Metadata-Version: 2.1
Name: wopmars
Version: 0.1.5
Summary: Workflow Python Manager for Reproducible Science
Home-page: https://github.com/aitgon/wopmars
Download-URL: https://github.com/aitgon/wopmars/archive/0.1.5.tar.gz
Author: Aitor Gonzalez, Luc Giffon, Lionel Spinelli
Author-email: aitor.gonzalez@univ-amu.fr
License: MIT
Keywords: workflow manager python object-oriented reproducible science database framework
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Database :: Front-Ends
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Software Development
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Provides-Extra: pygraphviz
License-File: LICENSE.txt

WopMars: Workflow Python Manager for Reproducible Science
======================================================================

.. image:: https://img.shields.io/pypi/v/wopmars.svg
    :target: https://pypi.python.org/pypi/wopmars

.. image:: https://img.shields.io/pypi/pyversions/wopmars.svg
    :target: https://www.python.org

.. image:: https://readthedocs.org/projects/wopmars/badge/?version=latest
    :target: http://wopmars.readthedocs.io/en/latest/?badge=latest

.. image:: https://github.com/aitgon/wopmars/workflows/CI/badge.svg
    :target: https://github.com/aitgon/wopmars/actions?query=branch%3Amaster+workflow%3ACI

.. image:: https://codecov.io/gh/aitgon/wopmars/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/aitgon/wopmars

.. image:: https://static.pepy.tech/personalized-badge/wopmars?period=month&units=international_system&left_color=black&right_color=blue&left_text=Downloads
    :target: https://pepy.tech/project/wopmars

WopMars is a database-driven workflow manager written in python similar to GNU Makefile or Snakemake.
The difference is that the definition file of WopMars takes into account input/output SQLITE table defined as python
paths to SQLAlchemy models.

You can install the latest WopMars version via "pypi":

.. code-block:: bash

    pip install wopmars

Run a quick example:

.. code-block:: bash

    wopmars example
    cd example
    pip install -e .
    wopmars -D sqlite:///db.sqlite -w Wopfile.yml -v

If there were not errors, you can look at the content of the sqlite db.

.. code-block:: bash

    $ sqlite3 db.sqlite '.tables'

    Piece                            wom_TableInputOutputInformation
    PieceCar                         wom_TableModificationTime
    wom_Execution                    wom_ToolWrapper
    wom_FileInputOutputInformation   wom_TypeInputOrOutput
    wom_Option

    $ sqlite3 db.sqlite "select * from Piece limit 5"

    1|UC8T9P7D0F|wheel|664.24
    2|2BPN653B9D|engine|550.49
    3|T808AHY3DS|engine|672.09
    4|977FPG7QJZ|bodywork|667.23
    5|KJ6WPB3N56|engine|678.83

The `WopMars documentation <http://wopmars.readthedocs.org/>`_ with user guide and
API reference is hosted at Read The Docs.

