bugfix

NVIDIA · Nov 7, 2024 · 7e80ad1 · 7e80ad1
1 parent 5c52c1b
commit 7e80ad1
Showing 1 changed file with 7 additions and 8 deletions.
diff --git a/docs/bionemo/notebooks/Geneformer-celltype-classification-example.ipynb b/docs/bionemo/notebooks/Geneformer-celltype-classification-example.ipynb
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "id": "b2f70fc3-3eb5-4de5-a24a-a7167584caaf",
    "metadata": {
     "tags": []
@@ -59,7 +59,7 @@
        "       'intestinal tuft cell'], dtype=object)"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "id": "8f9a2731",
    "metadata": {},
    "outputs": [
@@ -136,7 +136,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[NeMo W 2024-09-12 10:48:57 sc_memmap:291] Data path found, not writing over it. If you want to override the data, re-run with --override-metadata\n"
+      "[NeMo W 2024-11-07 04:50:59 sc_memmap:297] Data path found, not writing over it. If you want to override the data, re-run with --override-metadata\n"
      ]
     },
     {
@@ -145,14 +145,14 @@
      "text": [
       "Metadata already exists, loading...\n",
       "Writing data into memmaps to /workspace/bionemo/celltype-bench-dataset...\n",
-      "[NeMo I 2024-09-12 10:48:57 sc_memmap:219] pt_running_el: 0, cur_count: 0\n"
+      "[NeMo I 2024-11-07 04:50:59 sc_memmap:225] pt_running_el: 0, cur_count: 0\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Merging AnnData into numpy memaps...: 100%|██████████| 1/1 [00:00<00:00,  1.45it/s]\n"
+      "Merging AnnData into numpy memaps...: 100%|██████████| 1/1 [00:00<00:00,  1.37it/s]\n"
      ]
     },
     {
@@ -184,7 +184,6 @@
       "gene_expression_ind.npy\n",
       "gene_expression_ptr.npy\n",
       "human_dataset.h5ad\n",
-      "infer_results_106M.pkl\n",
       "metadata.json\n"
      ]
     }
@@ -215,7 +214,7 @@
     "\n",
     "cd $BIONEMO_HOME\n",
     "\n",
-    "python download_artifacts.py --models geneformer_106M_240530 geneformer_10M_240530 geneformer --source pbss --model_dir $BIONEMO_HOME/models --verbose\n",
+    "python download_artifacts.py --models geneformer_106M_240530 geneformer_10M_240530 --source pbss --model_dir $BIONEMO_HOME/models --verbose\n",
     "\n",
     "mkdir -p $BIONEMO_HOME/examples/tests/test_data/cellxgene_2023-12-15_small/processed_data/train\n",
     "mkdir -p $BIONEMO_HOME/examples/tests/test_data/cellxgene_2023-12-15_small/processed_data/val\n",