Merge pull request #1 from martinvonk/dev

Update main to version 0.0.2

.github/workflows/python-publish.yml

@@ -0,0 +1,30 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python3 -m build
+          python3 -m twine upload --repository pypi dist/*

.gitignore

@@ -1,7 +1,13 @@
-
 *.pyc
 
+.mypy_cache/
+.pytest_cache/
+.ruff_cache/
+.tox/
+
 doc/examples/fig/
-.tox/*
+doc/literature/
+dist/
 src/pedon.egg-info/
 
+

README.md

@@ -2,9 +2,35 @@
 
 *from Greek: πέδον, pedon -> soil*
 
-Python package for (unsaturated) soil properties including pedotransfer functions. This package takes an object-oriented approach to soils, soil samples and soil models. Soil models include:
-- Mualem - Van Genuchten
-- Brooks - Corey
-- Fredlund & Xing
-- Gardner
-- Sorab Panday (Modflow-USG)
+Python package for (unsaturated) soil properties including pedotransfer functions. This package takes an object-oriented approach to soils, soil samples and soil models. Soil models that are available in this package are:
+  - [Mualem-Van Genuchten](http://www.soilphysics.okstate.edu/teaching/soil-6583/references-folder/van%20Genuchten%201980.pdf)
+  - [Brooks-Corey](https://www.wipp.energy.gov/library/cra/2009_cra/references/Others/Brooks_Corey_1964_Hydraulic_Properties_ERMS241117.pdf)
+  - [Fredlund & Xing](http://projects.mans.edu.eg/heepf/ilppp/cources/12/pdf%20course/1/pressure/osmotic%20soilsalinity22.pdf)
+  - Gardner
+  - Panday ([Modflow-USG](https://www.gsienv.com/product/modflow-usg/))
+
+This package can fit soil water retention curves and  using least squares (same as [RETC](https://www.pc-progress.com/Documents/programs/retc.pdf)) to measurements.
+
+Measurements for different soil properties and parameters are available from these datasets:
+  - [HYDRUS](https://www2.pc-progress.com/downloads/Pgm_Hydrus3D5/HYDRUS_user_Manual_V5.pdf)
+  - [VS2D](https://pubs.usgs.gov/wri/1983/4099/report.pdf)
+  - Staring Series ([2001](https://edepot.wur.nl/43272) & [2018](https://edepot.wur.nl/512761))
+
+Additionaly, there are pedotransfer functions implemented such as:
+  - Van Genuchten: [Wösten](https://www.sciencedirect.com/science/article/pii/S0016706198001323/pdfft?md5=6844f89c07deb81001c2a6eea6fc9e32&pid=1-s2.0-S0016706198001323-main.pdf)
+  - Van Genuchten: [Staring Series](https://edepot.wur.nl/43272)
+  - Brooks-Corey: [Cosby](https://hess.copernicus.org/articles/25/2445/2021/hess-25-2445-2021.pdf)
+
+## Installation
+To get the latest stable version install using:
+
+`pip install pedon`
+
+To get the development version download the GitHub code to your computer. Use cd to get to the download directory and install using:
+
+`pip install -e .`
+
+
+## Todo
+- [ ] Rosetta Pedotransfer Function
+- [ ] Other soil models such as Haverkamp

pyproject.toml

@@ -33,11 +33,17 @@ pytesting = ["pytest>=7", "pytest-cov", "pytest-sugar"]
 coveraging = ["coverage"]
 dev = ["pedon[linting,formatting,typing,pytesting]", "tox"]
 
+[tool.setuptools]
+include-package-data = true
+
 [tool.setuptools.dynamic]
 version = { attr = "pedon._version.__version__" }
 
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.setuptools.package-data]
-myModule = ["*.xlsx"]
+"pedon.datasets" = ["*.xlsx"]
 
 [tool.black]
 line-length = 88

src/pedon/__init__.py

@@ -3,4 +3,4 @@
 from . import _params, soil, soilmodel
 from ._version import __version__
 from .soil import Soil, SoilSample
-from .soilmodel import Brooks, Fredlund, Gardner, Genuchten, Sorab, plot_hcf, plot_swrc
+from .soilmodel import Brooks, Fredlund, Gardner, Genuchten, Panday, plot_hcf, plot_swrc

src/pedon/_params.py

@@ -66,7 +66,7 @@
 ].astype(float)
 pBrooks.loc[:, "swrc"] = pBrooks.loc[:, "swrc"].astype(bool)
 
-pSorab = DataFrame(
+pPanday = DataFrame(
     data={
         "p_ini": {
             "k_s": 50.0,
@@ -102,12 +102,12 @@
         },
     },
 )
-pSorab.loc[:, ["p_ini", "p_min", "p_max"]] = pSorab.loc[
+pPanday.loc[:, ["p_ini", "p_min", "p_max"]] = pPanday.loc[
     :, ["p_ini", "p_min", "p_max"]
 ].astype(float)
-pSorab.loc[:, "swrc"] = pSorab.loc[:, "swrc"].astype(bool)
+pPanday.loc[:, "swrc"] = pPanday.loc[:, "swrc"].astype(bool)
 
 
 def get_params(sm_name: str) -> DataFrame:
-    params = {"Genuchten": pGenuchten, "Brooks": pBrooks, "Sorab": pSorab}
+    params = {"Genuchten": pGenuchten, "Brooks": pBrooks, "Panday": pPanday}
     return params[sm_name].copy()

src/pedon/_version.py

@@ -1 +1 @@
-__version__ = "0.0.1"
+__version__ = "0.0.2"

src/pedon/soilmodel.py

@@ -28,6 +28,12 @@ def plot(self):
 
 @dataclass
 class Genuchten:
+    """Mualem- van Genuchten Soil Model
+
+    van Genuchten, M. Th. (1970) - A Closed-form Equation for Predicting the
+    Hydraulic Conductivity of Unsaturated Soil
+    """
+
     k_s: float
     theta_r: float
     theta_s: float
@@ -60,6 +66,11 @@ def plot(self):
 
 @dataclass
 class Brooks:
+    """Brooks and Corey Soil Model
+
+    Brooks, R.H. and Corey, A.T. (1964) - Hydraulic Properties of Porous Media
+    """
+
     k_s: float
     theta_r: float
     theta_s: float
@@ -103,6 +114,11 @@ def plot(self):
 
 @dataclass
 class Gardner:
+    """Gardner Soil Model
+
+    Gardner et al (1970) - Post-irrigation movement of soil water
+    """
+
     k_s: float
     theta_r: float
     theta_s: float
@@ -111,25 +127,28 @@ class Gardner:
     m: float
 
     def theta(self, h: FloatArray) -> FloatArray:
-        return self.theta_r + (self.theta_s - self.theta_r) * self.s(h)
+        return self.a * npabs(h) ** -self.b
 
     def s(self, h: FloatArray) -> FloatArray:
-        return 1 / (1 + npabs(h / self.a) ** self.b)
+        return (self.theta(h) - self.theta_r) / (self.theta_s - self.theta_r)
 
     def k(self, h: FloatArray, s: FloatArray | None = None) -> FloatArray:
         if s is not None:
-            raise NotImplementedError(
-                "Can only calculate the hydraulic conductivity"
-                "using the pressure head, not the saturation"
-            )
-        return self.k_s * exp(-self.a * h)
+            theta = s * (self.theta_s - self.theta_r) + self.theta_r
+            return self.k_s * self.a * theta**self.m
+        return self.k_s * (self.a / (self.b + npabs(h) ** self.m))
 
     def plot(self):
         return plot_swrc(self)
 
 
 @dataclass
-class Sorab:
+class Panday:
+    """Panday Soil Model (MODFLOW-USG)
+
+    Panday, S. - USG-Transport: Transport and other Enhancements to MODFLOW-USG
+    """
+
     k_s: float
     theta_r: float
     theta_s: float
@@ -158,6 +177,12 @@ def plot(self):
 
 @dataclass
 class Fredlund:
+    """Fredlund and Xing Soil Model
+
+    Fredlund, D.G. and Xing, A. (1994) - Equations for the soil-water
+    characteristic curve
+    """
+
     k_s: float
     theta_s: float
     a: float

tests/test_fit.py

@@ -1,5 +1,6 @@
-from numpy import array
 import pytest
+from numpy import array
+
 import pedon as pe
 
 

tests/test_ptf.py

@@ -1,4 +1,5 @@
 import pytest
+
 import pedon as pe
 
 

tests/test_soilmodel.py

@@ -1,5 +1,6 @@
 import pytest
 from numpy import logspace
+
 import pedon as pe
 from pedon._typing import FloatArray
 
@@ -18,7 +19,7 @@ def bro() -> pe.soilmodel.SoilModel:
 
 @pytest.fixture
 def sor() -> pe.soilmodel.SoilModel:
-    return pe.Sorab(k_s=10, theta_r=0.01, theta_s=0.43, alpha=0.02, beta=1.1, brook=3)
+    return pe.Panday(k_s=10, theta_r=0.01, theta_s=0.43, alpha=0.02, beta=1.1, brook=3)
 
 
 def test_theta_genuchten(gen: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
@@ -45,13 +46,13 @@ def test_k_brooks(bro: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
     bro.k(h=h)
 
 
-def test_theta_sorab(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
+def test_theta_panday(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
     sor.theta(h=h)
 
 
-def test_s_sorab(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
+def test_s_panday(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
     sor.s(h=h)
 
 
-def test_k_sorab(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
+def test_k_panday(sor: pe.soilmodel.SoilModel, h: FloatArray = h) -> None:
     sor.k(h=h)