pip/conda dependency version constraints not guaranteed in all environments

[victorlin]

Note

This isn't an issue with Augur. It's really about the interaction within or between Python package managers, e.g. conda and pip, but I couldn't find a good external issue describing this behavior.

Augur defines dependency version constraints in setup.py and Bioconda recipe. However, there's been cases of users ending up with environments that don't follow these constraints:

• jsonschema v4 issues - this happens with conda install augur followed by pip install <something-that-depends-on-jsonschema>.
• @genehack's pains when using Augur in seasonal-cov. Not sure how this happened since all packages seem to be installed by conda, but somehow it happened.