core Package

`core` Package

class LocMgr[source]

Bases: object

_locations = {'rootdir': '/home/docs/checkouts/readthedocs.org/user_builds/morphforge/envs/latest/local/lib/python2.7/site-packages'}

classmethod ensure_dir_exists(dir_location)[source]

Helper function that will make directories if they don’t exist.

Useful for temporary locations

classmethod get_bin_path()[source]

classmethod get_default_channel_summary_output_dir()[source]

classmethod get_default_mod_builddir()[source]

classmethod get_default_mod_outdir()[source]

classmethod get_default_output_dir()[source]

classmethod get_default_summary_output_dir()[source]

classmethod get_log_path()[source]

classmethod get_path_from_rcfile(subsection, default)[source]

classmethod get_ply_parsetab_path(subdir)[source]

classmethod get_root_path()[source]

classmethod get_simulation_results_tmp_dir()[source]

classmethod get_simulation_tmp_dir()[source]

classmethod get_temporary_filename(suffix='', filedirectory=None)[source]

classmethod get_test_mods_path()[source]

classmethod get_test_srcs_path()[source]

classmethod get_tmp_path()[source]

classmethod validate_exists(cell_location)[source]: Helper function to ensure that returned path actually does exist

class LogMgr[source]

Bases: object

_initialised_state = 'Ready'

classmethod _is_logging_active_and_ready()[source]

classmethod _pyfile_to_modulename(filename)[source]

classmethod config()[source]

classmethod create_logger(log_name)[source]

classmethod debug(msg)[source]

classmethod get_caller()[source]

classmethod get_logger()[source]

classmethod info(msg)[source]

classmethod info_from_logger(msg)[source]

loggers = {'morphforge.core.logmgr': <logging.Logger object at 0x7f0ab1dbd290>, 'DISABLEDLOGGING': <logging.Logger object at 0x7f0ab1dbd4d0>}

classmethod warning(msg)[source]

class SettingsMgr[source]

Bases: object

Doc String for Settings Manager

_clearTempAllAt_start = True

_logging = False

classmethod get_ply_yacc_debug_flag()[source]

classmethod is_logging()[source]

classmethod simulator_is_verbose()[source]

class RCMgr[source]

Bases: object

_rc_config_parser = None

_rc_filename = '/home/docs/.morphforgerc'

classmethod get(section, option)[source]

classmethod get_config()[source]

classmethod has(section, option)[source]

classmethod has_config()[source]

merge_dictionaries(dictionaries)[source]

Merge a sequence of dictionaries safely.

This function merges dictionaries together, but ensures that there are not same keys which point to different values. That is, merge_dictionaries({‘alpha’:True}, {‘alpha’:True}) is OK, but merge_dictionaries({‘alpha’:True}, {‘alpha’:False}) will raise an exception

class FileIO[source]

Bases: object

A collection of file utility functions

classmethod append_to_file(txt, filename, file_expected=True)[source]

Appends text to an existing file.

By default the file is expected to already exist, otherwise an IOError exception be thrown. This can be overridden with the file_expected parameter. Returns filename

classmethod get_hash_md5(filename)[source]

Returns the md5 checksum of a file.

This function should not be used for large files, since it loads the entire file into memory.

classmethod read_from_file(filename)[source]: Reads text from a file

classmethod write_to_file(txt, filename=None, filedirectory=None, suffix=None)[source]: Writes text to a file This function will overwrite an existing file. If no filename is given, a filename will be invented, using LocMgr.get_temporary_filename(). The name of the file written to will be returned.

class SeqUtils[source]

Bases: object

A collection of utility functions for working with sequences

classmethod expect_single(l)[source]

Expects a sequence containing a single object and returns it.

If 0 or more than 1 objects are found, it raises an error.

classmethod filter_expect_single(seq, filter_func)[source]: Filters a sequence according to the predicate filter_func, then expects a single item to remain, which it returns. If 0 or more than 1 objects are found, it raises an error.

classmethod filter_with_prob(lst, p)[source]: Returns a copy of the sequence, in which each item in the original has a fixed probability of being in the new sequence.

classmethod flatten(seq, flatten_types=(<type 'tuple'>, <type 'list'>))[source]

‘Flattens’ a sequence recursively.

The objects types to flatten are specified by the flatten_types parameter, which must by a tuple of classes. By default it flattens lists and tuples.

classmethod max_with_unique_check(collection, key)[source]

Return the maximum from a sequence, based on a key, but verify that there is a unique maximum.

This is designed to be used when the key generates integers.

class StrUtils[source]

Bases: object

A collection of string utility functions

classmethod get_hash_md5(s)[source]: Returns the md5 digest hash of a string

classmethod strip_comments_and_blank_lines(text, cmt_sym='#')[source]: Removes comments and blank lines from block of text

check_cstyle_varname(name)[source]: Check a string conforms to a C-style variable name.

is_iterable(f)[source]: Returns True if an object can be iterated over by using iter(obj)

class ObjectLabeller[source]

Bases: object

Provides names for internal use for annoymous objects

Often, we need to automatically generate names for objects. For example, a user might not nessesarily provide names for all cells in simulations, but the simulator will expect variable names to refer to them. This class provides methods to create new names of objects, based on their type.

classmethod get_next_count_for_type(obj)[source]

classmethod get_next_unamed_object_name(obj_type, prefix=None, num_fmt_string=None)[source]: Returns the next ‘anonymous’ name for an object of ‘obj_type’.

objectcount = {}

Join(a, *p): Join two or more pathname components, inserting ‘/’ as needed. If any component is an absolute path, all previous path components will be discarded. An empty last part will result in a path that ends with a separator.

class PluginDict[source]

Bases: object

Basic component for making features of morphforge ‘pluggable’.

This class simply wraps a dictionary, and exposes some methods to make the intention of code clearer.

__init__()[source]

__iter__()[source]

get_plugin(plugin_name)[source]: Returns a previously registered plugin

keys()[source]

register_plugin(plugin_name, plugin)[source]: Registers a plugin

class MFRandom[source]

Bases: object

A class to centralise random numbers.

This is centralised so that a seed can be set in a single place in order to make simulations repeatable. This is particularly relevant in the case of NEURON simulations, which are saved and spawned in another process.

classmethod _reseed()[source]

_seed = None

classmethod get_seed()[source]: Returns the current seed used

classmethod seed(seed)[source]

Seed the random number generator

This method simply calls ‘random.seed()’ and ‘numpy.random.seed()’

class ParameterSweepValues(values)[source]

Bases: object

__getitem__(index)[source]

__init__(values)[source]

__iter__()[source]

__len__()[source]

_short_iter()[source]

`mfrandom` Module

class MFRandom[source]

Bases: object

A class to centralise random numbers.

classmethod _reseed()[source]

_seed = None

classmethod get_seed()[source]: Returns the current seed used

classmethod seed(seed)[source]

Seed the random number generator

This method simply calls ‘random.seed()’ and ‘numpy.random.seed()’

`misc` Module

A collection of utility functions. Often these are not the most efficient implementations, especially when dealing with large files, but for most files morphforge has to deal with, they work fine and make code more readable.

class FileIO[source]

Bases: object

A collection of file utility functions

classmethod append_to_file(txt, filename, file_expected=True)[source]

Appends text to an existing file.

By default the file is expected to already exist, otherwise an IOError exception be thrown. This can be overridden with the file_expected parameter. Returns filename

classmethod get_hash_md5(filename)[source]

Returns the md5 checksum of a file.

This function should not be used for large files, since it loads the entire file into memory.

classmethod read_from_file(filename)[source]: Reads text from a file

classmethod write_to_file(txt, filename=None, filedirectory=None, suffix=None)[source]: Writes text to a file This function will overwrite an existing file. If no filename is given, a filename will be invented, using LocMgr.get_temporary_filename(). The name of the file written to will be returned.

class ParameterSweepValues(values)[source]

Bases: object

__getitem__(index)[source]

__init__(values)[source]

__iter__()[source]

__len__()[source]

_short_iter()[source]

class SeqUtils[source]

Bases: object

A collection of utility functions for working with sequences

classmethod expect_single(l)[source]

Expects a sequence containing a single object and returns it.

If 0 or more than 1 objects are found, it raises an error.

classmethod filter_expect_single(seq, filter_func)[source]: Filters a sequence according to the predicate filter_func, then expects a single item to remain, which it returns. If 0 or more than 1 objects are found, it raises an error.

classmethod filter_with_prob(lst, p)[source]: Returns a copy of the sequence, in which each item in the original has a fixed probability of being in the new sequence.

classmethod flatten(seq, flatten_types=(<type 'tuple'>, <type 'list'>))[source]

‘Flattens’ a sequence recursively.

The objects types to flatten are specified by the flatten_types parameter, which must by a tuple of classes. By default it flattens lists and tuples.

classmethod max_with_unique_check(collection, key)[source]

Return the maximum from a sequence, based on a key, but verify that there is a unique maximum.

This is designed to be used when the key generates integers.

class StrUtils[source]

Bases: object

A collection of string utility functions

classmethod get_hash_md5(s)[source]: Returns the md5 digest hash of a string

classmethod strip_comments_and_blank_lines(text, cmt_sym='#')[source]: Removes comments and blank lines from block of text

class TracePrints[source]

Bases: object

__init__()[source]

write(s)[source]

class benchmark(name)[source]

Bases: object

__enter__()[source]

__exit__(ty, val, tb)[source]

__init__(name)[source]

check_cstyle_varname(name)[source]: Check a string conforms to a C-style variable name.

find_files_recursively(directory, pattern)[source]

Recursive ‘glob’ for files.

This function walks over a directory looking for filenames matching a certain pattern

class flushfile(f)[source]

Bases: file

__init__(f)[source]

write(x)[source]

is_float(f)[source]: Deprecated

is_int(f)[source]: Deprecated

is_iterable(f)[source]: Returns True if an object can be iterated over by using iter(obj)

merge_dictionaries(dictionaries)[source]

Merge a sequence of dictionaries safely.

`mockcontrol` Module

class MockControl[source]

Bases: object

is_mock_simulation = None

`monkey_patching` Module

`objectnumberer` Module

class ObjectLabeller[source]

Bases: object

Provides names for internal use for annoymous objects

classmethod get_next_count_for_type(obj)[source]

classmethod get_next_unamed_object_name(obj_type, prefix=None, num_fmt_string=None)[source]: Returns the next ‘anonymous’ name for an object of ‘obj_type’.

objectcount = {}

`plugindict` Module

class PluginDict[source]

Bases: object

Basic component for making features of morphforge ‘pluggable’.

This class simply wraps a dictionary, and exposes some methods to make the intention of code clearer.

__init__()[source]

__iter__()[source]

get_plugin(plugin_name)[source]: Returns a previously registered plugin

keys()[source]

register_plugin(plugin_name, plugin)[source]: Registers a plugin

Subpackages

mgrs Package

core Package

core Package

mfrandom Module

misc Module

mockcontrol Module

monkey_patching Module

objectnumberer Module

plugindict Module

Subpackages

`core` Package

`mfrandom` Module

`misc` Module

`mockcontrol` Module

`monkey_patching` Module

`objectnumberer` Module

`plugindict` Module