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Add support for reference sequences #59

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Merged
merged 1 commit into from
Jan 26, 2022
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benjeffery
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@benjeffery benjeffery commented Jan 25, 2022

It#s not very pretty, but that will have to wait for the refactor.

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Codecov Report

Merging #59 (41f35ac) into main (55bc8c4) will increase coverage by 0.05%.
The diff coverage is 100.00%.

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@@            Coverage Diff             @@
##             main      #59      +/-   ##
==========================================
+ Coverage   97.70%   97.76%   +0.05%     
==========================================
  Files           6        6              
  Lines         305      313       +8     
  Branches       55       62       +7     
==========================================
+ Hits          298      306       +8     
  Misses          5        5              
  Partials        2        2              
Impacted Files Coverage Δ
tszip/cli.py 100.00% <100.00%> (ø)
tszip/compression.py 98.90% <100.00%> (+0.01%) ⬆️

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@jeromekelleher jeromekelleher left a comment

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Looks good, ugly is the right approach for now.

Can you verify that verify actually verifies the reference sequence stuff? I suspect this was written before the assert_equals methods for tables and they may not be getting checked.

# NOTE: it's unclear whether we'll want to have this set at the same time as
# 'data', but it's useful to have something in all columns for now.
tables.reference_sequence.url = "http://example.com/a_reference"
self.verify(tables.tree_sequence())
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I assume verify calls tables.assert_equals() somewhere along the line? Otherwise we won't actually be testing much here I think.

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I have verified that verify actually verifies. I changed to use assert_equals anyway as it gives better errors.

@mergify mergify bot merged commit c4acfa2 into tskit-dev:main Jan 26, 2022
@benjeffery benjeffery deleted the ref_seq branch January 26, 2022 11:49
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3 participants