LF-59602 Upgrade PyTOUGH master to v1.6.6

.github/workflows/publish.yml

@@ -0,0 +1,27 @@
+name: Build and publish PyTOUGH to PyPI
+
+on:
+  push:
+    branches:
+    - master
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        pip install setuptools wheel build
+    - name: Build
+      run: |
+        python -m build
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pythontest.yml

@@ -10,16 +10,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install --user numpy scipy
+        pip install --user numpy scipy layermesh
         pip install --user .
     - name: Unit tests
       run: |

.readthedocs.yaml

@@ -0,0 +1,21 @@
+# File: .readthedocs.yaml
+
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: doc/source/requirements.txt
+
+formats:
+  - pdf
+  - epub

IAPWS97.py

@@ -467,9 +467,11 @@ def density_temperature_plot(plt, subplot = 111):
     plt.plot(t, dw, color = 'k', marker = '', linestyle = '-')
     t = np.linspace(350, tcritical, 50)
     p = np.array([sat(tx) for tx in t])
-    def f(dx): return super(dx, tx)[0] - px
-    ds = np.array([fsolve(f, 120. + 25. / 200 * (tx - 350.)) for tx, px in zip(t, p)])
-    dw = np.array([fsolve(f, 560. - 25. / 200 * (tx - 350.)) for tx, px in zip(t, p)])
+    def f(dx, tx, px): return super(dx, tx)[0] - px
+    ds = np.array([fsolve(f, 120. + 25. / 200 * (tx - 350.), (tx, px))
+                   for tx, px in zip(t, p)])
+    dw = np.array([fsolve(f, 560. - 25. / 200 * (tx - 350.), (tx, px))
+                   for tx, px in zip(t, p)])
     plt.plot(t, ds, color = 'k', marker = '', linestyle = '-')
     plt.plot(t, dw, color = 'k', marker = '', linestyle = '-')
 
@@ -495,8 +497,8 @@ def f(dx): return super(dx, tx)[0] - px
     d = np.array([cowat(tx, p)[0] for tx in t])
     plt.plot(t, d, color = 'k', marker = '', linestyle = '--')
     t = np.linspace(350, 800, 100)
-    def g(dx): return super(dx, tx)[0] - p
-    d = np.array([fsolve(g, 1100 - tx) for tx in t])
+    def g(dx, tx, p): return super(dx, tx)[0] - p
+    d = np.array([fsolve(g, 1100 - tx, (tx, p)) for tx in t])
     plt.plot(t, d, color = 'k', marker = '', linestyle = '--')
 
     plt.axis([0, 800, 0, 1100])

LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
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README.md

@@ -1,28 +1,37 @@
-![Unit tests](https://github.com/acroucher/PyTOUGH/workflows/Unit%20tests/badge.svg)
+![Unit tests](https://github.com/acroucher/PyTOUGH/workflows/Unit%20tests/badge.svg) [![Documentation Status](https://readthedocs.org/projects/PyTOUGH/badge/?version=latest)](https://PyTOUGH.readthedocs.io/en/latest/?badge=latest) [![PyPI version](https://badge.fury.io/py/PyTOUGH.svg)](https://badge.fury.io/py/PyTOUGH) ![PyPI - Downloads](https://img.shields.io/pypi/dm/PyTOUGH)
+
 
 # What is PyTOUGH?
 
 PyTOUGH (Python TOUGH) is a Python library for simplifying, extending and automating the use of the [TOUGH2](http://esd.lbl.gov/research/projects/tough/) subsurface fluid and heat flow simulator. Using PyTOUGH, it is possible to automate the creation and editing of TOUGH2 model grids and data files, and the analysis and display of model simulation results, using Python scripts.
 
 # Installing PyTOUGH:
 
-First, make sure you have [Python](http://www.python.org) and the [Numerical Python](http://numpy.scipy.org/) library installed on your machine.  (For some features you will need other libraries such as [Scientific Python](http://www.scipy.org/) or [Matplotlib](http://matplotlib.sourceforge.net/)- consult the user guide for details.)
-
-Click the _Clone or download_ button at the right of the PyTOUGH web page and then click [Download ZIP](https://github.com/acroucher/PyTOUGH/archive/master.zip) , and save the .zip file to your computer.  Unzip this to any directory on your computer.  This will create a directory containing a file called `setup.py`.  At the command line type `python setup.py install`.
-
-(Alternatively, if you are confident using the Git version control system, you can clone the PyTOUGH repository instead of downloading a .zip file.)
+From version 1.6.0, PyTOUGH can be installed via the [`pip`](https://pip.pypa.io) Python package installer:
+
+```
+pip install PyTOUGH
+```
+You can also install a particular version of PyTOUGH, e.g. to install version 1.6.0:
+
+```
+pip install PyTOUGH==1.6.0
+```
+To uninstall PyTOUGH:
+```
+pip uninstall PyTOUGH
+```
+To install the `testing` branch, to get the most recent changes being tested for the next stable release:
+```
+pip install git+https://github.com/acroucher/PyTOUGH.git@testing
+```
 
 # More information:
 
-For more detailed information on PyTOUGH, consult the user guide (PDF format, in the 'doc' directory of your PyTOUGH install) and the PyTOUGH [wiki](https://github.com/acroucher/PyTOUGH/wiki/), which has links to published articles on PyTOUGH.
+For more detailed information on PyTOUGH, consult the [user guide](https://pytough.readthedocs.io) (html, or you can download PDF or Epub versions) and the PyTOUGH [wiki](https://github.com/acroucher/PyTOUGH/wiki/), which has links to published articles on PyTOUGH.
 
 # What's new in PyTOUGH?
 
-The latest stable version is 1.5.5, which has:
-
-* various bug fixes and other minor enhancements.
-
-# Where's the user guide?
-
-Since PyTOUGH version 1.3.6, the PyTOUGH user guide (PyTOUGH-guide.pdf) is now included in the 'doc' directory of your PyTOUGH install.  Previously this was available separately from the 'Downloads' section on the website, but GitHub decided to phase out this 'Downloads' section.
+The latest stable version is 1.6.6, which has:
 
+* ability to convert EOS3 models to Waiwera JSON input