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AllenInstitute · Nov 20, 2024 · f23d211 · f23d211
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diff --git a/notebooks/10x_snRNASeq_tutorial_part_1.ipynb b/notebooks/10x_snRNASeq_tutorial_part_1.ipynb
@@ -46,7 +46,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -214,7 +214,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cell_metadata.csv: 100%|█████████████████████████████████████████████████████████████████████| 1.01G/1.01G [00:38<00:00, 26.0MMB/s]\n"
+      "cell_metadata.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.01G/1.01G [00:40<00:00, 25.0MMB/s]\n"
      ]
     },
     {
@@ -832,7 +832,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "region_of_interest_metadata.csv: 100%|███████████████████████████████████████████████████████| 1.40k/1.40k [00:00<00:00, 23.7kMB/s]\n"
+      "region_of_interest_metadata.csv: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.40k/1.40k [00:00<00:00, 23.7kMB/s]\n"
      ]
     },
     {
@@ -1810,7 +1810,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-TH-log2.h5ad: 100%|████████████████████████████████████████████████████████████████| 4.04G/4.04G [02:35<00:00, 25.9MMB/s]"
+      "WMB-10Xv2-TH-log2.h5ad: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4.04G/4.04G [02:38<00:00, 25.4MMB/s]"
      ]
     },
     {
@@ -2095,7 +2095,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "time taken:  3.9703891139999996\n",
+      "time taken:  3.743057188999984\n",
       "AnnData object with n_obs × n_vars = 131212 × 10\n",
       "    obs: 'cell_barcode', 'library_label', 'anatomical_division_label'\n",
       "    var: 'gene_symbol'\n",
@@ -2246,7 +2246,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_5015/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
+      "/tmp/ipykernel_3679/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
       "  grouped = grouped.sort_values(by=gnames[0], ascending=False)\n"
      ]
     },
@@ -2283,7 +2283,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_5015/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
+      "/tmp/ipykernel_3679/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
       "  grouped = grouped.sort_values(by=gnames[0], ascending=False)\n"
      ]
     },
@@ -2320,7 +2320,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_5015/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
+      "/tmp/ipykernel_3679/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
       "  grouped = grouped.sort_values(by=gnames[0], ascending=False)\n"
      ]
     },
@@ -2357,7 +2357,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_5015/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
+      "/tmp/ipykernel_3679/199257058.py:4: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
       "  grouped = grouped.sort_values(by=gnames[0], ascending=False)\n"
      ]
     },

diff --git a/notebooks/10x_snRNASeq_tutorial_part_2a.ipynb b/notebooks/10x_snRNASeq_tutorial_part_2a.ipynb
@@ -45,7 +45,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -438,38 +438,38 @@
      "output_type": "stream",
      "text": [
       "WMB-10XMulti\n",
-      " - time taken:  0.1917191869999968\n",
+      " - time taken:  0.1909020649999995\n",
       "WMB-10Xv2-CTXsp\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|█████████████████████████████████████████████████████████████| 1.74G/1.74G [01:06<00:00, 26.4MMB/s]\n"
+      "WMB-10Xv2-CTXsp-log2.h5ad: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.74G/1.74G [01:06<00:00, 26.0MMB/s]\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  2.700235495000001\n",
+      " - time taken:  2.6437265510000003\n",
       "WMB-10Xv2-HPF\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "WMB-10Xv2-HPF-log2.h5ad: 100%|███████████████████████████████████████████████████████████████| 6.10G/6.10G [03:40<00:00, 27.7MMB/s]\n"
+      "WMB-10Xv2-HPF-log2.h5ad: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 6.10G/6.10G [03:42<00:00, 27.4MMB/s]\n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      " - time taken:  9.575340357000002\n",
-      "total time taken:  92.364425141\n"
+      " - time taken:  8.835037850000006\n",
+      "total time taken:  91.33585639500001\n"
      ]
     }
    ],

diff --git a/notebooks/10x_snRNASeq_tutorial_part_2b.ipynb b/notebooks/10x_snRNASeq_tutorial_part_2b.ipynb
@@ -43,7 +43,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -74,8 +74,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cell_metadata_with_cluster_annotation.csv: 100%|█████████████████████████████████████████████| 1.39G/1.39G [00:52<00:00, 26.3MMB/s]\n",
-      "/allen/aibs/informatics/chris.morrison/miniconda/envs/abc_atlas_access/lib/python3.11/site-packages/abc_atlas_access/abc_atlas_cache/abc_project_cache.py:429: DtypeWarning: Columns (16) have mixed types. Specify dtype option on import or set low_memory=False.\n",
+      "cell_metadata_with_cluster_annotation.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.39G/1.39G [00:52<00:00, 26.5MMB/s]\n",
+      "/allen/scratch/aibstemp/chris.morrison/src/abc_atlas_access/src/abc_atlas_access/abc_atlas_cache/abc_project_cache.py:429: DtypeWarning: Columns (16) have mixed types. Specify dtype option on import or set low_memory=False.\n",
       "  return pd.read_csv(path, **kwargs)\n"
      ]
     }
@@ -101,7 +101,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "example_genes_all_cells_expression.csv: 100%|██████████████████████████████████████████████████| 318M/318M [00:13<00:00, 24.4MMB/s]\n"
+      "example_genes_all_cells_expression.csv: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 318M/318M [00:13<00:00, 23.8MMB/s]\n"
      ]
     }
    ],

diff --git a/notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb b/notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb
@@ -47,7 +47,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -136,13 +136,6 @@
    "execution_count": 5,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "cell_metadata.csv: 100%|███████████████████████████████████████████████████████████████████████| 830M/830M [00:42<00:00, 19.7MMB/s]\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -653,7 +646,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "region_of_interest_structure_map.csv: 100%|██████████████████████████████████████████████████| 8.82k/8.82k [00:00<00:00, 90.7kMB/s]\n"
+      "region_of_interest_structure_map.csv: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8.82k/8.82k [00:00<00:00, 124kMB/s]\n"
      ]
     },
     {

diff --git a/notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb b/notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb
@@ -43,7 +43,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -440,27 +440,13 @@
    "execution_count": 5,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "gene.csv: 100%|██████████████████████████████████████████████████████████████████████████████| 4.23M/4.23M [00:00<00:00, 17.1MMB/s]"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Number of genes =  59357\n"
      ]
     },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n"
-     ]
-    },
     {
      "data": {
       "text/html": [
@@ -576,7 +562,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "example_genes_all_cells_expression.csv: 100%|██████████████████████████████████████████████████| 233M/233M [00:18<00:00, 12.9MMB/s]\n"
+      "example_genes_all_cells_expression.csv: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 233M/233M [00:09<00:00, 24.5MMB/s]\n"
      ]
     },
     {

diff --git a/notebooks/WHB_cluster_annotation_tutorial.ipynb b/notebooks/WHB_cluster_annotation_tutorial.ipynb
@@ -44,7 +44,7 @@
     {
      "data": {
       "text/plain": [
-       "'releases/20241115/manifest.json'"
+       "'releases/20241130/manifest.json'"
       ]
      },
      "execution_count": 2,
@@ -108,7 +108,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cluster.csv: 100%|████████████████████████████████████████████████████████████████████████████| 84.8k/84.8k [00:00<00:00, 568kMB/s]"
+      "cluster.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 84.8k/84.8k [00:00<00:00, 529kMB/s]"
      ]
     },
     {
@@ -268,7 +268,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cluster_annotation_term_set.csv: 100%|███████████████████████████████████████████████████████| 1.33k/1.33k [00:00<00:00, 23.0kMB/s]\n"
+      "cluster_annotation_term_set.csv: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.33k/1.33k [00:00<00:00, 22.7kMB/s]\n"
      ]
     },
     {
@@ -414,7 +414,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cluster_annotation_term.csv: 100%|█████████████████████████████████████████████████████████████| 547k/547k [00:00<00:00, 4.19MMB/s]\n"
+      "cluster_annotation_term.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 547k/547k [00:00<00:00, 4.53MMB/s]\n"
      ]
     },
     {
@@ -669,7 +669,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "cluster_to_cluster_annotation_membership.csv: 100%|██████████████████████████████████████████| 1.02M/1.02M [00:00<00:00, 5.60MMB/s]\n"
+      "cluster_to_cluster_annotation_membership.csv: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.02M/1.02M [00:00<00:00, 7.56MMB/s]\n"
      ]
     },
     {
@@ -1525,7 +1525,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_7193/1772253940.py:9: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
+      "/tmp/ipykernel_27919/1772253940.py:9: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`\n",
       "  ax.barh(AxB.index, AxB[col], left=bottom, label=col[1], color=B_colors[i])\n"
      ]
     },