You will need Python >= 3.6.
Please favor Conda, as Conda will seamlessly install the HDF5 standard library which is a required dependency.
pip install tramway
pip install will install some Python dependencies if missing, but you may still need to install the HDF5 reference library.
Note that the HDF5 library can usually be installed using any OS’ package manager. Only Windows users may have to manually download and install the HDF5 library, if they do not wish to use Conda instead of pip.
Several installation targets are available, including
full, that install optional dependencies:
pip install tramway[full]
Most of the functionalities and code examples described in this documentation will run without the optional dependencies this target installs in addition to the required dependencies.
It is safe to first install TRamWAy with minimal requirements and then
pip install the missing dependencies as you hit
ImportError while using TRamWAy.
conda install tramway -c conda-forge
Compared with the bare package
pip installs (with no installation targets), the
conda package specifies some optional dependencies as required, so that the above command installs them.
However, many other optional dependencies are omitted.
git clone https://github.com/DecBayComp/TRamWAy cd TRamWAy pip install -e .
Can be updated with
git pull run in the local repository.
To compile the documentation and get a local copy, after installing TRamWAy do:
cd doc make html
The generated documentation will be available at
_build/html/index.html from the
Building the documentation requires Sphinx.
OS and version specific notes¶
Some modules require Python>=3.7. These are bayes_factor for force “detection” based on Bayesian statistics, snr that extracts signal-to-noise ratios required by the bayes_factor module, and d.conj_prior which estimates the diffusion similarly to ddrift with no regularization but with additional confidence intervals.