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clean-up example
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@r-trimbour
r-trimbour committed Jul 12, 2024
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52 changes: 2 additions & 50 deletions Examples/Minimal_example.ipynb
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"cells": [
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "4f0a488c-3d0c-481b-a63f-0d4e76f89c95",
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: circe-py in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (0.1.8)\n",
"Requirement already satisfied: joblib<2.0.0,>=1.1.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (1.4.2)\n",
"Requirement already satisfied: numpy<2.0.0,>=1.25.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (1.26.4)\n",
"Requirement already satisfied: pandas<3.0.0,>=2.1.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (2.2.2)\n",
"Requirement already satisfied: rich<11.0.0,>=10.12.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (10.16.2)\n",
"Requirement already satisfied: scanpy<2.0.0,>=1.8.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (1.10.2)\n",
"Requirement already satisfied: scikit-learn<2.0.0,>=1.3.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from circe-py) (1.5.1)\n",
"Requirement already satisfied: python-dateutil>=2.8.2 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from pandas<3.0.0,>=2.1.1->circe-py) (2.9.0)\n",
"Requirement already satisfied: pytz>=2020.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from pandas<3.0.0,>=2.1.1->circe-py) (2024.1)\n",
"Requirement already satisfied: tzdata>=2022.7 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from pandas<3.0.0,>=2.1.1->circe-py) (2024.1)\n",
"Requirement already satisfied: colorama<0.5.0,>=0.4.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from rich<11.0.0,>=10.12.0->circe-py) (0.4.6)\n",
"Requirement already satisfied: commonmark<0.10.0,>=0.9.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from rich<11.0.0,>=10.12.0->circe-py) (0.9.1)\n",
"Requirement already satisfied: pygments<3.0.0,>=2.6.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from rich<11.0.0,>=10.12.0->circe-py) (2.18.0)\n",
"Requirement already satisfied: anndata>=0.8 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.10.8)\n",
"Requirement already satisfied: h5py>=3.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (3.11.0)\n",
"Requirement already satisfied: legacy-api-wrap>=1.4 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (1.4)\n",
"Requirement already satisfied: matplotlib>=3.6 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (3.9.1)\n",
"Requirement already satisfied: natsort in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (8.4.0)\n",
"Requirement already satisfied: networkx>=2.7 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (3.3)\n",
"Requirement already satisfied: numba>=0.56 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.60.0)\n",
"Requirement already satisfied: packaging>=21.3 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (24.1)\n",
"Requirement already satisfied: patsy in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.5.6)\n",
"Requirement already satisfied: pynndescent>=0.5 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.5.13)\n",
"Requirement already satisfied: scipy>=1.8 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (1.14.0)\n",
"Requirement already satisfied: seaborn>=0.13 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.13.2)\n",
"Requirement already satisfied: session-info in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (1.0.0)\n",
"Requirement already satisfied: statsmodels>=0.13 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.14.2)\n",
"Requirement already satisfied: tqdm in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (4.66.4)\n",
"Requirement already satisfied: umap-learn!=0.5.0,>=0.5 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scanpy<2.0.0,>=1.8.1->circe-py) (0.5.6)\n",
"Requirement already satisfied: threadpoolctl>=3.1.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from scikit-learn<2.0.0,>=1.3.1->circe-py) (3.5.0)\n",
"Requirement already satisfied: array-api-compat!=1.5,>1.4 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from anndata>=0.8->scanpy<2.0.0,>=1.8.1->circe-py) (1.7.1)\n",
"Requirement already satisfied: contourpy>=1.0.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (1.2.1)\n",
"Requirement already satisfied: cycler>=0.10 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (0.12.1)\n",
"Requirement already satisfied: fonttools>=4.22.0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (4.53.1)\n",
"Requirement already satisfied: kiwisolver>=1.3.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (1.4.5)\n",
"Requirement already satisfied: pillow>=8 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (10.4.0)\n",
"Requirement already satisfied: pyparsing>=2.3.1 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy<2.0.0,>=1.8.1->circe-py) (3.1.2)\n",
"Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from numba>=0.56->scanpy<2.0.0,>=1.8.1->circe-py) (0.43.0)\n",
"Requirement already satisfied: six>=1.5 in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from python-dateutil>=2.8.2->pandas<3.0.0,>=2.1.1->circe-py) (1.16.0)\n",
"Requirement already satisfied: stdlib-list in /home/rtrimbou/miniconda3/envs/test_circe_pip/lib/python3.12/site-packages (from session-info->scanpy<2.0.0,>=1.8.1->circe-py) (0.10.0)\n",
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"outputs": [],
"source": [
"pip install circe-py"
]
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