Deleted conflicting files from main to keep dev version

FAIRChemistry · Sep 21, 2024 · 96f4370 · 96f4370
2 parents bdc6ec2 + 6d27a7f
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -27,4 +27,8 @@ jobs:
 
       - name: Run tests with pytest
         run: |
+<<<<<<< HEAD
           poetry run pytest --nbval --nbval-lax
+=======
+          poetry run pytest
+>>>>>>> main
diff --git a/README.md b/README.md
@@ -1,13 +1,25 @@
+<<<<<<< HEAD
 # MTPHandler
 
 [![Documentation](https://img.shields.io/badge/Documentation-Online-blue.svg)](https://fairchemistry.github.io/MTPHandler/)
 [![Tests](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml/badge.svg)](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml)
 [![PyPI version](https://badge.fury.io/py/mtphandler.svg)](https://badge.fury.io/py/mtphandler)
+=======
+# MTPHandler - _🚧 currently unstable 🚧_
+
+[![Documentation](https://img.shields.io/badge/Documentation-Online-blue.svg)](https://fairchemistry.github.io/MTPHandler/)
+[![Tests](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml/badge.svg)](https://github.com/FAIRChemistry/MTPHandler/actions/workflows/tests.yml)
+[![PyPI version](https://badge.fury.io/py/MTPHandler.svg)](https://badge.fury.io/py/MTPHandler)
+>>>>>>> main
 
 
 ## ℹ️ Overview
 
+<<<<<<< HEAD
 `mtphandler` is a tool for managing and processing data from microtiter plates. It allows to directly read in the output files of various photometers, enabling low friction data processing. The tool facilitates a workflow for reading in raw data, assigning molecules with their respective concentration and and unit to wells. Furthermore, wells for creating a standard curve can be automatically detected and applied to different calibration models, which can be used to calculate the concentration of unknown samples. Finally, the plate data can be transformed into time-course concentration data in the EnzymeML format for subsequent analysis of the concentration data.
+=======
+MTPHandler is a tool for managing and processing data from microtiter plates. It allows to directly read in the output files of various photometers, enabling low friction data processing. The tool facilitates a workflow for reading in raw data, assigning molecules with their respective concentration and and unit to wells. Furthermore, wells for creating a standard curve can be automatically detected and applied to different calibration models, which can be used to calculate the concentration of unknown samples. Finally, the plate data can be transformed into time-course concentration data in the EnzymeML format for subsequent analysis of the concentration data.
+>>>>>>> main
 
 ``` mermaid
 graph LR
@@ -69,11 +81,21 @@ Install `MTPHandler` via pip:
 
 ```bash
 pip install MTPHandler # 🚧 not released yet
+<<<<<<< HEAD
 ```
 or from source:
 
 ```bash
 pip install git+https://github.com/FAIRChemistry/MTPHandler.git
+=======
+>>>>>>> main
 ```
+or from source:
 
-Please refer to the [documentation](https://fairchemistry.github.io/MTPHandler/) for more information on how to use the package.
+<<<<<<< HEAD
+Please refer to the [documentation](https://fairchemistry.github.io/MTPHandler/) for more information on how to use the package.
+=======
+```bash
+pip install git+https://github.com/FAIRChemistry/MTPHandler.git
+```
+>>>>>>> main
diff --git a/docs/examples/Untitled.ipynb b/docs/examples/Untitled.ipynb
@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "c07890c3-104b-44fd-80be-036ba82b90da",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%reload_ext autoreload\n",
+    "%autoreload 2\n",
+    "\n",
+    "from MTPHandler.core import Plate"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f3056b2c-3065-49e4-9b92-ca4047768f56",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ValueError",
+     "evalue": "Could not read file with implemented readers.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 4\u001b[0m\n\u001b[1;32m      1\u001b[0m path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/Users/max/Documents/GitHub/MTPHandler/tests/data/ BioTek_Epoch2.xlsx\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m----> 4\u001b[0m plate \u001b[38;5;241m=\u001b[39m \u001b[43mPlate\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfrom_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpath\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/Documents/GitHub/MTPHandler/MTPHandler/core/plate.py:920\u001b[0m, in \u001b[0;36mPlate.from_file\u001b[0;34m(cls, path, ph, wavelength, time, time_unit, temperature, temperature_unit)\u001b[0m\n\u001b[1;32m    909\u001b[0m \u001b[38;5;129m@classmethod\u001b[39m\n\u001b[1;32m    910\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mfrom_file\u001b[39m(\n\u001b[1;32m    911\u001b[0m     \u001b[38;5;28mcls\u001b[39m: Plate,\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    918\u001b[0m     temperature_unit: Optional[\u001b[38;5;28mstr\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m    919\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Plate:\n\u001b[0;32m--> 920\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mMTPReaderFactory\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m    921\u001b[0m \u001b[43m        \u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m    922\u001b[0m \u001b[43m        \u001b[49m\u001b[43mpath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpath\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    923\u001b[0m \u001b[43m        \u001b[49m\u001b[43mph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mph\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    924\u001b[0m \u001b[43m        \u001b[49m\u001b[43mwavelength\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mwavelength\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    925\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtime\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtime\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    926\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtime_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtime_unit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    927\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtemperature\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtemperature\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    928\u001b[0m \u001b[43m        \u001b[49m\u001b[43mtemperature_unit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtemperature_unit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m    929\u001b[0m \u001b[43m    \u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m~/Documents/GitHub/MTPHandler/MTPHandler/readers/factory.py:68\u001b[0m, in \u001b[0;36mMTPReaderFactory.read\u001b[0;34m(cls, path, ph, wavelength, time, time_unit, temperature, temperature_unit)\u001b[0m\n\u001b[1;32m     65\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m:\n\u001b[1;32m     66\u001b[0m     \u001b[38;5;28;01mpass\u001b[39;00m\n\u001b[0;32m---> 68\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCould not read file with implemented readers.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
+      "\u001b[0;31mValueError\u001b[0m: Could not read file with implemented readers."
+     ]
+    }
+   ],
+   "source": [
+    "path = \"/Users/max/Documents/GitHub/MTPHandler/tests/data/ BioTek_Epoch2.xlsx\"\n",
+    "\n",
+    "\n",
+    "plate = Plate.from_file(path)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "d5a1d177-cf90-4f20-824e-40f8063b9a58",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datetime import datetime as df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "dbf8c2e1-7945-4f69-8348-d340df36fe25",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<attribute 'day' of 'datetime.date' objects>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5860b0d3-97ae-43f7-8d92-a9c41f79451c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/examples/data/ BioTek_Epoch2.xlsx b/docs/examples/data/ BioTek_Epoch2.xlsx