There are various ways of installing or downloading the benchmark models:
The repository containing the benchmark models can be cloned from GitHub via:
git clone git@github.com:Benchmarking-Initiative/Benchmark-Models-PEtab.git
The Benchmark files can be downloaded from GitHub as a ZIP file.
We provide a Python utility package that simplifies the installation and provides access functionality at src/python.
It can be installed directly from GitHub via:
pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python
Alternatively, when the whole repository has been cloned (see above), the python package can be installed via
cd src/python
followed by either an in-place develop mode installation:
pip install -e .
or a packaged installation:
./build.sh
pip install build/dist/*
Note that when the repository models are updated, also the python package needs to be updated, as it does not actively synchronize.
Once installed, the python package can be used via:
import benchmark_models_petab as models
# print models base folder
print(models.MODELS_DIR)
# print all model names
print(models.MODELS)
# generate petab problem
petab_problem = models.get_problem("Zheng_PNAS2012")For provided functionality, see the source code documentation.