:mod:`biotransformers`
======================

.. py:module:: biotransformers


Subpackages
-----------
.. toctree::
   :titlesonly:
   :maxdepth: 3

   lightning_utils/index.rst
   tests/index.rst
   utils/index.rst
   wrappers/index.rst


Submodules
----------
.. toctree::
   :titlesonly:
   :maxdepth: 1

   bio_transformers/index.rst
   version/index.rst


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

Classes
~~~~~~~

.. autoapisummary::

   biotransformers.BioTransformers



Functions
~~~~~~~~~

.. autoapisummary::

   biotransformers.logger



Attributes
~~~~~~~~~~

.. autoapisummary::

   biotransformers.VERSION
   biotransformers.log
   biotransformers.__version__


.. class:: BioTransformers(backend: str = 'esm1_t6_43M_UR50S', num_gpus: int = 0)


   Bases: :py:obj:`biotransformers.wrappers.transformers_wrappers.TransformersWrapper`

   General class to choose an ESM or ProtBert backend
   Abstract method are implemented in transformers

   .. method:: list_backend() -> None
      :staticmethod:

      Get all possible backend for the model



.. function:: logger(module_name: str) -> logging.Logger

   Configure the logger with formatter and handlers.

   The log level depends on the environment variable `BIO_LOG_LEVEL`.

   - 0: NOTSET, will be set to DEBUG
   - 1: DEBUG
   - 2: INFO (default)
   - 3: WARNING
   - 4: ERROR
   - 5: CRITICAL
   https://docs.python.org/3/library/logging.html#levels

   :param module_name: module name
   :type module_name: str

   :returns: instantiate logger object
   :rtype: [Logger]


.. data:: VERSION
   :annotation: = 0.1.17

   

.. data:: log
   

   

.. data:: __version__