Linux & macOS¶
Installing OpenEye Python Toolkits As A Conda package¶
The simplest way to install the OpenEye Python Toolkits is as a Conda package.
The Anaconda package can be downloaded from https://www.anaconda.com/distribution/ for Windows, macOS and Linux platforms. Follow the very simple instructions given there for installation.
While Anaconda is available free of charge for personal use, users may need to purchase an Anaconda license if they are doing commercial development. Please check the Anaconda license terms.
We recommend the installation of PYTHON 3 Anaconda packages. This version will default to Python 3 when creating new environments and building packages.
After downloading and installing Anaconda, the OpenEye Python Toolkit package can be installed by the following steps:
First create a new conda environment with the OpenEye Python Toolkit package
$ conda create -n oepython -c openeye openeye-toolkits Solving environment: done ## Package Plan ## environment location: /home/username/anaconda3/envs/oepython added / updated specs: - openeye-toolkits The following packages will be downloaded: ... The following NEW packages will be INSTALLED: ... openeye-toolkits: |pypkgversion| -py37_0 openeye ... Proceed ([y]/n)?
After entering “y” to proceed, a new ‘oepython’ environment will be created be activated with the OpenEye Python Toolkit package.
Activate the newly created ‘oepython3’ environment:
$ source activate oepython
Run the OpenEye example oecheminfo.py to verify the installation has completed successfully:
(oepython) $ oecheminfo.py Installed OEChem version: |oechemversion| platform: linux-g++4.x-x64 built: |builddate| ...
Alternative Installation Strategies¶
To install OpenEye Python Toolkits in existing environments:
The above two ways are highly recommended since it is considered harmful to install packages into your global Python installation.
To install OpenEye Python Toolkits across multiple Linux versions:
To install OpenEye Python Toolkits with no root access available:
For assistance with unusual installation environments such as systems without network access or heterogeneous clusters, please contact support at firstname.lastname@example.org.
In order to follow the PEP 440 guidelines on versions, the version label for the python toolkit is 2021.1.1 instead of 2021.1.1.
The OpenEye Python Toolkits ship with a simple set of integration tests to make sure all the libraries function as intended. The test suite is not as exhaustive as the test suite used internally, it is just meant to ensure the OpenEye Python Toolkits infrastructure is working as intended.
Running the integration test requires scripttest and nose Python packages. These packages will be installed on-the-fly, if necessary. Again using conda or virtualenv environments will ensure that these packages will not be installed into the global Python environment.
To run the integration test suite (after activating the environment into which OpenEye Python Toolkits has been installed), execute the following command:
$ python -m openeye.examples.openeye_tests
A message like the following will be shown if all the tests were run successfully:
Requirement already satisfied: pytest Requirement already satisfied: py>=1.4.29 Collecting scripttest Installing collected packages: scripttest Successfully installed scripttest-1.3 Ran 42 tests in 95.877s OK
Tests are skipped when the license is invalid/expired/doesn’t exist or if functionally is not supported on the OS/platform. For example, when using a license file that only contains an OEChem TK license, a large number of tests will be skipped:
SSSSSSSSSSSSSSS.......SSSSSSSSSSSSSSSSSSS ---------------------------------------------------------------------- Ran 42 tests in 0.956s OK (SKIP=34)
Similarly, FastROCS, GPU-OMEGA, and GPU-GRAPHSIM tests are skipped on macOS, Windows, and Linux systems without appropriate GPU hardware since their functionality is not available.