:py:mod:`cobra.summary.summary`
===============================

.. py:module:: cobra.summary.summary

.. autoapi-nested-parse::

   Provide the abstract base summary class.



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

Classes
~~~~~~~

.. autoapisummary::

   cobra.summary.summary.Summary




Attributes
~~~~~~~~~~

.. autoapisummary::

   cobra.summary.summary.logger


.. py:data:: logger

   

.. py:class:: Summary(**kwargs)


   Bases: :py:obj:`abc.ABC`

   Define the abstract base summary.

   .. seealso:: :obj:`MetaboliteSummary`, :obj:`ReactionSummary`, :obj:`ModelSummary`

   .. py:property:: tolerance
      :type: float

      Return the set threshold.

   .. py:method:: _generate(model: cobra.Model, solution: Optional[cobra.Solution], fva: Optional[Union[float, pandas.DataFrame]]) -> None

      Prepare the data for the summary instance.

      :param model: The metabolic model for which to generate a metabolite summary.
      :type model: cobra.Model
      :param solution: A previous model solution to use for generating the summary. If
                       ``None``, the summary method will generate a parsimonious flux
                       distribution.
      :type solution: cobra.Solution, optional
      :param fva: Whether or not to include flux variability analysis in the output.
                  If given, `fva` should either be a previous FVA solution matching the
                  model or a float between 0 and 1 representing the fraction of the
                  optimum objective to be searched.
      :type fva: pandas.DataFrame or float, optional


   .. py:method:: __str__() -> str

      Return a string representation of the summary.


   .. py:method:: _repr_html_() -> str

      Return a rich HTML representation of the summary.


   .. py:method:: _normalize_threshold(threshold: Optional[float])

      Return a sensible threshold value.


   .. py:method:: to_string(names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G', column_width: int = 79) -> str
      :abstractmethod:

      Return a pretty string representation of the summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, optional
      :param threshold: Hide fluxes below the threshold from being displayed. If no value is
                        given, the model tolerance is used (default None).
      :type threshold: float, optional
      :param float_format: Format string for floats (default '.4G').
      :type float_format: str, optional
      :param column_width: The maximum column width for each row (default 79).
      :type column_width: int, optional

      :returns: The summary formatted as a pretty string.
      :rtype: str


   .. py:method:: to_html(names: bool = False, threshold: Optional[float] = None, float_format: str = '.4G') -> str
      :abstractmethod:

      Return a rich HTML representation of the metabolite summary.

      :param names: Whether or not elements should be displayed by their common names
                    (default False).
      :type names: bool, optional
      :param threshold: Hide fluxes below the threshold from being displayed. If no value is
                        given, the model tolerance is used (default None).
      :type threshold: float, optional
      :param float_format: Format string for floats (default '.4G').
      :type float_format: str, optional

      :returns: The summary formatted as HTML.
      :rtype: str


   .. py:method:: to_frame() -> pandas.DataFrame

      Return the a data frame representation of the summary.