Updated projects before checkout

Author: TineClaeys

.gitignore

@@ -1,3 +1,6 @@
 *.pkl
 ./Projects/Arnaud/*
-*.csv
+*.csv
+Projects/SCP_slavov/2024_Khan_testis/npop5_DIANN_report.tsv
+Projects/Cell_lines/metadata.xlsx
+Projects/Cell_lines/data.xlsx

Projects/Cell_lines/classify.ipynb

@@ -7,6 +7,49 @@
     "PROBLEEM in sample validation"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Processing /home/compomics/git/MLMarker/dist/mlmarker-0.1.0-py3-none-any.whl\n",
+      "Requirement already satisfied: shap==0.46.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.46.0)\n",
+      "Requirement already satisfied: numpy in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (1.26.4)\n",
+      "Requirement already satisfied: scipy in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (1.12.0)\n",
+      "Requirement already satisfied: scikit-learn in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (1.1.3)\n",
+      "Requirement already satisfied: pandas in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (2.2.2)\n",
+      "Requirement already satisfied: tqdm>=4.27.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (4.66.4)\n",
+      "Requirement already satisfied: packaging>20.9 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (23.2)\n",
+      "Requirement already satisfied: slicer==0.0.8 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (0.0.8)\n",
+      "Requirement already satisfied: numba in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (0.60.0)\n",
+      "Requirement already satisfied: cloudpickle in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (3.0.0)\n",
+      "Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from numba->shap==0.46.0->mlmarker==0.1.0) (0.43.0)\n",
+      "Requirement already satisfied: python-dateutil>=2.8.2 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pandas->shap==0.46.0->mlmarker==0.1.0) (2.9.0)\n",
+      "Requirement already satisfied: pytz>=2020.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pandas->shap==0.46.0->mlmarker==0.1.0) (2024.1)\n",
+      "Requirement already satisfied: tzdata>=2022.7 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pandas->shap==0.46.0->mlmarker==0.1.0) (2023.3)\n",
+      "Requirement already satisfied: joblib>=1.0.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from scikit-learn->shap==0.46.0->mlmarker==0.1.0) (1.1.0)\n",
+      "Requirement already satisfied: threadpoolctl>=2.0.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from scikit-learn->shap==0.46.0->mlmarker==0.1.0) (3.5.0)\n",
+      "Requirement already satisfied: six>=1.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from python-dateutil>=2.8.2->pandas->shap==0.46.0->mlmarker==0.1.0) (1.16.0)\n",
+      "mlmarker is already installed with the same version as the provided wheel. Use --force-reinstall to force an installation of the wheel.\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
+   "source": [
+    "pip install /home/compomics/git/MLMarker/dist/mlmarker-0.1.0-py3-none-any.whl\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

Projects/SCP_slavov/2024_Khan_testis/classify.ipynb

@@ -4,10 +4,12 @@
     name='MLMarker_app',
     version='0.1',
     description="MLMarker is a Python package for tissue-specific protein marker prediction",
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
     author="Tine Claeys",
     author_email="tineclae.claeys@ugent.be",
-    packages=find_packages(),
-    include_package_data=True,
+    packages=find_packages(include=["mlmarker", "mlmarker.*"]),  # Include only relevant package
+    include_package_data=True,  # Respect MANIFEST.in
     package_data={
         "mlmarker": ["models/*.joblib", "models/*.txt"]
     },

results_quant.tar.gz

@@ -2,19 +2,105 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import MLMarker_app\n",
     "import pandas as pd\n",
     "import numpy as np\n",
-    "from MLMarker_app import MLMarker\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "import random\n",
     "import re"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Processing ./dist/mlmarker-0.1.0-py3-none-any.whl\n",
+      "Requirement already satisfied: ace in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.3.3)\n",
+      "Requirement already satisfied: dask in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (2024.8.0)\n",
+      "Requirement already satisfied: datashader in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.16.3)\n",
+      "Requirement already satisfied: easydev in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.13.2)\n",
+      "Requirement already satisfied: joblib in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (1.1.0)\n",
+      "Requirement already satisfied: matplotlib in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (3.7.2)\n",
+      "Requirement already satisfied: numpy in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (1.26.4)\n",
+      "Requirement already satisfied: pandas in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (2.2.2)\n",
+      "Requirement already satisfied: plotly in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (5.24.0)\n",
+      "Requirement already satisfied: scipy in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (1.12.0)\n",
+      "Requirement already satisfied: seaborn in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.13.2)\n",
+      "Requirement already satisfied: shap==0.46.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.46.0)\n",
+      "Requirement already satisfied: sklearn in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.0)\n",
+      "Requirement already satisfied: umap-learn in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from mlmarker==0.1.0) (0.5.6)\n",
+      "Requirement already satisfied: scikit-learn in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (1.1.3)\n",
+      "Requirement already satisfied: tqdm>=4.27.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (4.66.4)\n",
+      "Requirement already satisfied: packaging>20.9 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (23.2)\n",
+      "Requirement already satisfied: slicer==0.0.8 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (0.0.8)\n",
+      "Requirement already satisfied: numba in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (0.60.0)\n",
+      "Requirement already satisfied: cloudpickle in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from shap==0.46.0->mlmarker==0.1.0) (3.0.0)\n",
+      "Requirement already satisfied: click>=8.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (8.1.7)\n",
+      "Requirement already satisfied: fsspec>=2021.09.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (2024.9.0)\n",
+      "Requirement already satisfied: partd>=1.4.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (1.4.2)\n",
+      "Requirement already satisfied: pyyaml>=5.3.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (6.0.1)\n",
+      "Requirement already satisfied: toolz>=0.10.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (0.12.0)\n",
+      "Requirement already satisfied: importlib-metadata>=4.13.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from dask->mlmarker==0.1.0) (7.0.1)\n",
+      "Requirement already satisfied: colorcet in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (3.1.0)\n",
+      "Requirement already satisfied: multipledispatch in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (1.0.0)\n",
+      "Requirement already satisfied: param in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (2.1.1)\n",
+      "Requirement already satisfied: pillow in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (10.4.0)\n",
+      "Requirement already satisfied: pyct in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (0.5.0)\n",
+      "Requirement already satisfied: requests in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (2.32.3)\n",
+      "Requirement already satisfied: xarray in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from datashader->mlmarker==0.1.0) (2024.7.0)\n",
+      "Requirement already satisfied: colorama<0.5.0,>=0.4.6 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from easydev->mlmarker==0.1.0) (0.4.6)\n",
+      "Requirement already satisfied: colorlog<7.0.0,>=6.8.2 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from easydev->mlmarker==0.1.0) (6.8.2)\n",
+      "Requirement already satisfied: line-profiler<5.0.0,>=4.1.2 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from easydev->mlmarker==0.1.0) (4.1.3)\n",
+      "Requirement already satisfied: pexpect<5.0.0,>=4.9.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from easydev->mlmarker==0.1.0) (4.9.0)\n",
+      "Requirement already satisfied: platformdirs<5.0.0,>=4.2.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from easydev->mlmarker==0.1.0) (4.2.2)\n",
+      "Requirement already satisfied: contourpy>=1.0.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (1.2.0)\n",
+      "Requirement already satisfied: cycler>=0.10 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (0.11.0)\n",
+      "Requirement already satisfied: fonttools>=4.22.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (4.51.0)\n",
+      "Requirement already satisfied: kiwisolver>=1.0.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (1.4.4)\n",
+      "Requirement already satisfied: pyparsing<3.1,>=2.3.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (3.0.9)\n",
+      "Requirement already satisfied: python-dateutil>=2.7 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (2.9.0)\n",
+      "Requirement already satisfied: importlib-resources>=3.2.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from matplotlib->mlmarker==0.1.0) (6.4.0)\n",
+      "Requirement already satisfied: pytz>=2020.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pandas->mlmarker==0.1.0) (2024.1)\n",
+      "Requirement already satisfied: tzdata>=2022.7 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pandas->mlmarker==0.1.0) (2023.3)\n",
+      "Requirement already satisfied: tenacity>=6.2.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from plotly->mlmarker==0.1.0) (8.2.3)\n",
+      "Requirement already satisfied: pynndescent>=0.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from umap-learn->mlmarker==0.1.0) (0.5.13)\n",
+      "Requirement already satisfied: zipp>=0.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from importlib-metadata>=4.13.0->dask->mlmarker==0.1.0) (3.17.0)\n",
+      "Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from numba->shap==0.46.0->mlmarker==0.1.0) (0.43.0)\n",
+      "Requirement already satisfied: locket in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from partd>=1.4.0->dask->mlmarker==0.1.0) (1.0.0)\n",
+      "Requirement already satisfied: ptyprocess>=0.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from pexpect<5.0.0,>=4.9.0->easydev->mlmarker==0.1.0) (0.7.0)\n",
+      "Requirement already satisfied: six>=1.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib->mlmarker==0.1.0) (1.16.0)\n",
+      "Requirement already satisfied: threadpoolctl>=2.0.0 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from scikit-learn->shap==0.46.0->mlmarker==0.1.0) (3.5.0)\n",
+      "Requirement already satisfied: charset-normalizer<4,>=2 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from requests->datashader->mlmarker==0.1.0) (3.3.2)\n",
+      "Requirement already satisfied: idna<4,>=2.5 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from requests->datashader->mlmarker==0.1.0) (3.7)\n",
+      "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from requests->datashader->mlmarker==0.1.0) (2.2.2)\n",
+      "Requirement already satisfied: certifi>=2017.4.17 in /home/compomics/miniconda3/envs/mlmarker/lib/python3.9/site-packages (from requests->datashader->mlmarker==0.1.0) (2024.8.30)\n",
+      "mlmarker is already installed with the same version as the provided wheel. Use --force-reinstall to force an installation of the wheel.\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
+   "source": [
+    "pip install dist/mlmarker-0.1.0-py3-none-any.whl"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import mlmarker"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 22,