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Refactor low-level code #830

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Merged
jeromekelleher merged 34 commits into from
Mar 27, 2026
Merged

Refactor low-level code #830

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cb44642
Initial rough work on getting ancstor_matcher decoupled
jeromekelleher Apr 13, 2023
df2b3db
Port tests to new layout
jeromekelleher Mar 26, 2026
74d8f9f
Fixup lint
jeromekelleher Mar 26, 2026
48b0267
Fix build issue with packaging
jeromekelleher Mar 26, 2026
e0fb690
Add matching fixture tests for AncestorMatcher2 transition
jeromekelleher Mar 26, 2026
3cbd349
Make AncestorMatcher2 API-compatible with AncestorMatcher
jeromekelleher Mar 26, 2026
0bdeeef
Tests on windows
jeromekelleher Mar 26, 2026
a8e0012
Remove dead file
jeromekelleher Mar 26, 2026
0e165be
Add TSINFER_MATCHER env var to switch between AncestorMatcher and Anc…
jeromekelleher Mar 26, 2026
8e98012
Fix missing fstrings
jeromekelleher Mar 26, 2026
29a4039
Add tsinfer-topology fixture tests to test_lshmm
jeromekelleher Mar 27, 2026
97ac289
Add C Matcher2 comparison path for tsinfer-topology tests
jeromekelleher Mar 27, 2026
ab9e466
Add tsinfer-topology fixtures to C test suite
jeromekelleher Mar 27, 2026
135d238
Fix uninitialised sites arrays in matcher_indexes
jeromekelleher Mar 27, 2026
481145f
Add a plan with some analysis on matching implementation
jeromekelleher Mar 27, 2026
b1ac387
Add exact expected match paths to C fixture tests
jeromekelleher Mar 27, 2026
1590a9b
Unify matcher path coordinates to genomic positions
jeromekelleher Mar 27, 2026
49f7bfe
Add memory diagnostics: RSS after Matcher, per-group, cache budget
jeromekelleher Mar 27, 2026
d7d5476
Pass num_alleles through to MatcherIndexes on construction
jeromekelleher Mar 27, 2026
6cab450
Fix OOM: lazy reader registered with zero chunk_bytes bypassing cache…
jeromekelleher Mar 27, 2026
b99beac
Require functions at the top.
jeromekelleher Mar 27, 2026
9d98abd
Add periodic memory diagnostics: GC, tracemalloc, RSS within groups
jeromekelleher Mar 27, 2026
e599fda
Fix memory leak: delete completed futures in Matcher.match()
jeromekelleher Mar 27, 2026
69555e8
Turn off tracemalloc
jeromekelleher Mar 27, 2026
6a93e1b
Add informative error for multiple mutations per site in matcher_indexes
jeromekelleher Mar 27, 2026
b032846
Fix memory leak in find_path: use Py_BuildValue N format to transfer …
jeromekelleher Mar 27, 2026
2228934
Add a plan to remove the legacyh matcher code.
jeromekelleher Mar 27, 2026
a6da166
Tidy up tests
jeromekelleher Mar 27, 2026
e272b1e
Port likelihood_threshold and weight_by_n to AncestorMatcher2
jeromekelleher Mar 27, 2026
e2aee50
Enable C engine comparison in all test_lshmm fixture tests
jeromekelleher Mar 27, 2026
29699c6
Use atomic block allocator for AncestorMatcher2 total_memory
jeromekelleher Mar 27, 2026
6d423f5
Use tsi_blkalloc in matcher_indexes_t
jeromekelleher Mar 27, 2026
c53d30c
Fix C tests: pass DBL_MIN as likelihood_threshold instead of old prec…
jeromekelleher Mar 27, 2026
92c35ac
Fix windows tests
jeromekelleher Mar 27, 2026
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3 changes: 2 additions & 1 deletion .github/workflows/tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,11 +28,12 @@ jobs:

test:
name: Python
uses: tskit-dev/.github/.github/workflows/python-tests.yml@v15
uses: tskit-dev/.github/.github/workflows/python-tests.yml@v16
with:
os: ${{ matrix.os }}
python-version: ${{ matrix.python }}
coverage-directory: tsinfer
fix-lwt-symlink: "true"
secrets: inherit
strategy:
matrix:
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1 change: 1 addition & 0 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
include lwt_interface/*.h
include lib/*.h
include git-submodules/tskit/c/*.h
include git-submodules/tskit/c/tskit/*.h
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