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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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install.py doesn't correctly request pytables #42

Closed ebzheng closed 7 years ago

ebzheng commented 7 years ago

When running the packaged setup.py script ("pip install ." from a fresh Ubuntu LTS 16.04 image with miniconda installed), the script completes successfully, but MAGIC fails to run with the following error:

  File "/home/ubuntu/miniconda3/bin/MAGIC.py", line 8, in <module>
    import magic
  File "/home/ubuntu/miniconda3/lib/python3.6/site-packages/magic/__init__.py", line 2, in <module>
    from . import mg
  File "/home/ubuntu/miniconda3/lib/python3.6/site-packages/magic/mg.py", line 12, in <module>
    import tables
ModuleNotFoundError: No module named 'tables'

This is rectified by installing pytables separately.

This may also underlie the discrepancy referenced in issue #39 (he installs pytables when explicit getting dependencies, but everything else gets properly installed as needed).

pkathail commented 7 years ago

Thanks for catching this, will add pytables as a dependency!