Metadata-Version: 2.1
Name: petab
Version: 0.2.8
Summary: Parameter estimation tabular data
Home-page: https://github.com/PEtab-dev/libpetab-python
Author: The PEtab developers
Author-email: daniel.weindl@helmholtz-muenchen.de
Requires-Python: >=3.9.0
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.15.1
Requires-Dist: pandas>=1.2.0
Requires-Dist: pyarrow
Requires-Dist: python-libsbml>=5.17.0
Requires-Dist: sympy
Requires-Dist: colorama
Requires-Dist: pyyaml
Requires-Dist: jsonschema
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Requires-Dist: simplesbml; extra == "tests"
Requires-Dist: scipy; extra == "tests"
Requires-Dist: pysb; extra == "tests"
Provides-Extra: quality
Requires-Dist: flake8>=3.8.3; extra == "quality"
Provides-Extra: reports
Requires-Dist: Jinja2==3.0.3; extra == "reports"
Provides-Extra: combine
Requires-Dist: python-libcombine>=0.2.6; extra == "combine"
Provides-Extra: doc
Requires-Dist: sphinx!=5.1.0,>=3.5.3; extra == "doc"
Requires-Dist: sphinxcontrib-napoleon>=0.7; extra == "doc"
Requires-Dist: sphinx-markdown-tables>=0.0.15; extra == "doc"
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Requires-Dist: myst-nb>=0.14.0; extra == "doc"
Requires-Dist: ipython!=8.7.0,>=7.21.0; extra == "doc"
Provides-Extra: vis
Requires-Dist: matplotlib>=3.6.0; extra == "vis"
Requires-Dist: seaborn; extra == "vis"
Requires-Dist: scipy; extra == "vis"

[![CI](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml/badge.svg?branch=main)](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml)
[![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/main/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
[![PyPI version](https://badge.fury.io/py/petab.svg)](https://badge.fury.io/py/petab)

# petab - a Python package for handling PEtab files

[PEtab](https://petab.readthedocs.io/) is a data format for specifying
parameter estimation problems in systems biology. This repository provides
the `petab` Python package for reading, writing and validating PEtab files.

## Documentation

Documentation of the `petab` Python package is available at
[https://libpetab-python.readthedocs.io/en/latest/](https://libpetab-python.readthedocs.io/en/latest/).
Documentation of the PEtab format in general is available at
[https://petab.readthedocs.io/en/latest/](https://petab.readthedocs.io/en/latest/).

## Installation

The PEtab library is available on [pypi](https://pypi.org/project/petab/)
and the easiest way to install it is running

    pip3 install petab

It will require Python>=3.9 to run. (We are following the
[numpy Python support policy](https://numpy.org/neps/nep-0029-deprecation_policy.html)).

Development versions of the PEtab library can be installed using

    pip3 install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip

(replace `develop` by the branch or commit you would like to install).

When setting up a new parameter estimation problem, the most useful tools will
be:

  - The [PEtab validator](https://petab.readthedocs.io/projects/libpetab-python/en/latest/example/example_petablint.html),
    which is automatically installed using Python
    entrypoints to be available as a shell command from anywhere, called
    `petablint`

  - [`petab.create_parameter_df`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.parameters.html#petab.parameters.create_parameter_df)
    to create the parameter table, once you have set up the model,
    condition table, observable table and measurement table

  - [`petab.create_combine_archive`](https://petab.readthedocs.io/projects/libpetab-python/en/latest/build/_autosummary/petab.core.html#petab.core.create_combine_archive)
    to create a [COMBINE Archive](https://combinearchive.org/index/) from PEtab
    files

## Examples

Examples for PEtab Python library usage:

* [Validation](https://github.com/PEtab-dev/libpetab-python/blob/main/doc/example/example_petablint.ipynb)
* [Visualization](https://github.com/PEtab-dev/libpetab-python/blob/main/doc/example/example_visualization.ipynb)


## Getting help

If you have any question or problems with this package, feel free to post them
at our GitHub [issue tracker](https://github.com/PEtab-dev/libpetab-python/issues/).

## Contributing

Contributions and feedback to this package are very welcome, see our
[contribution guide](https://github.com/petab-dev/libpetab-python/tree/master/CONTRIBUTING.md).
