Update main to v0.0.6

doc/examples/00_pedon_structure.ipynb

@@ -0,0 +1,169 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Package Structure**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Python Packages"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "import inspect\n",
+    "import pedon as pe"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Pedon Structure\n",
+    "\n",
+    "Pedon knows three classes;\n",
+    "- Soil\n",
+    "- SoilModel\n",
+    "- SoilSample\n",
+    "\n",
+    "The Soil class encapsulates the SoilModel and SoilSample class. The soil class has the following attributes:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'name': str,\n",
+       " 'model': pedon.soilmodel.SoilModel | None,\n",
+       " 'sample': pedon.soil.SoilSample | None,\n",
+       " 'source': str | None,\n",
+       " 'description': str | None}"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# main class\n",
+    "# containing both SoilModel and SoilSample\n",
+    "pe.Soil.__annotations__"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The name of the soil, the soil type (e.g. sand or clay) are strings. The source is the origin of the soil, and description contains extra information. The SoilModel is the relation between the pressure head, hydraulic conducitivity and water content. Possible SoilModels are:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['Brooks',\n",
+       " 'Fredlund',\n",
+       " 'Gardner',\n",
+       " 'Genuchten',\n",
+       " 'Panday',\n",
+       " 'Protocol',\n",
+       " 'SoilModel']"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# classes for soil models\n",
+    "soilmodels = [\n",
+    "    cls_name\n",
+    "    for cls_name, cls_obj in inspect.getmembers(sys.modules[\"pedon.soilmodel\"])\n",
+    "    if inspect.isclass(cls_obj)\n",
+    "]\n",
+    "soilmodels"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The SoilSample atttribute can contain measurements of the sand percentage `sand_p`, silt percentage `silt_p`, bulkd density `rho` or measurements of the pressure head `h` and the resulting hydraulic conductivity `k` or water content `theta`. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'sand_p': float | None,\n",
+       " 'silt_p': float | None,\n",
+       " 'clay_p': float | None,\n",
+       " 'rho': float | None,\n",
+       " 'th33': float | None,\n",
+       " 'th1500': float | None,\n",
+       " 'om_p': float | None,\n",
+       " 'm50': float | None,\n",
+       " 'h': float | numpy.ndarray[typing.Any, numpy.dtype[numpy.float64]] | None,\n",
+       " 'k': float | numpy.ndarray[typing.Any, numpy.dtype[numpy.float64]] | None,\n",
+       " 'theta': float | numpy.ndarray[typing.Any, numpy.dtype[numpy.float64]] | None}"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# class for sample measurements\n",
+    "pe.SoilSample.__annotations__"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pydon",
+   "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": "3.10.12"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

pyproject.toml

@@ -10,7 +10,7 @@ description = "Python package for (unsaturated) soil properties including pedotr
 readme = "README.md"
 license = { file = "LICENSE" }
 requires-python = ">=3.10"
-dependencies = ["numpy", "matplotlib", "pandas", "scipy", "openpyxl"]
+dependencies = ["numpy", "matplotlib", "pandas", "scipy"]
 classifiers = [
         'Programming Language :: Python :: 3 :: Only',
         'Programming Language :: Python :: 3.10',
@@ -33,6 +33,33 @@ pytesting = ["pytest>=7", "pytest-cov", "pytest-sugar"]
 coveraging = ["coverage"]
 dev = ["pedon[linting,formatting,typing,pytesting]", "tox"]
 
+[tool.poetry]
+name = "pedonenv"
+version = "0.0.0"
+description = "Development Virtual Environment"
+authors = ["poetry"]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+numpy = "^1.3"
+scipy = "^1.6"
+pandas = "^2.0"
+matplotlib = "^3.6"
+openpyxl = "^3.0"
+flake8 = "^6.1.0"
+ruff = "^0.1.9"
+black = { extras = ["jupyter"], version = "^23.12.1" }
+isort = "^5.13.2"
+mypy = "^1.8.0"
+pandas-stubs = "^2.1.4.231218"
+pytest = "^7.4.3"
+pytest-cov = "^4.1.0"
+pytest-sugar = "^0.9.7"
+coverage = "^7.3.4"
+tox = "^4.11.4"
+setuptools = "^69.0.3"
+ipykernel = "^6.28.0"
+
 [tool.setuptools]
 include-package-data = true
 
@@ -43,7 +70,7 @@ version = { attr = "pedon._version.__version__" }
 where = ["src"]
 
 [tool.setuptools.package-data]
-"pedon.datasets" = ["*.xlsx"]
+"pedon.datasets" = ["*.csv"]
 
 [tool.black]
 line-length = 88

src/pedon/_params.py

@@ -16,30 +16,19 @@
             "theta_s": 0.2,
             "alpha": 0.001,
             "n": 1.000001,
-            "l": -7,
+            "l": -7.0,
         },
         "p_max": {
             "k_s": 100000.0,
             "theta_r": 0.2,
             "theta_s": 0.9,
             "alpha": 0.20,
-            "n": 12,
-            "l": 8,
-        },
-        "swrc": {
-            "k_s": False,
-            "theta_r": True,
-            "theta_s": True,
-            "alpha": True,
-            "n": True,
-            "l": False,
+            "n": 12.0,
+            "l": 8.0,
         },
     },
+    dtype=float,
 )
-pGenuchten.loc[:, ["p_ini", "p_min", "p_max"]] = pGenuchten.loc[
-    :, ["p_ini", "p_min", "p_max"]
-].astype(float)
-pGenuchten.loc[:, "swrc"] = pGenuchten.loc[:, "swrc"].astype(bool)
 
 pBrooks = DataFrame(
     data={
@@ -51,21 +40,16 @@
             "h_b": 0.0001,
             "l": 0.1,
         },
-        "p_max": {"k_s": 100000.0, "theta_r": 0.2, "theta_s": 0.5, "h_b": 100, "l": 5},
-        "swrc": {
-            "k_s": False,
-            "theta_r": True,
-            "theta_s": True,
-            "h_b": True,
-            "l": True,
+        "p_max": {
+            "k_s": 100000.0,
+            "theta_r": 0.2,
+            "theta_s": 0.5,
+            "h_b": 100.0,
+            "l": 5.0,
         },
     },
+    dtype=float,
 )
-pBrooks.loc[:, ["p_ini", "p_min", "p_max"]] = pBrooks.loc[
-    :, ["p_ini", "p_min", "p_max"]
-].astype(float)
-pBrooks.loc[:, "swrc"] = pBrooks.loc[:, "swrc"].astype(bool)
-
 pPanday = DataFrame(
     data={
         "p_ini": {
@@ -89,23 +73,12 @@
             "theta_r": 0.2,
             "theta_s": 0.5,
             "alpha": 0.30,
-            "beta": 12,
+            "beta": 12.0,
             "brook": 50.0,
         },
-        "swrc": {
-            "k_s": False,
-            "theta_r": True,
-            "theta_s": True,
-            "alpha": True,
-            "beta": True,
-            "brook": False,
-        },
     },
+    dtype=float,
 )
-pPanday.loc[:, ["p_ini", "p_min", "p_max"]] = pPanday.loc[
-    :, ["p_ini", "p_min", "p_max"]
-].astype(float)
-pPanday.loc[:, "swrc"] = pPanday.loc[:, "swrc"].astype(bool)
 
 
 def get_params(sm_name: str) -> DataFrame: