Metadata-Version: 2.1
Name: yaml2sbml
Version: 0.2.2
Summary: A small package to convert ODEs specified in a YAML file to SBML/PEtab
Home-page: https://github.com/yaml2sbml-dev/yaml2sbml
Author: Jakob Vanhoefer, Marta R. A. Matos, Dilan Pathirana, Yannik Schälte
Author-email: jakob.vanhoefer@uni-bonn.de,marta.ra.matos@gmail.com
License: MIT
Download-URL: https://github.com/yaml2sbml-dev/yaml2sbml/releases
Project-URL: Bug Tracker, https://github.com/yaml2sbml-dev/yaml2sbml/issues
Project-URL: Documentation, https://yaml2sbml.readthedocs.io
Project-URL: Changelog, https://yaml2sbml.readthedocs.io/en/latest/release_notes.html
Description: <img src="https://raw.githubusercontent.com/yaml2sbml-dev/yaml2sbml/main/doc/logo/logo_yaml2sbml_long.svg" alt="yaml2sbml logo"/>
        
        [![CI](https://github.com/yaml2sbml-dev/yaml2sbml/workflows/CI/badge.svg)](https://github.com/yaml2sbml-dev/yaml2sbml/actions)
        [![codecov](https://codecov.io/gh/yaml2sbml-dev/yaml2sbml/branch/master/graph/badge.svg)](https://codecov.io/gh/yaml2sbml-dev/yaml2sbml)
        [![Documentation Status](https://readthedocs.org/projects/yaml2sbml/badge/?version=latest)](https://yaml2sbml.readthedocs.io/en/latest/?badge=latest)
        [![Codacy Badge](https://app.codacy.com/project/badge/Grade/632acdc8d4ef4f50bf69892b8862fd24)](https://www.codacy.com/gh/yaml2sbml-dev/yaml2sbml/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=yaml2sbml-dev/yaml2sbml&amp;utm_campaign=Badge_Grade)
        [![PyPI](https://badge.fury.io/py/yaml2sbml.svg)](https://badge.fury.io/py/yaml2sbml)
        
        ## Table of contents
        
        * [About](#about)
        
        * [Installation](#installation)
        
        * [Getting Started](#getting-started)
        
        * [Basic Syntax](#basic-syntax)
        
        * [Contact](#contact)
        
        
        ## About
        
        `yaml2sbml` is a small package in Python to convert an ODE model specified in a YAML file into 
        [**SBML**](http://www.sbml.org/) for ODE simulation and into 
        [**PEtab**](https://github.com/PEtab-dev/PEtab/) for parameter fitting. `yaml2sbml` offers:
        
        
        * a translator of ODE models specified in YAML into SBML/PEtab via a Python and a command-line interface;
        * a format validator for the input YAML; and
        * a model editor, which provides a simplified interface to generate, import and export YAML models.
        
        ## Installation
        
        `yaml2sbml` can be installed from PyPI with
        
        ```shell
        pip install yaml2sbml
        ```
        For more info see the [docs](https://yaml2sbml.readthedocs.io/en/latest/).
        
        ## Getting Started
        
        * The documentation of the tool is hosted on [Read the Docs](https://yaml2sbml.readthedocs.io/en/latest/).
        * The [format documentation](https://yaml2sbml.readthedocs.io/en/latest/format_specification.html) describes the input YAML. 
        
        * Jupyter notebooks containing examples can be found under [`doc/examples`](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples).  Most notably:
            * [Lotka_Volterra.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb) showing the Python package,
            * [Lotka_Volterra_CLI.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_CLI.ipynb) showing the command-line interface, and
            * [Lotka_Volterra_Model_Editor.ipynb](https://github.com/yaml2sbml-dev/yaml2sbml/tree/main/doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb) demonstrates the Model Editor.
        
        ## Basic Syntax
        
        ### Python
        
        A YAML model can be translated to SBML/PEtab in Python via
        ```python
        import yaml2sbml
        
        # SBML conversion
        yaml2sbml.yaml2sbml(yaml_dir, sbml_dir)
        
        #PEtab conversion
        yaml2sbml.yaml2petab(yaml_dir, 
                             output_dir,
                             sbml_name)
        ```
        ### Command-Line Interface
        
        and in the command-line via 
        ```shell
        # SBML conversion
        yaml2sbml <yaml_dir> <sbml_dir>
        
        #PEtab conversion
        yaml2petab <yaml_dir> <output_dir> <sbml_name>
        ```
        
        ### Format Validation
        
        Format validation is possible in Python via `yaml2sbml.validate_yaml` and in the command-line via `yaml2sbml_validate`.
        
        ## Contact
        If you have a question regarding the tool: Please drop us an [issue](https://github.com/yaml2sbml-dev/yaml2sbml/issues/new) or a [mail](mailto:jakob.vanhoefer@uni-bonn.de), we are happy to help.
        
Keywords: YAML,SBML,PEtab,ODE
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: examples
Provides-Extra: doc
