Merge pull request #75 from sgfsweden/dev

release v0.3.0

Author: officialankan

README.md

@@ -7,11 +7,11 @@
 <p>
   <a href="https://pypi.org/project/gwrefpy/"><img src="https://img.shields.io/pypi/v/gwrefpy.svg" alt="PyPI version"></a>
   <a href="https://pypi.org/project/gwrefpy/"><img src="https://img.shields.io/pypi/pyversions/gwrefpy.svg" alt="Python versions"></a>
-  <a href="https://github.com/andersretznersgu/gwrefpy/blob/main/LICENSE"><img src="https://img.shields.io/github/license/andersretznersgu/gwrefpy.svg" alt="License"></a>
-  <a href="https://andersretznersgu.github.io/gwrefpy/"><img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" alt="Documentation"></a>
-  <a href="https://github.com/andersretznersgu/gwrefpy/actions"><img src="https://img.shields.io/github/actions/workflow/status/andersretznersgu/gwrefpy/ci.yml?branch=main" alt="Build status"></a>
+  <a href="https://github.com/sgfsweden/gwrefpy/blob/main/LICENSE"><img src="https://img.shields.io/github/license/andersretznersgu/gwrefpy.svg" alt="License"></a>
+  <a href="https://sgfsweden.github.io/gwrefpy/"><img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" alt="Documentation"></a>
+  <a href="https://github.com/sgfsweden/gwrefpy/actions"><img src="https://img.shields.io/github/actions/workflow/status/sgfsweden/gwrefpy/.github/workflows/publish_on_pypi.yml?branch=main" alt="Build status"></a>
   <a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff"></a>
-  <a href="https://github.com/andersretznersgu/gwrefpy"><img src="https://img.shields.io/github/stars/andersretznersgu/gwrefpy?style=social" alt="GitHub stars"></a>
+  <a href="https://github.com/sgfsweden/gwrefpy"><img src="https://img.shields.io/github/stars/sgfsweden/gwrefpy?style=social" alt="GitHub stars"></a>
 </p>
 
 A Python implementation of the Akvifär reference method for detecting deviations in groundwater level time series.

docs/conf.py

@@ -14,7 +14,7 @@
 project = "gwrefpy"
 copyright = ""
 author = ""
-release = "0.2.0"
+release = "0.3.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -50,6 +50,7 @@
 html_theme = "pydata_sphinx_theme"
 html_title = "gwrefpy"
 html_logo = "_static/figures/logo.png"
+html_favicon = "_static/figures/logo.png"
 html_theme_options = {
     "navbar_align": "content",
     "icon_links": [

docs/tutorials/exercises/1_exercise1.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "This notebook introduces how to create and fit a simple `gwrefpy` model. \n",
     "\n",
-    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorial/exercises/1_exerciese1.ipynb).\n",
+    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorials/exercises/1_exercise1.ipynb).\n",
     "\n",
     "In this exercise, you will:\n",
     "1. Import the `gwrefpy` package (already done for you)\n",

docs/tutorials/exercises/2_exercise2.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "This notebook introduces how to use the best fit method for a large `gwrefpy` model. \n",
     "\n",
-    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorial/exercises/1_exerciese1.ipynb).\n",
+    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorials/exercises/2_exercise2.ipynb).\n",
     "\n",
     "In this exercise, you will:\n",
     "1. Import the `gwrefpy` package and load the model (already done for you)\n",

docs/tutorials/exercises/3_exercise3.ipynb

@@ -8,7 +8,7 @@
     "\n",
     "This notebook introduces how to create and fit a simple `gwrefpy` model. \n",
     "\n",
-    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorial/exercises/1_exerciese1.ipynb).\n",
+    "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/tutorials/exercises/3_exercise3.ipynb).\n",
     "\n",
     "```{warning}\n",
     "This exercise is not completed yet.\n",

docs/tutorials/livedata.ipynb

@@ -1,55 +1,51 @@
 {
  "cells": [
   {
-   "metadata": {},
    "cell_type": "markdown",
+   "id": "f8ebfe5589158bd0",
+   "metadata": {},
    "source": [
     "# Saving and loading models\n",
     "\n",
     "This notebook introduces the concept of saving and loading `.gwref` files.\n",
     "\n",
     "This notebook can be downloaded from the source code [here](https://github.com/andersretznerSGU/gwrefpy/blob/main/docs/user_guide/5_io.ipynb).\n",
     "\n",
-    "# Saving a model 💾\n",
+    "## Saving a model 💾\n",
     "\n",
     "You can save a `gwrefpy` model to a `.gwref` file using the `save_project` function of the `Model` class. This function saves the model, including all wells and fits, to a specified file."
-   ],
-   "id": "f8ebfe5589158bd0"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "We will first create a simple model with one observed well and one reference well.",
-   "id": "a7d320daa081a770"
+   "id": "a7d320daa081a770",
+   "metadata": {},
+   "source": [
+    "We will first create a simple model with one observed well and one reference well."
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-19T06:19:23.202275Z",
-     "start_time": "2025-09-19T06:19:21.423475Z"
-    }
-   },
    "cell_type": "code",
+   "execution_count": 1,
+   "id": "ae7b6686cad2a72f",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import gwrefpy as gr\n",
     "import numpy as np\n",
     "import pandas as pd"
-   ],
-   "id": "ae7b6686cad2a72f",
-   "outputs": [],
-   "execution_count": 3
+   ]
   },
   {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "e9337241bbe35e1a",
    "metadata": {
     "tags": [
      "hide-input"
-    ],
-    "ExecuteTime": {
-     "end_time": "2025-09-19T06:19:23.878Z",
-     "start_time": "2025-09-19T06:19:23.865523Z"
-    }
+    ]
    },
-   "cell_type": "code",
+   "outputs": [],
    "source": [
     "# Create some example data\n",
     "n_days = 100\n",
@@ -68,19 +64,14 @@
     "    + np.random.normal(0, 0.05, n_days)\n",
     ")\n",
     "values_ref1 = pd.Series(values_ref1, index=dates)"
-   ],
-   "id": "e9337241bbe35e1a",
-   "outputs": [],
-   "execution_count": 4
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-19T06:19:25.524811Z",
-     "start_time": "2025-09-19T06:19:25.522288Z"
-    }
-   },
    "cell_type": "code",
+   "execution_count": 3,
+   "id": "dd1b89e7b780e90d",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# Creat the observed and reference wells\n",
     "obs1 = gr.Well(name=\"Obs. well\", is_reference=False)\n",
@@ -92,171 +83,150 @@
     "model1 = gr.Model(name=\"IO Model\")\n",
     "model1.add_well(obs1)\n",
     "model1.add_well(ref1)"
-   ],
-   "id": "dd1b89e7b780e90d",
-   "outputs": [],
-   "execution_count": 5
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
+   "id": "3f437ef415865dca",
+   "metadata": {},
    "source": [
     "We can now save the model to a `.gwref` file using the `save_project` function.\n",
     "```{note}\n",
     "The funciton will create the file in the current working directory if no path is specified.\n",
     "```"
-   ],
-   "id": "3f437ef415865dca"
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-19T06:21:35.698499Z",
-     "start_time": "2025-09-19T06:21:35.680754Z"
-    }
-   },
    "cell_type": "code",
-   "source": [
-    "# Save the model to a .gwref file\n",
-    "model1.save_project(\"my_model.gwref\")"
-   ],
+   "execution_count": 4,
    "id": "cff5a365dc580981",
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Model 'Logging Example Model' saved to 'example_model.gwref'.\n"
+      "Model 'IO Model' saved to 'my_model.gwref'.\n"
      ]
     }
    ],
-   "execution_count": 9
+   "source": [
+    "# Save the model to a .gwref file\n",
+    "model1.save_project(\"my_model.gwref\")"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
+   "id": "d2a3d40fe6011460",
+   "metadata": {},
    "source": [
     "You can now find the `my_model.gwref` files in your working directory. You can also give a path with the filename and the fild will be saved to that path, e.g. `\"path//to//folder//my_model.gwref\"`. \n",
     "```{warning}\n",
     "If the file already exists, a warning will be logged and the file will not be overwritten. You can set the ``overwrite`` variable to `True` to overwrite the existing file.\n",
     "\n",
     "The funciton will not create any folders in the specified path if they do not exist.\n",
     "```"
-   ],
-   "id": "d2a3d40fe6011460"
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-19T06:21:50.470844Z",
-     "start_time": "2025-09-19T06:21:50.464055Z"
-    }
-   },
    "cell_type": "code",
-   "source": [
-    "# Save the model to a .gwref file, allowing overwriting\n",
-    "model1.save_project(\"my_model.gwref\") # This will not overwrite the existing file and a warning will be logged\n",
-    "model1.save_project(\"my_model.gwref\", overwrite=True) # This will overwrite the existing file"
-   ],
+   "execution_count": 5,
    "id": "8927630e5d539af5",
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The file 'example_model.gwref' already exists. To overwrite the existing file set the argument 'overwrite' to True.\n",
-      "Model 'Logging Example Model' saved to 'example_model.gwref'.\n"
+      "The file 'my_model.gwref' already exists. To overwrite the existing file set the argument 'overwrite' to True.\n",
+      "Model 'IO Model' saved to 'my_model.gwref'.\n"
      ]
     }
    ],
-   "execution_count": 10
+   "source": [
+    "# Save the model to a .gwref file, allowing overwriting\n",
+    "model1.save_project(\"my_model.gwref\") # This will not overwrite the existing file and a warning will be logged\n",
+    "model1.save_project(\"my_model.gwref\", overwrite=True) # This will overwrite the existing file"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
+   "id": "ab0429e99fb8f13e",
+   "metadata": {},
    "source": [
     "## Loading Models 📦\n",
     "You can load a model from a `.gwref` file using the `open_project` function from the `Model` class. This function reads the model from the specified file and saves it to the `Model` object. The model will include all wells and fits that were saved in the file.\n",
     "\n",
     "There are two ways to load a model:\n",
     "1. Create a new `Model` object and use the `open_project` method.\n",
     "2. Specify the `.gwref` file directly when creating a new `Model` object."
-   ],
-   "id": "ab0429e99fb8f13e"
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-18T11:56:24.801814Z",
-     "start_time": "2025-09-18T11:56:24.769652Z"
-    }
-   },
    "cell_type": "code",
-   "source": [
-    "# Method 1: Create a new Model object and load the project\n",
-    "loaded_model1 = gr.Model(name=\"Name will be overwritten\")\n",
-    "loaded_model1.open_project(\"my_model.gwref\")"
-   ],
+   "execution_count": 6,
    "id": "30f2208061681fe",
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Model 'Logging Example Model' loaded from 'example_model.gwref'.\n"
+      "Model 'IO Model' loaded from 'my_model.gwref'.\n"
      ]
     }
    ],
-   "execution_count": 3
+   "source": [
+    "# Method 1: Create a new Model object and load the project\n",
+    "loaded_model1 = gr.Model(name=\"Name will be overwritten\")\n",
+    "loaded_model1.open_project(\"my_model.gwref\")"
+   ]
   },
   {
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-09-18T11:56:24.887100Z",
-     "start_time": "2025-09-18T11:56:24.877035Z"
-    }
-   },
    "cell_type": "code",
-   "source": [
-    "# Method 2: Directly load the project into a new Model object\n",
-    "loaded_model2 = gr.Model(\"my_model.gwref\")"
-   ],
+   "execution_count": 7,
    "id": "5b2b524c40b0d03",
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Model 'Logging Example Model' loaded from 'example_model.gwref'.\n"
+      "Model 'IO Model' loaded from 'my_model.gwref'.\n"
      ]
     }
    ],
-   "execution_count": 4
+   "source": [
+    "# Method 2: Directly load the project into a new Model object\n",
+    "loaded_model2 = gr.Model(\"my_model.gwref\")"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "This concludes this notebook on saving and loading models in `gwrefpy`.",
-   "id": "e30b422c68de2ecf"
+   "id": "e30b422c68de2ecf",
+   "metadata": {},
+   "source": [
+    "This concludes this notebook on saving and loading models in `gwrefpy`."
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "pygments_lexer": "ipython3",
+   "version": "3.11.2"
   }
  },
  "nbformat": 4,