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Virtual root in trees #1704

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Merged
merged 8 commits into from
Oct 18, 2021
Merged

Virtual root in trees #1704

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62e829a
Add virtual_root to tree arrays
jeromekelleher Sep 15, 2021
0a98866
Update drawing samples with arbitrary node reordering
jeromekelleher Oct 9, 2021
a0af17b
Refactor node traversal tests
jeromekelleher Oct 9, 2021
364a009
Revert changes to timeasc ordering.
jeromekelleher Oct 12, 2021
07faaf2
Numpy versions of timeasc and timedesc
jeromekelleher Oct 12, 2021
d670511
Count edges in the tree.
jeromekelleher Oct 12, 2021
edbaaca
Add tsk_tree_size_bound to enable safe allocations
jeromekelleher Oct 13, 2021
a882a5d
Document orderings
jeromekelleher Oct 14, 2021
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3 changes: 3 additions & 0 deletions c/CHANGELOG.rst
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Expand Up @@ -14,6 +14,7 @@

- The previously deprecated option ``TSK_SAMPLE_COUNTS`` has been removed. (:user:`benjeffery`, :issue:`1744`, :pr:`1761`).

- FIXME breaking changes for tree API and virtual root

**Features**

Expand All @@ -37,6 +38,8 @@
tree sequence. This is then used to generate an error if ``time_units`` is ``uncalibrated`` when
using the branch lengths in statistics. (:user:`benjeffery`, :issue:`1644`, :pr:`1760`)

- FIXME add features for virtual root, num_edges, stack allocation size etc

**Fixes**

----------------------
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