Don't sort individuals by default #1789
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This is tricky - let's have a chat about it tomorrow, see if we can figure out a clean path forward? |
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@@ Coverage Diff @@
## main #1789 +/- ##
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+ Coverage 93.41% 93.43% +0.01%
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Files 27 27
Lines 24756 24716 -40
Branches 1095 1095
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- Hits 23127 23093 -34
+ Misses 1594 1588 -6
Partials 35 35
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@jeromekelleher I think this is ready, although do we need to check integrity before we sort? |
c/tskit/tables.h
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| @return Return 0 on success or a negative value on failure. | ||
| */ | ||
| int tsk_table_collection_sort( | ||
| tsk_table_collection_t *self, const tsk_bookmark_t *start, tsk_flags_t options); | ||
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| /** | ||
| @brief Sorts the indivdual table in this collection. |
python/tskit/tables.py
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| @@ -3165,6 +3164,15 @@ def sort(self, edge_start=0): | |||
| self._ll_tables.sort(edge_start) | |||
| # TODO add provenance | |||
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| def sort_individuals(self, edge_start=0): | |||
c/tskit/tables.c
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| @@ -6379,7 +6380,7 @@ tsk_table_sorter_run(tsk_table_sorter_t *self, const tsk_bookmark_t *start) | |||
| goto out; | |||
| } | |||
| } | |||
| if (!skip_individuals) { | |||
| if (!skip_individuals && self->sort_individuals) { | |||
There was a problem hiding this comment.
Comparisons to NULL are usually explicit, i.e., && (self->sort_individuals != NULL)
Reading this I assumed that self->sort_individuals is a boolean
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We should update the CHANGELOGs in case we forget. |
4th times the charm.... Did you see the question about checking integrity before sort, I think as it stands you could make python segfault with this. |
I haven't thought about it, but the answer is in the question if this is true! |
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@jerome all fixed up and changlog added, assuming CI is now happy this is good to go. |
Part of #1774
I started ripping loads of code out, then realised that maybe this is a less destructive way to do this. (Commented out code will return when the individual sort method uses it.)
WIP for feedback, next is removing the requirement from checks