def powerline_shell(): '''Install and set up powerline-shell prompt. More infos: * https://github.com/banga/powerline-shell * https://github.com/ohnonot/powerline-shell * https://askubuntu.com/questions/283908/how-can-i-install-and-use-powerline-plugin ''' assert env.host == 'localhost', 'This task cannot run on a remote host' # set up fonts for powerline checkup_git_repo_legacy('https://github.com/powerline/fonts.git', name='powerline-fonts') run('cd ~/repos/powerline-fonts && ./install.sh') # run('fc-cache -vf ~/.local/share/fonts') prefix = 'URxvt*font: ' from config import fontlist line = prefix + fontlist update_or_append_line(filename='~/.Xresources', prefix=prefix, new_line=line) if env.host_string == 'localhost': run('xrdb ~/.Xresources') # set up powerline-shell checkup_git_repo_legacy('https://github.com/banga/powerline-shell.git') # checkup_git_repo_legacy('https://github.com/ohnonot/powerline-shell.git') install_file_legacy(path='~/repos/powerline-shell/config.py') run('cd ~/repos/powerline-shell && ./install.py') question = 'Use normal question mark (u003F) for untracked files instead '\ 'of fancy "black question mark ornament" (u2753, which may not work)?' if query_yes_no(question, default='yes'): filename = '~/repos/powerline-shell/powerline-shell.py' update_or_append_line(filename, keep_backup=False, prefix=" 'untracked': u'\u2753',", new_line=" 'untracked': u'\u003F',") run(flo('chmod u+x {filename}')) bash_snippet = '~/.bashrc_powerline_shell' install_file_legacy(path=bash_snippet) prefix = flo('if [ -f {bash_snippet} ]; ') enabler = flo('if [ -f {bash_snippet} ]; then source {bash_snippet}; fi') uncomment_or_update_or_append_line(filename='~/.bashrc', prefix=prefix, new_line=enabler)

Install and set up powerline-shell prompt. More infos: * https://github.com/banga/powerline-shell * https://github.com/ohnonot/powerline-shell * https://askubuntu.com/questions/283908/how-can-i-install-and-use-powerline-plugin

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/__init__.py#L378-L423

train

muckamuck/stackility

stackility/drift.py

DriftTool._init_boto3_clients

def _init_boto3_clients(self, profile, region): """ The utililty requires boto3 clients to CloudFormation. Args: None Returns: Good or Bad; True or False """ try: session = None if profile and region: session = boto3.session.Session(profile_name=profile, region_name=region) elif profile: session = boto3.session.Session(profile_name=profile) elif region: session = boto3.session.Session(region_name=region) else: session = boto3.session.Session() self._cloud_formation = session.client('cloudformation') return True except Exception as wtf: logging.error(wtf, exc_info=True) return False

python

def _init_boto3_clients(self, profile, region): """ The utililty requires boto3 clients to CloudFormation. Args: None Returns: Good or Bad; True or False """ try: session = None if profile and region: session = boto3.session.Session(profile_name=profile, region_name=region) elif profile: session = boto3.session.Session(profile_name=profile) elif region: session = boto3.session.Session(region_name=region) else: session = boto3.session.Session() self._cloud_formation = session.client('cloudformation') return True except Exception as wtf: logging.error(wtf, exc_info=True) return False

The utililty requires boto3 clients to CloudFormation. Args: None Returns: Good or Bad; True or False

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/drift.py#L54-L79

train

muckamuck/stackility

stackility/drift.py

DriftTool.determine_drift

def determine_drift(self): """ Determine the drift of the stack. Args: None Returns: Good or Bad; True or False """ try: response = self._cloud_formation.detect_stack_drift(StackName=self._stack_name) drift_request_id = response.get('StackDriftDetectionId', None) if drift_request_id: logging.info('drift_request_id: %s - polling', drift_request_id) drift_calc_done = False while not drift_calc_done: time.sleep(self.nap_time) response = self._cloud_formation.describe_stack_drift_detection_status( StackDriftDetectionId=drift_request_id ) current_state = response.get('DetectionStatus', None) logging.info( 'describe_stack_drift_detection_status(): {}'.format(current_state) ) drift_calc_done = current_state in CALC_DONE_STATES drift_answer = response.get('StackDriftStatus', 'UNKNOWN') logging.info('drift of {}: {}'.format( self._stack_name, drift_answer )) if drift_answer == 'DRIFTED': if self._verbose: self._print_drift_report() return False else: return True else: logging.warning('drift_request_id is None') return False except Exception as wtf: logging.error(wtf, exc_info=True) return False

python

def determine_drift(self): """ Determine the drift of the stack. Args: None Returns: Good or Bad; True or False """ try: response = self._cloud_formation.detect_stack_drift(StackName=self._stack_name) drift_request_id = response.get('StackDriftDetectionId', None) if drift_request_id: logging.info('drift_request_id: %s - polling', drift_request_id) drift_calc_done = False while not drift_calc_done: time.sleep(self.nap_time) response = self._cloud_formation.describe_stack_drift_detection_status( StackDriftDetectionId=drift_request_id ) current_state = response.get('DetectionStatus', None) logging.info( 'describe_stack_drift_detection_status(): {}'.format(current_state) ) drift_calc_done = current_state in CALC_DONE_STATES drift_answer = response.get('StackDriftStatus', 'UNKNOWN') logging.info('drift of {}: {}'.format( self._stack_name, drift_answer )) if drift_answer == 'DRIFTED': if self._verbose: self._print_drift_report() return False else: return True else: logging.warning('drift_request_id is None') return False except Exception as wtf: logging.error(wtf, exc_info=True) return False

Determine the drift of the stack. Args: None Returns: Good or Bad; True or False

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/drift.py#L81-L126

train

muckamuck/stackility

stackility/drift.py

DriftTool._print_drift_report

def _print_drift_report(self): """ Report the drift of the stack. Args: None Returns: Good or Bad; True or False Note: not yet implemented """ try: response = self._cloud_formation.describe_stack_resources(StackName=self._stack_name) rows = [] for resource in response.get('StackResources', []): row = [] row.append(resource.get('LogicalResourceId', 'unknown')) row.append(resource.get('PhysicalResourceId', 'unknown')) row.append(resource.get('ResourceStatus', 'unknown')) row.append(resource.get('DriftInformation', {}).get('StackResourceDriftStatus', 'unknown')) rows.append(row) print('Drift Report:') print(tabulate(rows, headers=[ 'Logical ID', 'Physical ID', 'Resource Status', 'Drift Info' ])) except Exception as wtf: logging.error(wtf, exc_info=True) return False return True

python

def _print_drift_report(self): """ Report the drift of the stack. Args: None Returns: Good or Bad; True or False Note: not yet implemented """ try: response = self._cloud_formation.describe_stack_resources(StackName=self._stack_name) rows = [] for resource in response.get('StackResources', []): row = [] row.append(resource.get('LogicalResourceId', 'unknown')) row.append(resource.get('PhysicalResourceId', 'unknown')) row.append(resource.get('ResourceStatus', 'unknown')) row.append(resource.get('DriftInformation', {}).get('StackResourceDriftStatus', 'unknown')) rows.append(row) print('Drift Report:') print(tabulate(rows, headers=[ 'Logical ID', 'Physical ID', 'Resource Status', 'Drift Info' ])) except Exception as wtf: logging.error(wtf, exc_info=True) return False return True

Report the drift of the stack. Args: None Returns: Good or Bad; True or False Note: not yet implemented

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/drift.py#L128-L162

train

jaraco/jaraco.windows

jaraco/windows/dpapi.py

DATA_BLOB.set_data

def set_data(self, data): "Use this method to set the data for this blob" if data is None: self.data_size = 0 self.data = None return self.data_size = len(data) # create a string buffer so that null bytes aren't interpreted # as the end of the string self.data = ctypes.cast(ctypes.create_string_buffer(data), ctypes.c_void_p)

python

def set_data(self, data): "Use this method to set the data for this blob" if data is None: self.data_size = 0 self.data = None return self.data_size = len(data) # create a string buffer so that null bytes aren't interpreted # as the end of the string self.data = ctypes.cast(ctypes.create_string_buffer(data), ctypes.c_void_p)

Use this method to set the data for this blob

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/dpapi.py#L43-L52

train

jaraco/jaraco.windows

jaraco/windows/dpapi.py

DATA_BLOB.get_data

def get_data(self): "Get the data for this blob" array = ctypes.POINTER(ctypes.c_char * len(self)) return ctypes.cast(self.data, array).contents.raw

python

def get_data(self): "Get the data for this blob" array = ctypes.POINTER(ctypes.c_char * len(self)) return ctypes.cast(self.data, array).contents.raw

Get the data for this blob

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/dpapi.py#L54-L57

train

sbmlteam/libCombine

examples/python/printExample.py

printMetaDataFor

def printMetaDataFor(archive, location): """ Prints metadata for given location. :param archive: CombineArchive instance :param location: :return: """ desc = archive.getMetadataForLocation(location) if desc.isEmpty(): print(" no metadata for '{0}'".format(location)) return None print(" metadata for '{0}':".format(location)) print(" Created : {0}".format(desc.getCreated().getDateAsString())) for i in range(desc.getNumModified()): print(" Modified : {0}".format(desc.getModified(i).getDateAsString())) print(" # Creators: {0}".format(desc.getNumCreators())) for i in range(desc.getNumCreators()): creator = desc.getCreator(i) print(" {0} {1}".format(creator.getGivenName(), creator.getFamilyName()))

python

def printMetaDataFor(archive, location): """ Prints metadata for given location. :param archive: CombineArchive instance :param location: :return: """ desc = archive.getMetadataForLocation(location) if desc.isEmpty(): print(" no metadata for '{0}'".format(location)) return None print(" metadata for '{0}':".format(location)) print(" Created : {0}".format(desc.getCreated().getDateAsString())) for i in range(desc.getNumModified()): print(" Modified : {0}".format(desc.getModified(i).getDateAsString())) print(" # Creators: {0}".format(desc.getNumCreators())) for i in range(desc.getNumCreators()): creator = desc.getCreator(i) print(" {0} {1}".format(creator.getGivenName(), creator.getFamilyName()))

Prints metadata for given location. :param archive: CombineArchive instance :param location: :return:

d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4

https://github.com/sbmlteam/libCombine/blob/d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4/examples/python/printExample.py#L11-L31

train

sbmlteam/libCombine

examples/python/printExample.py

printArchive

def printArchive(fileName): """ Prints content of combine archive :param fileName: path of archive :return: None """ archive = CombineArchive() if archive.initializeFromArchive(fileName) is None: print("Invalid Combine Archive") return None print('*'*80) print('Print archive:', fileName) print('*' * 80) printMetaDataFor(archive, ".") print("Num Entries: {0}".format(archive.getNumEntries())) for i in range(archive.getNumEntries()): entry = archive.getEntry(i) print(" {0}: location: {1} format: {2}".format(i, entry.getLocation(), entry.getFormat())) printMetaDataFor(archive, entry.getLocation()) for j in range(entry.getNumCrossRefs()): print(" {0}: crossRef location {1}".format(j, entry.getCrossRef(j).getLocation())) # the entry could now be extracted via # archive.extractEntry(entry.getLocation(), <filename or folder>) # or used as string # content = archive.extractEntryToString(entry.getLocation()); archive.cleanUp()

python

def printArchive(fileName): """ Prints content of combine archive :param fileName: path of archive :return: None """ archive = CombineArchive() if archive.initializeFromArchive(fileName) is None: print("Invalid Combine Archive") return None print('*'*80) print('Print archive:', fileName) print('*' * 80) printMetaDataFor(archive, ".") print("Num Entries: {0}".format(archive.getNumEntries())) for i in range(archive.getNumEntries()): entry = archive.getEntry(i) print(" {0}: location: {1} format: {2}".format(i, entry.getLocation(), entry.getFormat())) printMetaDataFor(archive, entry.getLocation()) for j in range(entry.getNumCrossRefs()): print(" {0}: crossRef location {1}".format(j, entry.getCrossRef(j).getLocation())) # the entry could now be extracted via # archive.extractEntry(entry.getLocation(), <filename or folder>) # or used as string # content = archive.extractEntryToString(entry.getLocation()); archive.cleanUp()

Prints content of combine archive :param fileName: path of archive :return: None

d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4

https://github.com/sbmlteam/libCombine/blob/d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4/examples/python/printExample.py#L34-L65

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

mklink

def mklink(): """ Like cmd.exe's mklink except it will infer directory status of the target. """ from optparse import OptionParser parser = OptionParser(usage="usage: %prog [options] link target") parser.add_option( '-d', '--directory', help="Target is a directory (only necessary if not present)", action="store_true") options, args = parser.parse_args() try: link, target = args except ValueError: parser.error("incorrect number of arguments") symlink(target, link, options.directory) sys.stdout.write("Symbolic link created: %(link)s --> %(target)s\n" % vars())

python

def mklink(): """ Like cmd.exe's mklink except it will infer directory status of the target. """ from optparse import OptionParser parser = OptionParser(usage="usage: %prog [options] link target") parser.add_option( '-d', '--directory', help="Target is a directory (only necessary if not present)", action="store_true") options, args = parser.parse_args() try: link, target = args except ValueError: parser.error("incorrect number of arguments") symlink(target, link, options.directory) sys.stdout.write("Symbolic link created: %(link)s --> %(target)s\n" % vars())

Like cmd.exe's mklink except it will infer directory status of the target.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L28-L45

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

is_reparse_point

def is_reparse_point(path): """ Determine if the given path is a reparse point. Return False if the file does not exist or the file attributes cannot be determined. """ res = api.GetFileAttributes(path) return ( res != api.INVALID_FILE_ATTRIBUTES and bool(res & api.FILE_ATTRIBUTE_REPARSE_POINT) )

python

def is_reparse_point(path): """ Determine if the given path is a reparse point. Return False if the file does not exist or the file attributes cannot be determined. """ res = api.GetFileAttributes(path) return ( res != api.INVALID_FILE_ATTRIBUTES and bool(res & api.FILE_ATTRIBUTE_REPARSE_POINT) )

Determine if the given path is a reparse point. Return False if the file does not exist or the file attributes cannot be determined.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L78-L88

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

is_symlink

def is_symlink(path): """ Assuming path is a reparse point, determine if it's a symlink. """ path = _patch_path(path) try: return _is_symlink(next(find_files(path))) # comment below workaround for PyCQA/pyflakes#376 except WindowsError as orig_error: # noqa: F841 tmpl = "Error accessing {path}: {orig_error.message}" raise builtins.WindowsError(tmpl.format(**locals()))

python

def is_symlink(path): """ Assuming path is a reparse point, determine if it's a symlink. """ path = _patch_path(path) try: return _is_symlink(next(find_files(path))) # comment below workaround for PyCQA/pyflakes#376 except WindowsError as orig_error: # noqa: F841 tmpl = "Error accessing {path}: {orig_error.message}" raise builtins.WindowsError(tmpl.format(**locals()))

Assuming path is a reparse point, determine if it's a symlink.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L113-L123

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

get_final_path

def get_final_path(path): r""" For a given path, determine the ultimate location of that path. Useful for resolving symlink targets. This functions wraps the GetFinalPathNameByHandle from the Windows SDK. Note, this function fails if a handle cannot be obtained (such as for C:\Pagefile.sys on a stock windows system). Consider using trace_symlink_target instead. """ desired_access = api.NULL share_mode = ( api.FILE_SHARE_READ | api.FILE_SHARE_WRITE | api.FILE_SHARE_DELETE ) security_attributes = api.LPSECURITY_ATTRIBUTES() # NULL pointer hFile = api.CreateFile( path, desired_access, share_mode, security_attributes, api.OPEN_EXISTING, api.FILE_FLAG_BACKUP_SEMANTICS, api.NULL, ) if hFile == api.INVALID_HANDLE_VALUE: raise WindowsError() buf_size = api.GetFinalPathNameByHandle( hFile, LPWSTR(), 0, api.VOLUME_NAME_DOS) handle_nonzero_success(buf_size) buf = create_unicode_buffer(buf_size) result_length = api.GetFinalPathNameByHandle( hFile, buf, len(buf), api.VOLUME_NAME_DOS) assert result_length < len(buf) handle_nonzero_success(result_length) handle_nonzero_success(api.CloseHandle(hFile)) return buf[:result_length]

python

def get_final_path(path): r""" For a given path, determine the ultimate location of that path. Useful for resolving symlink targets. This functions wraps the GetFinalPathNameByHandle from the Windows SDK. Note, this function fails if a handle cannot be obtained (such as for C:\Pagefile.sys on a stock windows system). Consider using trace_symlink_target instead. """ desired_access = api.NULL share_mode = ( api.FILE_SHARE_READ | api.FILE_SHARE_WRITE | api.FILE_SHARE_DELETE ) security_attributes = api.LPSECURITY_ATTRIBUTES() # NULL pointer hFile = api.CreateFile( path, desired_access, share_mode, security_attributes, api.OPEN_EXISTING, api.FILE_FLAG_BACKUP_SEMANTICS, api.NULL, ) if hFile == api.INVALID_HANDLE_VALUE: raise WindowsError() buf_size = api.GetFinalPathNameByHandle( hFile, LPWSTR(), 0, api.VOLUME_NAME_DOS) handle_nonzero_success(buf_size) buf = create_unicode_buffer(buf_size) result_length = api.GetFinalPathNameByHandle( hFile, buf, len(buf), api.VOLUME_NAME_DOS) assert result_length < len(buf) handle_nonzero_success(result_length) handle_nonzero_success(api.CloseHandle(hFile)) return buf[:result_length]

r""" For a given path, determine the ultimate location of that path. Useful for resolving symlink targets. This functions wraps the GetFinalPathNameByHandle from the Windows SDK. Note, this function fails if a handle cannot be obtained (such as for C:\Pagefile.sys on a stock windows system). Consider using trace_symlink_target instead.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L163-L203

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

join

def join(*paths): r""" Wrapper around os.path.join that works with Windows drive letters. >>> join('d:\\foo', '\\bar') 'd:\\bar' """ paths_with_drives = map(os.path.splitdrive, paths) drives, paths = zip(*paths_with_drives) # the drive we care about is the last one in the list drive = next(filter(None, reversed(drives)), '') return os.path.join(drive, os.path.join(*paths))

python

def join(*paths): r""" Wrapper around os.path.join that works with Windows drive letters. >>> join('d:\\foo', '\\bar') 'd:\\bar' """ paths_with_drives = map(os.path.splitdrive, paths) drives, paths = zip(*paths_with_drives) # the drive we care about is the last one in the list drive = next(filter(None, reversed(drives)), '') return os.path.join(drive, os.path.join(*paths))

r""" Wrapper around os.path.join that works with Windows drive letters. >>> join('d:\\foo', '\\bar') 'd:\\bar'

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L292-L303

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

resolve_path

def resolve_path(target, start=os.path.curdir): r""" Find a path from start to target where target is relative to start. >>> tmp = str(getfixture('tmpdir_as_cwd')) >>> findpath('d:\\') 'd:\\' >>> findpath('d:\\', tmp) 'd:\\' >>> findpath('\\bar', 'd:\\') 'd:\\bar' >>> findpath('\\bar', 'd:\\foo') # fails with '\\bar' 'd:\\bar' >>> findpath('bar', 'd:\\foo') 'd:\\foo\\bar' >>> findpath('\\baz', 'd:\\foo\\bar') # fails with '\\baz' 'd:\\baz' >>> os.path.abspath(findpath('\\bar')).lower() 'c:\\bar' >>> os.path.abspath(findpath('bar')) '...\\bar' >>> findpath('..', 'd:\\foo\\bar') 'd:\\foo' The parent of the root directory is the root directory. >>> findpath('..', 'd:\\') 'd:\\' """ return os.path.normpath(join(start, target))

python

def resolve_path(target, start=os.path.curdir): r""" Find a path from start to target where target is relative to start. >>> tmp = str(getfixture('tmpdir_as_cwd')) >>> findpath('d:\\') 'd:\\' >>> findpath('d:\\', tmp) 'd:\\' >>> findpath('\\bar', 'd:\\') 'd:\\bar' >>> findpath('\\bar', 'd:\\foo') # fails with '\\bar' 'd:\\bar' >>> findpath('bar', 'd:\\foo') 'd:\\foo\\bar' >>> findpath('\\baz', 'd:\\foo\\bar') # fails with '\\baz' 'd:\\baz' >>> os.path.abspath(findpath('\\bar')).lower() 'c:\\bar' >>> os.path.abspath(findpath('bar')) '...\\bar' >>> findpath('..', 'd:\\foo\\bar') 'd:\\foo' The parent of the root directory is the root directory. >>> findpath('..', 'd:\\') 'd:\\' """ return os.path.normpath(join(start, target))

r""" Find a path from start to target where target is relative to start. >>> tmp = str(getfixture('tmpdir_as_cwd')) >>> findpath('d:\\') 'd:\\' >>> findpath('d:\\', tmp) 'd:\\' >>> findpath('\\bar', 'd:\\') 'd:\\bar' >>> findpath('\\bar', 'd:\\foo') # fails with '\\bar' 'd:\\bar' >>> findpath('bar', 'd:\\foo') 'd:\\foo\\bar' >>> findpath('\\baz', 'd:\\foo\\bar') # fails with '\\baz' 'd:\\baz' >>> os.path.abspath(findpath('\\bar')).lower() 'c:\\bar' >>> os.path.abspath(findpath('bar')) '...\\bar' >>> findpath('..', 'd:\\foo\\bar') 'd:\\foo' The parent of the root directory is the root directory. >>> findpath('..', 'd:\\') 'd:\\'

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L306-L343

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

trace_symlink_target

def trace_symlink_target(link): """ Given a file that is known to be a symlink, trace it to its ultimate target. Raises TargetNotPresent when the target cannot be determined. Raises ValueError when the specified link is not a symlink. """ if not is_symlink(link): raise ValueError("link must point to a symlink on the system") while is_symlink(link): orig = os.path.dirname(link) link = readlink(link) link = resolve_path(link, orig) return link

python

def trace_symlink_target(link): """ Given a file that is known to be a symlink, trace it to its ultimate target. Raises TargetNotPresent when the target cannot be determined. Raises ValueError when the specified link is not a symlink. """ if not is_symlink(link): raise ValueError("link must point to a symlink on the system") while is_symlink(link): orig = os.path.dirname(link) link = readlink(link) link = resolve_path(link, orig) return link

Given a file that is known to be a symlink, trace it to its ultimate target. Raises TargetNotPresent when the target cannot be determined. Raises ValueError when the specified link is not a symlink.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L349-L364

train

jaraco/jaraco.windows

jaraco/windows/filesystem/__init__.py

patch_os_module

def patch_os_module(): """ jaraco.windows provides the os.symlink and os.readlink functions. Monkey-patch the os module to include them if not present. """ if not hasattr(os, 'symlink'): os.symlink = symlink os.path.islink = islink if not hasattr(os, 'readlink'): os.readlink = readlink

python

def patch_os_module(): """ jaraco.windows provides the os.symlink and os.readlink functions. Monkey-patch the os module to include them if not present. """ if not hasattr(os, 'symlink'): os.symlink = symlink os.path.islink = islink if not hasattr(os, 'readlink'): os.readlink = readlink

jaraco.windows provides the os.symlink and os.readlink functions. Monkey-patch the os module to include them if not present.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/filesystem/__init__.py#L398-L407

train

theno/fabsetup

fabsetup/fabutils.py

task

def task(func, *args, **kwargs): '''Composition of decorator functions for inherent self-documentation on task execution. On execution, each task prints out its name and its first docstring line. ''' prefix = '\n# ' tail = '\n' return fabric.api.task( print_full_name(color=magenta, prefix=prefix, tail=tail)(print_doc1(func)), *args, **kwargs)

python

def task(func, *args, **kwargs): '''Composition of decorator functions for inherent self-documentation on task execution. On execution, each task prints out its name and its first docstring line. ''' prefix = '\n# ' tail = '\n' return fabric.api.task( print_full_name(color=magenta, prefix=prefix, tail=tail)(print_doc1(func)), *args, **kwargs)

Composition of decorator functions for inherent self-documentation on task execution. On execution, each task prints out its name and its first docstring line.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L191-L204

train

theno/fabsetup

fabsetup/fabutils.py

subtask

def subtask(*args, **kwargs): '''Decorator which prints out the name of the decorated function on execution. ''' depth = kwargs.get('depth', 2) prefix = kwargs.get('prefix', '\n' + '#' * depth + ' ') tail = kwargs.get('tail', '\n') doc1 = kwargs.get('doc1', False) color = kwargs.get('color', cyan) def real_decorator(func): if doc1: return print_full_name(color=color, prefix=prefix, tail=tail)(print_doc1(func)) return print_full_name(color=color, prefix=prefix, tail=tail)(func) invoked = bool(not args or kwargs) if not invoked: # invoke decorator function which returns the wrapper function return real_decorator(func=args[0]) return real_decorator

python

def subtask(*args, **kwargs): '''Decorator which prints out the name of the decorated function on execution. ''' depth = kwargs.get('depth', 2) prefix = kwargs.get('prefix', '\n' + '#' * depth + ' ') tail = kwargs.get('tail', '\n') doc1 = kwargs.get('doc1', False) color = kwargs.get('color', cyan) def real_decorator(func): if doc1: return print_full_name(color=color, prefix=prefix, tail=tail)(print_doc1(func)) return print_full_name(color=color, prefix=prefix, tail=tail)(func) invoked = bool(not args or kwargs) if not invoked: # invoke decorator function which returns the wrapper function return real_decorator(func=args[0]) return real_decorator

Decorator which prints out the name of the decorated function on execution.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L213-L233

train

theno/fabsetup

fabsetup/fabutils.py

_is_sudoer

def _is_sudoer(what_for=''): '''Return True if current user is a sudoer, else False. Should be called non-eager if sudo is wanted only. ''' if env.get('nosudo', None) is None: if what_for: print(yellow(what_for)) with quiet(): # possible outputs: # en: "Sorry, user winhost-tester may not run sudo on <hostname>" # en: "sudo: a password is required" (=> is sudoer) # de: "sudo: Ein Passwort ist notwendig" (=> is sudoer) output = run('sudo -nv', capture=True) env.nosudo = not (output.startswith('sudo: ') or output == '') if env.nosudo: print('Cannot execute sudo-commands') return not env.nosudo

python

def _is_sudoer(what_for=''): '''Return True if current user is a sudoer, else False. Should be called non-eager if sudo is wanted only. ''' if env.get('nosudo', None) is None: if what_for: print(yellow(what_for)) with quiet(): # possible outputs: # en: "Sorry, user winhost-tester may not run sudo on <hostname>" # en: "sudo: a password is required" (=> is sudoer) # de: "sudo: Ein Passwort ist notwendig" (=> is sudoer) output = run('sudo -nv', capture=True) env.nosudo = not (output.startswith('sudo: ') or output == '') if env.nosudo: print('Cannot execute sudo-commands') return not env.nosudo

Return True if current user is a sudoer, else False. Should be called non-eager if sudo is wanted only.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L248-L265

train

theno/fabsetup

fabsetup/fabutils.py

install_packages

def install_packages(packages, what_for='for a complete setup to work properly'): '''Try to install .deb packages given by list. Return True, if packages could be installed or are installed already, or if they cannot be installed but the user gives feedback to continue. Else return False. ''' res = True non_installed_packages = _non_installed(packages) packages_str = ' '.join(non_installed_packages) if non_installed_packages: with quiet(): dpkg = _has_dpkg() hint = ' (You may have to install them manually)' do_install = False go_on = True if dpkg: if _is_sudoer('Want to install dpkg packages'): do_install = True else: do_install is False # cannot install anything info = yellow(' '.join([ 'This deb packages are missing to be installed', flo("{what_for}: "), ', '.join(non_installed_packages), ])) question = ' Continue anyway?' go_on = query_yes_no(info + hint + question, default='no') else: # dpkg == False, unable to determine if packages are installed do_install = False # cannot install anything info = yellow(' '.join([ flo('Required {what_for}: '), ', '.join(non_installed_packages), ])) go_on = query_yes_no(info + hint + ' Continue?', default='yes') if not go_on: sys.exit('Abort') if do_install: command = flo('sudo apt-get install {packages_str}') res = run(command).return_code == 0 return res

python

def install_packages(packages, what_for='for a complete setup to work properly'): '''Try to install .deb packages given by list. Return True, if packages could be installed or are installed already, or if they cannot be installed but the user gives feedback to continue. Else return False. ''' res = True non_installed_packages = _non_installed(packages) packages_str = ' '.join(non_installed_packages) if non_installed_packages: with quiet(): dpkg = _has_dpkg() hint = ' (You may have to install them manually)' do_install = False go_on = True if dpkg: if _is_sudoer('Want to install dpkg packages'): do_install = True else: do_install is False # cannot install anything info = yellow(' '.join([ 'This deb packages are missing to be installed', flo("{what_for}: "), ', '.join(non_installed_packages), ])) question = ' Continue anyway?' go_on = query_yes_no(info + hint + question, default='no') else: # dpkg == False, unable to determine if packages are installed do_install = False # cannot install anything info = yellow(' '.join([ flo('Required {what_for}: '), ', '.join(non_installed_packages), ])) go_on = query_yes_no(info + hint + ' Continue?', default='yes') if not go_on: sys.exit('Abort') if do_install: command = flo('sudo apt-get install {packages_str}') res = run(command).return_code == 0 return res

Try to install .deb packages given by list. Return True, if packages could be installed or are installed already, or if they cannot be installed but the user gives feedback to continue. Else return False.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L273-L315

train

theno/fabsetup

fabsetup/fabutils.py

checkup_git_repos_legacy

def checkup_git_repos_legacy(repos, base_dir='~/repos', verbose=False, prefix='', postfix=''): '''Checkout or update git repos. repos must be a list of dicts each with an url and optional with a name value. ''' run(flo('mkdir -p {base_dir}')) for repo in repos: cur_base_dir = repo.get('base_dir', base_dir) checkup_git_repo_legacy(url=repo['url'], name=repo.get('name', None), base_dir=cur_base_dir, verbose=verbose, prefix=prefix, postfix=postfix)

python

def checkup_git_repos_legacy(repos, base_dir='~/repos', verbose=False, prefix='', postfix=''): '''Checkout or update git repos. repos must be a list of dicts each with an url and optional with a name value. ''' run(flo('mkdir -p {base_dir}')) for repo in repos: cur_base_dir = repo.get('base_dir', base_dir) checkup_git_repo_legacy(url=repo['url'], name=repo.get('name', None), base_dir=cur_base_dir, verbose=verbose, prefix=prefix, postfix=postfix)

Checkout or update git repos. repos must be a list of dicts each with an url and optional with a name value.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L324-L336

train

theno/fabsetup

fabsetup/fabutils.py

checkup_git_repo_legacy

def checkup_git_repo_legacy(url, name=None, base_dir='~/repos', verbose=False, prefix='', postfix=''): '''Checkout or update a git repo.''' if not name: match = re.match(r'.*/(.+)\.git', url) assert match, flo("Unable to extract repo name from '{url}'") name = match.group(1) assert name is not None, flo('Cannot extract repo name from repo: {url}') assert name != '', flo('Cannot extract repo name from repo: {url} (empty)') if verbose: name_blue = blue(name) print_msg(flo('{prefix}Checkout or update {name_blue}{postfix}')) if not exists(base_dir): run(flo('mkdir -p {base_dir}')) if not exists(flo('{base_dir}/{name}/.git')): run(flo(' && '.join([ 'cd {base_dir}', 'git clone {url} {name}'])), msg='clone repo') else: if verbose: print_msg('update: pull from origin') run(flo('cd {base_dir}/{name} && git pull')) return name

python

def checkup_git_repo_legacy(url, name=None, base_dir='~/repos', verbose=False, prefix='', postfix=''): '''Checkout or update a git repo.''' if not name: match = re.match(r'.*/(.+)\.git', url) assert match, flo("Unable to extract repo name from '{url}'") name = match.group(1) assert name is not None, flo('Cannot extract repo name from repo: {url}') assert name != '', flo('Cannot extract repo name from repo: {url} (empty)') if verbose: name_blue = blue(name) print_msg(flo('{prefix}Checkout or update {name_blue}{postfix}')) if not exists(base_dir): run(flo('mkdir -p {base_dir}')) if not exists(flo('{base_dir}/{name}/.git')): run(flo(' && '.join([ 'cd {base_dir}', 'git clone {url} {name}'])), msg='clone repo') else: if verbose: print_msg('update: pull from origin') run(flo('cd {base_dir}/{name} && git pull')) return name

Checkout or update a git repo.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L339-L362

train

theno/fabsetup

fabsetup/fabutils.py

install_file_legacy

def install_file_legacy(path, sudo=False, from_path=None, **substitutions): '''Install file with path on the host target. The from file is the first of this list which exists: * custom file * custom file.template * common file * common file.template ''' # source paths 'from_custom' and 'from_common' from_path = from_path or path # remove beginning '/' (if any), eg '/foo/bar' -> 'foo/bar' from_tail = join('files', from_path.lstrip(os.sep)) if from_path.startswith('~/'): from_tail = join('files', 'home', 'USERNAME', from_path[2:]) # without beginning '~/' from_common = join(FABFILE_DATA_DIR, from_tail) from_custom = join(FABSETUP_CUSTOM_DIR, from_tail) # target path 'to_' (path or tempfile) for subst in ['SITENAME', 'USER', 'ADDON', 'TASK']: sitename = substitutions.get(subst, False) if sitename: path = path.replace(subst, sitename) to_ = path if sudo: to_ = join(os.sep, 'tmp', 'fabsetup_' + os.path.basename(path)) path_dir = dirname(path) # copy file if isfile(from_custom): run(flo('mkdir -p {path_dir}')) put(from_custom, to_) elif isfile(from_custom + '.template'): _install_file_from_template_legacy(from_custom + '.template', to_=to_, **substitutions) elif isfile(from_common): run(flo('mkdir -p {path_dir}')) put(from_common, to_) else: _install_file_from_template_legacy(from_common + '.template', to_=to_, **substitutions) if sudo: run(flo('sudo mv --force {to_} {path}'))

python

def install_file_legacy(path, sudo=False, from_path=None, **substitutions): '''Install file with path on the host target. The from file is the first of this list which exists: * custom file * custom file.template * common file * common file.template ''' # source paths 'from_custom' and 'from_common' from_path = from_path or path # remove beginning '/' (if any), eg '/foo/bar' -> 'foo/bar' from_tail = join('files', from_path.lstrip(os.sep)) if from_path.startswith('~/'): from_tail = join('files', 'home', 'USERNAME', from_path[2:]) # without beginning '~/' from_common = join(FABFILE_DATA_DIR, from_tail) from_custom = join(FABSETUP_CUSTOM_DIR, from_tail) # target path 'to_' (path or tempfile) for subst in ['SITENAME', 'USER', 'ADDON', 'TASK']: sitename = substitutions.get(subst, False) if sitename: path = path.replace(subst, sitename) to_ = path if sudo: to_ = join(os.sep, 'tmp', 'fabsetup_' + os.path.basename(path)) path_dir = dirname(path) # copy file if isfile(from_custom): run(flo('mkdir -p {path_dir}')) put(from_custom, to_) elif isfile(from_custom + '.template'): _install_file_from_template_legacy(from_custom + '.template', to_=to_, **substitutions) elif isfile(from_common): run(flo('mkdir -p {path_dir}')) put(from_common, to_) else: _install_file_from_template_legacy(from_common + '.template', to_=to_, **substitutions) if sudo: run(flo('sudo mv --force {to_} {path}'))

Install file with path on the host target. The from file is the first of this list which exists: * custom file * custom file.template * common file * common file.template

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L481-L524

train

theno/fabsetup

fabsetup/fabutils.py

install_user_command_legacy

def install_user_command_legacy(command, **substitutions): '''Install command executable file into users bin dir. If a custom executable exists it would be installed instead of the "normal" one. The executable also could exist as a <command>.template file. ''' path = flo('~/bin/{command}') install_file_legacy(path, **substitutions) run(flo('chmod 755 {path}'))

python

def install_user_command_legacy(command, **substitutions): '''Install command executable file into users bin dir. If a custom executable exists it would be installed instead of the "normal" one. The executable also could exist as a <command>.template file. ''' path = flo('~/bin/{command}') install_file_legacy(path, **substitutions) run(flo('chmod 755 {path}'))

Install command executable file into users bin dir. If a custom executable exists it would be installed instead of the "normal" one. The executable also could exist as a <command>.template file.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L527-L535

train

theno/fabsetup

fabsetup/fabutils.py

_line_2_pair

def _line_2_pair(line): '''Return bash variable declaration as name-value pair. Name as lower case str. Value itself only without surrounding '"' (if any). For example, _line_2_pair('NAME="Ubuntu"') will return ('name', 'Ubuntu') ''' key, val = line.split('=') return key.lower(), val.strip('"')

python

def _line_2_pair(line): '''Return bash variable declaration as name-value pair. Name as lower case str. Value itself only without surrounding '"' (if any). For example, _line_2_pair('NAME="Ubuntu"') will return ('name', 'Ubuntu') ''' key, val = line.split('=') return key.lower(), val.strip('"')

Return bash variable declaration as name-value pair. Name as lower case str. Value itself only without surrounding '"' (if any). For example, _line_2_pair('NAME="Ubuntu"') will return ('name', 'Ubuntu')

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L735-L743

train

theno/fabsetup

fabsetup/fabutils.py

extract_minors_from_setup_py

def extract_minors_from_setup_py(filename_setup_py): '''Extract supported python minor versions from setup.py and return them as a list of str. Return example: ['2.6', '2.7', '3.3', '3.4', '3.5', '3.6'] ''' # eg: minors_str = '2.6\n2.7\n3.3\n3.4\n3.5\n3.6' minors_str = fabric.api.local( flo('grep --perl-regexp --only-matching ' '"(?<=Programming Language :: Python :: )\\d+\\.\\d+" ' '{filename_setup_py}'), capture=True) # eg: minors = ['2.6', '2.7', '3.3', '3.4', '3.5', '3.6'] minors = minors_str.split() return minors

python

def extract_minors_from_setup_py(filename_setup_py): '''Extract supported python minor versions from setup.py and return them as a list of str. Return example: ['2.6', '2.7', '3.3', '3.4', '3.5', '3.6'] ''' # eg: minors_str = '2.6\n2.7\n3.3\n3.4\n3.5\n3.6' minors_str = fabric.api.local( flo('grep --perl-regexp --only-matching ' '"(?<=Programming Language :: Python :: )\\d+\\.\\d+" ' '{filename_setup_py}'), capture=True) # eg: minors = ['2.6', '2.7', '3.3', '3.4', '3.5', '3.6'] minors = minors_str.split() return minors

Extract supported python minor versions from setup.py and return them as a list of str. Return example: ['2.6', '2.7', '3.3', '3.4', '3.5', '3.6']

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabutils.py#L834-L850

train

theno/fabsetup

fabsetup/fabfile/setup/vim_janus.py

vim_janus

def vim_janus(uninstall=None): '''Install or update Janus, a distribution of addons and mappings for vim. More info: https://github.com/carlhuda/janus Customization: https://github.com/carlhuda/janus/wiki/Customization Args: uninstall: If not None, Uninstall janus and restore old vim config ''' if uninstall is not None: uninstall_janus() else: if not exists('~/.vim/janus'): print_msg('not installed => install') install_janus() else: print_msg('already installed => update') update_janus() customize_janus() show_files_used_by_vim_and_janus()

python

def vim_janus(uninstall=None): '''Install or update Janus, a distribution of addons and mappings for vim. More info: https://github.com/carlhuda/janus Customization: https://github.com/carlhuda/janus/wiki/Customization Args: uninstall: If not None, Uninstall janus and restore old vim config ''' if uninstall is not None: uninstall_janus() else: if not exists('~/.vim/janus'): print_msg('not installed => install') install_janus() else: print_msg('already installed => update') update_janus() customize_janus() show_files_used_by_vim_and_janus()

Install or update Janus, a distribution of addons and mappings for vim. More info: https://github.com/carlhuda/janus Customization: https://github.com/carlhuda/janus/wiki/Customization Args: uninstall: If not None, Uninstall janus and restore old vim config

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/vim_janus.py#L18-L38

train

yahoo/serviceping

serviceping/network.py

scan

def scan(host, port=80, url=None, https=False, timeout=1, max_size=65535): """ Scan a network port Parameters ---------- host : str Host or ip address to scan port : int, optional Port to scan, default=80 url : str, optional URL to perform get request to on the host and port specified https : bool, optional Perform ssl connection on the socket, default=False timeout : float Timeout for network operations, default=1 Returns ------- dict Result dictionary that contains the following keys: host - The host or IP address that was scanned port - The port number that was scanned state - The state of the port, will be either "open" or "closed" durations - An ordered dictionary with floating point value of the time elapsed for each connection operation Raises ------ ScanFailed - The scan operation failed """ starts = OrderedDict() ends = OrderedDict() port = int(port) result = dict( host=host, port=port, state='closed', durations=OrderedDict() ) if url: timeout = 1 result['code'] = None starts['all'] = starts['dns'] = datetime.datetime.now() # DNS Lookup try: hostip = socket.gethostbyname(host) result['ip'] = hostip ends['dns'] = datetime.datetime.now() except socket.gaierror: raise ScanFailed('DNS Lookup failed', result=result) # TCP Connect starts['connect'] = datetime.datetime.now() network_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) network_socket.settimeout(timeout) result_connection = network_socket.connect_ex((hostip, port)) ends['connect'] = datetime.datetime.now() # SSL if https: starts['ssl'] = datetime.datetime.now() try: network_socket = ssl.wrap_socket(network_socket) except socket.timeout: raise ScanFailed('SSL socket timeout', result=result) ends['ssl'] = datetime.datetime.now() # Get request if result_connection == 0 and url: starts['request'] = datetime.datetime.now() network_socket.send( "GET {0} HTTP/1.0\r\nHost: {1}\r\n\r\n".format( url, host ).encode('ascii')) if max_size: data = network_socket.recv(max_size) else: data = network_socket.recv() result['length'] = len(data) data = data.decode('ascii', errors='ignore') result['response'] = (data) try: result['code'] = int(data.split('\n')[0].split()[1]) except IndexError: pass ends['request'] = datetime.datetime.now() network_socket.close() # Calculate durations ends['all'] = datetime.datetime.now() for duration in starts.keys(): if duration in ends.keys(): result['durations'][duration] = ends[duration] - starts[duration] if result_connection == 0: result['state'] = 'open' return result

python

def scan(host, port=80, url=None, https=False, timeout=1, max_size=65535): """ Scan a network port Parameters ---------- host : str Host or ip address to scan port : int, optional Port to scan, default=80 url : str, optional URL to perform get request to on the host and port specified https : bool, optional Perform ssl connection on the socket, default=False timeout : float Timeout for network operations, default=1 Returns ------- dict Result dictionary that contains the following keys: host - The host or IP address that was scanned port - The port number that was scanned state - The state of the port, will be either "open" or "closed" durations - An ordered dictionary with floating point value of the time elapsed for each connection operation Raises ------ ScanFailed - The scan operation failed """ starts = OrderedDict() ends = OrderedDict() port = int(port) result = dict( host=host, port=port, state='closed', durations=OrderedDict() ) if url: timeout = 1 result['code'] = None starts['all'] = starts['dns'] = datetime.datetime.now() # DNS Lookup try: hostip = socket.gethostbyname(host) result['ip'] = hostip ends['dns'] = datetime.datetime.now() except socket.gaierror: raise ScanFailed('DNS Lookup failed', result=result) # TCP Connect starts['connect'] = datetime.datetime.now() network_socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM) network_socket.settimeout(timeout) result_connection = network_socket.connect_ex((hostip, port)) ends['connect'] = datetime.datetime.now() # SSL if https: starts['ssl'] = datetime.datetime.now() try: network_socket = ssl.wrap_socket(network_socket) except socket.timeout: raise ScanFailed('SSL socket timeout', result=result) ends['ssl'] = datetime.datetime.now() # Get request if result_connection == 0 and url: starts['request'] = datetime.datetime.now() network_socket.send( "GET {0} HTTP/1.0\r\nHost: {1}\r\n\r\n".format( url, host ).encode('ascii')) if max_size: data = network_socket.recv(max_size) else: data = network_socket.recv() result['length'] = len(data) data = data.decode('ascii', errors='ignore') result['response'] = (data) try: result['code'] = int(data.split('\n')[0].split()[1]) except IndexError: pass ends['request'] = datetime.datetime.now() network_socket.close() # Calculate durations ends['all'] = datetime.datetime.now() for duration in starts.keys(): if duration in ends.keys(): result['durations'][duration] = ends[duration] - starts[duration] if result_connection == 0: result['state'] = 'open' return result

Scan a network port Parameters ---------- host : str Host or ip address to scan port : int, optional Port to scan, default=80 url : str, optional URL to perform get request to on the host and port specified https : bool, optional Perform ssl connection on the socket, default=False timeout : float Timeout for network operations, default=1 Returns ------- dict Result dictionary that contains the following keys: host - The host or IP address that was scanned port - The port number that was scanned state - The state of the port, will be either "open" or "closed" durations - An ordered dictionary with floating point value of the time elapsed for each connection operation Raises ------ ScanFailed - The scan operation failed

1f9df5ee5b3cba466426b1164262278472ba4977

https://github.com/yahoo/serviceping/blob/1f9df5ee5b3cba466426b1164262278472ba4977/serviceping/network.py#L25-L124

train

yahoo/serviceping

serviceping/network.py

ping

def ping(host, port=80, url=None, https=False, timeout=1, max_size=65535, sequence=0): """ Ping a host Parameters ---------- host: str The host or ip address to ping port: int, optional The port to ping, default=80 url: str, optional URL to ping, will do a host/port ping if not provided https: bool, optional Connect via ssl, default=False timeout: int, optional Number of seconds to wait for a response before timing out, default=1 second max_size: int, optional The max size of response that can be retrieved. This should be a power of 2 default=65535. sequence: int, optional Sequence number for the ping request Returns ------- PingResponse: The ping response object """ try: result = scan(host=host, port=port, url=url, https=https, timeout=timeout, max_size=max_size) except ScanFailed as failure: result = failure.result result['error'] = True result['error_message'] = str(failure) result_obj = PingResponse( host=host, port=port, ip=result.get('ip', None), sequence=sequence, durations=result.get('durations', None), code=result.get('code', None), state=result.get('state', 'unknown'), length=result.get('length', 0), response=result.get('response', None), error=result.get('error', False), error_message=result.get('error_message', None), responding=True if result.get('state', 'unknown') in ['open'] else False, start=datetime.datetime.now(), end=datetime.datetime.now() + result['durations'].get('all', datetime.timedelta(0)) if result.get('durations', None) else None ) return result_obj

python

def ping(host, port=80, url=None, https=False, timeout=1, max_size=65535, sequence=0): """ Ping a host Parameters ---------- host: str The host or ip address to ping port: int, optional The port to ping, default=80 url: str, optional URL to ping, will do a host/port ping if not provided https: bool, optional Connect via ssl, default=False timeout: int, optional Number of seconds to wait for a response before timing out, default=1 second max_size: int, optional The max size of response that can be retrieved. This should be a power of 2 default=65535. sequence: int, optional Sequence number for the ping request Returns ------- PingResponse: The ping response object """ try: result = scan(host=host, port=port, url=url, https=https, timeout=timeout, max_size=max_size) except ScanFailed as failure: result = failure.result result['error'] = True result['error_message'] = str(failure) result_obj = PingResponse( host=host, port=port, ip=result.get('ip', None), sequence=sequence, durations=result.get('durations', None), code=result.get('code', None), state=result.get('state', 'unknown'), length=result.get('length', 0), response=result.get('response', None), error=result.get('error', False), error_message=result.get('error_message', None), responding=True if result.get('state', 'unknown') in ['open'] else False, start=datetime.datetime.now(), end=datetime.datetime.now() + result['durations'].get('all', datetime.timedelta(0)) if result.get('durations', None) else None ) return result_obj

Ping a host Parameters ---------- host: str The host or ip address to ping port: int, optional The port to ping, default=80 url: str, optional URL to ping, will do a host/port ping if not provided https: bool, optional Connect via ssl, default=False timeout: int, optional Number of seconds to wait for a response before timing out, default=1 second max_size: int, optional The max size of response that can be retrieved. This should be a power of 2 default=65535. sequence: int, optional Sequence number for the ping request Returns ------- PingResponse: The ping response object

1f9df5ee5b3cba466426b1164262278472ba4977

https://github.com/yahoo/serviceping/blob/1f9df5ee5b3cba466426b1164262278472ba4977/serviceping/network.py#L213-L265

train

muckamuck/stackility

stackility/command.py

delete

def delete(stack, region, profile): """ Delete the given CloudFormation stack. """ ini_data = {} environment = {} environment['stack_name'] = stack if region: environment['region'] = region else: environment['region'] = find_myself() if profile: environment['profile'] = profile ini_data['environment'] = environment if start_smash(ini_data): sys.exit(0) else: sys.exit(1)

python

def delete(stack, region, profile): """ Delete the given CloudFormation stack. """ ini_data = {} environment = {} environment['stack_name'] = stack if region: environment['region'] = region else: environment['region'] = find_myself() if profile: environment['profile'] = profile ini_data['environment'] = environment if start_smash(ini_data): sys.exit(0) else: sys.exit(1)

Delete the given CloudFormation stack.

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/command.py#L81-L102

train

muckamuck/stackility

stackility/command.py

list

def list(region, profile): """ List all the CloudFormation stacks in the given region. """ ini_data = {} environment = {} if region: environment['region'] = region else: environment['region'] = find_myself() if profile: environment['profile'] = profile ini_data['environment'] = environment if start_list(ini_data): sys.exit(0) else: sys.exit(1)

python

def list(region, profile): """ List all the CloudFormation stacks in the given region. """ ini_data = {} environment = {} if region: environment['region'] = region else: environment['region'] = find_myself() if profile: environment['profile'] = profile ini_data['environment'] = environment if start_list(ini_data): sys.exit(0) else: sys.exit(1)

List all the CloudFormation stacks in the given region.

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/command.py#L108-L127

train

muckamuck/stackility

stackility/command.py

drift

def drift(stack, region, profile): """ Produce a CloudFormation drift report for the given stack. """ logging.debug('finding drift - stack: {}'.format(stack)) logging.debug('region: {}'.format(region)) logging.debug('profile: {}'.format(profile)) tool = DriftTool( Stack=stack, Region=region, Profile=profile, Verbose=True ) if tool.determine_drift(): sys.exit(0) else: sys.exit(1)

python

def drift(stack, region, profile): """ Produce a CloudFormation drift report for the given stack. """ logging.debug('finding drift - stack: {}'.format(stack)) logging.debug('region: {}'.format(region)) logging.debug('profile: {}'.format(profile)) tool = DriftTool( Stack=stack, Region=region, Profile=profile, Verbose=True ) if tool.determine_drift(): sys.exit(0) else: sys.exit(1)

Produce a CloudFormation drift report for the given stack.

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/command.py#L134-L151

train

muckamuck/stackility

stackility/command.py

start_upsert

def start_upsert(ini_data): """ Helper function to facilitate upsert. Args: ini_date - the dictionary of info to run upsert Exit: 0 - good 1 - bad """ stack_driver = CloudStackUtility(ini_data) poll_stack = not ini_data.get('no_poll', False) if stack_driver.upsert(): logging.info('stack create/update was started successfully.') if poll_stack: stack_tool = None try: profile = ini_data.get('environment', {}).get('profile') if profile: boto3_session = boto3.session.Session(profile_name=profile) else: boto3_session = boto3.session.Session() region = ini_data['environment']['region'] stack_name = ini_data['environment']['stack_name'] cf_client = stack_driver.get_cloud_formation_client() if not cf_client: cf_client = boto3_session.client('cloudformation', region_name=region) stack_tool = stack_tool = StackTool( stack_name, region, cf_client ) except Exception as wtf: logging.warning('there was a problems creating stack tool: {}'.format(wtf)) if stack_driver.poll_stack(): try: logging.info('stack create/update was finished successfully.') stack_tool.print_stack_info() except Exception as wtf: logging.warning('there was a problems printing stack info: {}'.format(wtf)) sys.exit(0) else: try: logging.error('stack create/update was did not go well.') stack_tool.print_stack_events() except Exception as wtf: logging.warning('there was a problems printing stack events: {}'.format(wtf)) sys.exit(1) else: logging.error('start of stack create/update did not go well.') sys.exit(1)

python

def start_upsert(ini_data): """ Helper function to facilitate upsert. Args: ini_date - the dictionary of info to run upsert Exit: 0 - good 1 - bad """ stack_driver = CloudStackUtility(ini_data) poll_stack = not ini_data.get('no_poll', False) if stack_driver.upsert(): logging.info('stack create/update was started successfully.') if poll_stack: stack_tool = None try: profile = ini_data.get('environment', {}).get('profile') if profile: boto3_session = boto3.session.Session(profile_name=profile) else: boto3_session = boto3.session.Session() region = ini_data['environment']['region'] stack_name = ini_data['environment']['stack_name'] cf_client = stack_driver.get_cloud_formation_client() if not cf_client: cf_client = boto3_session.client('cloudformation', region_name=region) stack_tool = stack_tool = StackTool( stack_name, region, cf_client ) except Exception as wtf: logging.warning('there was a problems creating stack tool: {}'.format(wtf)) if stack_driver.poll_stack(): try: logging.info('stack create/update was finished successfully.') stack_tool.print_stack_info() except Exception as wtf: logging.warning('there was a problems printing stack info: {}'.format(wtf)) sys.exit(0) else: try: logging.error('stack create/update was did not go well.') stack_tool.print_stack_events() except Exception as wtf: logging.warning('there was a problems printing stack events: {}'.format(wtf)) sys.exit(1) else: logging.error('start of stack create/update did not go well.') sys.exit(1)

Helper function to facilitate upsert. Args: ini_date - the dictionary of info to run upsert Exit: 0 - good 1 - bad

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/command.py#L154-L212

train

muckamuck/stackility

stackility/command.py

read_config_info

def read_config_info(ini_file): """ Read the INI file Args: ini_file - path to the file Returns: A dictionary of stuff from the INI file Exits: 1 - if problems are encountered """ try: config = RawConfigParser() config.optionxform = lambda option: option config.read(ini_file) the_stuff = {} for section in config.sections(): the_stuff[section] = {} for option in config.options(section): the_stuff[section][option] = config.get(section, option) return the_stuff except Exception as wtf: logging.error('Exception caught in read_config_info(): {}'.format(wtf)) traceback.print_exc(file=sys.stdout) return sys.exit(1)

python

def read_config_info(ini_file): """ Read the INI file Args: ini_file - path to the file Returns: A dictionary of stuff from the INI file Exits: 1 - if problems are encountered """ try: config = RawConfigParser() config.optionxform = lambda option: option config.read(ini_file) the_stuff = {} for section in config.sections(): the_stuff[section] = {} for option in config.options(section): the_stuff[section][option] = config.get(section, option) return the_stuff except Exception as wtf: logging.error('Exception caught in read_config_info(): {}'.format(wtf)) traceback.print_exc(file=sys.stdout) return sys.exit(1)

Read the INI file Args: ini_file - path to the file Returns: A dictionary of stuff from the INI file Exits: 1 - if problems are encountered

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/command.py#L257-L284

train

muckamuck/stackility

stackility/stack_tool.py

StackTool.print_stack_info

def print_stack_info(self): ''' List resources from the given stack Args: None Returns: A dictionary filled resources or None if things went sideways ''' try: rest_api_id = None deployment_found = False response = self._cf_client.describe_stack_resources( StackName=self._stack_name ) print('\nThe following resources were created:') rows = [] for resource in response['StackResources']: if resource['ResourceType'] == 'AWS::ApiGateway::RestApi': rest_api_id = resource['PhysicalResourceId'] elif resource['ResourceType'] == 'AWS::ApiGateway::Deployment': deployment_found = True row = [] row.append(resource['ResourceType']) row.append(resource['LogicalResourceId']) row.append(resource['PhysicalResourceId']) rows.append(row) ''' print('\t{}\t{}\t{}'.format( resource['ResourceType'], resource['LogicalResourceId'], resource['PhysicalResourceId'] ) ) ''' print(tabulate(rows, headers=['Resource Type', 'Logical ID', 'Physical ID'])) if rest_api_id and deployment_found: url = 'https://{}.execute-api.{}.amazonaws.com/{}'.format( rest_api_id, self._region, '<stage>' ) print('\nThe deployed service can be found at this URL:') print('\t{}\n'.format(url)) return response except Exception as wtf: print(wtf) return None

python

def print_stack_info(self): ''' List resources from the given stack Args: None Returns: A dictionary filled resources or None if things went sideways ''' try: rest_api_id = None deployment_found = False response = self._cf_client.describe_stack_resources( StackName=self._stack_name ) print('\nThe following resources were created:') rows = [] for resource in response['StackResources']: if resource['ResourceType'] == 'AWS::ApiGateway::RestApi': rest_api_id = resource['PhysicalResourceId'] elif resource['ResourceType'] == 'AWS::ApiGateway::Deployment': deployment_found = True row = [] row.append(resource['ResourceType']) row.append(resource['LogicalResourceId']) row.append(resource['PhysicalResourceId']) rows.append(row) ''' print('\t{}\t{}\t{}'.format( resource['ResourceType'], resource['LogicalResourceId'], resource['PhysicalResourceId'] ) ) ''' print(tabulate(rows, headers=['Resource Type', 'Logical ID', 'Physical ID'])) if rest_api_id and deployment_found: url = 'https://{}.execute-api.{}.amazonaws.com/{}'.format( rest_api_id, self._region, '<stage>' ) print('\nThe deployed service can be found at this URL:') print('\t{}\n'.format(url)) return response except Exception as wtf: print(wtf) return None

List resources from the given stack Args: None Returns: A dictionary filled resources or None if things went sideways

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/stack_tool.py#L39-L92

train

muckamuck/stackility

stackility/stack_tool.py

StackTool.print_stack_events

def print_stack_events(self): ''' List events from the given stack Args: None Returns: None ''' first_token = '7be7981bd6287dd8112305e8f3822a6f' keep_going = True next_token = first_token current_request_token = None rows = [] try: while keep_going and next_token: if next_token == first_token: response = self._cf_client.describe_stack_events( StackName=self._stack_name ) else: response = self._cf_client.describe_stack_events( StackName=self._stack_name, NextToken=next_token ) next_token = response.get('NextToken', None) for event in response['StackEvents']: row = [] event_time = event.get('Timestamp') request_token = event.get('ClientRequestToken', 'unknown') if current_request_token is None: current_request_token = request_token elif current_request_token != request_token: keep_going = False break row.append(event_time.strftime('%x %X')) row.append(event.get('LogicalResourceId')) row.append(event.get('ResourceStatus')) row.append(event.get('ResourceStatusReason', '')) rows.append(row) if len(rows) > 0: print('\nEvents for the current upsert:') print(tabulate(rows, headers=['Time', 'Logical ID', 'Status', 'Message'])) return True else: print('\nNo stack events found\n') except Exception as wtf: print(wtf) return False

python

def print_stack_events(self): ''' List events from the given stack Args: None Returns: None ''' first_token = '7be7981bd6287dd8112305e8f3822a6f' keep_going = True next_token = first_token current_request_token = None rows = [] try: while keep_going and next_token: if next_token == first_token: response = self._cf_client.describe_stack_events( StackName=self._stack_name ) else: response = self._cf_client.describe_stack_events( StackName=self._stack_name, NextToken=next_token ) next_token = response.get('NextToken', None) for event in response['StackEvents']: row = [] event_time = event.get('Timestamp') request_token = event.get('ClientRequestToken', 'unknown') if current_request_token is None: current_request_token = request_token elif current_request_token != request_token: keep_going = False break row.append(event_time.strftime('%x %X')) row.append(event.get('LogicalResourceId')) row.append(event.get('ResourceStatus')) row.append(event.get('ResourceStatusReason', '')) rows.append(row) if len(rows) > 0: print('\nEvents for the current upsert:') print(tabulate(rows, headers=['Time', 'Logical ID', 'Status', 'Message'])) return True else: print('\nNo stack events found\n') except Exception as wtf: print(wtf) return False

List events from the given stack Args: None Returns: None

b1696f02661134d31b99b4dea7c0d21d09482d33

https://github.com/muckamuck/stackility/blob/b1696f02661134d31b99b4dea7c0d21d09482d33/stackility/stack_tool.py#L94-L147

train

theno/fabsetup

fabsetup/fabfile/setup/service/trac.py

trac

def trac(): '''Set up or update a trac project. This trac installation uses python2, git, sqlite (trac-default), gunicorn, and nginx. The connection is https-only and secured by a letsencrypt certificate. This certificate must be created separately with task setup.server_letsencrypt. This task installes or updates to the latest trac version hosted at https://pypi.python.org/pypi/Trac Created and modified files and dirs of this task: ``` ~/sites/<sitename> <--- example: sitename = trac.example.com │ ├── backup.sh <--- create a local backup (deletes dir backup/ ├── backup | before it creates │   └── <sitename>_tracenv_hotcopy.tar.gz <--´ the tarball) ├── run │   └── trac.sock <--- file-socket for binding to nginx ├── scripts │   └── tracwsgi.py ├── tracenv │   ├── conf │   │   ├── trac.htpasswd <--- trac user password hashes │   │   └── trac.ini <--- trac config file │   ├── db │   │   └── trac.db <--- sqlite database │   ├── files │   ├── git │   ├── htdocs │   ├── log │   ├── plugins │   ├── README │   ├── templates │   └── VERSION └── virtualenv ├── bin ├── include ├── lib ├── local └── pip-selfcheck.json ``` How to create a backup tarball "manually": `~/sites/<sitename>/backup/tracenv_hotcopy_<yyyy-mm-dd>.tar.gz`: ``` cd ~/sites/<sitename> && rm -rf ./backup ./virtualenv/bin/trac-admin ./tracenv hotcopy ./backup/tracenv_hotcopy mkdir -p ./backup && cd ./backup tar czf <sitename>_tracenv_hotcopy_$(date +%F).tar.gz tracenv_hotcopy/ rm -rf tracenv_hotcopy; ls -hl ``` More infos: https://trac.edgewall.org/wiki/TracInstall https://trac.edgewall.org/wiki/TracFastCgi#NginxConfiguration https://trac.edgewall.org/wiki/TracNginxRecipe https://trac.edgewall.org/wiki/Gunicorn http://www.obeythetestinggoat.com/book/chapter_08.html#_getting_to_a_production_ready_deployment Setting REMOTE_USER for Trac in Gunicorn behind Nginx: http://serverfault.com/a/392096 https://trac.edgewall.org/wiki/TracBackup ''' hostname = re.sub(r'^[^@]+@', '', env.host) # without username if any sitename = query_input( question='\nEnter site-name of Your trac web service', default=flo('trac.{hostname}')) username = env.user site_dir = flo('/home/{username}/sites/{sitename}') bin_dir = flo('{site_dir}/virtualenv/bin') # provisioning steps install_or_upgrade_virtualenv_pip_package() create_directory_structure(site_dir) update_virtualenv(site_dir, sitename) set_up_trac_plugins(sitename, site_dir, bin_dir) set_up_gunicorn(site_dir, sitename) configure_nginx(username, sitename, hostname) if query_yes_no('\nRestore trac environment from backup tarball?', default='no'): restore_tracenv_from_backup_tarball(site_dir, bin_dir) elif not tracenv_exists(site_dir): init_tracenv(site_dir, bin_dir, username) upgrade_tracenv(site_dir, bin_dir) set_up_upstart_for_gunicorn(sitename, username, site_dir)

python

def trac(): '''Set up or update a trac project. This trac installation uses python2, git, sqlite (trac-default), gunicorn, and nginx. The connection is https-only and secured by a letsencrypt certificate. This certificate must be created separately with task setup.server_letsencrypt. This task installes or updates to the latest trac version hosted at https://pypi.python.org/pypi/Trac Created and modified files and dirs of this task: ``` ~/sites/<sitename> <--- example: sitename = trac.example.com │ ├── backup.sh <--- create a local backup (deletes dir backup/ ├── backup | before it creates │   └── <sitename>_tracenv_hotcopy.tar.gz <--´ the tarball) ├── run │   └── trac.sock <--- file-socket for binding to nginx ├── scripts │   └── tracwsgi.py ├── tracenv │   ├── conf │   │   ├── trac.htpasswd <--- trac user password hashes │   │   └── trac.ini <--- trac config file │   ├── db │   │   └── trac.db <--- sqlite database │   ├── files │   ├── git │   ├── htdocs │   ├── log │   ├── plugins │   ├── README │   ├── templates │   └── VERSION └── virtualenv ├── bin ├── include ├── lib ├── local └── pip-selfcheck.json ``` How to create a backup tarball "manually": `~/sites/<sitename>/backup/tracenv_hotcopy_<yyyy-mm-dd>.tar.gz`: ``` cd ~/sites/<sitename> && rm -rf ./backup ./virtualenv/bin/trac-admin ./tracenv hotcopy ./backup/tracenv_hotcopy mkdir -p ./backup && cd ./backup tar czf <sitename>_tracenv_hotcopy_$(date +%F).tar.gz tracenv_hotcopy/ rm -rf tracenv_hotcopy; ls -hl ``` More infos: https://trac.edgewall.org/wiki/TracInstall https://trac.edgewall.org/wiki/TracFastCgi#NginxConfiguration https://trac.edgewall.org/wiki/TracNginxRecipe https://trac.edgewall.org/wiki/Gunicorn http://www.obeythetestinggoat.com/book/chapter_08.html#_getting_to_a_production_ready_deployment Setting REMOTE_USER for Trac in Gunicorn behind Nginx: http://serverfault.com/a/392096 https://trac.edgewall.org/wiki/TracBackup ''' hostname = re.sub(r'^[^@]+@', '', env.host) # without username if any sitename = query_input( question='\nEnter site-name of Your trac web service', default=flo('trac.{hostname}')) username = env.user site_dir = flo('/home/{username}/sites/{sitename}') bin_dir = flo('{site_dir}/virtualenv/bin') # provisioning steps install_or_upgrade_virtualenv_pip_package() create_directory_structure(site_dir) update_virtualenv(site_dir, sitename) set_up_trac_plugins(sitename, site_dir, bin_dir) set_up_gunicorn(site_dir, sitename) configure_nginx(username, sitename, hostname) if query_yes_no('\nRestore trac environment from backup tarball?', default='no'): restore_tracenv_from_backup_tarball(site_dir, bin_dir) elif not tracenv_exists(site_dir): init_tracenv(site_dir, bin_dir, username) upgrade_tracenv(site_dir, bin_dir) set_up_upstart_for_gunicorn(sitename, username, site_dir)

Set up or update a trac project. This trac installation uses python2, git, sqlite (trac-default), gunicorn, and nginx. The connection is https-only and secured by a letsencrypt certificate. This certificate must be created separately with task setup.server_letsencrypt. This task installes or updates to the latest trac version hosted at https://pypi.python.org/pypi/Trac Created and modified files and dirs of this task: ``` ~/sites/<sitename> <--- example: sitename = trac.example.com │ ├── backup.sh <--- create a local backup (deletes dir backup/ ├── backup | before it creates │   └── <sitename>_tracenv_hotcopy.tar.gz <--´ the tarball) ├── run │   └── trac.sock <--- file-socket for binding to nginx ├── scripts │   └── tracwsgi.py ├── tracenv │   ├── conf │   │   ├── trac.htpasswd <--- trac user password hashes │   │   └── trac.ini <--- trac config file │   ├── db │   │   └── trac.db <--- sqlite database │   ├── files │   ├── git │   ├── htdocs │   ├── log │   ├── plugins │   ├── README │   ├── templates │   └── VERSION └── virtualenv ├── bin ├── include ├── lib ├── local └── pip-selfcheck.json ``` How to create a backup tarball "manually": `~/sites/<sitename>/backup/tracenv_hotcopy_<yyyy-mm-dd>.tar.gz`: ``` cd ~/sites/<sitename> && rm -rf ./backup ./virtualenv/bin/trac-admin ./tracenv hotcopy ./backup/tracenv_hotcopy mkdir -p ./backup && cd ./backup tar czf <sitename>_tracenv_hotcopy_$(date +%F).tar.gz tracenv_hotcopy/ rm -rf tracenv_hotcopy; ls -hl ``` More infos: https://trac.edgewall.org/wiki/TracInstall https://trac.edgewall.org/wiki/TracFastCgi#NginxConfiguration https://trac.edgewall.org/wiki/TracNginxRecipe https://trac.edgewall.org/wiki/Gunicorn http://www.obeythetestinggoat.com/book/chapter_08.html#_getting_to_a_production_ready_deployment Setting REMOTE_USER for Trac in Gunicorn behind Nginx: http://serverfault.com/a/392096 https://trac.edgewall.org/wiki/TracBackup

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/service/trac.py#L28-L120

train

push-things/wallabag_api

wallabag_api/wallabag.py

Wallabag.query

async def query(self, path, method='get', **params): """ Do a query to the System API :param path: url to the API :param method: the kind of query to do :param params: a dict with all the necessary things to query the API :return json data """ if method in ('get', 'post', 'patch', 'delete', 'put'): full_path = self.host + path if method == 'get': resp = await self.aio_sess.get(full_path, params=params) elif method == 'post': resp = await self.aio_sess.post(full_path, data=params) elif method == 'patch': resp = await self.aio_sess.patch(full_path, data=params) elif method == 'delete': resp = await self.aio_sess.delete(full_path, params=params, headers=params) elif method == 'put': resp = await self.aio_sess.put(full_path, data=params) async with resp: # return the content if its a binary one if resp.content_type.startswith('application/pdf') or \ resp.content_type.startswith('application/epub'): return await resp.read() return await self.handle_json_response(resp) else: raise ValueError('method expected: get, post, patch, delete, put')

python

async def query(self, path, method='get', **params): """ Do a query to the System API :param path: url to the API :param method: the kind of query to do :param params: a dict with all the necessary things to query the API :return json data """ if method in ('get', 'post', 'patch', 'delete', 'put'): full_path = self.host + path if method == 'get': resp = await self.aio_sess.get(full_path, params=params) elif method == 'post': resp = await self.aio_sess.post(full_path, data=params) elif method == 'patch': resp = await self.aio_sess.patch(full_path, data=params) elif method == 'delete': resp = await self.aio_sess.delete(full_path, params=params, headers=params) elif method == 'put': resp = await self.aio_sess.put(full_path, data=params) async with resp: # return the content if its a binary one if resp.content_type.startswith('application/pdf') or \ resp.content_type.startswith('application/epub'): return await resp.read() return await self.handle_json_response(resp) else: raise ValueError('method expected: get, post, patch, delete, put')

Do a query to the System API :param path: url to the API :param method: the kind of query to do :param params: a dict with all the necessary things to query the API :return json data

8d1e10a6ebc03d1ac9af2b38b57eb69f29b4216e

https://github.com/push-things/wallabag_api/blob/8d1e10a6ebc03d1ac9af2b38b57eb69f29b4216e/wallabag_api/wallabag.py#L60-L91

train

theno/fabsetup

fabsetup/fabfile/setup/revealjs.py

revealjs

def revealjs(basedir=None, title=None, subtitle=None, description=None, github_user=None, github_repo=None): '''Set up or update a reveals.js presentation with slides written in markdown. Several reveal.js plugins will be set up, too. More info: Demo: https://theno.github.io/revealjs_template http://lab.hakim.se/reveal-js/ https://github.com/hakimel/reveal.js plugins: https://github.com/hakimel/reveal.js/wiki/Plugins,-Tools-and-Hardware https://github.com/rajgoel/reveal.js-plugins/ https://github.com/e-gor/Reveal.js-TOC-Progress https://github.com/e-gor/Reveal.js-Title-Footer ''' basedir = basedir or query_input('Base dir of the presentation?', default='~/repos/my_presi') revealjs_repo_name = 'reveal.js' revealjs_dir = flo('{basedir}/{revealjs_repo_name}') _lazy_dict['presi_title'] = title _lazy_dict['presi_subtitle'] = subtitle _lazy_dict['presi_description'] = description _lazy_dict['github_user'] = github_user _lazy_dict['github_repo'] = github_repo question = flo("Base dir already contains a sub dir '{revealjs_repo_name}'." ' Reset (and re-download) reveal.js codebase?') if not exists(revealjs_dir) or query_yes_no(question, default='no'): run(flo('mkdir -p {basedir}')) set_up_revealjs_codebase(basedir, revealjs_repo_name) install_plugins(revealjs_dir) apply_customizations(repo_dir=revealjs_dir) if exists(revealjs_dir): install_files_in_basedir(basedir, repo_dir=revealjs_dir) init_git_repo(basedir) create_github_remote_repo(basedir) setup_npm(revealjs_dir) else: print('abort')

python

def revealjs(basedir=None, title=None, subtitle=None, description=None, github_user=None, github_repo=None): '''Set up or update a reveals.js presentation with slides written in markdown. Several reveal.js plugins will be set up, too. More info: Demo: https://theno.github.io/revealjs_template http://lab.hakim.se/reveal-js/ https://github.com/hakimel/reveal.js plugins: https://github.com/hakimel/reveal.js/wiki/Plugins,-Tools-and-Hardware https://github.com/rajgoel/reveal.js-plugins/ https://github.com/e-gor/Reveal.js-TOC-Progress https://github.com/e-gor/Reveal.js-Title-Footer ''' basedir = basedir or query_input('Base dir of the presentation?', default='~/repos/my_presi') revealjs_repo_name = 'reveal.js' revealjs_dir = flo('{basedir}/{revealjs_repo_name}') _lazy_dict['presi_title'] = title _lazy_dict['presi_subtitle'] = subtitle _lazy_dict['presi_description'] = description _lazy_dict['github_user'] = github_user _lazy_dict['github_repo'] = github_repo question = flo("Base dir already contains a sub dir '{revealjs_repo_name}'." ' Reset (and re-download) reveal.js codebase?') if not exists(revealjs_dir) or query_yes_no(question, default='no'): run(flo('mkdir -p {basedir}')) set_up_revealjs_codebase(basedir, revealjs_repo_name) install_plugins(revealjs_dir) apply_customizations(repo_dir=revealjs_dir) if exists(revealjs_dir): install_files_in_basedir(basedir, repo_dir=revealjs_dir) init_git_repo(basedir) create_github_remote_repo(basedir) setup_npm(revealjs_dir) else: print('abort')

Set up or update a reveals.js presentation with slides written in markdown. Several reveal.js plugins will be set up, too. More info: Demo: https://theno.github.io/revealjs_template http://lab.hakim.se/reveal-js/ https://github.com/hakimel/reveal.js plugins: https://github.com/hakimel/reveal.js/wiki/Plugins,-Tools-and-Hardware https://github.com/rajgoel/reveal.js-plugins/ https://github.com/e-gor/Reveal.js-TOC-Progress https://github.com/e-gor/Reveal.js-Title-Footer

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/revealjs.py#L50-L90

train

theno/fabsetup

fabsetup/fabfile/setup/revealjs.py

tweak_css

def tweak_css(repo_dir): '''Comment out some css settings.''' print_msg("* don't capitalize titles (no uppercase headings)") files = [ 'beige.css', 'black.css', 'blood.css', 'league.css', 'moon.css', 'night.css', 'serif.css', 'simple.css', 'sky.css', 'solarized.css', 'white.css', ] line = ' text-transform: uppercase;' for file_ in files: update_or_append_line(filename=flo('{repo_dir}/css/theme/{file_}'), prefix=line, new_line=flo('/*{line}*/')) print_msg('* images without border') data = [ {'file': 'beige.css', 'line': ' border: 4px solid #333;'}, {'file': 'black.css', 'line': ' border: 4px solid #fff;'}, {'file': 'blood.css', 'line': ' border: 4px solid #eee;'}, {'file': 'league.css', 'line': ' border: 4px solid #eee;'}, {'file': 'moon.css', 'line': ' border: 4px solid #93a1a1;'}, {'file': 'night.css', 'line': ' border: 4px solid #eee;'}, {'file': 'serif.css', 'line': ' border: 4px solid #000;'}, {'file': 'simple.css', 'line': ' border: 4px solid #000;'}, {'file': 'sky.css', 'line': ' border: 4px solid #333;'}, {'file': 'solarized.css', 'line': ' border: 4px solid #657b83;'}, {'file': 'white.css', 'line': ' border: 4px solid #222;'}, ] for item in data: file_ = item['file'] lines = [item['line'], ] lines.extend([' box-shadow: 0 0 10px rgba(0, 0, 0, 0.15); }', ' box-shadow: 0 0 20px rgba(0, 0, 0, 0.55); }']) for line in lines: update_or_append_line(filename=flo('{repo_dir}/css/theme/{file_}'), prefix=line, new_line=flo('/*{line}*/'))

python

def tweak_css(repo_dir): '''Comment out some css settings.''' print_msg("* don't capitalize titles (no uppercase headings)") files = [ 'beige.css', 'black.css', 'blood.css', 'league.css', 'moon.css', 'night.css', 'serif.css', 'simple.css', 'sky.css', 'solarized.css', 'white.css', ] line = ' text-transform: uppercase;' for file_ in files: update_or_append_line(filename=flo('{repo_dir}/css/theme/{file_}'), prefix=line, new_line=flo('/*{line}*/')) print_msg('* images without border') data = [ {'file': 'beige.css', 'line': ' border: 4px solid #333;'}, {'file': 'black.css', 'line': ' border: 4px solid #fff;'}, {'file': 'blood.css', 'line': ' border: 4px solid #eee;'}, {'file': 'league.css', 'line': ' border: 4px solid #eee;'}, {'file': 'moon.css', 'line': ' border: 4px solid #93a1a1;'}, {'file': 'night.css', 'line': ' border: 4px solid #eee;'}, {'file': 'serif.css', 'line': ' border: 4px solid #000;'}, {'file': 'simple.css', 'line': ' border: 4px solid #000;'}, {'file': 'sky.css', 'line': ' border: 4px solid #333;'}, {'file': 'solarized.css', 'line': ' border: 4px solid #657b83;'}, {'file': 'white.css', 'line': ' border: 4px solid #222;'}, ] for item in data: file_ = item['file'] lines = [item['line'], ] lines.extend([' box-shadow: 0 0 10px rgba(0, 0, 0, 0.15); }', ' box-shadow: 0 0 20px rgba(0, 0, 0, 0.55); }']) for line in lines: update_or_append_line(filename=flo('{repo_dir}/css/theme/{file_}'), prefix=line, new_line=flo('/*{line}*/'))

Comment out some css settings.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/revealjs.py#L184-L218

train

theno/fabsetup

fabsetup/fabfile/setup/revealjs.py

decktape

def decktape(): '''Install DeckTape. DeckTape is a "high-quality PDF exporter for HTML5 presentation frameworks". It can be used to create PDFs from reveal.js presentations. More info: https://github.com/astefanutti/decktape https://github.com/hakimel/reveal.js/issues/1252#issuecomment-198270915 ''' run('mkdir -p ~/bin/decktape') if not exists('~/bin/decktape/decktape-1.0.0'): print_msg('\n## download decktape 1.0.0\n') run('cd ~/bin/decktape && ' 'curl -L https://github.com/astefanutti/decktape/archive/' 'v1.0.0.tar.gz | tar -xz --exclude phantomjs') run('cd ~/bin/decktape/decktape-1.0.0 && ' 'curl -L https://github.com/astefanutti/decktape/releases/' 'download/v1.0.0/phantomjs-linux-x86-64 -o phantomjs') run('cd ~/bin/decktape/decktape-1.0.0 && ' 'chmod +x phantomjs') run('ln -snf ~/bin/decktape/decktape-1.0.0 ~/bin/decktape/active', msg='\n## link installed decktape version as active') print_msg('\nCreate PDF from reveal.js presentation:\n\n ' '# serve presentation:\n ' 'cd ~/repos/my_presi/reveal.js/ && npm start\n\n ' '# create pdf in another shell:\n ' 'cd ~/bin/decktape/active && \\\n ' './phantomjs decktape.js --size 1280x800 localhost:8000 ' '~/repos/my_presi/my_presi.pdf')

python

def decktape(): '''Install DeckTape. DeckTape is a "high-quality PDF exporter for HTML5 presentation frameworks". It can be used to create PDFs from reveal.js presentations. More info: https://github.com/astefanutti/decktape https://github.com/hakimel/reveal.js/issues/1252#issuecomment-198270915 ''' run('mkdir -p ~/bin/decktape') if not exists('~/bin/decktape/decktape-1.0.0'): print_msg('\n## download decktape 1.0.0\n') run('cd ~/bin/decktape && ' 'curl -L https://github.com/astefanutti/decktape/archive/' 'v1.0.0.tar.gz | tar -xz --exclude phantomjs') run('cd ~/bin/decktape/decktape-1.0.0 && ' 'curl -L https://github.com/astefanutti/decktape/releases/' 'download/v1.0.0/phantomjs-linux-x86-64 -o phantomjs') run('cd ~/bin/decktape/decktape-1.0.0 && ' 'chmod +x phantomjs') run('ln -snf ~/bin/decktape/decktape-1.0.0 ~/bin/decktape/active', msg='\n## link installed decktape version as active') print_msg('\nCreate PDF from reveal.js presentation:\n\n ' '# serve presentation:\n ' 'cd ~/repos/my_presi/reveal.js/ && npm start\n\n ' '# create pdf in another shell:\n ' 'cd ~/bin/decktape/active && \\\n ' './phantomjs decktape.js --size 1280x800 localhost:8000 ' '~/repos/my_presi/my_presi.pdf')

Install DeckTape. DeckTape is a "high-quality PDF exporter for HTML5 presentation frameworks". It can be used to create PDFs from reveal.js presentations. More info: https://github.com/astefanutti/decktape https://github.com/hakimel/reveal.js/issues/1252#issuecomment-198270915

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/revealjs.py#L366-L395

train

theno/fabsetup

fabsetup/fabfile/setup/revealjs.py

revealjs_template

def revealjs_template(): '''Create or update the template presentation demo using task `revealjs`. ''' from config import basedir, github_user, github_repo run(flo('rm -f {basedir}/index.html')) run(flo('rm -f {basedir}/slides.md')) run(flo('rm -f {basedir}/README.md')) run(flo('rm -rf {basedir}/img/')) title = 'reveal.js template' subtitle = '[reveal.js][3] presentation written ' \ 'in [markdown][4] set up with [fabric][5] & [fabsetup][6]' description = '''\ This presentation shows how to create a reveal.js presentation which will be set up with the fabric task `setup.revealjs` of fabsetup. Also, you can use this presentation source as a reveal.js template: * Checkout this repo * Then set the title in the `index.html` and edit the `slides.md`.''' execute(revealjs, basedir, title, subtitle, description, github_user, github_repo) # (README.md was removed, but not the github remote repo) print_msg('\n## Re-add github repo infos into README.md') basename = os.path.basename(basedir) _insert_repo_infos_into_readme(basedir, github_user=_lazy('github_user'), github_repo=_lazy('github_repo', default=basename)) print_msg('\n## Assure symbolic link not tracked by git exists\n') run(flo('ln -snf ../reveal.js {basedir}/reveal.js/reveal.js'))

python

def revealjs_template(): '''Create or update the template presentation demo using task `revealjs`. ''' from config import basedir, github_user, github_repo run(flo('rm -f {basedir}/index.html')) run(flo('rm -f {basedir}/slides.md')) run(flo('rm -f {basedir}/README.md')) run(flo('rm -rf {basedir}/img/')) title = 'reveal.js template' subtitle = '[reveal.js][3] presentation written ' \ 'in [markdown][4] set up with [fabric][5] & [fabsetup][6]' description = '''\ This presentation shows how to create a reveal.js presentation which will be set up with the fabric task `setup.revealjs` of fabsetup. Also, you can use this presentation source as a reveal.js template: * Checkout this repo * Then set the title in the `index.html` and edit the `slides.md`.''' execute(revealjs, basedir, title, subtitle, description, github_user, github_repo) # (README.md was removed, but not the github remote repo) print_msg('\n## Re-add github repo infos into README.md') basename = os.path.basename(basedir) _insert_repo_infos_into_readme(basedir, github_user=_lazy('github_user'), github_repo=_lazy('github_repo', default=basename)) print_msg('\n## Assure symbolic link not tracked by git exists\n') run(flo('ln -snf ../reveal.js {basedir}/reveal.js/reveal.js'))

Create or update the template presentation demo using task `revealjs`.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/revealjs.py#L401-L434

train

awickert/gFlex

gflex/f1d.py

F1D.spatialDomainNoGrid

def spatialDomainNoGrid(self): """ Superposition of analytical solutions without a gridded domain """ self.w = np.zeros(self.xw.shape) if self.Debug: print("w = ") print(self.w.shape) for i in range(len(self.q)): # More efficient if we have created some 0-load points # (e.g., for where we want output) if self.q[i] != 0: dist = np.abs(self.xw - self.x[i]) self.w -= self.q[i] * self.coeff * np.exp(-dist/self.alpha) * \ ( np.cos(dist/self.alpha) + np.sin(dist/self.alpha) )

python

def spatialDomainNoGrid(self): """ Superposition of analytical solutions without a gridded domain """ self.w = np.zeros(self.xw.shape) if self.Debug: print("w = ") print(self.w.shape) for i in range(len(self.q)): # More efficient if we have created some 0-load points # (e.g., for where we want output) if self.q[i] != 0: dist = np.abs(self.xw - self.x[i]) self.w -= self.q[i] * self.coeff * np.exp(-dist/self.alpha) * \ ( np.cos(dist/self.alpha) + np.sin(dist/self.alpha) )

Superposition of analytical solutions without a gridded domain

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/f1d.py#L143-L159

train

awickert/gFlex

gflex/f1d.py

F1D.build_diagonals

def build_diagonals(self): """ Builds the diagonals for the coefficient array """ ########################################################## # INCORPORATE BOUNDARY CONDITIONS INTO COEFFICIENT ARRAY # ########################################################## # Roll to keep the proper coefficients at the proper places in the # arrays: Python will naturally just do vertical shifts instead of # diagonal shifts, so this takes into account the horizontal compoent # to ensure that boundary values are at the right place. self.l2 = np.roll(self.l2, -2) self.l1 = np.roll(self.l1, -1) self.r1 = np.roll(self.r1, 1) self.r2 = np.roll(self.r2, 2) # Then assemble these rows: this is where the periodic boundary condition # can matter. if self.coeff_matrix is not None: pass elif self.BC_E == 'Periodic' and self.BC_W == 'Periodic': # In this case, the boundary-condition-related stacking has already # happened inside b.c.-handling function. This is because periodic # boundary conditions require extra diagonals to exist on the edges of # the solution array pass else: self.diags = np.vstack((self.l2,self.l1,self.c0,self.r1,self.r2)) self.offsets = np.array([-2,-1,0,1,2]) # Everybody now (including periodic b.c. cases) self.coeff_matrix = spdiags(self.diags, self.offsets, self.nx, self.nx, format='csr')

python

def build_diagonals(self): """ Builds the diagonals for the coefficient array """ ########################################################## # INCORPORATE BOUNDARY CONDITIONS INTO COEFFICIENT ARRAY # ########################################################## # Roll to keep the proper coefficients at the proper places in the # arrays: Python will naturally just do vertical shifts instead of # diagonal shifts, so this takes into account the horizontal compoent # to ensure that boundary values are at the right place. self.l2 = np.roll(self.l2, -2) self.l1 = np.roll(self.l1, -1) self.r1 = np.roll(self.r1, 1) self.r2 = np.roll(self.r2, 2) # Then assemble these rows: this is where the periodic boundary condition # can matter. if self.coeff_matrix is not None: pass elif self.BC_E == 'Periodic' and self.BC_W == 'Periodic': # In this case, the boundary-condition-related stacking has already # happened inside b.c.-handling function. This is because periodic # boundary conditions require extra diagonals to exist on the edges of # the solution array pass else: self.diags = np.vstack((self.l2,self.l1,self.c0,self.r1,self.r2)) self.offsets = np.array([-2,-1,0,1,2]) # Everybody now (including periodic b.c. cases) self.coeff_matrix = spdiags(self.diags, self.offsets, self.nx, self.nx, format='csr')

Builds the diagonals for the coefficient array

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/f1d.py#L344-L377

train

sbmlteam/libCombine

examples/python/createArchiveExample.py

createArchiveExample

def createArchiveExample(fileName): """ Creates Combine Archive containing the given file. :param fileName: file to include in the archive :return: None """ print('*' * 80) print('Create archive') print('*' * 80) archive = CombineArchive() archive.addFile( fileName, # filename "./models/model.xml", # target file name KnownFormats.lookupFormat("sbml"), # look up identifier for SBML models True # mark file as master ) # add metadata to the archive itself description = OmexDescription() description.setAbout(".") description.setDescription("Simple test archive including one SBML model") description.setCreated(OmexDescription.getCurrentDateAndTime()) creator = VCard() creator.setFamilyName("Bergmann") creator.setGivenName("Frank") creator.setEmail("[email protected]") creator.setOrganization("Caltech") description.addCreator(creator) archive.addMetadata(".", description) # add metadata to the added file location = "./models/model.xml" description = OmexDescription() description.setAbout(location) description.setDescription("SBML model") description.setCreated(OmexDescription.getCurrentDateAndTime()) archive.addMetadata(location, description) # write the archive out_file = "out.omex" archive.writeToFile(out_file) print('Archive created:', out_file)

python

def createArchiveExample(fileName): """ Creates Combine Archive containing the given file. :param fileName: file to include in the archive :return: None """ print('*' * 80) print('Create archive') print('*' * 80) archive = CombineArchive() archive.addFile( fileName, # filename "./models/model.xml", # target file name KnownFormats.lookupFormat("sbml"), # look up identifier for SBML models True # mark file as master ) # add metadata to the archive itself description = OmexDescription() description.setAbout(".") description.setDescription("Simple test archive including one SBML model") description.setCreated(OmexDescription.getCurrentDateAndTime()) creator = VCard() creator.setFamilyName("Bergmann") creator.setGivenName("Frank") creator.setEmail("[email protected]") creator.setOrganization("Caltech") description.addCreator(creator) archive.addMetadata(".", description) # add metadata to the added file location = "./models/model.xml" description = OmexDescription() description.setAbout(location) description.setDescription("SBML model") description.setCreated(OmexDescription.getCurrentDateAndTime()) archive.addMetadata(location, description) # write the archive out_file = "out.omex" archive.writeToFile(out_file) print('Archive created:', out_file)

Creates Combine Archive containing the given file. :param fileName: file to include in the archive :return: None

d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4

https://github.com/sbmlteam/libCombine/blob/d7c11a90129dedbcc8bdba8d204be03f1dd0c3e4/examples/python/createArchiveExample.py#L11-L57

train

yahoo/serviceping

serviceping/serviceping.py

calc_deviation

def calc_deviation(values, average): """ Calculate the standard deviation of a list of values @param values: list(float) @param average: @return: """ size = len(values) if size < 2: return 0 calc_sum = 0.0 for number in range(0, size): calc_sum += math.sqrt((values[number] - average) ** 2) return math.sqrt((1.0 / (size - 1)) * (calc_sum / size))

python

def calc_deviation(values, average): """ Calculate the standard deviation of a list of values @param values: list(float) @param average: @return: """ size = len(values) if size < 2: return 0 calc_sum = 0.0 for number in range(0, size): calc_sum += math.sqrt((values[number] - average) ** 2) return math.sqrt((1.0 / (size - 1)) * (calc_sum / size))

Calculate the standard deviation of a list of values @param values: list(float) @param average: @return:

1f9df5ee5b3cba466426b1164262278472ba4977

https://github.com/yahoo/serviceping/blob/1f9df5ee5b3cba466426b1164262278472ba4977/serviceping/serviceping.py#L106-L120

train

yahoo/serviceping

serviceping/serviceping.py

StatsList.append

def append(self, value): """ Append a value to the stats list Parameters ---------- value : float The value to add """ self.count += 1 if self.count == 1: self.old_m = self.new_m = value self.old_s = 0 else: self.new_m = self.old_m + (value - self.old_m) / self.count self.new_s = self.old_s + (value - self.old_m) * (value - self.new_m) self.old_m = self.new_m self.old_s = self.new_s

python

def append(self, value): """ Append a value to the stats list Parameters ---------- value : float The value to add """ self.count += 1 if self.count == 1: self.old_m = self.new_m = value self.old_s = 0 else: self.new_m = self.old_m + (value - self.old_m) / self.count self.new_s = self.old_s + (value - self.old_m) * (value - self.new_m) self.old_m = self.new_m self.old_s = self.new_s

Append a value to the stats list Parameters ---------- value : float The value to add

1f9df5ee5b3cba466426b1164262278472ba4977

https://github.com/yahoo/serviceping/blob/1f9df5ee5b3cba466426b1164262278472ba4977/serviceping/serviceping.py#L35-L54

train

bionikspoon/pureyaml

docs/github_docs.py

pipeline

def pipeline(steps, initial=None): """ Chain results from a list of functions. Inverted reduce. :param (function) steps: List of function callbacks :param initial: Starting value for pipeline. """ def apply(result, step): return step(result) return reduce(apply, steps, initial)

python

def pipeline(steps, initial=None): """ Chain results from a list of functions. Inverted reduce. :param (function) steps: List of function callbacks :param initial: Starting value for pipeline. """ def apply(result, step): return step(result) return reduce(apply, steps, initial)

Chain results from a list of functions. Inverted reduce. :param (function) steps: List of function callbacks :param initial: Starting value for pipeline.

784830b907ca14525c4cecdb6ae35306f6f8a877

https://github.com/bionikspoon/pureyaml/blob/784830b907ca14525c4cecdb6ae35306f6f8a877/docs/github_docs.py#L186-L197

train

jaraco/jaraco.windows

jaraco/windows/environ.py

RegisteredEnvironment.add

def add(class_, name, value, sep=';'): """ Add a value to a delimited variable, but only when the value isn't already present. """ values = class_.get_values_list(name, sep) if value in values: return new_value = sep.join(values + [value]) winreg.SetValueEx( class_.key, name, 0, winreg.REG_EXPAND_SZ, new_value) class_.notify()

python

def add(class_, name, value, sep=';'): """ Add a value to a delimited variable, but only when the value isn't already present. """ values = class_.get_values_list(name, sep) if value in values: return new_value = sep.join(values + [value]) winreg.SetValueEx( class_.key, name, 0, winreg.REG_EXPAND_SZ, new_value) class_.notify()

Add a value to a delimited variable, but only when the value isn't already present.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/environ.py#L84-L95

train

jaraco/jaraco.windows

jaraco/windows/timezone.py

Info.current

def current(class_): "Windows Platform SDK GetTimeZoneInformation" tzi = class_() kernel32 = ctypes.windll.kernel32 getter = kernel32.GetTimeZoneInformation getter = getattr(kernel32, 'GetDynamicTimeZoneInformation', getter) code = getter(ctypes.byref(tzi)) return code, tzi

python

def current(class_): "Windows Platform SDK GetTimeZoneInformation" tzi = class_() kernel32 = ctypes.windll.kernel32 getter = kernel32.GetTimeZoneInformation getter = getattr(kernel32, 'GetDynamicTimeZoneInformation', getter) code = getter(ctypes.byref(tzi)) return code, tzi

Windows Platform SDK GetTimeZoneInformation

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/timezone.py#L168-L175

train

jaraco/jaraco.windows

jaraco/windows/timezone.py

Info.dynamic_info

def dynamic_info(self): "Return a map that for a given year will return the correct Info" if self.key_name: dyn_key = self.get_key().subkey('Dynamic DST') del dyn_key['FirstEntry'] del dyn_key['LastEntry'] years = map(int, dyn_key.keys()) values = map(Info, dyn_key.values()) # create a range mapping that searches by descending year and matches # if the target year is greater or equal. return RangeMap(zip(years, values), RangeMap.descending, operator.ge) else: return AnyDict(self)

python

def dynamic_info(self): "Return a map that for a given year will return the correct Info" if self.key_name: dyn_key = self.get_key().subkey('Dynamic DST') del dyn_key['FirstEntry'] del dyn_key['LastEntry'] years = map(int, dyn_key.keys()) values = map(Info, dyn_key.values()) # create a range mapping that searches by descending year and matches # if the target year is greater or equal. return RangeMap(zip(years, values), RangeMap.descending, operator.ge) else: return AnyDict(self)

Return a map that for a given year will return the correct Info

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/timezone.py#L198-L210

train

jaraco/jaraco.windows

jaraco/windows/timezone.py

Info._locate_day

def _locate_day(year, cutoff): """ Takes a SYSTEMTIME object, such as retrieved from a TIME_ZONE_INFORMATION structure or call to GetTimeZoneInformation and interprets it based on the given year to identify the actual day. This method is necessary because the SYSTEMTIME structure refers to a day by its day of the week and week of the month (e.g. 4th saturday in March). >>> SATURDAY = 6 >>> MARCH = 3 >>> st = SYSTEMTIME(2000, MARCH, SATURDAY, 4, 0, 0, 0, 0) # according to my calendar, the 4th Saturday in March in 2009 was the 28th >>> expected_date = datetime.datetime(2009, 3, 28) >>> Info._locate_day(2009, st) == expected_date True """ # MS stores Sunday as 0, Python datetime stores Monday as zero target_weekday = (cutoff.day_of_week + 6) % 7 # For SYSTEMTIMEs relating to time zone inforamtion, cutoff.day # is the week of the month week_of_month = cutoff.day # so the following is the first day of that week day = (week_of_month - 1) * 7 + 1 result = datetime.datetime( year, cutoff.month, day, cutoff.hour, cutoff.minute, cutoff.second, cutoff.millisecond) # now the result is the correct week, but not necessarily # the correct day of the week days_to_go = (target_weekday - result.weekday()) % 7 result += datetime.timedelta(days_to_go) # if we selected a day in the month following the target month, # move back a week or two. # This is necessary because Microsoft defines the fifth week in a month # to be the last week in a month and adding the time delta might have # pushed the result into the next month. while result.month == cutoff.month + 1: result -= datetime.timedelta(weeks=1) return result

python

def _locate_day(year, cutoff): """ Takes a SYSTEMTIME object, such as retrieved from a TIME_ZONE_INFORMATION structure or call to GetTimeZoneInformation and interprets it based on the given year to identify the actual day. This method is necessary because the SYSTEMTIME structure refers to a day by its day of the week and week of the month (e.g. 4th saturday in March). >>> SATURDAY = 6 >>> MARCH = 3 >>> st = SYSTEMTIME(2000, MARCH, SATURDAY, 4, 0, 0, 0, 0) # according to my calendar, the 4th Saturday in March in 2009 was the 28th >>> expected_date = datetime.datetime(2009, 3, 28) >>> Info._locate_day(2009, st) == expected_date True """ # MS stores Sunday as 0, Python datetime stores Monday as zero target_weekday = (cutoff.day_of_week + 6) % 7 # For SYSTEMTIMEs relating to time zone inforamtion, cutoff.day # is the week of the month week_of_month = cutoff.day # so the following is the first day of that week day = (week_of_month - 1) * 7 + 1 result = datetime.datetime( year, cutoff.month, day, cutoff.hour, cutoff.minute, cutoff.second, cutoff.millisecond) # now the result is the correct week, but not necessarily # the correct day of the week days_to_go = (target_weekday - result.weekday()) % 7 result += datetime.timedelta(days_to_go) # if we selected a day in the month following the target month, # move back a week or two. # This is necessary because Microsoft defines the fifth week in a month # to be the last week in a month and adding the time delta might have # pushed the result into the next month. while result.month == cutoff.month + 1: result -= datetime.timedelta(weeks=1) return result

Takes a SYSTEMTIME object, such as retrieved from a TIME_ZONE_INFORMATION structure or call to GetTimeZoneInformation and interprets it based on the given year to identify the actual day. This method is necessary because the SYSTEMTIME structure refers to a day by its day of the week and week of the month (e.g. 4th saturday in March). >>> SATURDAY = 6 >>> MARCH = 3 >>> st = SYSTEMTIME(2000, MARCH, SATURDAY, 4, 0, 0, 0, 0) # according to my calendar, the 4th Saturday in March in 2009 was the 28th >>> expected_date = datetime.datetime(2009, 3, 28) >>> Info._locate_day(2009, st) == expected_date True

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/timezone.py#L213-L254

train

pmac/django-redirect-urls

redirect_urls/utils.py

redirect

def redirect(pattern, to, permanent=True, locale_prefix=True, anchor=None, name=None, query=None, vary=None, cache_timeout=12, decorators=None, re_flags=None, to_args=None, to_kwargs=None, prepend_locale=True, merge_query=False): """ Return a url matcher suited for urlpatterns. pattern: the regex against which to match the requested URL. to: either a url name that `reverse` will find, a url that will simply be returned, or a function that will be given the request and url captures, and return the destination. permanent: boolean whether to send a 301 or 302 response. locale_prefix: automatically prepend `pattern` with a regex for an optional locale in the url. This locale (or None) will show up in captured kwargs as 'locale'. anchor: if set it will be appended to the destination url after a '#'. name: if used in a `urls.py` the redirect URL will be available as the name for use in calls to `reverse()`. Does _NOT_ work if used in a `redirects.py` file. query: a dict of query params to add to the destination url. vary: if you used an HTTP header to decide where to send users you should include that header's name in the `vary` arg. cache_timeout: number of hours to cache this redirect. just sets the proper `cache-control` and `expires` headers. decorators: a callable (or list of callables) that will wrap the view used to redirect the user. equivalent to adding a decorator to any other view. re_flags: a string of any of the characters: "iLmsux". Will modify the `pattern` regex based on the documented meaning of the flags (see python re module docs). to_args: a tuple or list of args to pass to reverse if `to` is a url name. to_kwargs: a dict of keyword args to pass to reverse if `to` is a url name. prepend_locale: if true the redirect URL will be prepended with the locale from the requested URL. merge_query: merge the requested query params from the `query` arg with any query params from the request. Usage: urlpatterns = [ redirect(r'projects/$', 'mozorg.product'), redirect(r'^projects/seamonkey$', 'mozorg.product', locale_prefix=False), redirect(r'apps/$', 'https://marketplace.firefox.com'), redirect(r'firefox/$', 'firefox.new', name='firefox'), redirect(r'the/dude$', 'abides', query={'aggression': 'not_stand'}), ] """ if permanent: redirect_class = HttpResponsePermanentRedirect else: redirect_class = HttpResponseRedirect if locale_prefix: pattern = pattern.lstrip('^/') pattern = LOCALE_RE + pattern if re_flags: pattern = '(?{})'.format(re_flags) + pattern view_decorators = [] if cache_timeout is not None: view_decorators.append(cache_control_expires(cache_timeout)) if vary: if isinstance(vary, basestring): vary = [vary] view_decorators.append(vary_on_headers(*vary)) if decorators: if callable(decorators): view_decorators.append(decorators) else: view_decorators.extend(decorators) def _view(request, *args, **kwargs): # don't want to have 'None' in substitutions kwargs = {k: v or '' for k, v in kwargs.items()} args = [x or '' for x in args] # If it's a callable, call it and get the url out. if callable(to): to_value = to(request, *args, **kwargs) else: to_value = to if to_value.startswith('/') or HTTP_RE.match(to_value): redirect_url = to_value else: try: redirect_url = reverse(to_value, args=to_args, kwargs=to_kwargs) except NoReverseMatch: # Assume it's a URL redirect_url = to_value if prepend_locale and redirect_url.startswith('/') and kwargs.get('locale'): redirect_url = '/{locale}' + redirect_url.lstrip('/') # use info from url captures. if args or kwargs: redirect_url = strip_tags(force_text(redirect_url).format(*args, **kwargs)) if query: if merge_query: req_query = parse_qs(request.META.get('QUERY_STRING')) req_query.update(query) querystring = urlencode(req_query, doseq=True) else: querystring = urlencode(query, doseq=True) elif query is None: querystring = request.META.get('QUERY_STRING') else: querystring = '' if querystring: redirect_url = '?'.join([redirect_url, querystring]) if anchor: redirect_url = '#'.join([redirect_url, anchor]) if PROTOCOL_RELATIVE_RE.match(redirect_url): redirect_url = '/' + redirect_url.lstrip('/') return redirect_class(redirect_url) # Apply decorators try: # Decorators should be applied in reverse order so that input # can be sent in the order your would write nested decorators # e.g. dec1(dec2(_view)) -> [dec1, dec2] for decorator in reversed(view_decorators): _view = decorator(_view) except TypeError: log.exception('decorators not iterable or does not contain ' 'callable items') return url(pattern, _view, name=name)

python

def redirect(pattern, to, permanent=True, locale_prefix=True, anchor=None, name=None, query=None, vary=None, cache_timeout=12, decorators=None, re_flags=None, to_args=None, to_kwargs=None, prepend_locale=True, merge_query=False): """ Return a url matcher suited for urlpatterns. pattern: the regex against which to match the requested URL. to: either a url name that `reverse` will find, a url that will simply be returned, or a function that will be given the request and url captures, and return the destination. permanent: boolean whether to send a 301 or 302 response. locale_prefix: automatically prepend `pattern` with a regex for an optional locale in the url. This locale (or None) will show up in captured kwargs as 'locale'. anchor: if set it will be appended to the destination url after a '#'. name: if used in a `urls.py` the redirect URL will be available as the name for use in calls to `reverse()`. Does _NOT_ work if used in a `redirects.py` file. query: a dict of query params to add to the destination url. vary: if you used an HTTP header to decide where to send users you should include that header's name in the `vary` arg. cache_timeout: number of hours to cache this redirect. just sets the proper `cache-control` and `expires` headers. decorators: a callable (or list of callables) that will wrap the view used to redirect the user. equivalent to adding a decorator to any other view. re_flags: a string of any of the characters: "iLmsux". Will modify the `pattern` regex based on the documented meaning of the flags (see python re module docs). to_args: a tuple or list of args to pass to reverse if `to` is a url name. to_kwargs: a dict of keyword args to pass to reverse if `to` is a url name. prepend_locale: if true the redirect URL will be prepended with the locale from the requested URL. merge_query: merge the requested query params from the `query` arg with any query params from the request. Usage: urlpatterns = [ redirect(r'projects/$', 'mozorg.product'), redirect(r'^projects/seamonkey$', 'mozorg.product', locale_prefix=False), redirect(r'apps/$', 'https://marketplace.firefox.com'), redirect(r'firefox/$', 'firefox.new', name='firefox'), redirect(r'the/dude$', 'abides', query={'aggression': 'not_stand'}), ] """ if permanent: redirect_class = HttpResponsePermanentRedirect else: redirect_class = HttpResponseRedirect if locale_prefix: pattern = pattern.lstrip('^/') pattern = LOCALE_RE + pattern if re_flags: pattern = '(?{})'.format(re_flags) + pattern view_decorators = [] if cache_timeout is not None: view_decorators.append(cache_control_expires(cache_timeout)) if vary: if isinstance(vary, basestring): vary = [vary] view_decorators.append(vary_on_headers(*vary)) if decorators: if callable(decorators): view_decorators.append(decorators) else: view_decorators.extend(decorators) def _view(request, *args, **kwargs): # don't want to have 'None' in substitutions kwargs = {k: v or '' for k, v in kwargs.items()} args = [x or '' for x in args] # If it's a callable, call it and get the url out. if callable(to): to_value = to(request, *args, **kwargs) else: to_value = to if to_value.startswith('/') or HTTP_RE.match(to_value): redirect_url = to_value else: try: redirect_url = reverse(to_value, args=to_args, kwargs=to_kwargs) except NoReverseMatch: # Assume it's a URL redirect_url = to_value if prepend_locale and redirect_url.startswith('/') and kwargs.get('locale'): redirect_url = '/{locale}' + redirect_url.lstrip('/') # use info from url captures. if args or kwargs: redirect_url = strip_tags(force_text(redirect_url).format(*args, **kwargs)) if query: if merge_query: req_query = parse_qs(request.META.get('QUERY_STRING')) req_query.update(query) querystring = urlencode(req_query, doseq=True) else: querystring = urlencode(query, doseq=True) elif query is None: querystring = request.META.get('QUERY_STRING') else: querystring = '' if querystring: redirect_url = '?'.join([redirect_url, querystring]) if anchor: redirect_url = '#'.join([redirect_url, anchor]) if PROTOCOL_RELATIVE_RE.match(redirect_url): redirect_url = '/' + redirect_url.lstrip('/') return redirect_class(redirect_url) # Apply decorators try: # Decorators should be applied in reverse order so that input # can be sent in the order your would write nested decorators # e.g. dec1(dec2(_view)) -> [dec1, dec2] for decorator in reversed(view_decorators): _view = decorator(_view) except TypeError: log.exception('decorators not iterable or does not contain ' 'callable items') return url(pattern, _view, name=name)

Return a url matcher suited for urlpatterns. pattern: the regex against which to match the requested URL. to: either a url name that `reverse` will find, a url that will simply be returned, or a function that will be given the request and url captures, and return the destination. permanent: boolean whether to send a 301 or 302 response. locale_prefix: automatically prepend `pattern` with a regex for an optional locale in the url. This locale (or None) will show up in captured kwargs as 'locale'. anchor: if set it will be appended to the destination url after a '#'. name: if used in a `urls.py` the redirect URL will be available as the name for use in calls to `reverse()`. Does _NOT_ work if used in a `redirects.py` file. query: a dict of query params to add to the destination url. vary: if you used an HTTP header to decide where to send users you should include that header's name in the `vary` arg. cache_timeout: number of hours to cache this redirect. just sets the proper `cache-control` and `expires` headers. decorators: a callable (or list of callables) that will wrap the view used to redirect the user. equivalent to adding a decorator to any other view. re_flags: a string of any of the characters: "iLmsux". Will modify the `pattern` regex based on the documented meaning of the flags (see python re module docs). to_args: a tuple or list of args to pass to reverse if `to` is a url name. to_kwargs: a dict of keyword args to pass to reverse if `to` is a url name. prepend_locale: if true the redirect URL will be prepended with the locale from the requested URL. merge_query: merge the requested query params from the `query` arg with any query params from the request. Usage: urlpatterns = [ redirect(r'projects/$', 'mozorg.product'), redirect(r'^projects/seamonkey$', 'mozorg.product', locale_prefix=False), redirect(r'apps/$', 'https://marketplace.firefox.com'), redirect(r'firefox/$', 'firefox.new', name='firefox'), redirect(r'the/dude$', 'abides', query={'aggression': 'not_stand'}), ]

21495194b0b2a2bdd1013e13ec0d54d34dd7f750

https://github.com/pmac/django-redirect-urls/blob/21495194b0b2a2bdd1013e13ec0d54d34dd7f750/redirect_urls/utils.py#L128-L257

train

jaraco/jaraco.windows

jaraco/windows/inet.py

AllocatedTable.__get_table_size

def __get_table_size(self): """ Retrieve the size of the buffer needed by calling the method with a null pointer and length of zero. This should trigger an insufficient buffer error and return the size needed for the buffer. """ length = ctypes.wintypes.DWORD() res = self.method(None, length, False) if res != errors.ERROR_INSUFFICIENT_BUFFER: raise RuntimeError("Error getting table length (%d)" % res) return length.value

python

def __get_table_size(self): """ Retrieve the size of the buffer needed by calling the method with a null pointer and length of zero. This should trigger an insufficient buffer error and return the size needed for the buffer. """ length = ctypes.wintypes.DWORD() res = self.method(None, length, False) if res != errors.ERROR_INSUFFICIENT_BUFFER: raise RuntimeError("Error getting table length (%d)" % res) return length.value

Retrieve the size of the buffer needed by calling the method with a null pointer and length of zero. This should trigger an insufficient buffer error and return the size needed for the buffer.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/inet.py#L49-L60

train

jaraco/jaraco.windows

jaraco/windows/inet.py

AllocatedTable.get_table

def get_table(self): """ Get the table """ buffer_length = self.__get_table_size() returned_buffer_length = ctypes.wintypes.DWORD(buffer_length) buffer = ctypes.create_string_buffer(buffer_length) pointer_type = ctypes.POINTER(self.structure) table_p = ctypes.cast(buffer, pointer_type) res = self.method(table_p, returned_buffer_length, False) if res != errors.NO_ERROR: raise RuntimeError("Error retrieving table (%d)" % res) return table_p.contents

python

def get_table(self): """ Get the table """ buffer_length = self.__get_table_size() returned_buffer_length = ctypes.wintypes.DWORD(buffer_length) buffer = ctypes.create_string_buffer(buffer_length) pointer_type = ctypes.POINTER(self.structure) table_p = ctypes.cast(buffer, pointer_type) res = self.method(table_p, returned_buffer_length, False) if res != errors.NO_ERROR: raise RuntimeError("Error retrieving table (%d)" % res) return table_p.contents

Get the table

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/inet.py#L62-L74

train

jaraco/jaraco.windows

jaraco/windows/inet.py

AllocatedTable.entries

def entries(self): """ Using the table structure, return the array of entries based on the table size. """ table = self.get_table() entries_array = self.row_structure * table.num_entries pointer_type = ctypes.POINTER(entries_array) return ctypes.cast(table.entries, pointer_type).contents

python

def entries(self): """ Using the table structure, return the array of entries based on the table size. """ table = self.get_table() entries_array = self.row_structure * table.num_entries pointer_type = ctypes.POINTER(entries_array) return ctypes.cast(table.entries, pointer_type).contents

Using the table structure, return the array of entries based on the table size.

51811efed50b46ad08daa25408a1cc806bc8d519

https://github.com/jaraco/jaraco.windows/blob/51811efed50b46ad08daa25408a1cc806bc8d519/jaraco/windows/inet.py#L77-L85

train

theno/fabsetup

fabsetup/fabfile/setup/service/__init__.py

owncloud

def owncloud(): '''Set up owncloud. Package 'owncloud' pulls package 'mysql' which asks for a password. ''' hostname = re.sub(r'^[^@]+@', '', env.host) # without username if any sitename = query_input( question='\nEnter site-name of Your Owncloud web service', default=flo('owncloud.{hostname}'), color=cyan) username = env.user fabfile_data_dir = FABFILE_DATA_DIR print(magenta(' install owncloud')) repository = ''.join([ 'http://download.opensuse.org/repositories/', 'isv:/ownCloud:/community/Debian_7.0/', ]) with hide('output'): sudo(flo('wget -O - {repository}Release.key | apt-key add -')) filename = '/etc/apt/sources.list.d/owncloud.list' sudo(flo("echo 'deb {repository} /' > {filename}")) sudo('apt-get update') install_packages([ 'owncloud', 'php5-fpm', 'php-apc', 'memcached', 'php5-memcache', ]) # This server uses nginx. owncloud pulls apache2 => Disable apache2 print(magenta(' disable apache')) with hide('output'): sudo('service apache2 stop') sudo('update-rc.d apache2 disable') print(magenta(' nginx setup for owncloud')) filename = 'owncloud_site_config.template' path = flo('{fabfile_data_dir}/files/etc/nginx/sites-available/{filename}') from_str = filled_out_template(path, username=username, sitename=sitename, hostname=hostname) with tempfile.NamedTemporaryFile(prefix=filename) as tmp_file: with open(tmp_file.name, 'w') as fp: fp.write(from_str) put(tmp_file.name, flo('/tmp/{filename}')) to = flo('/etc/nginx/sites-available/{sitename}') sudo(flo('mv /tmp/{filename} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) sudo(flo(' '.join([ 'ln -snf ../sites-available/{sitename}', '/etc/nginx/sites-enabled/{sitename}', ]))) # php5 fpm fast-cgi config template = 'www.conf' to = flo('/etc/php5/fpm/pool.d/{template}') from_ = flo('{fabfile_data_dir}/files{to}') put(from_, '/tmp/') sudo(flo('mv /tmp/{template} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) template = 'php.ini' to = flo('/etc/php5/fpm/{template}') from_ = flo('{fabfile_data_dir}/files{to}') put(from_, '/tmp/') sudo(flo('mv /tmp/{template} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) sudo('service php5-fpm restart') sudo('service nginx reload')

python

def owncloud(): '''Set up owncloud. Package 'owncloud' pulls package 'mysql' which asks for a password. ''' hostname = re.sub(r'^[^@]+@', '', env.host) # without username if any sitename = query_input( question='\nEnter site-name of Your Owncloud web service', default=flo('owncloud.{hostname}'), color=cyan) username = env.user fabfile_data_dir = FABFILE_DATA_DIR print(magenta(' install owncloud')) repository = ''.join([ 'http://download.opensuse.org/repositories/', 'isv:/ownCloud:/community/Debian_7.0/', ]) with hide('output'): sudo(flo('wget -O - {repository}Release.key | apt-key add -')) filename = '/etc/apt/sources.list.d/owncloud.list' sudo(flo("echo 'deb {repository} /' > {filename}")) sudo('apt-get update') install_packages([ 'owncloud', 'php5-fpm', 'php-apc', 'memcached', 'php5-memcache', ]) # This server uses nginx. owncloud pulls apache2 => Disable apache2 print(magenta(' disable apache')) with hide('output'): sudo('service apache2 stop') sudo('update-rc.d apache2 disable') print(magenta(' nginx setup for owncloud')) filename = 'owncloud_site_config.template' path = flo('{fabfile_data_dir}/files/etc/nginx/sites-available/{filename}') from_str = filled_out_template(path, username=username, sitename=sitename, hostname=hostname) with tempfile.NamedTemporaryFile(prefix=filename) as tmp_file: with open(tmp_file.name, 'w') as fp: fp.write(from_str) put(tmp_file.name, flo('/tmp/{filename}')) to = flo('/etc/nginx/sites-available/{sitename}') sudo(flo('mv /tmp/{filename} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) sudo(flo(' '.join([ 'ln -snf ../sites-available/{sitename}', '/etc/nginx/sites-enabled/{sitename}', ]))) # php5 fpm fast-cgi config template = 'www.conf' to = flo('/etc/php5/fpm/pool.d/{template}') from_ = flo('{fabfile_data_dir}/files{to}') put(from_, '/tmp/') sudo(flo('mv /tmp/{template} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) template = 'php.ini' to = flo('/etc/php5/fpm/{template}') from_ = flo('{fabfile_data_dir}/files{to}') put(from_, '/tmp/') sudo(flo('mv /tmp/{template} {to}')) sudo(flo('chown root.root {to}')) sudo(flo('chmod 644 {to}')) sudo('service php5-fpm restart') sudo('service nginx reload')

Set up owncloud. Package 'owncloud' pulls package 'mysql' which asks for a password.

ced728abff93551ba5677e63bc1bdc0ef5ca5777

https://github.com/theno/fabsetup/blob/ced728abff93551ba5677e63bc1bdc0ef5ca5777/fabsetup/fabfile/setup/service/__init__.py#L23-L98

train

bionikspoon/pureyaml

docs/source/conf.py

doctree_read_handler

def doctree_read_handler(app, doctree): """ Add 'orphan' to metadata for partials :type app: sphinx.application.Sphinx :type doctree: docutils.nodes.document """ # noinspection PyProtectedMember docname = sys._getframe(2).f_locals['docname'] if docname.startswith('_partial'): app.env.metadata[docname]['orphan'] = True

python

def doctree_read_handler(app, doctree): """ Add 'orphan' to metadata for partials :type app: sphinx.application.Sphinx :type doctree: docutils.nodes.document """ # noinspection PyProtectedMember docname = sys._getframe(2).f_locals['docname'] if docname.startswith('_partial'): app.env.metadata[docname]['orphan'] = True

Add 'orphan' to metadata for partials :type app: sphinx.application.Sphinx :type doctree: docutils.nodes.document

784830b907ca14525c4cecdb6ae35306f6f8a877

https://github.com/bionikspoon/pureyaml/blob/784830b907ca14525c4cecdb6ae35306f6f8a877/docs/source/conf.py#L26-L36

train

bionikspoon/pureyaml

docs/source/conf.py

autodoc_skip_member_handler

def autodoc_skip_member_handler(app, what, name, obj, skip, options): """ Skip un parseable functions. :type app: sphinx.application.Sphinx :param str what: the type of the object which the docstring belongs to (one of "module", "class", "exception", "function", "method", "attribute") :param str name: the fully qualified name of the object :param type obj: the object itself :param bool skip: a boolean indicating if autodoc will skip this member :param sphinx.ext.autodoc.Options options: the options given to the directive :rtype: bool """ if 'YAMLTokens' in name: return True return False

python

def autodoc_skip_member_handler(app, what, name, obj, skip, options): """ Skip un parseable functions. :type app: sphinx.application.Sphinx :param str what: the type of the object which the docstring belongs to (one of "module", "class", "exception", "function", "method", "attribute") :param str name: the fully qualified name of the object :param type obj: the object itself :param bool skip: a boolean indicating if autodoc will skip this member :param sphinx.ext.autodoc.Options options: the options given to the directive :rtype: bool """ if 'YAMLTokens' in name: return True return False

Skip un parseable functions. :type app: sphinx.application.Sphinx :param str what: the type of the object which the docstring belongs to (one of "module", "class", "exception", "function", "method", "attribute") :param str name: the fully qualified name of the object :param type obj: the object itself :param bool skip: a boolean indicating if autodoc will skip this member :param sphinx.ext.autodoc.Options options: the options given to the directive :rtype: bool

784830b907ca14525c4cecdb6ae35306f6f8a877

https://github.com/bionikspoon/pureyaml/blob/784830b907ca14525c4cecdb6ae35306f6f8a877/docs/source/conf.py#L39-L54

train

awickert/gFlex

gflex/base.py

Plotting.surfplot

def surfplot(self, z, titletext): """ Plot if you want to - for troubleshooting - 1 figure """ if self.latlon: plt.imshow(z, extent=(0, self.dx*z.shape[0], self.dy*z.shape[1], 0)) #,interpolation='nearest' plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(z, extent=(0, self.dx/1000.*z.shape[0], self.dy/1000.*z.shape[1], 0)) #,interpolation='nearest' plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar() plt.title(titletext,fontsize=16)

python

def surfplot(self, z, titletext): """ Plot if you want to - for troubleshooting - 1 figure """ if self.latlon: plt.imshow(z, extent=(0, self.dx*z.shape[0], self.dy*z.shape[1], 0)) #,interpolation='nearest' plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(z, extent=(0, self.dx/1000.*z.shape[0], self.dy/1000.*z.shape[1], 0)) #,interpolation='nearest' plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar() plt.title(titletext,fontsize=16)

Plot if you want to - for troubleshooting - 1 figure

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/base.py#L376-L390

train

awickert/gFlex

gflex/base.py

Plotting.twoSurfplots

def twoSurfplots(self): """ Plot multiple subplot figure for 2D array """ # Could more elegantly just call surfplot twice # And also could include xyzinterp as an option inside surfplot. # Noted here in case anyone wants to take that on in the future... plt.subplot(211) plt.title('Load thickness, mantle equivalent [m]',fontsize=16) if self.latlon: plt.imshow(self.qs/(self.rho_m*self.g), extent=(0, self.dx*self.qs.shape[0], self.dy*self.qs.shape[1], 0)) plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(self.qs/(self.rho_m*self.g), extent=(0, self.dx/1000.*self.qs.shape[0], self.dy/1000.*self.qs.shape[1], 0)) plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar() plt.subplot(212) plt.title('Deflection [m]') if self.latlon: plt.imshow(self.w, extent=(0, self.dx*self.w.shape[0], self.dy*self.w.shape[1], 0)) plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(self.w, extent=(0, self.dx/1000.*self.w.shape[0], self.dy/1000.*self.w.shape[1], 0)) plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar()

python

def twoSurfplots(self): """ Plot multiple subplot figure for 2D array """ # Could more elegantly just call surfplot twice # And also could include xyzinterp as an option inside surfplot. # Noted here in case anyone wants to take that on in the future... plt.subplot(211) plt.title('Load thickness, mantle equivalent [m]',fontsize=16) if self.latlon: plt.imshow(self.qs/(self.rho_m*self.g), extent=(0, self.dx*self.qs.shape[0], self.dy*self.qs.shape[1], 0)) plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(self.qs/(self.rho_m*self.g), extent=(0, self.dx/1000.*self.qs.shape[0], self.dy/1000.*self.qs.shape[1], 0)) plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar() plt.subplot(212) plt.title('Deflection [m]') if self.latlon: plt.imshow(self.w, extent=(0, self.dx*self.w.shape[0], self.dy*self.w.shape[1], 0)) plt.xlabel('longitude [deg E]', fontsize=12, fontweight='bold') plt.ylabel('latitude [deg N]', fontsize=12, fontweight='bold') else: plt.imshow(self.w, extent=(0, self.dx/1000.*self.w.shape[0], self.dy/1000.*self.w.shape[1], 0)) plt.xlabel('x [km]', fontsize=12, fontweight='bold') plt.ylabel('y [km]', fontsize=12, fontweight='bold') plt.colorbar()

Plot multiple subplot figure for 2D array

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/base.py#L392-L422

train

awickert/gFlex

gflex/base.py

Flexure.outputDeflections

def outputDeflections(self): """ Outputs a grid of deflections if an output directory is defined in the configuration file If the filename given in the configuration file ends in ".npy", then a binary numpy grid will be exported. Otherwise, an ASCII grid will be exported. """ try: # If wOutFile exists, has already been set by a setter self.wOutFile if self.Verbose: print("Output filename provided.") # Otherwise, it needs to be set by an configuration file except: try: self.wOutFile = self.configGet("string", "output", "DeflectionOut", optional=True) except: # if there is no parsable output string, do not generate output; # this allows the user to leave the line blank and produce no output if self.Debug: print("No output filename provided:") print(" not writing any deflection output to file") if self.wOutFile: if self.wOutFile[-4:] == '.npy': from numpy import save save(self.wOutFile,self.w) else: from numpy import savetxt # Shouldn't need more than mm precision, at very most savetxt(self.wOutFile,self.w,fmt='%.3f') if self.Verbose: print("Saving deflections --> " + self.wOutFile)

python

def outputDeflections(self): """ Outputs a grid of deflections if an output directory is defined in the configuration file If the filename given in the configuration file ends in ".npy", then a binary numpy grid will be exported. Otherwise, an ASCII grid will be exported. """ try: # If wOutFile exists, has already been set by a setter self.wOutFile if self.Verbose: print("Output filename provided.") # Otherwise, it needs to be set by an configuration file except: try: self.wOutFile = self.configGet("string", "output", "DeflectionOut", optional=True) except: # if there is no parsable output string, do not generate output; # this allows the user to leave the line blank and produce no output if self.Debug: print("No output filename provided:") print(" not writing any deflection output to file") if self.wOutFile: if self.wOutFile[-4:] == '.npy': from numpy import save save(self.wOutFile,self.w) else: from numpy import savetxt # Shouldn't need more than mm precision, at very most savetxt(self.wOutFile,self.w,fmt='%.3f') if self.Verbose: print("Saving deflections --> " + self.wOutFile)

Outputs a grid of deflections if an output directory is defined in the configuration file If the filename given in the configuration file ends in ".npy", then a binary numpy grid will be exported. Otherwise, an ASCII grid will be exported.

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/base.py#L762-L796

train

awickert/gFlex

gflex/base.py

Flexure.TeArraySizeCheck

def TeArraySizeCheck(self): """ Checks that Te and q0 array sizes are compatible For finite difference solution. """ # Only if they are both defined and are arrays # Both being arrays is a possible bug in this check routine that I have # intentionally introduced if type(self.Te) == np.ndarray and type(self.qs) == np.ndarray: # Doesn't touch non-arrays or 1D arrays if type(self.Te) is np.ndarray: if (np.array(self.Te.shape) != np.array(self.qs.shape)).any(): sys.exit("q0 and Te arrays have incompatible shapes. Exiting.") else: if self.Debug: print("Te and qs array sizes pass consistency check")

python

def TeArraySizeCheck(self): """ Checks that Te and q0 array sizes are compatible For finite difference solution. """ # Only if they are both defined and are arrays # Both being arrays is a possible bug in this check routine that I have # intentionally introduced if type(self.Te) == np.ndarray and type(self.qs) == np.ndarray: # Doesn't touch non-arrays or 1D arrays if type(self.Te) is np.ndarray: if (np.array(self.Te.shape) != np.array(self.qs.shape)).any(): sys.exit("q0 and Te arrays have incompatible shapes. Exiting.") else: if self.Debug: print("Te and qs array sizes pass consistency check")

Checks that Te and q0 array sizes are compatible For finite difference solution.

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/base.py#L907-L921

train

awickert/gFlex

gflex/base.py

Flexure.FD

def FD(self): """ Set-up for the finite difference solution method """ if self.Verbose: print("Finite Difference Solution Technique") # Used to check for coeff_matrix here, but now doing so in self.bc_check() # called by f1d and f2d at the start # # Define a stress-based qs = q0 # But only if the latter has not already been defined # (e.g., by the getters and setters) try: self.qs except: self.qs = self.q0.copy() # Remove self.q0 to avoid issues with multiply-defined inputs # q0 is the parsable input to either a qs grid or contains (x,(y),q) del self.q0 # Give it x and y dimensions for help with plotting tools # (not implemented internally, but a help with external methods) self.x = np.arange(self.dx/2., self.dx * self.qs.shape[0], self.dx) if self.dimension == 2: self.y = np.arange(self.dy/2., self.dy * self.qs.shape[1], self.dy) # Is there a solver defined try: self.Solver # See if it exists already except: # Well, will fail if it doesn't see this, maybe not the most reasonable # error message. if self.filename: self.Solver = self.configGet("string", "numerical", "Solver") else: sys.exit("No solver defined!") # Check consistency of size if coeff array was loaded if self.filename: # In the case that it is iterative, find the convergence criterion self.iterative_ConvergenceTolerance = self.configGet("float", "numerical", "ConvergenceTolerance") # Try to import Te grid or scalar for the finite difference solution try: self.Te = self.configGet("float", "input", "ElasticThickness", optional=False) if self.Te is None: Tepath = self.configGet("string", "input", "ElasticThickness", optional=False) self.Te = Tepath else: Tepath = None except: Tepath = self.configGet("string", "input", "ElasticThickness", optional=False) self.Te = Tepath if self.Te is None: if self.coeff_matrix is not None: pass else: # Have to bring this out here in case it was discovered in the # try statement that there is no value given sys.exit("No input elastic thickness or coefficient matrix supplied.") # or if getter/setter if type(self.Te) == str: # Try to import Te grid or scalar for the finite difference solution Tepath = self.Te else: Tepath = None # in case no self.filename present (like for GRASS GIS) # If there is a Tepath, import Te # Assume that even if a coeff_matrix is defined # That the user wants Te if they gave the path if Tepath: self.Te = self.loadFile(self.Te, close_on_fail = False) if self.Te is None: print("Requested Te file is provided but cannot be located.") print("No scalar elastic thickness is provided in configuration file") print("(Typo in path to input Te grid?)") if self.coeff_matrix is not None: print("But a coefficient matrix has been found.") print("Calculations will be carried forward using it.") else: print("Exiting.") sys.exit() # Check that Te is the proper size if it was loaded # Will be array if it was loaded if self.Te.any(): self.TeArraySizeCheck()

python

def FD(self): """ Set-up for the finite difference solution method """ if self.Verbose: print("Finite Difference Solution Technique") # Used to check for coeff_matrix here, but now doing so in self.bc_check() # called by f1d and f2d at the start # # Define a stress-based qs = q0 # But only if the latter has not already been defined # (e.g., by the getters and setters) try: self.qs except: self.qs = self.q0.copy() # Remove self.q0 to avoid issues with multiply-defined inputs # q0 is the parsable input to either a qs grid or contains (x,(y),q) del self.q0 # Give it x and y dimensions for help with plotting tools # (not implemented internally, but a help with external methods) self.x = np.arange(self.dx/2., self.dx * self.qs.shape[0], self.dx) if self.dimension == 2: self.y = np.arange(self.dy/2., self.dy * self.qs.shape[1], self.dy) # Is there a solver defined try: self.Solver # See if it exists already except: # Well, will fail if it doesn't see this, maybe not the most reasonable # error message. if self.filename: self.Solver = self.configGet("string", "numerical", "Solver") else: sys.exit("No solver defined!") # Check consistency of size if coeff array was loaded if self.filename: # In the case that it is iterative, find the convergence criterion self.iterative_ConvergenceTolerance = self.configGet("float", "numerical", "ConvergenceTolerance") # Try to import Te grid or scalar for the finite difference solution try: self.Te = self.configGet("float", "input", "ElasticThickness", optional=False) if self.Te is None: Tepath = self.configGet("string", "input", "ElasticThickness", optional=False) self.Te = Tepath else: Tepath = None except: Tepath = self.configGet("string", "input", "ElasticThickness", optional=False) self.Te = Tepath if self.Te is None: if self.coeff_matrix is not None: pass else: # Have to bring this out here in case it was discovered in the # try statement that there is no value given sys.exit("No input elastic thickness or coefficient matrix supplied.") # or if getter/setter if type(self.Te) == str: # Try to import Te grid or scalar for the finite difference solution Tepath = self.Te else: Tepath = None # in case no self.filename present (like for GRASS GIS) # If there is a Tepath, import Te # Assume that even if a coeff_matrix is defined # That the user wants Te if they gave the path if Tepath: self.Te = self.loadFile(self.Te, close_on_fail = False) if self.Te is None: print("Requested Te file is provided but cannot be located.") print("No scalar elastic thickness is provided in configuration file") print("(Typo in path to input Te grid?)") if self.coeff_matrix is not None: print("But a coefficient matrix has been found.") print("Calculations will be carried forward using it.") else: print("Exiting.") sys.exit() # Check that Te is the proper size if it was loaded # Will be array if it was loaded if self.Te.any(): self.TeArraySizeCheck()

Set-up for the finite difference solution method

3ac32249375b0f8d342a142585d86ea4d905a5a0

https://github.com/awickert/gFlex/blob/3ac32249375b0f8d342a142585d86ea4d905a5a0/gflex/base.py#L927-L1008

train