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Make dump tables operations const. #1337

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Merged
merged 1 commit into from
May 5, 2021
Merged

Make dump tables operations const. #1337

merged 1 commit into from
May 5, 2021

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@molpopgen
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@molpopgen molpopgen commented May 3, 2021 •
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Fixes #1327

PR Checklist:

  • Tests that fully cover new/changed functionality.
  • Documentation including tutorial content if appropriate.
  • Changelogs, if there are API changes.

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codecov bot commented May 3, 2021 •
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Codecov Report

Merging #1337 (6e906bc) into main (cf38edb) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

❗ Current head 6e906bc differs from pull request most recent head 6760f6e. Consider uploading reports for the commit 6760f6e to get more accurate results
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@@            Coverage Diff             @@
##             main    #1337      +/-   ##
==========================================
- Coverage   93.85%   93.83%   -0.02%     
==========================================
  Files          26       26              
  Lines       22349    22344       -5     
  Branches     1060     1060              
==========================================
- Hits        20975    20967       -8     
- Misses       1340     1343       +3     
  Partials       34       34
Flag Coverage Δ
c-tests 92.41% <100.00%> (-0.04%) ⬇️
lwt-tests 92.97% <ø> (ø)
python-c-tests 95.19% <ø> (ø)
python-tests 98.80% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
c/tskit/tables.c 90.80% <100.00%> (-0.06%) ⬇️
c/tskit/trees.c 94.87% <100.00%> (ø)

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@jeromekelleher
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jeromekelleher commented May 4, 2021 •
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Looks great, thanks for this @molpopgen. I'd be inclined to do a "hard break" here by removing the TSK_NO_BUILD_INDEXES flag and not adding the new TSK_BUILD_INDEXES_IF_ABSENT. The old behaviour is just plain weird I think, and the only code we're likely to break is the test suite (which we can fix by calling build_indexes after load, if we need to). I'd see it as a pre-1.0 opportunity to clean things up a bit.

What do you think?

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benjeffery commented May 4, 2021

What do you think?

I know I originally suggested the flag, as a way to avoid any breakage, but now thinking about it I think it will be such a rare thing that it isn't worth the complexity.

@molpopgen
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molpopgen commented May 4, 2021

Sounds good. I'll undo the new flag, remove the old, etc..

jeromekelleher
jeromekelleher approved these changes May 4, 2021
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Looks great, thanks @molpopgen. Some minor tweaks to the tests and we're good to merge.

We should also update the CHANGELOG, since this is an API and semantics breaking change.

c/tests/test_tables.c Outdated
unlink(_tmp_file_name);
errno = 0;

/* Trying to dump without first sorting fails */
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@jeromekelleher jeromekelleher May 4, 2021

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We should be able to dump and load the unsorted tables without problems. Can just change the test to asserting ret is 0.

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@molpopgen molpopgen May 4, 2021

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I think this is taken care of.

jeromekelleher
jeromekelleher reviewed May 5, 2021
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c/tests/test_tables.c Outdated
/* Trying to dump without first sorting fails */
ret = tsk_table_collection_dump(&t1, _tmp_file_name, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME);
/* ret = tsk_table_collection_dump(&t1, _tmp_file_name, 0); */
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stray comments here

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jeromekelleher commented May 5, 2021

Looks great @molpopgen - just need to delete a few stray comments and squash

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Make dump tables operations const.
6760f6e 
* API/behaviour change: remove TSK_NO_BUILD_INDEXES
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molpopgen commented May 5, 2021

@jeromekelleher -- I think this is ready. Go ahead and merge!

@mergify mergify bot merged commit 495f8df into tskit-dev:main May 5, 2021
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benjeffery commented May 5, 2021

Sorry, meant to check this over earlier, but LGTM too! Thanks @molpopgen

@castedo castedo mentioned this pull request May 15, 2021
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@jeromekelleher jeromekelleher jeromekelleher approved these changes

@benjeffery benjeffery Awaiting requested review from benjeffery

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Semantics for table/treeseq "dump" functions.

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@molpopgen @jeromekelleher @benjeffery