attribute and argument fixes (#80)

Co-authored-by: Arina Danilina <danilina@cip.ifi.lmu.de>

examples/problems/1100_callback.ipynb

@@ -392,7 +392,7 @@
     "df_graph = pd.DataFrame(\n",
     "    index=adata_concat.obs_names,\n",
     "    columns=adata_concat.obs_names,\n",
-    "    data=adata_concat.obsp[\"connectivities\"].A.astype(\"float64\"),\n",
+    "    data=adata_concat.obsp[\"connectivities\"].toarray().astype(\"float64\"),\n",
     ")"
    ]
   },
@@ -505,7 +505,8 @@
     "    normalize_spatial=False,\n",
     "    xy_callback=lambda term, src, tgt: TaggedArray(\n",
     "        *np.split(\n",
-    "            SparsePCA().fit_transform(np.vstack([src.X.A, tgt.X.A])), [src.shape[0]]\n",
+    "            SparsePCA().fit_transform(np.vstack([src.X.toarray(), tgt.X.toarray()])),\n",
+    "            [src.shape[0]],\n",
     "        )\n",
     "    ),\n",
     ")"

examples/problems/900_annotation_mapping.ipynb

@@ -202,7 +202,7 @@
    ],
    "source": [
     "mp = mp.prepare(\n",
-    "    sc_attr={\"attr\": \"obsm\", \"key\": \"X_pca\"}, **{\"xy_callback\": \"local-pca\"}\n",
+    "    sc_attr={\"attr\": \"obsm\", \"key\": \"X_pca\"}, xy_callback=\"local-pca\"\n",
     ").solve()"
    ]
   },
@@ -301,7 +301,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -339,7 +339,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -366,7 +366,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -375,7 +375,7 @@
        "0.8644290885159592"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }