Decouple SampleData from AncestorData #779
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## main #779 +/- ##
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- Coverage 93.33% 93.30% -0.03%
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Branches 991 990 -1
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- Hits 5209 5198 -11
Misses 246 246
- Partials 126 127 +1
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Hmm, tests are passing locally. Looking into it. |
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Not sure why docs are failing either. |
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Rebased onto #780 to fix the Ci issues. Should be good to go now. |
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tsinfer/formats.py
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| @@ -2252,7 +2242,7 @@ def __eq__(self, other): | |||
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| class AncestorData(DataContainer): | |||
| """ | |||
| AncestorData(sample_data, *, path=None, num_flush_threads=0, compressor=None, \ | |||
| AncestorData(position, *, path=None, num_flush_threads=0, compressor=None, \ | |||
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Missing sequence_length here
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Can you take a look through please @hyanwong? |
| @@ -819,7 +823,9 @@ def sim_true_and_inferred_ancestors(args): | |||
| sample_data = generate_samples(ts, args.error) | |||
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| inferred_anc = tsinfer.generate_ancestors(sample_data, engine=args.engine) | |||
| true_anc = tsinfer.AncestorData(sample_data) | |||
| true_anc = tsinfer.AncestorData( | |||
| sample_data.sites_position, sample_data.sequence_length | |||
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Trivial, but if you want to shorten sample_data to sd (which we do sometimes anyway in the tests), it will make all this fit on a single line. There are a whole set of other examples like this too.
| def match_ancestors_ancestors_unfinalised(self, path=None): | ||
| with tsinfer.SampleData(sequence_length=2) as sample_data: | ||
| sample_data.add_site(1, genotypes=[0, 1, 1, 0], alleles=["G", "C"]) | ||
| with tsinfer.AncestorData(sample_data, path=path) as ancestor_data: | ||
| with tsinfer.AncestorData( |
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Ditto, sd rather than sample_data might make it all more readable (fewer lines)
tsinfer/formats.py
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| self._num_alleles = self.sample_data.num_alleles() | ||
| position = self.sample_data.sites_position[:] | ||
| self.data.attrs["sequence_length"] = sequence_length | ||
| if self.sequence_length == 0: |
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Should this be if self.sequence_length <= 0?
| with tempfile.TemporaryDirectory(prefix="tsinf_inference_test") as tempdir: | ||
| filename = os.path.join(tempdir, "samples.tmp") | ||
| self.make_ancestor_data_unfinalised(filename) | ||
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| def test_match_ancestors_ancestors(self): | ||
| self.match_ancestors_ancestors_unfinalised() |
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Do we test match_ancestors_ancestors_unfinalised with the path argument anywhere?
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I thought this best done as a separate PR from the sgkit ancestors work.
This ended up a bit more invasive than I had hoped. It looks like
ancestor_data.sequence_lengthis used in quite a few places - mostly for making tree sequence tables of the ancestors, so I've also passed that through too, thought it might be possible to usemax(position)? The main changes are ingenerate_ancestorsandAncestorsGeneratoras theAncestorDatacan no longer be made ahead of time, and has to be made once the sites are known.