Conda Install Gensim For Mac

Do not pip install gdal, do not install GDAL inside a virtual-env. Instead, use Conda.

These are my instructions on how to install GDAL using Conda on a Mac. Before we dive in, let me explain why I am writing this guide. GDAL stands for the “Geospatial Data Abstraction Library” and it is released by the Open Source Geospatial Foundation. For Python, the GDAL package is released with a package called osgeo as well. And as it happens, I need both for a project I’m doing. And I want them neatly wrapped up inside a virtual environment.

When you run pip install or conda install, these commands are associated with a particular Python version: pip installs packages in the Python in its same path; conda installs packages in the current active conda environment; So, for example we see that pip install will install to the conda. Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. Target audience is the natural language processing (NLP).

I started by trying to use pip and virtual-env. This obscure how-to (and first post on Medium!) comes to you after hours of googling and trying to debug the errors I encountered along the way. In the end, I shifted gears, tried something new and switched over to Conda. This was the solution to all my problems. OK, except a few, but I fixed those too.

Conda is great because it’s a package manager like pip, but it also manages your virtual environments like virtual-env does. Except it does both way better and it’s a joy to use. Treat yo self and switch to Conda.

I wanted to spare you the trouble I experienced so I wrote up the following instructions.

Environment:

A quick note about the environment I’m working in:

Mac OS 10.12.6 Sierra
Miniconda2 for Python 2 (Conda 4.3.30) info
Python 2.7.14

optional python packages:
Jupyter notebook, installs with $ conda install jupyter
nb_conda, makes Jupyter play nice with Conda, $ conda install nb_conda

If you are working in a different development environment, your mileage may vary.

And now, the instructions that I myself needed hours ago…

How to Install GDAL 🌐 using Conda 🐍 on a Mac 🍎

This tutorial assumes you have Conda already installed and a Conda environment already created. Instructions here and here, respectively.

Step 1: Activate your Conda environment 🚀

Open up Terminal, run this:

For me, [yourEnvironmentName] = geoenv.

(We can deactivate with the command $ source deactivate.)

Step 2: Ok, now we get to install GDAL. 🔧

Still in Terminal, run this command:

Here’s what I got:

Great. As it turns out, for the osgeo subpackage to work, we actually need the dependency jpeg version 8, rather than 9. You can read more about how I came to that conclusion towards the end of this post, under #Diagnosing.

For now, all you need to do is run this:

The “-f” flag forces the install (which is really a downgrade of the the jpeg module).

OK, we should have a working version of GDAL now! Let’s just test it to make sure.

Step 3: Test the installation 🔍

You can do this in the command line or in a Jupyter notebook. Since I want to make sure gdal will work in Jupyter later, I’m going to test there.

To open a new Jupyter Notebook 📙, go back to Terminal, run this command:

This command will open up a new tab in your internet browser with the Jupyter Notebook file viewer. Navigate to the directory where you wish to save your notebook. Now, we want to start a new notebook. Go to the upper righthand corner, click “New”.

Make sure to choose the Conda environment you’ve been working with as the Python Kernel.

Let’s go ahead and test! Run these commands in the notebook.

The help for gdal works, so we’re off to the races.

Success! 🤗

We’ve finally got GDAL installed as well as osgeo. Everything is working (for now). This somewhat lengthy post was a joy to write, as this problem caused me innumerable hours of strife. I hope to save you from the same. Thanks in advance for your claps 👏🏽 Let me know if something needs an edit or clarification. With that, I’m off to explore graphs with networkx!

With ❤︎,

Filip

p.s.

#Motivation for this post

I generally like to use virtual environments on projects to keep things organized. First, I tried to install GDAL inside a python virtual-env which was a huge fail. There are instructions out there how to do that for Windows and Ubuntu, but I couldn’t get it to work for Mac. Virtual-env was more like virtual-enemy. Some folks on StackOverflow suggested to use Conda instead. I ran into a few snags anyways, so I decided to publish these instructions how to Install GDAL using Python/Conda on Mac. Dear reader, I hope this guide saves you some time.

#What am I using GDAL for

I need GDAL for a very particular reason. It’s required for and a dependency of the read_shp() function of the networkx Python module. That function reads in an ESRI shapefile (geospatial data) an converts it into a network/graph object. Obviously, you might need GDAL for something else.

To install, I tried using pip install gdal inside a Python virtual environment (a.k.a. virtual-env) at first. That failed. I guess you could say it was only a pip dream, sigh. Or maybe it had something to do with having QGIS via Kyngchaos installed. That distribution includes GDAL not as a Python package, but as a Framework.

Anyways, the bottom line is that I still needed GDAL to work inside a Python virtual environment.

#Diagnosing the Conda install issue:

It was not possible for me to get GDAL installed inside a virtual-env using pip. That’s why I switched to Conda.

When running the install in Conda, I ran into a few issues. Simply running the read_shp function from networkx was giving me a generic error, much like it was in virtual-env.

ImportError: read_shp requires OGR:

In the screenshot you can see that the code requires from osgeo import ogr which is actually included as part of the GDAL module.

So when we try to import gdal, we can see what’s actually happening:

Library not loaded: @rpath/libjpeg.8.dylib

The jpeg8 library is not loading. To investigate, we can check what packages conda has installed:$ conda list

Moreover, when I uninstall and reinstall only gdal, it actually becomes evident that gdal itself updates jpeg to version 9, only to break later.

The fix is to simply downgrade jpeg 9 to jpeg 8 after installing gdal. You can find the recipe for that in Step 3 of the #Instructions above. Thanks!

Sources I used:

egayer’s comment in this thread on the gdal GitHub
I’m not including my crazy, exhaustive searches for anything related to “pip install GDAL” or “GDAL python install mac virtual-env” in this list. Bless your heart if you try to go that path.