add better error handling if treetime fails

[anna-parker]

Resolves #1013

Description of proposed changes

Hi, after #1013 it appears that errors in augur (refine) that occur while running treetime are not handled in a clear way in augur, and give a very long and not very understandable error message. This is a small change that will make the errors more understandable.

For example the output of the error described in the issue above will change from

to

Testing

• install augur and treetime in local environment (branch fix/augur_bug has slightly better error messages but will hopefully soon be merged into the master)
• create an Exception in treetime, I added a line in _exp_lt to force and error in this function, as this is where the error arose in the issue above, e.g.

        """
        Parameters
        ----------

         t : float
            time to propagate

        Returns
        --------

         exp_lt : numpy.array
            Array of values exp(lambda(i) * t),
            where (i) - alphabet index (the eigenvalue number).
        """
        log_val = self.mu * t * self.eigenvals
        log_val = np.ones(len(log_val))*750 ##cause an exception
        if any(i > 10 for i in log_val):
            raise ValueError("Error in computing exp(Q * t): Q has positive eigenvalues or the branch length t \n"
                    "is too large. This is most likely caused by incorrect input data. If this error persists \n"
                    "please let us know by filing an issue at: https://github.com/neherlab/treetime/issues")

        return np.exp(log_val)

this can be done with other functions or using data which causes an exception.

• install modified treetime in local environment (pip install .)
• run augur refine on the CLI using data from the tests folder:

augur refine -t tests/functional/refine/tree.nwk -a tests/functional/refine/aligned.fasta --metadata tests/functional/refine/metadata.tsv --timetree --root 'min_dev' --coalescent 'opt' --output-tree augur.tree.nwk --output-node augur.branch_lengths.json --divergence-units 'mutations'

Checklist

• Add a message in CHANGES.md summarizing the changes in this PR. Keep headers and formatting consistent with the rest of the file.

[corneliusroemer]

Very nice, looks like you use Python's error handling how it's supposed to be used. As treetime often errors it's good to handle this!

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 61.74%. Comparing base (e8392b3) to head (f3634b8).
Report is 1265 commits behind head on master.

Files	Patch %	Lines
augur/refine.py	60.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1023      +/-   ##
==========================================
- Coverage   61.75%   61.74%   -0.01%     
==========================================
  Files          52       52              
  Lines        6275     6279       +4     
  Branches     1581     1581              
==========================================
+ Hits         3875     3877       +2     
- Misses       2129     2131       +2     
  Partials      271      271              

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