Merge pull request #557 from vespa-engine/kkraune/colab

Kkraune/colab
vespa-engine · Aug 31, 2023 · eab0e4b · eab0e4b
2 parents 91fddcb + 4284f9d
commit eab0e4b
Show file tree

Hide file tree

Showing 5 changed files with 94 additions and 116 deletions.
diff --git a/docs/sphinx/source/application-packages.ipynb b/docs/sphinx/source/application-packages.ipynb
@@ -18,10 +18,24 @@
     "  **_To configure setting an unsupported indexing option (or any other unsupported option),_**\n",
     "  **_export the application package like above, modify the schema or other files_**\n",
     "  **_and deploy the application package from the directory, or as a zipped file._**\n",
-    "  **_Find more details at the end of this notebook._**\n",
-    "\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vespa-engine/pyvespa/blob/master/docs/sphinx/source/application-packages.ipynb)\n",
-    "\n",
+    "  **_Find more details at the end of this notebook._**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e51d0086",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip3 install pyvespa"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b593d6e2",
+   "metadata": {},
+   "source": [
     "By exporting to disk, one can see the generated files:"
    ]
   },

diff --git a/docs/sphinx/source/examples/multi-vector-indexing.ipynb b/docs/sphinx/source/examples/multi-vector-indexing.ipynb
@@ -24,8 +24,24 @@
     "* How to control text search result highlighting.\n",
     "\n",
     "This notebook requires [pyvespa >= 0.37.1](https://pyvespa.readthedocs.io/en/latest/index.html#requirements)\n",
-    "and the [Vespa CLI](https://pyvespa.readthedocs.io/en/latest/reads-writes.html#Feed-using-Vespa-CLI).\n",
-    "\n",
+    "and the [Vespa CLI](https://pyvespa.readthedocs.io/en/latest/reads-writes.html#Feed-using-Vespa-CLI)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bf5137e2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip3 install pyvespa"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0d35f3da",
+   "metadata": {},
+   "source": [
     "## Create the application"
    ]
   },

diff --git a/docs/sphinx/source/examples/pyvespa-examples.ipynb b/docs/sphinx/source/examples/pyvespa-examples.ipynb
@@ -14,6 +14,16 @@
     "Refer to [troubleshooting](https://pyvespa.readthedocs.io/en/latest/troubleshooting.html), which also has utilies for debugging."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8fb6db5b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip3 install pyvespa"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c77bfca9",

diff --git a/docs/sphinx/source/getting-started-pyvespa.ipynb b/docs/sphinx/source/getting-started-pyvespa.ipynb
@@ -32,6 +32,7 @@
     }
    ],
    "source": [
+    "!pip3 install pyvespa\n",
     "!docker info | grep \"Total Memory\""
    ]
   },
@@ -451,9 +452,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "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": "3.11.4"
   }
  },
  "nbformat": 4,

diff --git a/docs/sphinx/source/query.ipynb b/docs/sphinx/source/query.ipynb
@@ -12,8 +12,22 @@
     "and https://cord19.vespa.ai/ app as an example.\n",
     "You can run this tutorial in Google Colab:\n",
     "\n",
-    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vespa-engine/pyvespa/blob/master/docs/sphinx/source/query.ipynb)\n",
-    "\n",
+    "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vespa-engine/pyvespa/blob/master/docs/sphinx/source/query.ipynb)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip3 install pyvespa"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "Set the query endpoint:"
    ]
   },
@@ -46,18 +60,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "10977"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "body = {\n",
     "  'yql':     'select cord_uid, title, abstract from sources * where userQuery()',\n",
@@ -81,18 +84,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "5"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "len(results.hits)"
    ]
@@ -108,18 +100,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['ysml5abq', 'zpcuwvn4', '8art2tyj', 'xej338lo', 'npoje09j']"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "[hit[\"fields\"][\"cord_uid\"] for hit in results.hits]"
    ]
@@ -135,23 +116,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'id': 'index:content/1/848ca5db53648911e0a58c78',\n",
-       " 'relevance': 30.531354743471304,\n",
-       " 'source': 'content',\n",
-       " 'fields': {'title': 'Cost utility analysis of <hi>Remdesivir</hi> and Dexamethasone <hi>treatment</hi> for hospitalised <hi>COVID</hi>-<hi>19</hi> patients - a hypothetical study',\n",
-       "  'abstract': '<sep />: Sars-Cov-2 is a novel corona virus associated with significant morbidity and mortality. <hi>Remdesivir</hi> and Dexamethasone are two <hi>treatments</hi> that have shown to be <hi>effective</hi> against the Sars-Cov-2 associated disease. However, a cost-effectiveness analysis of the two <hi>treatments</hi> is still lacking. OBJECTIVE: The cost-utility of <hi>Remdesivir</hi>, Dexamethasone and a simultaneous use of the two drugs with respect to standard of care for <hi>treatment</hi> <hi>Covid</hi>-<hi>19</hi> hospitalized patients is evaluated, together with the effect<sep />',\n",
-       "  'cord_uid': 'ysml5abq'}}"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "results.hits[0]"
    ]
@@ -168,59 +133,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'timing': {'querytime': 0.019,\n",
-       "  'summaryfetchtime': 0.001,\n",
-       "  'searchtime': 0.021},\n",
-       " 'root': {'id': 'toplevel',\n",
-       "  'relevance': 1.0,\n",
-       "  'fields': {'totalCount': 10977},\n",
-       "  'coverage': {'coverage': 100,\n",
-       "   'documents': 976355,\n",
-       "   'full': True,\n",
-       "   'nodes': 2,\n",
-       "   'results': 1,\n",
-       "   'resultsFull': 1},\n",
-       "  'children': [{'id': 'index:content/1/848ca5db53648911e0a58c78',\n",
-       "    'relevance': 30.531354743471304,\n",
-       "    'source': 'content',\n",
-       "    'fields': {'title': 'Cost utility analysis of <hi>Remdesivir</hi> and Dexamethasone <hi>treatment</hi> for hospitalised <hi>COVID</hi>-<hi>19</hi> patients - a hypothetical study',\n",
-       "     'abstract': '<sep />: Sars-Cov-2 is a novel corona virus associated with significant morbidity and mortality. <hi>Remdesivir</hi> and Dexamethasone are two <hi>treatments</hi> that have shown to be <hi>effective</hi> against the Sars-Cov-2 associated disease. However, a cost-effectiveness analysis of the two <hi>treatments</hi> is still lacking. OBJECTIVE: The cost-utility of <hi>Remdesivir</hi>, Dexamethasone and a simultaneous use of the two drugs with respect to standard of care for <hi>treatment</hi> <hi>Covid</hi>-<hi>19</hi> hospitalized patients is evaluated, together with the effect<sep />',\n",
-       "     'cord_uid': 'ysml5abq'}},\n",
-       "   {'id': 'index:content/1/afade29b15d5f83d8dd4d16a',\n",
-       "    'relevance': 30.124913401931195,\n",
-       "    'source': 'content',\n",
-       "    'fields': {'title': '<hi>Remdesivir</hi> is <hi>effective</hi> for moderately severe patients: A re-analysis of the first double-blind, placebo-controlled, randomized trial on <hi>remdesivir</hi> for <hi>treatment</hi> of severe <hi>covid</hi>-<hi>19</hi> patients conducted in wuhan city',\n",
-       "     'abstract': '<sep /> with baseline score, day of assessment, <hi>treatment</hi> group, baseline by <hi>treatment</hi> interaction, and day by <hi>treatment</hi> interaction as covariates. The binary endpoint was supported by the recent FDA<sep />oxygen (but not NIV/HFNC)) – the moderately severe category. The response rate was 85% for <hi>remdesivir</hi>-treated patients with baseline disease point=3 versus 70% response rate for likewise placebo-treated<sep />opinions. This result supports the preliminary findings of ACTT that <hi>remdesivir</hi> is <hi>effective</hi> for patients who were not critically severe. This result also suggests that<sep />',\n",
-       "     'cord_uid': 'zpcuwvn4'}},\n",
-       "   {'id': 'index:content/1/4678cba4fd31160fd163d063',\n",
-       "    'relevance': 29.876569304341285,\n",
-       "    'source': 'content',\n",
-       "    'fields': {'title': 'A Review on <hi>Remdesivir</hi>: A Possible Promising Agent for the <hi>Treatment</hi> of <hi>COVID</hi>-<hi>19</hi>',\n",
-       "     'abstract': '<sep />manufacturing of specific therapeutics and vaccines to treat <hi>COVID</hi>-<hi>19</hi> are time-consuming processes. At this time, using available conventional therapeutics along with other <hi>treatment</hi> options may be useful to fight <hi>COVID</hi>-<hi>19</hi>. In different clinical trials, efficacy of <hi>remdesivir</hi> (GS-5734) against Ebola virus has been demonstrated. Moreover, <hi>remdesivir</hi> may be an <hi>effective</hi> therapy in vitro and in animal models infected by SARS and MERS coronaviruses. Hence, the drug may be theoretically <hi>effective</hi> against SARS-CoV-2. <hi>Remdesivir</hi><sep />',\n",
-       "     'cord_uid': '8art2tyj'}},\n",
-       "   {'id': 'index:content/0/eec37c88ff9aa825c5c79d81',\n",
-       "    'relevance': 29.874123437446798,\n",
-       "    'source': 'content',\n",
-       "    'fields': {'title': 'A Review on <hi>Remdesivir</hi>: A Possible Promising Agent for the <hi>Treatment</hi> of <hi>COVID</hi>-<hi>19</hi>',\n",
-       "     'abstract': '<sep />manufacturing of specific therapeutics and vaccines to treat <hi>COVID</hi>-<hi>19</hi> are time-consuming processes. At this time, using available conventional therapeutics along with other <hi>treatment</hi> options may be useful to fight <hi>COVID</hi>-<hi>19</hi>. In different clinical trials, efficacy of <hi>remdesivir</hi> (GS-5734) against Ebola virus has been demonstrated. Moreover, <hi>remdesivir</hi> may be an <hi>effective</hi> therapy in vitro and in animal models infected by SARS and MERS coronaviruses. Hence, the drug may be theoretically <hi>effective</hi> against SARS-CoV-2. <hi>Remdesivir</hi><sep />',\n",
-       "     'cord_uid': 'xej338lo'}},\n",
-       "   {'id': 'index:content/0/a41b357fc6aa38c6b55a4685',\n",
-       "    'relevance': 29.481438680496694,\n",
-       "    'source': 'content',\n",
-       "    'fields': {'title': '<hi>Remdesivir</hi> for the <hi>Treatment</hi> of <hi>COVID</hi>-<hi>19</hi>: A Systematic Review of the Literature',\n",
-       "     'abstract': '<sep />CoV-2 a global pandemic. To date, coronavirus disease-2019 (<hi>COVID</hi>-<hi>19</hi>) has spread to over 200 countries, leading to over 1.6 million cases and over 99,000 deaths. Given that there is neither a vaccine nor proven <hi>treatment</hi> for <hi>COVID</hi>-<hi>19</hi>, there is currently an urgent need for <hi>effective</hi> pharmacotherapy. To address the need for an <hi>effective</hi> <hi>treatment</hi> of SARS-CoV-2 during the worldwide pandemic, this systematic review of intravenous (IV) <hi>remdesivir</hi> was performed. <hi>Remdesivir</hi>, an anti-viral prodrug originally developed to treat Ebola virus disease, has shown broad spectrum activity against the Coronavirus family. A recent case report reported improvement of clinical symptoms with <hi>remdesivir</hi> in a patient with <hi>COVID</hi>-<hi>19</hi>. After<sep />',\n",
-       "     'cord_uid': 'npoje09j'}}]}}"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "results.json"
    ]
@@ -239,9 +152,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "python3",
+   "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": "3.11.4"
   }
  },
  "nbformat": 4,