Metadata-Version: 2.4
Name: casq
Version: 1.4.4
Summary: CaSQ: Celldesigner as Sbml-Qual
Project-URL: Code, https://gitlab.inria.fr/soliman/casq/
Project-URL: Documentation, https://casq.readthedocs.io/en/latest/
Project-URL: Homepage, https://soliman.gitlabpages.inria.fr/casq/
Project-URL: Mirror, https://github.com/soli/casq
Author-email: Sylvain Soliman <Sylvain.Soliman@inria.fr>
License-Expression: GPL-3.0-or-later
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.7
Requires-Dist: loguru>=0.2.5
Requires-Dist: networkx>=2.2
Provides-Extra: dev
Requires-Dist: ruff>=0.0.289; extra == 'dev'
Provides-Extra: docs
Requires-Dist: sphinx; extra == 'docs'
Requires-Dist: sphinxcontrib-programoutput; extra == 'docs'
Description-Content-Type: text/x-rst

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|pipeline status| |coverage report| |black| |rtd| |gpl|

|pypi-version| |pypi-python| |pypi-wheel| |pypi-downloads| |deps|

|conda| |conda-down| |made-by-humans|

.. |pipeline status| image:: https://gitlab.inria.fr/soliman/casq/badges/master/pipeline.svg
   :target: https://gitlab.inria.fr/soliman/casq/commits/master
   :alt: pipeline status

.. |coverage report| image:: https://gitlab.inria.fr/soliman/casq/badges/master/coverage.svg
   :target: https://gitlab.inria.fr/soliman/casq/commits/master
   :alt: coverage report

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/python/black
   :alt: Code style: black

.. |rtd| image:: https://readthedocs.org/projects/casq/badge/?version=latest
   :target: https://casq.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

.. |gpl| image:: https://img.shields.io/pypi/l/casq
   :target: https://gitlab.inria.fr/soliman/casq/raw/master/LICENSE
   :alt: PyPI - License

.. |pypi-version| image:: https://img.shields.io/pypi/v/casq
   :target: https://pypi.org/project/casq/
   :alt: PyPI

.. |pypi-python| image:: https://img.shields.io/pypi/pyversions/casq
   :alt: PyPI - Python Version
   :target: https://pypi.org/project/casq/

.. |pypi-wheel| image:: https://img.shields.io/pypi/wheel/casq
   :target: https://pypi.org/project/casq/
   :alt: PyPI - Wheel

.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/casq
   :target: https://pypi.org/project/casq/
   :alt: PyPI - Downloads

.. |deps| image:: https://img.shields.io/librariesio/release/pypi/casq
   :target: https://pypi.org/project/casq/
   :alt: Libraries.io dependency status for latest release

.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/casq
   :target: https://anaconda.org/conda-forge/casq
   :alt: Conda-Forge CaSQ version

.. |conda-down| image:: https://img.shields.io/conda/d/conda-forge/casq
   :target: https://anaconda.org/conda-forge/casq
   :alt: Conda-Forge CaSQ total downloads badge

.. |made-by-humans| image:: https://img.shields.io/badge/Made_by-humans-darkviolet
   :alt: Made by humans

**CaSQ** converts `CellDesigner`_ and `SBGN-ML`_ models to Boolean models
encoded in `SBML-Qual`_ with a rather strict semantics defined in a `published
article`_.

.. _`CellDesigner`: http://celldesigner.org
.. _`SBML-Qual`: http://sbml.org
.. _`SBGN-ML`: https://github.com/sbgn/sbgn/wiki/SBGN_ML
.. _`published article`: https://academic.oup.com/bioinformatics/article/36/16/4473/5836892

Install
=======

CaSQ is provided as a Python3 package, you can install it from the `Python package index`_ with ``pip``, ``conda`` or your Python package manager of choice:

.. _`Python package index`: https://pypi.org/project/casq/

.. code:: bash

   $ python3 -m pip install casq

Note that we currently recommend that you use the excellent `uv` tool from Astral, which allows you to run CaSQ without worrying about any installation procedure at all:

.. _`uv`: https://docs.astral.sh/uv/

.. code:: bash

   $ uvx casq -v
   casq v1.4.3

Command-line usage
==================

Just follow the instructions::

   $ casq --help
   usage: casq [-h] [-v] [-D] [-c] [-s] [-r S] [-f FIXED] [-n]
               [-u [UPSTREAM ...]] [-d [DOWNSTREAM ...]] [-b] [-g GRANULARITY]
               [-i INPUT] [-C]
               [infile] [outfile]

   Convert CellDesigner/SBGNML models to SBML-qual with a rather strict
   semantics. Copyright (C) 2019, Sylvain.Soliman@inria.fr GPLv3

   positional arguments:
     infile                CellDesigner or SBGN-ML File
     outfile               SBML-Qual/BMA json File

   optional arguments:
     -h, --help            show this help message and exit
     -v, --version         show program's version number and exit
     -D, --debug           Display a lot of debug information
     -c, --csv             Additionally store the information in a .bnet and
                           separate CSV files compatible with the Spreadsheet-
                           SBML-qual format
     -s, --sif             Store the influence information in a separate SIF file
     -r S, --remove S      Delete connected components in the resulting model if
                           their size is smaller than S. A negative S leads to
                           keep only the biggest(s) connected component(s)
     -f FIXED, --fixed FIXED
                           A CSV file containing input values or knock-ins/knock-
                           outs, one per line, with name in the first column and
                           the value in the second.
     -n, --names           Use the names as IDs in the SBML file
     -u [UPSTREAM ...], --upstream [UPSTREAM ...]
                           Only species upstream of this/these species will be
                           kept
     -d [DOWNSTREAM ...], --downstream [DOWNSTREAM ...]
                           Only species downstream of this/these species will be
                           kept
     -b, --bma             Output to BMA json format
     -g GRANULARITY, --granularity GRANULARITY
                           When exporting to BMA, use this granularity
     -i INPUT, --input INPUT
                           When exporting to BMA, nodes with no input should be
                           set to this value
     -C, --colourConstant  When exporting to BMA, colour all variables pink
                           (defaults to colour by compartment)
