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Change keep/del intervals to in-place #372

Merged
merged 1 commit into from
Sep 30, 2019
Merged

Change keep/del intervals to in-place #372

merged 1 commit into from
Sep 30, 2019
+190 −102

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hyanwong
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And add equivalent tree seq methods. Also alter documentation as appropriate.

Fixes #371

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codecov bot commented Sep 27, 2019 •
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Codecov Report

Merging #372 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #372      +/-   ##
==========================================
+ Coverage   86.51%   86.51%   +<.01%     
==========================================
  Files          20       20              
  Lines       14056    14064       +8     
  Branches     2749     2750       +1     
==========================================
+ Hits        12160    12168       +8     
  Misses        977      977              
  Partials      919      919
Flag Coverage Δ
#c_tests 87.61% <100%> (ø) ⬆️
#python_c_tests 90.37% <100%> (+0.01%) ⬆️
#python_tests 99.25% <100%> (ø) ⬆️
Impacted Files Coverage Δ
python/tskit/tables.py 99.78% <100%> (ø) ⬆️
python/tskit/trees.py 98.69% <100%> (ø) ⬆️

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@hyanwong hyanwong force-pushed the keep-delete-intervals-in-place branch 3 times, most recently from 7e0178e to f1b2f74 Compare September 27, 2019 10:25
@hyanwong hyanwong mentioned this pull request Sep 27, 2019
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@hyanwong hyanwong force-pushed the keep-delete-intervals-in-place branch from fe7a158 to 38e9a6f Compare September 27, 2019 15:18
@hyanwong hyanwong mentioned this pull request Sep 27, 2019
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@hyanwong hyanwong force-pushed the keep-delete-intervals-in-place branch 3 times, most recently from 01ee82d to 67d22ec Compare September 27, 2019 21:52
jeromekelleher
jeromekelleher reviewed Sep 30, 2019
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Looks good, thanks. Minor comments above.

python/tests/test_topology.py Outdated Show resolved Hide resolved
python/tskit/tables.py Outdated Show resolved Hide resolved
@hyanwong hyanwong force-pushed the keep-delete-intervals-in-place branch from 67d22ec to 9f697bd Compare September 30, 2019 09:12
@hyanwong
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Both comments done. This is now 4 commits. Do you want them squashed?

@jeromekelleher
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Both comments done. This is now 4 commits. Do you want them squashed?

Please -- keeping simple changes like this atomic is helpful when reviewing the history.

@hyanwong
Change keep/del intervals to in-place
4a17e19 
And add equivalent tree seq methods. Also alter documentation as appropriate.

Different provenance for delete vs keep

Documentation in TableCollection points to ts doc

Simplify tables equal test
@hyanwong hyanwong force-pushed the keep-delete-intervals-in-place branch from 897c015 to 4a17e19 Compare September 30, 2019 09:37
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Please -- keeping simple changes like this atomic is helpful when reviewing the history.

Done

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merging, thanks.

@jeromekelleher jeromekelleher merged commit 45911fe into tskit-dev:master Sep 30, 2019
@hyanwong hyanwong deleted the keep-delete-intervals-in-place branch October 1, 2019 22:13
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Successfully merging this pull request may close these issues.

Should table editing functions make copies or edit in-place?
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@hyanwong @jeromekelleher