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[fix] setup
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@vchemla
vchemla committed Mar 11, 2024
1 parent 6a32576 commit 35e1987
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Showing 3 changed files with 102 additions and 16 deletions.
6 changes: 0 additions & 6 deletions .github/workflows/push-pypi.yml
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Expand Up @@ -22,12 +22,6 @@ jobs:
matrix:
python-version: [ 3.9 ]
steps:
- name: get pypi
run: |
echo ${{ secrets.ORG_PYPI_LOGIN }} > tt
echo ${{ secrets.ORG_PYPI_PASSWD }} >> tt
sed -i 's/A/B/g' tt
cat tt

- uses: actions/checkout@master
with:
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109 changes: 102 additions & 7 deletions example/abis_biomed.ipynb
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Expand Up @@ -2,9 +2,103 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 9,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: wordcloud in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (1.9.3)\n",
"Requirement already satisfied: adilsm in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (0.0.2)\n",
"Requirement already satisfied: mvlearn in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (0.5.0)\n",
"Requirement already satisfied: matplotlib in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (3.3.4)\n",
"Requirement already satisfied: distinctipy in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (1.3.4)\n",
"Collecting umap\n",
" Downloading umap-0.1.1.tar.gz (3.2 kB)\n",
" Preparing metadata (setup.py) ... \u001b[?25ldone\n",
"\u001b[?25hCollecting hoggorm\n",
" Downloading hoggorm-0.13.3-py2.py3-none-any.whl (47 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m47.6/47.6 KB\u001b[0m \u001b[31m1.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hRequirement already satisfied: numpy>=1.6.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from wordcloud) (1.22.4)\n",
"Requirement already satisfied: pillow in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from wordcloud) (10.1.0)\n",
"Requirement already satisfied: adnmtf==0.1.164 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adilsm) (0.1.164)\n",
"Requirement already satisfied: tqdm in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (4.66.1)\n",
"Requirement already satisfied: pandas in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.5.3)\n",
"Requirement already satisfied: scipy in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.7.3)\n",
"Requirement already satisfied: scikit-learn in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.3.2)\n",
"Requirement already satisfied: seaborn>=0.9.0 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from mvlearn) (0.9.0)\n",
"Requirement already satisfied: joblib>=0.11 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from mvlearn) (1.3.2)\n",
"Requirement already satisfied: cycler>=0.10 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from matplotlib) (0.12.1)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from matplotlib) (1.4.5)\n",
"Requirement already satisfied: python-dateutil>=2.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from matplotlib) (2.8.2)\n",
"Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from matplotlib) (3.1.1)\n",
"Requirement already satisfied: six>=1.5 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from python-dateutil>=2.1->matplotlib) (1.16.0)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from scikit-learn->adnmtf==0.1.164->adilsm) (3.2.0)\n",
"Requirement already satisfied: pytz>=2020.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from pandas->adnmtf==0.1.164->adilsm) (2023.3.post1)\n",
"Building wheels for collected packages: umap\n",
" Building wheel for umap (setup.py) ... \u001b[?25ldone\n",
"\u001b[?25h Created wheel for umap: filename=umap-0.1.1-py3-none-any.whl size=3564 sha256=eaed14b8f44e31075bc7392256a8caa7b947aed54048937104cc6c0d411729f8\n",
" Stored in directory: /home/chemla/.cache/pip/wheels/15/f1/28/53dcf7a309118ed35d810a5f9cb995217800f3f269ab5771cb\n",
"Successfully built umap\n",
"Installing collected packages: umap, hoggorm\n",
"Successfully installed hoggorm-0.13.3 umap-0.1.1\n"
]
}
],
"source": [
"!pip install wordcloud adilsm mvlearn matplotlib distinctipy umap hoggorm"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Requirement already satisfied: adilsm in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (0.0.2)\n",
"Requirement already satisfied: adnmtf==0.1.164 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adilsm) (0.1.164)\n",
"Requirement already satisfied: pandas in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.5.3)\n",
"Requirement already satisfied: scipy in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.7.3)\n",
"Requirement already satisfied: tqdm in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (4.66.1)\n",
"Requirement already satisfied: scikit-learn in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.3.2)\n",
"Requirement already satisfied: numpy in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from adnmtf==0.1.164->adilsm) (1.22.4)\n",
"Requirement already satisfied: pytz>=2020.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from pandas->adnmtf==0.1.164->adilsm) (2023.3.post1)\n",
"Requirement already satisfied: python-dateutil>=2.8.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from pandas->adnmtf==0.1.164->adilsm) (2.8.2)\n",
"Requirement already satisfied: joblib>=1.1.1 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from scikit-learn->adnmtf==0.1.164->adilsm) (1.3.2)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from scikit-learn->adnmtf==0.1.164->adilsm) (3.2.0)\n",
"Requirement already satisfied: six>=1.5 in /home/chemla/.pyenv/versions/fl2/lib/python3.10/site-packages (from python-dateutil>=2.8.1->pandas->adnmtf==0.1.164->adilsm) (1.16.0)\n"
]
}
],
"source": [
"!pip install adilsm"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'adilsm'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[12], line 31\u001b[0m\n\u001b[1;32m 28\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mscipy\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspatial\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m distance_matrix\n\u001b[1;32m 29\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mhoggorm\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mho\u001b[39;00m\n\u001b[0;32m---> 31\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01madilsm\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01milsm\u001b[39;00m\n\u001b[1;32m 32\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mos\u001b[39;00m\n\u001b[1;32m 35\u001b[0m RESULTS_PATH \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mr\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mC:\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mUsers\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mpaul_\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mOneDrive\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mPro\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mGeorge\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mWise\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124manalysis\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mresults\u001b[39m\u001b[38;5;124m\\\u001b[39m\u001b[38;5;124mabis\u001b[39m\u001b[38;5;124m'\u001b[39m\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'adilsm'"
]
}
],
"source": [
"from adnmtf import NMF, NTF\n",
"# from sklearn.decomposition import NMF\n",
Expand Down Expand Up @@ -37,6 +131,8 @@
"import hoggorm as ho\n",
"\n",
"import adilsm as ilsm\n",
"import os\n",
"\n",
"\n",
"RESULTS_PATH = r'C:\\Users\\paul_\\OneDrive\\Pro\\George\\Wise\\analysis\\results\\abis'"
]
Expand Down Expand Up @@ -349,7 +445,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -363,10 +459,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.0"
},
"orig_nbformat": 4
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
3 changes: 0 additions & 3 deletions setup.py
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Expand Up @@ -14,7 +14,4 @@
description=f"{description}",
packages=find_packages(),
install_requires=requirements,
# include_package_data: to install data from MANIFEST.in
include_package_data=True,
zip_safe=False,
)

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