update cell_census python package dependency tiledbsoma 0.5.0a11 (#176)

* update package dep to tiledbsoma 0.5.0a11 * rerun notebooks on latest
chanzuckerberg · Feb 14, 2023 · bca525d · bca525d
1 parent 543d870
commit bca525d
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Showing 7 changed files with 350 additions and 350 deletions.
diff --git a/api/python/cell_census/pyproject.toml b/api/python/cell_census/pyproject.toml
@@ -35,7 +35,7 @@ dependencies= [
     # of TileDB on-disk storage format. Make sure this doesn't fall behind the builder's tiledbsoma version.
     # NOTE: tiledb is also a requirement of the API, but tiledbsoma also has a tiledb dependency, so just use 
     # the same version here
-    "tiledbsoma==0.5.0a10",
+    "tiledbsoma==0.5.0a11",
     "typing_extensions",
     "s3fs",
     "scikit-misc",

diff --git a/api/python/notebooks/api_demo/census_axis_query.ipynb b/api/python/notebooks/api_demo/census_axis_query.ipynb
@@ -22,7 +22,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 9,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2023-01-31T19:40:26.784214Z",
@@ -62,7 +62,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 10,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2023-01-31T19:40:27.870658Z",
@@ -76,19 +76,19 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "There are 560 cell types in the Cell Census! The first 10 are: ['CL:0000649', 'CL:0002187', 'CL:0000148', 'CL:0000312', 'CL:0000242', 'CL:0000988', 'CL:2000092', 'CL:0002189', 'CL:0000084', 'CL:0000576']\n",
+      "There are 569 cell types in the Cell Census! The first 10 are: ['CL:0000649', 'CL:0002187', 'CL:0000148', 'CL:0000312', 'CL:0000242', 'CL:0000988', 'CL:2000092', 'CL:0002189', 'CL:0000084', 'CL:0000576']\n",
       "\n",
       "The top 10 cell types and their counts are:\n",
       "CL:0000540    5177999\n",
       "CL:0000679    1889047\n",
       "CL:0000128    1744101\n",
-      "CL:0000235    1387771\n",
+      "CL:0000235    1394590\n",
       "CL:0000624    1286352\n",
       "CL:0000860    1251739\n",
       "CL:0000625    1243990\n",
       "CL:0000623    1027763\n",
+      "CL:0000057     982731\n",
       "CL:0000236     959462\n",
-      "CL:0000057     947376\n",
       "Name: cell_type_ontology_term_id, dtype: int64\n"
      ]
     }
@@ -125,7 +125,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 11,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2023-01-31T19:40:34.239947Z",
@@ -139,7 +139,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "There are 176 cell types in the Cell Census where tissue_ontology_term_id == UBERON:0002048! The first 10 are: ['CL:0002632', 'CL:0000499', 'CL:0000763', 'CL:0002138', 'CL:0002139', 'CL:0000067', 'CL:0001065', 'CL:0000165', 'CL:0000077', 'CL:0000076']\n",
+      "There are 176 cell types in the Cell Census where tissue_ontology_term_id == UBERON:0002048! The first 10 are: ['CL:0000192', 'CL:0002503', 'CL:0000057', 'CL:0002598', 'CL:0000359', 'CL:0000186', 'CL:0000669', 'CL:0000077', 'CL:0002063', 'CL:0002370']\n",
       "\n",
       "Top 10 cell types where tissue_ontology_term_id == UBERON:0002048\n",
       "CL:0000235    514828\n",
@@ -197,7 +197,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 12,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2023-01-31T19:40:38.379046Z",
@@ -258,7 +258,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 13,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2023-01-31T19:40:42.156087Z",
@@ -272,11 +272,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Complete cell census contains 47342221 cells.\n",
+      "Complete cell census contains 47665352 cells.\n",
       "homo_sapiens\n",
-      "\tUnique cell_type_ontology_term_id values: 560\n",
+      "\tUnique cell_type_ontology_term_id values: 569\n",
       "\tUnique assay_ontology_term_id values: 20\n",
-      "\tUnique tissue_ontology_term_id values: 198\n",
+      "\tUnique tissue_ontology_term_id values: 203\n",
       "mus_musculus\n",
       "\tUnique cell_type_ontology_term_id values: 211\n",
       "\tUnique assay_ontology_term_id values: 9\n",
@@ -314,7 +314,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [