Add cython example #3194
Merged
Add cython example #3194
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Member
Author
|
Mostly cribbed from https://github.com/terhorst/tskit_cython_example with a few modernisations and using the local tskit. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3194 +/- ##
=======================================
Coverage 89.62% 89.62%
=======================================
Files 28 28
Lines 31969 31969
Branches 5873 5873
=======================================
Hits 28653 28653
Misses 1886 1886
Partials 1430 1430
Flags with carried forward coverage won't be shown. Click here to find out more. 🚀 New features to boost your workflow:
|
Member
jeromekelleher
left a comment
jeromekelleher
left a comment
There was a problem hiding this comment.
Cool! Spotted a few things
| lwtc = LightweightTableCollection() | ||
| lwtc.fromdict(pyts.dump_tables().asdict()) | ||
| cdef tsk_treeseq_t ts | ||
| cdef int err = tsk_table_collection_build_index(lwtc.tables, 0) # this recently became necessary? |
Member
There was a problem hiding this comment.
Why do we need to build an index if we're getting a TreeSequence in as parameter? The indexes should be there already
| check_tsk_error(ret) | ||
|
|
||
| print("Iterate forwards") | ||
| cdef int iter = tsk_tree_first(&tree) |
Member
There was a problem hiding this comment.
iter might not be a great name, seems to hav some meaning in cytyhon?
| check_tsk_error(iter) | ||
|
|
||
| print("Iterate backwards") | ||
| iter = tsk = tsk_tree_last(&tree) |
benjeffery
force-pushed
the
cython-example
branch
from
7e00007 to
a89df54
Compare
Member
Author
|
Thanks - fixed up! |
jeromekelleher
approved these changes
Jun 8, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #1124
Fixes #1018