booldog
=======

.. py:module:: booldog

.. autoapi-nested-parse::

   `booldog`: A Python package for analyses of Boolean and semi-quantitative Boolean networks



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/booldog/boolean/index
   /autoapi/booldog/classes/index
   /autoapi/booldog/continuous/index
   /autoapi/booldog/io/index
   /autoapi/booldog/network/index
   /autoapi/booldog/resources/index
   /autoapi/booldog/simulation_result/index
   /autoapi/booldog/utils/index


Attributes
----------

.. autoapisummary::

   booldog.__version__
   booldog.logger


Classes
-------

.. autoapisummary::

   booldog.BoolDogModel
   booldog.BooleanStateSpace


Functions
---------

.. autoapisummary::

   booldog.get_pkg_version
   booldog.setup_logger


Package Contents
----------------

.. py:function:: get_pkg_version()

   Get version of booldog package

   :returns: **version** -- Version of booldog package
   :rtype: str


.. py:function:: setup_logger(level=logging.INFO)

   Set up logger for BoolDog



.. py:class:: BoolDogModel(nodes=None, primes=None, modelinfo=None)

   Bases: :py:obj:`booldog.boolean.BooleanNetworkMixin`, :py:obj:`booldog.boolean.BooleanNetworkModificationMixin`, :py:obj:`booldog.continuous.ContinuousMixin`, :py:obj:`booldog.io.BoolDogModelIOFromMixin`, :py:obj:`booldog.io.BoolDogModelIOToMixin`


   A class to represent a Boolean network.

   .. attribute:: n

      The number of nodes/variables in the network

      :type: int

   .. attribute:: primes

      Prime implicants of the Boolean network. See
      `PyBoolNet:prime implicants
      <https://pyboolnet.readthedocs.io/en/latest/Manual.html#prime-implicants>`_
      for more information.

      :type: dict

   .. attribute:: nodes

      List of `booldog.network.BoolDogNode` objects representing the nodes

      :type: tuple of str

   .. attribute:: index

      Dictionary of node name to integer index for indexing arrays

      :type: dict


   .. py:attribute:: nodes


   .. py:attribute:: _primes_cached
      :value: True



   .. py:attribute:: modifications
      :value: []



   .. py:method:: _set_node_ids_and_index()

      Set the sorted node identifiers and index mapping to integers.



   .. py:property:: n

      Number of nodes in the network


   .. py:property:: primes

      Prime implicants of the Boolean network. See
      `PyBoolNet:prime implicants` <https://pyboolnet.readthedocs.io/en/latest/Manual.html
      #prime-implicants> for more information.


   .. py:method:: __repr__()


   .. py:method:: __len__()


.. py:class:: BooleanStateSpace(network, state_space)

   Class to contain a subspace of a Boolean Network.


   .. py:attribute:: network


   .. py:attribute:: state_space


   .. py:method:: set_node_state(node_id, state)

      Set the state of a node in all states of the state space.

      :param node_id: The identifier of the node to set the state for.
      :type node_id: str
      :param state: The state to set for the node (0 or 1).
      :type state: int

      :raises ValueError: If `node_id` is not a valid node identifier in the network, or if `state` is not 0 or 1.



   .. py:method:: plot_state_space(title='State Heatmap', cmap=None)

      Plot the states of the Boolean network as a heatmap.

      :param title: Title of the heatmap, default is "State Heatmap".
      :type title: str, optional
      :param cmap: Colormap to use for the heatmap. Default is binary with green (1) and grey (0).
      :type cmap: ListedColormap, optional



   .. py:method:: __repr__()


.. py:data:: __version__

.. py:data:: logger