Plugins: what are they?¶

Plugins in pyCIF are the elementary block of the python library. They are the basic class on which all other classes are built.

All data and meta-data in pyCIF are stored as attributes of Plugin class instance.

Dependencies and links between each plugin are automatically dealt with, as further explained here.

The list of classes in the CIF is detailed below. Click to expand the code of each class. For each class, please refer to the corresponding page for the list of available plugins and further documentation:

Plugin class

Click here to expand the code of the Plugin class

class pycif.utils.classes.baseclass.Plugin(plg_orig=None, **kwargs)[source]¶

The Plugin class is the parent class of all other pyCIF classes. It is used to store all information about sub-parts of pyCIF and loads if needed sub-modules.

classmethod childclass_factory(plg_orig, child_type=None, parent_plg=None, overwrite=False)[source]¶

Generates an instance of one of Plugin’s child classes. Transfers all existing attributes in the argument plugin to the output child-class instance

Parameters

plg_orig (Plugin) – the plugin to turn into a child-class instance

child_type (str) – sub-class type to generate if not available in plg_orig.plugin.type

overwrite (bool) – overwrite the class type of the origin plugin

Returns

a plugin with all the attributes from plg_orig, but as a child-class instance

Return type

child_plg

classmethod dump_incorrect(file_dump)[source]¶

Dump incorrect arguments from the Yaml into a file

Parameters

file_dump – File where to dump

Returns

classmethod from_dict(def_dict, orig_name='', convert_none=False, **kwargs)[source]¶

Loads a recursive dictionary structure into a Plugin

Parameters

def_dict (dict) – the definition dictionary

orig_dict (dict) – the definition dictionary used at level 0

Returns

Plugin

classmethod from_yaml(def_file)[source]¶

Generates a dictionary including all pyCIF parameters

Parameters

def_file (string) – Path to the definition file Handles both absolute and relative paths

Returns

Dictionary populated with all pyCIF parameters

Return type

config_dict (dictionary)

classmethod get_loaded(name, version, plugin_type, subtype='')[source]¶

Get the correct loaded plugin, given its name, version and type (and optionally subtype)

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

Returns

plugin module for plugin version

Return type

Plugin

classmethod get_registered(name, version, plugin_type, subtype='')[source]¶

Get the correct registered plugin, given its name, version and type

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

Returns

plugin module for plugin version

Return type

Plugin

classmethod get_subclass(plg_type, plg_subtype='')[source]¶

Get the plugin class template from a given type

Parameters

plg_type (str) – the plugin type to load

plg_subtype (str) – the plugin sub-type to load

Returns

Empty instance of the correct class type

initiate(plg_type=None)[source]¶

Initializes a Plugin, i.e., loads functions from registered plugins

Parameters

plg_type (str) – the type of plugin to load; this should

to one of the defined child-classes (correspond) –

Returns

a python module as registered in pyCIF

Return type

module

initiate_template(plg_type=None, default_functions={})[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

classmethod is_allowed(plugin_type)[source]¶

Check whether a plugin type is allowed in pyCIF or not

Parameters

plugin_type (str) – type of plugin

Returns

True if allowed plugin

Return type

bool

classmethod is_allowed_as_subtype(plugin_type)[source]¶

Check whether a plugin type is allowed as the sub-type of a main type in pyCIF or not

Parameters

plugin_type (str) – type of plugin

Returns

True if allowed plugin

Return type

bool

classmethod is_loaded(name, version, plugin_type, subtype='')[source]¶

Check whether a plugin is loaded

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

Returns

bool

classmethod is_registered(name, version, plugin_type, subtype)[source]¶

Check if a plugin is registered

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

Returns

True if a parser is registered key: the key of the registered Plugin if registered

Return type

bool

classmethod load_registered(name, version, plg_type, plg_subtype='', plg_orig=None)[source]¶

Get a sub-class instance of a registered plugin. This can be used to get default required plugins.

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plg_type (str) – type of plugin

plg_subtype (str) – sub-type of plugin

plg_orig (Plugin) – Original plugin from which to copy attributes to the new plugin

Returns

a new plugin of correct type

Return type

Plugin

static plugin_key(name, version, plugin_type, subtype)[source]¶

Creates the key for a name, version and plugin type

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

Returns

dict key for a plugin and version

Return type

set

classmethod print_default(plg)[source]¶

Print default values if available

classmethod print_registered(print_requirement=False, print_rst=False, types=[], names=[], versions=[], stream=None)[source]¶

Print in a user-friendly format the list of available plugins

Parameters

print_requirement (bool) – for each registered plugin, print its requirements

print_rst (bool) – print in rst format for automatic use in the documentations

types (list) – list of types of Plugins to print

names (list) – list of names of Plugins to print

version (list) – list of versions of Plugins to print

stream – stream to which send the display. By default, stdout is used. A stream to a given file can be used instead.

classmethod register_plugin(name, version, module, plugin_type='', subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

plugin_type (str) – type of plugin

subtype (str) – sub-type of plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

**kwargs (dictionary) – default options for module

classmethod save_loaded(plg)[source]¶

Saves all loaded plugins to the class

Parameters

plg (Plugin) – plugin to save

set_requirements()[source]¶

Update requirements depending on the Plugin properties

By default, this method does nothing. It can be included in any new Plugin depending on the developer needs.

Parameters

self (Plugin) – the Plugin to update

classmethod to_dict(plg, exclude_patterns=None, full=False)[source]¶

Turns a Plugin to a dictionary for easier saving.

Parameters

plg (Plugin) – a Plugin instance to be saved as a dictionary

classmethod to_yaml(plg, yaml_file, full=True)[source]¶

Write a Yaml from a loaded plugin

Setup class

Click here to expand the code of the Setup class

class pycif.utils.classes.setup.Setup(plg_orig=None, **kwargs)[source]¶

classmethod config_info(setup)[source]¶

Prints out main input parameters for pyCIF

classmethod load_setup(plg, parent_plg_type=None, level=999, tree='', list_levels=None, ignore_parent_type=False, **kwargs)[source]¶

Loads a Setup plugin. Loops recursively over all attributes of the setup to load: 1) sub-plugins are initialized as Plugin child-class templates ( Domain, ObsVect, Model, etc); 2) instances are saved to the Plugin class to be accessible for anywhere later one.

This allows modifications of the data of a given plugin at some place of the code to be automatically forwarded to the rest of the code

Parameters

self (Setup) – the setup to load

parent_plg_type (str) – the last recognized plugin type that is

by children (inherited) –

Chemistry class

Click here to expand the code of the Chemistry class

class pycif.utils.classes.chemistries.Chemistry(plg_orig=None, **kwargs)[source]¶

create_chemicalscheme(*args, **kwargs)[source]¶

Creates a chemical scheme if needed

Parameters

chemistry (dictionary) – dictionary defining the chelical scheme

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

read_chemicalscheme(*args, **kwargs)[source]¶

Read a chemical scheme from an existing file

Parameters

self (Chemistry) – plugin defining the chemistry. Should include

grid to be able to read the chemistry from files (dirscheme) –

Returns

Characteristics of the chemical scheme

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Controlvect class

Click here to expand the code of the Controlvect class

class pycif.utils.classes.controlvects.ControlVect(**kwargs)[source]¶

control2native(*args, **kwargs)[source]¶

Default empty control2native method

crop(*args, **kwargs)[source]¶

Default crop dump method

dump(*args, **kwargs)[source]¶

Default empty dump method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

load(*args, **kwargs)[source]¶

Default empty load method

native2control(*args, **kwargs)[source]¶

Default empty native2control method

outputs2state(*args, **kwargs)[source]¶

Default empty outputs2state method

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

sqrtbprod(*args, **kwargs)[source]¶

Default empty sqrtbprod method

sqrtbprod_ad(*args, **kwargs)[source]¶

Default empty sqrtbprod_ad method

state2inputs(*args, **kwargs)[source]¶

Default empty state2inputs method

Datastream class

Click here to expand the code of the Datastream class

class pycif.utils.classes.datastreams.DataStream(plg_orig=None, **kwargs)[source]¶

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Datavect class

Click here to expand the code of the Datavect class

class pycif.utils.classes.datavects.DataVect(plg_orig=None, **kwargs)[source]¶

control2native(*args, **kwargs)[source]¶

Default empty control2native method

dump(*args, **kwargs)[source]¶

Default empty dump method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

load(*args, **kwargs)[source]¶

Default empty load method

native2control(*args, **kwargs)[source]¶

Default empty native2control method

outputs2state(*args, **kwargs)[source]¶

Default empty outputs2state method

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

sqrtbprod(*args, **kwargs)[source]¶

Default empty sqrtbprod method

sqrtbprod_ad(*args, **kwargs)[source]¶

Default empty sqrtbprod_ad method

state2inputs(*args, **kwargs)[source]¶

Default empty state2inputs method

Domain class

Click here to expand the code of the Domain class

class pycif.utils.classes.domains.Domain(**kwargs)[source]¶

calc_areas(*args, **kwargs)[source]¶

Computes the area of each grid cell in your domain.

create_domain(*args, **kwargs)[source]¶

Creates a grid if needed

Parameters

domain (dictionary) – dictionary defining the domain.

get_sides()[source]¶

Gets the sides of the domain

ini_data(**kwargs)[source]¶

Initializes the domain depending on the model used for the inversion. Defines a domain grid from a grid file or a set of parameters if the domain was not already defined. Domains are model dependant, so the outputs can be different depending on the model.

Parameters

plugin (DomainPlugin) – domain definition

Returns

Updates on the fly the domain

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

read_grid(*args, **kwargs)[source]¶

Read a grid from an existing file

Parameters

self (Domain) – plugin defining the domain. Should include

to be able to read the grid from a file (filegrid) –

Returns

Grid domain with meshgrids for center lon/lat and corner lon/lat

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Measurement class

Click here to expand the code of the Measurement class

class pycif.utils.classes.measurements.Measurement(plg_orig=None, **kwargs)[source]¶

ini_data(**kwargs)[source]¶

Initializes the measurement plugin. This is pased on iterating over multiple species and providers

Parameters

plugin (MeasurementPlugin) – Measurement definition

Returns

Updates on the fly the measurements

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

parse_tracers(*args, **kwargs)[source]¶

Default empty minimize function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Minimizer class

Click here to expand the code of the Minimizer class

class pycif.utils.classes.minimizers.Minimizer(plg_orig=None, **kwargs)[source]¶

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

minimize(*args, **kwargs)[source]¶

Default empty minimize function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Model class

Click here to expand the code of the Model class

class pycif.utils.classes.models.Model(**kwargs)[source]¶

flushrun(*args, **kwargs)[source]¶

Default empty flushrun method

ini_mapper(*args, **kwargs)[source]¶

Default empty ini_mapper method

ini_periods(*args, **kwargs)[source]¶

Default empty ini_periods method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

make_auxiliary(*args, **kwargs)[source]¶

Default empty make_auxiliary method

make_input(*args, **kwargs)[source]¶

Default empty make_input method

native2inputs(*args, **kwargs)[source]¶

Default empty native2inputs method

native2inputs_adj(*args, **kwargs)[source]¶

Default empty native2inputs_adj method

outputs2native(*args, **kwargs)[source]¶

Default empty outputs2native method

outputs2native_adj(*args, **kwargs)[source]¶

Default empty outputs2native_adj method

perturb_model(*args, **kwargs)[source]¶

Default empty perturb_model method

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

run(*args, **kwargs)[source]¶

Default empty run method

Mode class

Click here to expand the code of the Mode class

class pycif.utils.classes.modes.Mode(plg_orig=None, **kwargs)[source]¶

execute(*args, **kwargs)[source]¶

Default empty execute method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Obsoperator class

Click here to expand the code of the Obsoperator class

class pycif.utils.classes.obsoperators.ObsOperator(plg_orig=None, **kwargs)[source]¶

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

obsoper(inputs, mode, run_id=0, datei=datetime.datetime(1979, 1, 1, 0, 0), datef=datetime.datetime(2100, 1, 1, 0, 0), workdir='./', **kwargs)[source]¶

The observation operator. This function maps information from the control space to the observation space and conversely depending on the running mode.

Parameters

self (ObsOperator) – the ObsOperator plugin

inputs (Controlvect or Obsvect) – the inputs of the fwd or adj mode

mode (str) – the running mode

run_id (int) – the ID of the current run (determines the

name (sub-directory) –

datei (datetime.datetime) – beginning of the simulation window

datef (datetime.datetime) – end of the simulation window

workdir (str) – path to the parent directory

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Obsparser class

Click here to expand the code of the Obsparser class

class pycif.utils.classes.obsparsers.ObsParser(plg_orig=None, **kwargs)[source]¶

Class for handling time series parsing from different data providers and data file formats.

static check_df(df, **kwargs)[source]¶

Check that all required columns have been loaded

Parameters

df –

kwargs –

Returns

classmethod get_parser(plg)[source]¶

Get the correct Parser for a provider and file_format_id

Parameters

provider (str) – provider of the input file

file_format_id (str) – name of the type of file with a given format

Returns

Parser for provider and file_format_id

Return type

Parser

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

parse_file(obs_file, **kwargs)[source]¶

This function does the parsing (and post processing if necessary).

Parameters

obs_file (str) – path to input file

Keyword Arguments

encoding (str) – Encoding of input files

freq (str) – frequency after resampling see `Offset Aliases`_ for valid strings

src_freq (str) – explicit setting of the frequency in the input file shouldn’t be necessary

Returns

renamed, shifted, resampled Dataframe df[obssite_id, parameter] with t as index

Return type

pandas.DataFrame

parse_multiple_files(**kwargs)[source]¶

Parses multiple files specified by a glob pattern and stores the content into a datastore.

Parameters

self – the plugin with its describing arguments (in particular dir_obs)

Returns

{obs_file} = df[obssite_id, parameter]

Return type

dict

Note

By default, the function calls self.parse_file, which filters out NaNs and check that all required columns are available.

classmethod register_parser(provider, file_format_id, parse_module, **kwargs)[source]¶

Register a parsing function for provider and format with default options

Parameters

provider (str) – provider of the input file

file_format_id (str) – name of the type of file with a given format

parse_module (Module) – returns file content as pandas.DataFrame df[obssite_id, parameter]

**kwargs – default options for parse_function

Notes

The parse_function signature is the same as the Parser.parse_file()

Obsvect class

Click here to expand the code of the Obsvect class

class pycif.utils.classes.obsvects.ObsVect(**kwargs)[source]¶

dump(*args, **kwargs)[source]¶

Default empty dump method

init_invprod(*args, **kwargs)[source]¶

Default empty init_invprod method

init_y0(*args, **kwargs)[source]¶

Default empty init_y0 method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

read(*args, **kwargs)[source]¶

Default empty read method

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

rinvprod(*args, **kwargs)[source]¶

Default empty rinvprod method

Platform class

Click here to expand the code of the Platform class

class pycif.utils.classes.platforms.Platform(**kwargs)[source]¶

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Simulator class

Click here to expand the code of the Simulator class

class pycif.utils.classes.simulators.Simulator(plg_orig=None, **kwargs)[source]¶

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

simul(*args, **kwargs)[source]¶

Default empty simul method

Transform class

Click here to expand the code of the Transform class

class pycif.utils.classes.transforms.Transform(plg_orig=None, **kwargs)[source]¶

flushrun(*args, **kwargs)[source]¶

Default empty flushrun method for transforms

classmethod get_transform(plg)[source]¶

Get the correct Parser for a provider and file_format_id

Parameters

provider (str) – provider of the input file

file_format_id (str) – name of the type of file with a given format

Returns

Parser for provider and file_format_id

Return type

Parser

ini_mapper(*args, **kwargs)[source]¶

Default empty ini_mapper method

initiate_template()[source]¶

Initializes a Plugin template, with methods from the corresponding module.

Parameters

self – the plugin to initialize

plg_type – the type of the plugin to initialize

default_functions (dict[str, bool]) – functions to load from the module and to attach to the plugin. Each key names the function and each value is a boolean to determine whether the corresponding function is a class method (with a reflective self as argument) or a classical static function

mapper2batch(nsamples, transf_mapper, all_mapper, all_transforms, dir_samples, **kwargs)[source]¶

Default mapper2batch method.

Perturb the mapper to simulate a batch of samples at once.

Propagate perturbations from precursors to outputs.

For transformations with no inputs, perturb outputs if “fromcontrol”

perturb_transform(*args, **kwargs)[source]¶

Default empty perturb_transform method.

Do nothing by default.

If specified in the corresponding plugin, the function should perturb its own behaviour beyond the mapper if necessary.

For instance, for models, it is necessary to update the chemical scheme to know which species should be accounted for

classmethod register_plugin(name, version, module, subtype='', **kwargs)[source]¶

Register a module for a plugin and version with possibly options

Parameters

name (str) – name of the plugin

version (str) – version of the plugin

module (types.ModuleType) – module defining the interface between pyCIF and the plugin

plugin_type (str) – type of plugin

**kwargs (dictionary) – default options for module

Plugins: what are they?¶

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