Add notebook example for cohort group metadata

Author: Sharon-codes

notebooks/cohort_group_metadata.ipynb

@@ -0,0 +1,94 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Cohort group metadata quick demo\n",
+    "\n",
+    "This notebook shows how to load cohort-group metadata tables and filter them with `cohort_group_query`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from malariagen_data import ag3 as _ag3\n",
+    "from malariagen_data.anoph.cohort_group_metadata import AnophelesCohortGroupMetadata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cohort_meta = AnophelesCohortGroupMetadata(\n",
+    "    url=\"simplecache::gs://vo_agam_release_master_us_central1\",\n",
+    "    public_url=\"gs://vo_agam_release_master_us_central1/\",\n",
+    "    config_path=_ag3.CONFIG_PATH,\n",
+    "    major_version_number=_ag3.MAJOR_VERSION_NUMBER,\n",
+    "    major_version_path=_ag3.MAJOR_VERSION_PATH,\n",
+    "    pre=True,\n",
+    "    simplecache={\"cache_storage\": \"../gcs_cache\"},\n",
+    ")\n",
+    "cohort_meta"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_admin1_month = cohort_meta.cohort_group_metadata(\"admin1_month\")\n",
+    "df_admin1_month.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_bf = cohort_meta.cohort_group_metadata(\n",
+    "    \"admin1_month\",\n",
+    "    cohort_group_query=\"country == 'Burkina Faso' and year >= 2010\",\n",
+    ")\n",
+    "df_bf.loc[:, [\"cohort_id\", \"cohort_size\", \"country\", \"year\", \"month\", \"admin1_name\"]].head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_bf.groupby([\"year\", \"month\"], as_index=False)[\"cohort_size\"].sum().head()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

tests/anoph/test_cohort_group_metadata.py

@@ -16,6 +16,7 @@ def ag3_sim_api(ag3_sim_fixture):
         pre=True,
     )
 
+
 def case_ag3_sim(ag3_sim_fixture, ag3_sim_api):
     return ag3_sim_fixture, ag3_sim_api