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REINVENT 3.0

Installation

  1. Install Conda

  2. Clone this Git repository

  3. Open a shell, and go to the repository and create the Conda environment:

     $ conda env create -f reinvent.yml
    
  4. Activate the environment:

     $ conda activate reinvent.v3.0
    
  5. Use the tool.

Tutorials / jupyter notebooks

There is another repository containing useful jupyter notebooks related to REINVENT called ReinventCommunity. Note, that it uses a different conda environment to execute, so you have to set up a separate environment.

Usage

For concrete examples, you can check out the Jupyter notebook examples in the ReinventCommunity repo. Running each example will result in a template file.There are templates for many running modes. Each running mode can be executed by python input.py some_running_mode.json after activating the environment.

Templates can be manually edited before using. The only thing that needs modification for a standard run are the file and folder paths. Most running modes produce logs that can be monitored by tensorboard.

Tests

The REINVENT project uses the unittest framework for its tests; before you run them you first have to create a configuration, which the tests will use.

In the project directory, create a config.json file in the configs/ directory; you can use the example config (example.config.json) as a base. Make sure that you set MAIN_TEST_PATH to a non-existent directory; it is where temporary files will be written during the tests; if it is set to an existing directory, that directory will be removed once the tests have finished.

Some tests require a proprietary OpenEye license; you have to set up a few things to make the tests read your license. The simple way is to just set the OE_LICENSE environment variable to the path of the file containing the license. If you just want to set the license in the reinvent_scoring Conda environment, it is a bit more complicated, but you only have to do it once.

(reinvent-scoring) $ cd $CONDA_PREFIX
$ mkdir -p etc/conda/activate.d
$ mkdir -p etc/conda/deactivate.d

Put the following in etc/conda/activate.d/env_vars.sh.

#!/bin/sh
export OE_LICENSE='</path/to/your/oe_license/file>'

And put the following in etc/conda/deactivate.d/env_vars.sh.

#!/bin/sh
unset OE_LICENSE

Once you have created the files, deactivate and re-activate the environment, and echo $OE_LICENSE should output the path to the license file. Once you have a configuration and your license can be read, you can run the tests.

$ python main_test.py