ecDNA simulator

[mattjones315]

This PR implements a special simulator described in Hung*, Jones*, Wong*, Curtis* et al.

It extends the basic BirthDeathFitnessSimulator implemented Cassiopeia to simulate copy-numbers of extrachromosomal DNA (ecDNA) on top of the phylogeny. An arbitrary number of particles can be simulated according to various selection and co-segregation parameters.

It also makes a few changes to the BirthDeathFitnessSimulator to support passing in an intermediate tree. This is especially relevant when users would like to simulate experiments with different phases - for example, drug-on and drug-off cases.

Another miscellaneous change is the support for passing specific lineage_profiles for tree plotting.

[codecov]

Codecov Report

Attention: Patch coverage is 79.18782% with 41 lines in your changes are missing coverage. Please review.

Project coverage is 79.77%. Comparing base (41dbff8) to head (8bbcd10).

❗ Current head 8bbcd10 differs from pull request most recent head fca94b2. Consider uploading reports for the commit fca94b2 to get more accurate results

Files	Patch %	Lines
cassiopeia/simulator/ecDNABirthDeathSimulator.py	77.14%	32 Missing ⚠️
cassiopeia/simulator/BirthDeathFitnessSimulator.py	83.33%	9 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #240      +/-   ##
==========================================
- Coverage   79.84%   79.77%   -0.08%     
==========================================
  Files          90       91       +1     
  Lines        8173     8347     +174     
==========================================
+ Hits         6526     6659     +133     
- Misses       1647     1688      +41     

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[mattjones315]

Hey @colganwi --

I know that this PR is very much outside of the normal scope of Cassiopeia, but there are a few items here that are relevant to the BirthDeathSimulator. Requesting your review here just in case you want to see if any of my suggested changes would be non-optimal with how you are using Cassiopeia.

[colganwi]

Looks good to me. Just added a few comments.

[mattjones315]

Thanks so much for the review, @colganwi -- I believe I've addressed your comments and it looks like this is ready to be merged in!