add pandas req to notebook test

ersilia-os · Dec 19, 2023 · 911528b · 911528b
1 parent 98f5b4b
commit 911528b
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Showing 3 changed files with 37 additions and 32 deletions.
diff --git a/.github/workflows/test-colab.yml b/.github/workflows/test-colab.yml
@@ -24,11 +24,15 @@ jobs:
           source activate
           conda init
           conda install google-colab -c conda-forge
+          pip install pandas
           jupyter --version
 
       - name: Test Google Colab Notebook with CLI shell commands
         run: jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-cli.ipynb --output=output-cli.ipynb --ExecutePreprocessor.timeout=-1
 
+      - name: Test Google Colab Notebook with Python API commands
+        run: jupyter nbconvert --to notebook --execute notebooks/test-colab-notebook-python-api.ipynb --output=output-python-api.ipynb --ExecutePreprocessor.timeout=-1
+
       - name: Upload Output of the Google Colab Notebook CLI
         uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # [email protected]
         with:

diff --git a/notebooks/test-colab-notebook-cli.ipynb b/notebooks/test-colab-notebook-cli.ipynb
@@ -1,25 +1,10 @@
 {
- "nbformat": 4,
- "nbformat_minor": 0,
- "metadata": {
-  "colab": {
-   "provenance": [],
-   "include_colab_link": true
-  },
-  "kernelspec": {
-   "name": "python3",
-   "display_name": "Python 3"
-  },
-  "language_info": {
-   "name": "python"
-  }
- },
  "cells": [
   {
    "cell_type": "markdown",
    "metadata": {
-    "id": "view-in-github",
-    "colab_type": "text"
+    "colab_type": "text",
+    "id": "view-in-github"
    },
    "source": [
     "<a href=\"https://colab.research.google.com/github/ersilia-os/ersilia/blob/master/notebooks/test-colab-notebook-cli.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
@@ -51,28 +36,44 @@
   },
   {
    "cell_type": "code",
-   "source": [
-    "model_name = \"eos4e40\"\n",
-    "smi = \"CC(C)CC1=CC=C(C=C1)C(C)C(=O)O\""
-   ],
+   "execution_count": 2,
    "metadata": {
     "id": "28yw34ZaV9rA"
    },
-   "execution_count": 2,
-   "outputs": []
+   "outputs": [],
+   "source": [
+    "model_name = \"eos4e41\"\n",
+    "smi = \"CC(C)CC1=CC=C(C=C1)C(C)C(=O)O\""
+   ]
   },
   {
    "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "id": "MOROJyhcWBvV"
+   },
+   "outputs": [],
    "source": [
     "!ersilia fetch $model_name\n",
     "!ersilia serve $model_name\n",
     "!ersilia api -i \"$smi\" -o output-cli.csv"
-   ],
-   "metadata": {
-    "id": "MOROJyhcWBvV"
-   },
-   "execution_count": null,
-   "outputs": []
+   ]
   }
- ]
-}
+ ],
+ "metadata": {
+  "colab": {
+   "include_colab_link": true,
+   "provenance": []
+  },
+  "kernelspec": {
+   "display_name": "Python 3",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/notebooks/test-colab-notebook-python-api.ipynb b/notebooks/test-colab-notebook-python-api.ipynb
@@ -166,7 +166,7 @@
    "source": [
     "from ersilia import ErsiliaModel\n",
     "\n",
-    "em = ErsiliaModel(\"chemprop-antibiotic\")"
+    "em = ErsiliaModel(\"chemprop-antibiotic-lite\")"
    ]
   },
   {