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SBRG / cobradb

COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.
http://bigg.ucsd.edu
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setup.py install_packages is broken #53

Open Schmoho opened 2 years ago

Schmoho commented 2 years ago

The version ranges are not specific enough, running setup.py on a blank conda env with just python 3.7 installed yields a dependency resolution error because a jupyter version > 6 is installed that requires tornado version > 6, but 4.5.3 is installed earlier.

Furthermore, even after fixating all requirements accordingly, there are requirements missing, in particular cython.

More generally, this project would benefit greatly from a pip freeze requirements.txt file which is suitable for building.

Since BiGG no longer provides SQL dumps, building cobradb has become prerequisite for acquiring a dump, and it is unfortunate that this is not easily accomplished.

Schmoho commented 2 years ago

It seems like this requirements file is at least suitable for running the setup and load_db scripts.

requirements.txt