Skip to content

Efficient metadata #658

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bhaller merged 7 commits into from
Aug 15, 2026
Merged

Efficient metadata #658

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
36d89fe
draft fix for metadata inefficiency
bhaller Aug 14, 2026
1a1214a
fixup of python recipe
petrelharp Aug 14, 2026
d6def05
bug fixup
petrelharp Aug 15, 2026
1321d0d
Merge pull request #659 from petrelharp/efficient_metadata
bhaller Aug 15, 2026
316e7a0
final (?) revisions
bhaller Aug 15, 2026
37054fe
add newlines since they fit
bhaller Aug 15, 2026
0b1dd8b
remove semicolons, sigh
bhaller Aug 15, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion .../recipes/Recipe 18.10 - Adding a neutral burn-in after simulation with recapitation II.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,11 @@

# Calculate tree heights, giving uncoalesced sites the maximum time
def tree_heights(ts):
uncoalesced_height = ts.metadata['SLiM']['tick']
heights = np.zeros(ts.num_trees + 1)
for tree in ts.trees():
if tree.num_roots > 1: # not fully coalesced
heights[tree.index] = ts.metadata['SLiM']['tick']
heights[tree.index] = uncoalesced_height

@petrelharp petrelharp Aug 14, 2026

Copy link
Copy Markdown
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is not necessary any more! I see that below we recapitate, implying that this tree sequence has all the input roots, and so the heights of all the roots should all be equal to the tick value (+/- 1) already!

else:
children = tree.children(tree.root)
real_root = tree.root if len(children) > 1 else children[0]
Expand Down
3 changes: 2 additions & 1 deletion .../Recipes/Recipe 18.10 - Adding a neutral burn-in after simulation with recapitation II.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,11 @@

# Calculate tree heights, giving uncoalesced sites the maximum time
def tree_heights(ts):
uncoalesced_height = ts.metadata['SLiM']['tick']
heights = np.zeros(ts.num_trees + 1)
for tree in ts.trees():
if tree.num_roots > 1: # not fully coalesced
heights[tree.index] = ts.metadata['SLiM']['tick']
heights[tree.index] = uncoalesced_height
else:
children = tree.children(tree.root)
real_root = tree.root if len(children) > 1 else children[0]
Expand Down
1 change: 1 addition & 0 deletions VERSIONS
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -204,6 +204,7 @@ multitrait branch:
add a built-in "Multispecies Multitrait Phenotype ~ Time" plot for phenotype ~ time, with one line per trait across all species
add a built-in "Phenotype ~ Time" plot for phenotype ~ time, focusing on a single user-selected trait across subpopulations
clean up the way pedigree IDs get recorded, for better efficiency and parallelization
fix recipe 18.10 to reduce metadata accesses (see discussion at https://github.com/tskit-dev/tskit/issues/3472#issuecomment-5210734749)


version 5.2 (Eidos version 4.2):
Expand Down
Loading