booldog.boolean.modifications
=============================

.. py:module:: booldog.boolean.modifications

.. autoapi-nested-parse::

   Module containing functions to manipulate Boolean networks.
   It is not intended to be used directly, but rather as a mixin
   for other classes.



Attributes
----------

.. autoapisummary::

   booldog.boolean.modifications.logger


Classes
-------

.. autoapisummary::

   booldog.boolean.modifications.ModificationTypes
   booldog.boolean.modifications.Modification
   booldog.boolean.modifications.BooleanNetworkModificationMixin


Module Contents
---------------

.. py:data:: logger

.. py:class:: ModificationTypes

   Bases: :py:obj:`booldog.utils.ExtendedEnum`


   Types of modifications to the Boolean network.

   :meta private:


   .. py:attribute:: ADD
      :value: 'add_node'



   .. py:attribute:: REMOVE
      :value: 'remove_node'



   .. py:attribute:: UPDATE
      :value: 'update'



.. py:class:: Modification(modification_type, node_id, rule=None)

   Class to represent a modification to the Boolean network.


   .. py:attribute:: type


   .. py:attribute:: node_id


   .. py:attribute:: rule
      :value: None



   .. py:method:: __repr__()


.. py:class:: BooleanNetworkModificationMixin

   Mixin class to modify a Boolean network.
   This class is not intended to be used directly, but rather as a mixin.


   .. py:method:: _track_network_modifications(modification_type, node_id, rule=None)

      Keep track of network modifications



   .. py:method:: _update_model_object(uncache_primes=True)

      Update the model attributes after a modification.



   .. py:method:: modify_network(modifications)

      Modify the network according to the given modifications.

      :param modifications: List of Modification objects.
      :type modifications: list

      :returns: The network is modified in place.
      :rtype: None

      .. rubric:: Notes

      Each Modification object must have the following attributes:
      - modification_type : str
          Type of modification. One of "add_node", "remove_node", "update".
      - node : str or list
          Name of node(s) to modify.
      - rule : str or None
          Rule to define the update function of `node`, in bnet form.
          All nodes in `rule` need to be defined in Network.

      The modifications are applied in the order they are given.
      A node cannot be removed if other nodes depend on it (i.e. it occurs in
      their update logic). To remove such a node, either also remove all of
      its dependants, or first update the logic rule of its dependants to
      remove dependency.

      This is a wrapper for pyboolnet.prime_implicants.create_variables and
      pyboolnet.prime_implicants.remove_variables.



   .. py:method:: remove_node(node_id)

      Removes `node` from the network.

      :param node: Names of node to remove
      :type node: str

      :rtype: None

      .. rubric:: Notes

      A node cannot be removed if other nodes depend on it (i.e. it occurs in
      their update logic). To remove such a node, either also remove all of
      its dependants, or first update the logic rule of its dependants to
      remove dependency.

      This is a wrapper for pyboolnet.prime_implicants.remove_variables.



   .. py:method:: _test_node_removabilty(node_ids)

      Test if a node (set) can be removed from the network.




   .. py:method:: remove_nodes(node_ids)

      Removes all nodes in `node_ids` from the network.

      :param node_ids: List of identifiers of nodes to remove
      :type node_ids: list

      :rtype: None

      .. rubric:: Notes

      A node cannot be removed if other nodes depend on it (i.e. it occurs in
      their update logic). To remove such a node, either also remove all of
      its dependants, or first update the logic rule of its dependants to
      remove dependency.

      This is a wrapper for pyboolnet.prime_implicants.remove_variables.



   .. py:method:: add_node(node_id, rule, name=None)

      Add a new node to Network.

      :param node: Node name
      :type node: str
      :param rule: Rule to define update of `node`, in bnet form. All nodes in
                   `rule` need to be defined in Network.
      :type rule: str

      :returns: * *None*
                * *This is a wrapper for pyboolnet.prime_implicants.create_variables.*



   .. py:method:: update_node(node_id, rule, modification_type=ModificationTypes.UPDATE)

      Update (modify) or add the logic rule defining the update of `node`.
      If `node` does not yet exist, it will be added, if it does exist, its
      update logic will be overwritten.

      :param node_id: Node identifier
      :type node_id: str
      :param rule: New rule to define update of `node`, in bnet form. All nodes in
                   `rule` need to be defined in Network.
      :type rule: str

      :returns: * *None*
                * *This is a wrapper for pyboolnet.prime_implicants.create_variables.*