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Install and Import MDAnalysis on Google Colaboratory for Python? Problems

I'm trying to install and import MDAnalysis and MDAnalysisTests libraries on Google Colaboratory, I've tried three ways but nothing works:

  1. Using default: !pip install library
!pip install MDAnalysis

But I get:

Collecting MDAnalysis
  Using cached https://files.pythonhosted.org/packages/9e/19/1d32ded1891605facf6faf6e0de4ff6bd33db3f7983d84cfc10074363990/MDAnalysis-1.0.1.tar.gz
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I read that this kind of error is related to a lack of a complementary library or something, but I have no idea where find more information about, so I was hoping that, maybe someone in this forum knows if MDAnalysis requeries something specific. I don´t know what is egg_info, searching I found an example here with the text #egg= in the code, but I talk more about of this option in my last try.

  1. Using default: !apt-get -qq install -y library
!apt-get -qq install -y MDAnalysis

Output:

E: Unable to locate package MDAnalysis

Neither works.

  1. From GitHub

In a preview question I discovery that I can import libraries from GitHub! Awesome! (to be honest I didn´t understand at all the syntaxis), so I looked for the MDAnalysis GitHub respository and I wrote the next code:

!pip install git+https://github.com/MDAnalysis/mdanalysis.git

Output:

Collecting git+https://github.com/MDAnalysis/mdanalysis.git
  Cloning https://github.com/MDAnalysis/mdanalysis.git to /tmp/pip-req-build-4e7svv83
  Running command git clone -q https://github.com/MDAnalysis/mdanalysis.git /tmp/pip-req-build-4e7svv83
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I found variants with git+git:, git+ssh: but didn't work.

Is this a specific problem of MDAnalysis to work on Colab? or is something wrong in the code? I even tried changing "MDAnalysis" by "mdanalysis". I was following the Colab's guide to install and preview questions on this forum, but I haven´t results. Thanks for read.

Solution

  • Since MDAnalysis 2.0.0, you can directly install MDAnalysis in Colab with pip

    !pip install MDAnalysis

    See the example Colab notebook mda_colab_install.ipynb for a demonstration where I install MDAnalysis 2.1.0 together with the tests and the MDAnalysisData package (for example data).