Allow Demography init from provenance with preset pop IDs

[hyanwong]

The last step to allow demographies to be instantiated from provenance entries. We exceptionally allow a demography.Population object to be created with an existing ID, but only if generated when decoding provenance JSON. This ensures that the IDs in the events etc match with what we expect. It's a slight hack in that we check for the error message. The alternative is to pick a different error (?RuntimeError) or make our own bespoke error that can be allowed through in this case.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.23%. Comparing base (7f854ac) to head (dec2a42).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2370   +/-   ##
=======================================
  Coverage   91.23%   91.23%           
=======================================
  Files          20       20           
  Lines       11831    11836    +5     
  Branches     2296     2298    +2     
=======================================
+ Hits        10794    10799    +5     
  Misses        568      568           
  Partials      469      469           

Flag	Coverage Δ
C	91.23% <100.00%> (+<0.01%)	⬆️
python	98.69% <100.00%> (+<0.01%)	⬆️

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[hyanwong]

With this in place, you can plot a demes demography from a tree seq generated by stdpopsim, without having to install stedpopsim, know the model etc., which is neat:

import demesdraw
ts = tskit.load("from_msprime_stdpopsim.trees")

for provenance in ts.provenances():
    try:
        cmd, params = msprime.provenance.parse_provenance(provenance, ts)
        if cmd == "sim_ancestry":
            demesdraw.tubes(params["demography"].to_demes())
    except ValueError
        pass

[jeromekelleher]

I think we need a different way of instantiating Demography objects

[jeromekelleher]

This control flow by exception logic is fragile and distributes the logic of creating Demography objects around different modules. We should add a Demography.fromdict method that does this, and can be tested independently;.

[hyanwong]

I'm returning to some of my open PRs, and realise that this one has an easy fix, because I just found out that you can pass an InitVar parameter to a dataclass. In this case we use it to flag not to worry about making new population IDs in this specific case. I think this is probably the minimally intrusive thing to do.