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Use new scanpy umap connectivity fn in test #170

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Aug 21, 2024
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Use new scanpy umap connectivity fn in test #170

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7631412
Use new scanpy umap connectivity fn in test
adamgayoso Aug 21, 2024
b8c14bd
Update test_neighbors.py
adamgayoso Aug 21, 2024
5513040
Update CHANGELOG.md
adamgayoso Aug 21, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,10 @@ and this project adheres to [Semantic Versioning][].

- Add `progress_bar` argument to {class}`scib_metrics.benchmark.Benchmarker` {pr}`152`.

### Fixed

- Fix neighbors connectivities in test to use new scanpy fn {pr}`170`.

## 0.5.1 (2024-02-23)

### Changed
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7 changes: 3 additions & 4 deletions tests/test_neighbors.py
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Expand Up @@ -20,9 +20,8 @@ def test_neighbors_results(n):
new_connect = neigh_result.knn_graph_connectivities
new_dist = neigh_result.knn_graph_distances

sc_dist, sc_connect = sc.neighbors._compute_connectivities_umap(
neigh_result.indices[:, :n], neigh_result.distances[:, :n], adata.n_obs, n_neighbors=n
sc_connect = sc.neighbors._connectivity.umap(
neigh_result.indices[:, :n], neigh_result.distances[:, :n], n_obs=adata.n_obs, n_neighbors=n
)

np.testing.assert_allclose(new_dist.A, sc_dist.A)
np.testing.assert_allclose(new_connect.A, sc_connect.A)
np.testing.assert_allclose(new_connect.toarray(), sc_connect.toarray())
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