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Correctly decode tszip cols #213

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merged 2 commits into from
Oct 24, 2024
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benjeffery
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@benjeffery benjeffery commented Oct 23, 2024

Fixes #190
Fixed other odd columns too and added tests for all columns.

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edges.png

edges.png

mutations-popup.png

mutations-popup.png

mutations.png

mutations.png

nodes.png

nodes.png

out_edges.png

out_edges.png

out_mutations.png

out_mutations.png

out_nodes.png

out_nodes.png

overview.png

overview.png

tables.png

tables.png

trees.png

trees.png

github-actions bot pushed a commit that referenced this pull request Oct 23, 2024
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coveralls commented Oct 23, 2024

Pull Request Test Coverage Report for Build 11497469628

Details

  • 14 of 14 (100.0%) changed or added relevant lines in 1 file are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.08%) to 90.369%

Totals Coverage Status
Change from base Build 11486973043: 0.08%
Covered Lines: 760
Relevant Lines: 841

💛 - Coveralls

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@jeromekelleher jeromekelleher left a comment

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I don't understand why we need to do this tbh - shouldn't we let tszip handle this? If we do

ts = tszip.load(tsbrowse_path)
root = zarr.open(tsbrowse_path)
# e.g.
edges_df = {
     "left": ts.edges_left,
     "right": ts.edges_right, 
      ...
     "extra_col_1": root["edges"]["extra_col_1"]
 } 

then we let tszip deal with these details, and we don't become depending on an implementation detail of tszip?

github-actions bot pushed a commit that referenced this pull request Oct 24, 2024
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Minor perf issue

@@ -54,44 +43,35 @@ def __init__(self, tsbrowse_path):
"migrations",
"provenances",
]:
ts_table = getattr(self.ts.tables, table_name)
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That's generating a fresh copy of the tables each time. Get a reference to the tables before the loop body

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Fixed!

github-actions bot pushed a commit that referenced this pull request Oct 24, 2024
@benjeffery benjeffery merged commit 0452a25 into tskit-dev:main Oct 24, 2024
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edges table viewer: incorrect right coordinate displayed?
3 participants