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bugfix notebook pandas install
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@GemmaTuron
GemmaTuron committed Dec 19, 2023
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1 change: 0 additions & 1 deletion .github/workflows/test-colab.yml
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Expand Up @@ -24,7 +24,6 @@ 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
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226 changes: 226 additions & 0 deletions notebooks/output-python-api.ipynb
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{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {
"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-python-api.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"execution": {
"iopub.execute_input": "2023-12-19T10:09:00.078522Z",
"iopub.status.busy": "2023-12-19T10:09:00.078256Z",
"iopub.status.idle": "2023-12-19T10:09:18.851451Z",
"shell.execute_reply": "2023-12-19T10:09:18.849379Z"
},
"id": "tK-9NmDan9_r"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"env: MINICONDA_INSTALLER_SCRIPT=Miniconda3-py37_4.12.0-Linux-x86_64.sh\n",
"env: MINICONDA_PREFIX=/usr/local\n",
"env: PYTHONPATH=\"$PYTHONPATH:/usr/local/lib/python3.7/site-packages\"\n",
"env: PIP_ROOT_USER_ACTION=ignore\n",
"--2023-12-19 11:09:00-- https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh\r\n",
"Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.131.3, 104.16.130.3, 2606:4700::6810:8303, ...\r\n",
"Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.131.3|:443... connected.\r\n",
"HTTP request sent, awaiting response... 200 OK\r\n",
"Length: 104996770 (100M) [application/x-sh]\r\n",
"Saving to: ‘Miniconda3-py37_4.12.0-Linux-x86_64.sh’\r\n",
"\r\n",
"Miniconda3-py37_4.1 100%[===================>] 100,13M 8,87MB/s in 12s \r\n",
"\r\n",
"2023-12-19 11:09:12 (8,53 MB/s) - ‘Miniconda3-py37_4.12.0-Linux-x86_64.sh’ saved [104996770/104996770]\r\n",
"\r\n",
"PREFIX=/usr/local\r\n",
"./Miniconda3-py37_4.12.0-Linux-x86_64.sh: 396: cannot create /usr/local/conda.exe: Permission denied\r\n",
"chmod: cannot access '/usr/local/conda.exe': No such file or directory\r\n",
"Unpacking payload ...\r\n",
"./Miniconda3-py37_4.12.0-Linux-x86_64.sh: 412: /usr/local/conda.exe: not found\r\n",
"./Miniconda3-py37_4.12.0-Linux-x86_64.sh: 414: /usr/local/conda.exe: not found\r\n",
"Collecting git+https://github.com/ersilia-os/ersilia.git\r\n",
" Cloning https://github.com/ersilia-os/ersilia.git to /tmp/pip-req-build-enbhpjsb\r\n",
" Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/ersilia.git /tmp/pip-req-build-enbhpjsb\r\n",
" Resolved https://github.com/ersilia-os/ersilia.git to commit 911528b1d17a68bbe3f18a952ddcac865833c416\r\n",
" Installing build dependencies ... \u001b[?25l-\b \b\\\b \b|\b \bdone\r\n",
"\u001b[?25h Getting requirements to build wheel ... \u001b[?25ldone\r\n",
"\u001b[?25h Preparing metadata (pyproject.toml) ... \u001b[?25ldone\r\n",
"\u001b[?25hRequirement already satisfied: PyYAML<7.0.0,>=6.0.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (6.0.1)\r\n",
"Requirement already satisfied: boto3<2.0.0,>=1.28.40 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (1.28.50)\r\n",
"Requirement already satisfied: click<9.0.0,>=8.1.7 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (8.1.7)\r\n",
"Requirement already satisfied: docker<7.0.0,>=6.1.3 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (6.1.3)\r\n",
"Requirement already satisfied: dockerfile-parse<3.0.0,>=2.0.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (2.0.1)\r\n",
"Requirement already satisfied: emoji<3.0.0,>=2.8.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (2.8.0)\r\n",
"Requirement already satisfied: h5py<4.0.0,>=3.7.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (3.9.0)\r\n",
"Requirement already satisfied: inputimeout<2.0.0,>=1.0.4 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (1.0.4)\r\n",
"Requirement already satisfied: loguru<0.7.0,>=0.6.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (0.6.0)\r\n",
"Requirement already satisfied: pyairtable<3 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (1.5.0)\r\n",
"Requirement already satisfied: tqdm<5.0.0,>=4.66.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (4.66.1)\r\n",
"Requirement already satisfied: validators<0.22.0,>=0.21.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from ersilia==0.1.29) (0.21.2)\r\n",
"Requirement already satisfied: botocore<1.32.0,>=1.31.50 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from boto3<2.0.0,>=1.28.40->ersilia==0.1.29) (1.31.50)\r\n",
"Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from boto3<2.0.0,>=1.28.40->ersilia==0.1.29) (1.0.1)\r\n",
"Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from boto3<2.0.0,>=1.28.40->ersilia==0.1.29) (0.6.2)\r\n",
"Requirement already satisfied: packaging>=14.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from docker<7.0.0,>=6.1.3->ersilia==0.1.29) (23.1)\r\n",
"Requirement already satisfied: requests>=2.26.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from docker<7.0.0,>=6.1.3->ersilia==0.1.29) (2.31.0)\r\n",
"Requirement already satisfied: urllib3>=1.26.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from docker<7.0.0,>=6.1.3->ersilia==0.1.29) (1.26.16)\r\n",
"Requirement already satisfied: websocket-client>=0.32.0 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from docker<7.0.0,>=6.1.3->ersilia==0.1.29) (1.6.3)\r\n",
"Requirement already satisfied: numpy>=1.17.3 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from h5py<4.0.0,>=3.7.0->ersilia==0.1.29) (1.26.0)\r\n",
"Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from botocore<1.32.0,>=1.31.50->boto3<2.0.0,>=1.28.40->ersilia==0.1.29) (2.8.2)\r\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests>=2.26.0->docker<7.0.0,>=6.1.3->ersilia==0.1.29) (3.2.0)\r\n",
"Requirement already satisfied: idna<4,>=2.5 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests>=2.26.0->docker<7.0.0,>=6.1.3->ersilia==0.1.29) (3.4)\r\n",
"Requirement already satisfied: certifi>=2017.4.17 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests>=2.26.0->docker<7.0.0,>=6.1.3->ersilia==0.1.29) (2023.7.22)\r\n",
"Requirement already satisfied: six>=1.5 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.32.0,>=1.31.50->boto3<2.0.0,>=1.28.40->ersilia==0.1.29) (1.16.0)\r\n",
"Requirement already satisfied: requests in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (2.31.0)\r\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests) (3.2.0)\r\n",
"Requirement already satisfied: idna<4,>=2.5 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests) (3.4)\r\n",
"Requirement already satisfied: urllib3<3,>=1.21.1 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests) (1.26.16)\r\n",
"Requirement already satisfied: certifi>=2017.4.17 in /home/gturon/miniconda3/envs/ersilia/lib/python3.10/site-packages (from requests) (2023.7.22)\r\n"
]
}
],
"source": [
"%env MINICONDA_INSTALLER_SCRIPT=Miniconda3-py37_4.12.0-Linux-x86_64.sh\n",
"%env MINICONDA_PREFIX=/usr/local\n",
"%env PYTHONPATH= \"$PYTHONPATH:/usr/local/lib/python3.7/site-packages\"\n",
"%env PIP_ROOT_USER_ACTION=ignore\n",
"\n",
"!wget https://repo.anaconda.com/miniconda/$MINICONDA_INSTALLER_SCRIPT\n",
"!chmod +x $MINICONDA_INSTALLER_SCRIPT\n",
"!./$MINICONDA_INSTALLER_SCRIPT -b -f -p $MINICONDA_PREFIX\n",
"\n",
"!python -m pip install git+https://github.com/ersilia-os/ersilia.git\n",
"!python -m pip install requests --upgrade\n",
"!python -m pip install pandas\n",
"!rm $MINICONDA_INSTALLER_SCRIPT\n",
"import sys\n",
"\n",
"_ = sys.path.append(\"/usr/local/lib/python3.7/site-packages\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"execution": {
"iopub.execute_input": "2023-12-19T10:09:18.855989Z",
"iopub.status.busy": "2023-12-19T10:09:18.855723Z",
"iopub.status.idle": "2023-12-19T10:24:30.011293Z",
"shell.execute_reply": "2023-12-19T10:24:30.010724Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requested model eos4e41 is not available locally. Do you want to fetch it? [Y/n]🚀 Serving model eos4e41: chemprop-antibiotic-lite\n",
"\n",
" URL: http://0.0.0.0:52243\n",
" PID: -1\n",
" SRV: pulled_docker\n",
"\n",
"👉 To run model:\n",
" - run\n",
"\n",
" These APIs are also valid:\n",
" - predict\n",
"\n",
"💁 Information:\n",
" - info\n",
"⛔ Model eos4e41 closed\n"
]
}
],
"source": [
"from ersilia import ErsiliaModel\n",
"\n",
"em = ErsiliaModel(\"chemprop-antibiotic-lite\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"execution": {
"iopub.execute_input": "2023-12-19T10:24:30.013598Z",
"iopub.status.busy": "2023-12-19T10:24:30.013331Z",
"iopub.status.idle": "2023-12-19T10:24:50.154576Z",
"shell.execute_reply": "2023-12-19T10:24:50.153277Z"
}
},
"outputs": [],
"source": [
"smiles = [\n",
" \"CC1C2C(CC3(C=CC(=O)C(=C3C2OC1=O)C)C)O\",\n",
" \"C1=CN=CC=C1C(=O)NN\",\n",
" \"CC(CN1C=NC2=C(N=CN=C21)N)OCP(=O)(O)O\",\n",
" \"CC(=O)OC1=CC=CC=C1C(=O)O\",\n",
" \"CC(C)CC1=CC=C(C=C1)C(C)C(=O)O\",\n",
" \"CC1(OC2C(OC(C2O1)(C#N)C3=CC=C4N3N=CN=C4N)CO)C\",\n",
" \"COC1=CC23CCCN2CCC4=CC5=C(C=C4C3C1O)OCO5\",\n",
"]\n",
"\n",
"em.serve()\n",
"data = em.run(smiles, output=\"pandas\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"execution": {
"iopub.execute_input": "2023-12-19T10:24:50.160737Z",
"iopub.status.busy": "2023-12-19T10:24:50.160410Z",
"iopub.status.idle": "2023-12-19T10:24:50.166888Z",
"shell.execute_reply": "2023-12-19T10:24:50.166129Z"
}
},
"outputs": [],
"source": [
"data.to_csv(\"output-python-api.csv\", index=False)"
]
}
],
"metadata": {
"colab": {
"authorship_tag": "ABX9TyN10gxVjdZEkUFNqJRGD4EG",
"include_colab_link": true,
"provenance": []
},
"kernelspec": {
"display_name": "ersilia",
"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": "3.10.13"
},
"vscode": {
"interpreter": {
"hash": "f4425e10f64e35b5c2846e94987c1961ae0dce9f7acb7463ce8901870868cb33"
}
}
},
"nbformat": 4,
"nbformat_minor": 0
}

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