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Initial numba module #3225

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Initial numba module #3225

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1cd6ea9
Move example tree sequences to tsutil
benjeffery Jun 18, 2025
6b5bd0d
Initial numba edge diffs
benjeffery Jun 18, 2025
407eef1
Fix CI, add extra test
benjeffery Jun 18, 2025
54e4964
Refactor to remove iteration
benjeffery Jun 23, 2025
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1 change: 1 addition & 0 deletions python/requirements/CI-complete/requirements.txt
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Expand Up @@ -6,6 +6,7 @@ lshmm==0.0.8
msgpack==1.1.0
msprime==1.3.3
networkx==3.2.1
numba==0.61.2
portion==2.6.0
pytest==8.3.5
pytest-cov==6.0.0
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3 changes: 2 additions & 1 deletion python/requirements/CI-tests-pip/requirements.txt
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Expand Up @@ -11,4 +11,5 @@ networkx==3.2.1
msgpack==1.1.0
newick==1.10.0
kastore==0.3.3
jsonschema==4.23.0
jsonschema==4.23.0
numba>=0.60.0
2 changes: 1 addition & 1 deletion python/tests/test_balance_metrics.py
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Expand Up @@ -29,7 +29,7 @@

import tests
import tskit
from tests.test_highlevel import get_example_tree_sequences
from tests.tsutil import get_example_tree_sequences

# ↑ See https://github.com/tskit-dev/tskit/issues/1804 for when
# we can remove this.
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2 changes: 1 addition & 1 deletion python/tests/test_divmat.py
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Expand Up @@ -32,7 +32,7 @@

import tskit
from tests import tsutil
from tests.test_highlevel import get_example_tree_sequences
from tests.tsutil import get_example_tree_sequences

# ↑ See https://github.com/tskit-dev/tskit/issues/1804 for when
# we can remove this.
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2 changes: 1 addition & 1 deletion python/tests/test_extend_haplotypes.py
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Expand Up @@ -6,7 +6,7 @@
import tests.test_wright_fisher as wf
import tskit
from tests import tsutil
from tests.test_highlevel import get_example_tree_sequences
from tests.tsutil import get_example_tree_sequences

# ↑ See https://github.com/tskit-dev/tskit/issues/1804 for when
# we can remove this.
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2 changes: 1 addition & 1 deletion python/tests/test_genotypes.py
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Expand Up @@ -37,7 +37,7 @@
import tests.test_wright_fisher as wf
import tests.tsutil as tsutil
import tskit
from tests.test_highlevel import get_example_tree_sequences
from tests.tsutil import get_example_tree_sequences
from tskit import exceptions
from tskit.genotypes import allele_remap

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