Setting up a Windows environment to make Python contributions to the RDKit¶

There is an updated version of this post, combined with the instructions for Linux and the Mac, available here: https://greglandrum.github.io/rdkit-blog/posts/2020-03-30-setting-up-an-environment.html

This is a followup to a longer post on setting up an environment for Linux or the Mac, there's more background there.

I'm going to explain each of the required steps, but the complete set of steps required is at the bottom of this post. Assuming that you have the prerequisites (explained directly below), I hope that these will "just work" for you, but one never knows... I'd like to be able to include this in the RDKit documentation, so please me know how it goes if you try the recipe out. Please do not add a comment to this blog post, I've created a github issue so that we have the comments in one place. If you don't have a github account, please email me your comments and I'll add them to the issue.

The steps explained¶

Prerequisites:

• you need to have either anaconda python or miniconda installed and in your path
• you need to have git installed and in your path
• these instructions assume that you are running in git bash (or some other capable bash-type shell). I'm sure you can do all of this in powershell, but I haven't managed to figure that out.

You should start by changing into the directory where you want to clone the RDKit source repository and then running:

git clone https://github.com/rdkit/rdkit.git

That will clone the repo from github into a local directory called rdkit. We now change into that directory and use it to set our RDBASE environment variable:

cd rdkit
export RDBASE=`pwd`

The next step is to create the conda environment that we're going to use to hold the RDKit binary components and install a recent beta version of the RDKit into that environment:

conda create -y -n py37_rdkit_beta python=3.7
conda activate py37_rdkit_beta
conda install -y -c rdkit/label/beta rdkit

If you have other Python packages that you'd like to work with, go ahead and install them into the environment now.

Next we copy the RDKit binary components from that environment into our local clone of the RDKit repo:

cd $CONDA_PREFIX/lib/python3.7/site-packages/rdkit
find . -name '*.pyd' -exec cp --parents \{\} $RDBASE/rdkit \; 
cp Chem/inchi.py $RDBASE/rdkit/Chem

Finally we set our PYTHONPATH and then test that everything is working by importing the RDKit's Chem module:

export PYTHONPATH="$RDBASE"
cd $RDBASE/rdkit
python -c 'from rdkit import Chem;print(Chem.__file__)'

That last command should not generate errors and should show you a filename that is in your local github clone. As an example, I started the first step of this process in my Code\rdkit_tmp directory, so I see:

c:\Users\glandrum\Code\rdkit_tmp\rdkit\Chem\__init__.py

Running the tests¶

If you're planning on making an RDKit contribution, it's important to know how to run the Python tests to make sure that your changes work and don't break anything else. For historic reasons the RDKit uses a self-written framework for running tests, but it's easy enough to use. You need to run the script $RDBASE/rdkit/TestRunner.py and point it to the test_list.py file containing the tests to be run. For example, if you want to run all the tests in the directory $RDBASE/rdkit/Chem (this corresponds to the python module rdkit.Chem), you would do:

cd $RDBASE/rdkit/Chem
python $RDBASE/rdkit/TestRunner.py test_list.py

That will take a while and generate a lot of output, including things that look like exceptions and errors, but should finish with something like:

Script: test_list.py.  Passed 40 tests in 69.70 seconds

Finishing up¶

You're set. The one thing to remember is that whenever you want to use this environment in a new terminal window or shell, you need to activate the py37_rdkit_beta conda environment (don't delete it!), set RDBASE, and set your PYTHONPATH:

conda activate py37_rdkit_beta
cd your_local_rdkit_clone  # <- replace this with the real name of the directory
export RDBASE=`pwd`
export PYTHONPATH="$RDBASE"

If you are planning on working with the normal Windows command prompt or powershell, you'd do the equivalent things to set the RDBASE environment variable and the make sure your PYTHONPATH is pointing to the right place.

The recipe¶

Here's the complete recipe:

git clone https://github.com/rdkit/rdkit.git
cd rdkit
export RDBASE=`pwd`
conda create -y -n py37_rdkit_beta python=3.7
conda activate py37_rdkit_beta
conda install -y -c rdkit/label/beta rdkit
cd $CONDA_PREFIX/lib/python3.7/site-packages/rdkit
find . -name '*.pyd' -exec cp --parents \{\} $RDBASE/rdkit \; 
cp Chem/inchi.py $RDBASE/rdkit/Chem 
export PYTHONPATH="$RDBASE"
cd $RDBASE/rdkit
python -c 'from rdkit import Chem;print(Chem.__file__)'