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tskit-dev / pyslim

Tools for dealing with tree sequences coming to and from SLiM.
MIT License
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use metadata vector #299

Closed petrelharp closed 2 years ago

petrelharp commented 2 years ago

Over in https://github.com/popsim-consortium/stdpopsim/issues/1334 we found out that convert_alleles is taking way too long. I had a try at changing it to use metadata_vector (in this PR); however, there's no appreciable change in speed. (However, note that at least I noticed that the complicated stuff I was doing had no effect - either a bug or SLiM does always put the most recent mutation first.)

bhaller commented 2 years ago

...either a bug or SLiM does always put the most recent mutation first.)

I'm not sure whether that is guaranteed. It might be different for new mutations added by SLiM itself versus those added by addNewMutation() / addNewDrawnMutation(), and I'm not sure how removeMutations() might affect things. This could of course be checked, but I don't have time to get into it right at the moment. Might be easiest to determine empirically, rather than by looking at the code. :-> But then of course there is also the question of whether SLiM guarantees any particular behavior, or whether whatever it does right now could change in the future without a "breach of contract". I would lean towards the latter, especially since neither of us actually knows what the "contract" might be, and it might be inconsistent, and so forth. I don't think there's any "contract" in this area.

petrelharp commented 2 years ago

Codecov hasn't run for some reason (I've just added the action to github), but I've run it locally, and it looks good.

codecov-commenter commented 2 years ago

Codecov Report

Merging #299 (f3cd117) into main (9bc27db) will increase coverage by 0.15%. The diff coverage is 95.77%.

@@            Coverage Diff             @@
##             main     #299      +/-   ##
==========================================
+ Coverage   95.44%   95.59%   +0.15%     
==========================================
  Files           8        8              
  Lines         724      613     -111     
  Branches      145      127      -18     
==========================================
- Hits          691      586     -105     
+ Misses         22       18       -4     
+ Partials       11        9       -2
Impacted Files Coverage Δ
pyslim/provenance.py 83.78% <ø> (-4.73%) :arrow_down:
pyslim/slim_metadata.py 96.17% <93.80%> (-3.83%) :arrow_down:
pyslim/methods.py 97.39% <96.41%> (-2.61%) :arrow_down:
pyslim/slim_tree_sequence.py 98.11% <97.29%> (+3.77%) :arrow_up:
pyslim/_version.py 100.00% <100.00%> (ø)
pyslim/spatial.py 87.23% <100.00%> (-12.77%) :arrow_down:
pyslim/util.py 100.00% <100.00%> (ø)

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