petab - a Python package for handling PEtab files
PEtab 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/.
Documentation of the PEtab format in general is available at
https://petab.readthedocs.io/en/latest/.
Installation
The PEtab library is available on pypi and the easiest way to install it is running
pip3 install petab
It will require Python>=3.7.1 to run.
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, which is automatically installed using Python entrypoints to be available as a shell command from anywhere, called
petablint -
petab.create_parameter_dfto create the parameter table, once you have set up the model, condition table, observable table and measurement table -
petab.create_combine_archiveto create a COMBINE Archive from PEtab files
Examples
Examples for PEtab Python library usage:
Getting help
If you have any question or problems with this package, feel free to post them at our GitHub issue tracker.
Contributing
Contributions and feedback to this package are very welcome, see our contribution guide.
Release files for petab 0.1.23
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| petab-0.1.23.tar.gz | 75.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| petab-0.1.23-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 161.3 kB
Release files / petab-0.1.23.tar.gz
| Download URL | petab-0.1.23.tar.gz |
|---|---|
| Size | 75.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / petab-0.1.23-py3-none-any.whl
| Download URL | petab-0.1.23-py3-none-any.whl |
|---|---|
| Size | 86.0 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.8 tqdm/4.62.3 importlib-metadata/4.10.1 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.8.12
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