Enable assignment & visualisation with partial query graphs

[nickjcroucher]

To enable full database querying with beebop:

• This workflow saves a partial query graph after assignment, along with a list of the sequences in the network components containing queries
• This enables visusaliation of only the clusters that contain queries, rather than the full database
• A flag is added to enable distances to be recalculated for tree generation, rather than read from the file (question: would it be useful to have an option in which we sparsified the pairwise distance matrix to only include within-cluster distances?)
• I update the CI tests to allow testing of the beebop workflow
• This revealed a problem with the lineage assignment C++ code, which I think should now be resolved

[johnlees]

@nickjcroucher is this ready for review? I feel we should release and fix the conda builds as the dict bug keeps coming up

[nickjcroucher]

Yes! Sorry, I was still making some fixes with @absternator yesterday, but it should now be working