Installation
The default installations from PyPI and conda-forge don’t include any of the optional dependencies required for visualization (see below). This is done to avoid potential conflicts with user defined PyMOL installations.
Installation via conda
ConservedWaterSearch is available through conda-forge using conda
(or mamba
) and this is the recommended way to install it:
conda install -c conda-forge ConservedWaterSearch
Installation via PyPI
ConservedWaterSearch can be installed via pip
from PyPI:
pip install ConservedWaterSearch
Optional visualization dependencies
PyMOL is required for visualization only, if so desired. If not, it’s installation can be skipped. PyMOL is not available via PyPI (pip
), but can be installed from conda-forge. If PyMOL is already installed in your current python
environment it can be used with CWS. If not, the free (open-source) version can be installed from conda-forge via conda
(or mamba
):
conda install -c conda-forge pymol-open-source
and paid (licensed version) from schrodinger channel (see here for more details) via conda
(or mamba
):
conda install -c conda-forge -c schrodinger pymol-bundle
Optional dependencies for visualization can be installed through PyPI (pip
) except for PyMOL. To install CWS through pip
with nglview use:
pip install ConservedWaterSearch[nglview]
To install with matplotlib for clustering plots use:
pip install ConservedWaterSearch[debug]
To install with both nglview and matplotlib use:
pip install ConservedWaterSearch[all]
Known Issues
AttributeError: 'super' object has no attribute '_ipython_display_'
Some versions of Jupyter notebook are incpompatible with ipython (see here). To resolve install version of ipywidgets<8
using conda
:
conda install "ipywidgets <8" -c conda-forge
or pip
:
pip install ipywidgets==7.6.0
Tests
ConservedWaterSearch (CWS) uses pytest
for running unit tests. It can be installed via conda
:
conda install -c conda-forge pytest
Or via PyPI (using pip
):
pip install pytest
Unit tests can be run from the root directory:
python -m pytest
Documentation
To build the documentation following dependencies have to be installed, either using conda
:
conda install -c conda-forge sphinx sphinx_rtd_theme sphinxcontrib-bibtex
or pip
:
pip install sphinx sphinx_rtd_theme sphinxcontrib-bibtex
The documentation can be build from the docs
folder:
cd docs/
make html
open build/html/index.html