casanovoutils
=============

.. py:module:: casanovoutils

.. autoapi-nested-parse::

   casanovoutils — utilities for working with de novo peptide sequencing data.

   Provides MGF file processing, precision/coverage evaluation, sequence
   alignment, and residue mass vocabulary management. Exposes
   ``configure_logging`` for consistent log setup across submodules.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/casanovoutils/align/index
   /autoapi/casanovoutils/constants/index
   /autoapi/casanovoutils/datasets/index
   /autoapi/casanovoutils/denovoutils/index
   /autoapi/casanovoutils/graphloss/index
   /autoapi/casanovoutils/main/index
   /autoapi/casanovoutils/mgfutils/index
   /autoapi/casanovoutils/mzmlutils/index
   /autoapi/casanovoutils/preccov/index
   /autoapi/casanovoutils/residues/index
   /autoapi/casanovoutils/summarize_mgf/index
   /autoapi/casanovoutils/types/index


Functions
---------

.. autoapisummary::

   casanovoutils.configure_logging


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

.. py:function:: configure_logging(log_file: Optional[os.PathLike] = None, level: Optional[int] = None) -> None

   Configure logging to stdout, optionally also writing to a file.

   This function is a no-op if it's already been called.

   :param log_file: If provided, log output is written to this file in addition to stdout.
                    The file is opened in append mode. If ``None`` (default), only stdout
                    is used.
   :type log_file: PathLike, optional
   :param level: Logging level. If ``None`` (default), reads from the ``LOG_LEVEL``
                 environment variable. If that is not set, defaults to ``logging.INFO``.
   :type level: int, optional