fix test

YosefLab · Dec 28, 2023 · 78aaca2 · 78aaca2
1 parent 1a5d0f9
commit 78aaca2
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Showing 2 changed files with 34 additions and 9 deletions.
diff --git a/docs/notebooks/large_scale.ipynb b/docs/notebooks/large_scale.ipynb
@@ -56,7 +56,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "adata"
@@ -65,7 +69,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "# Number of unique cell types\n",
@@ -205,7 +213,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "import time\n",
@@ -241,7 +253,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bm.plot_results_table()"
@@ -250,7 +266,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "bm.plot_results_table(min_max_scale=False)"
@@ -267,7 +287,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "keep_output"
+    ]
+   },
    "outputs": [],
    "source": [
     "from rich import print\n",
@@ -293,7 +317,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {

diff --git a/tests/test_metrics.py b/tests/test_metrics.py
@@ -58,8 +58,9 @@ def test_compute_simpson_index():
     D = scib_metrics.utils.cdist(X, X)
     nbrs = NearestNeighbors(n_neighbors=30, algorithm="kd_tree").fit(X)
     D, knn_idx = nbrs.kneighbors(X)
+    row_idx = np.arange(X.shape[0])[:, None]
     scib_metrics.utils.compute_simpson_index(
-        jnp.array(D), jnp.array(knn_idx), jnp.array(labels), len(np.unique(labels))
+        jnp.array(D), jnp.array(knn_idx), jnp.array(row_idx), jnp.array(labels), len(np.unique(labels))
     )
 
 
@@ -72,7 +73,7 @@ def test_lisi_knn():
     harmonypy_lisi_res = harmonypy_lisi(
         X, pd.DataFrame(labels, columns=["labels"]), label_colnames=["labels"], perplexity=10
     )[:, 0]
-    assert np.testing.assert_allclose(lisi_res, harmonypy_lisi_res)
+    np.testing.assert_allclose(lisi_res, harmonypy_lisi_res)
 
 
 def test_ilisi_clisi_knn():