Merge pull request #3 from daavid00/dev

Using toml, updating the docs, and CI with OpenFOAM 12

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-name: Build and test pymm
+name: Run pymm
 
 on:
  push:
@@ -43,9 +43,9 @@ jobs:
 
     - name: Check code style and linting 
       run: |
-        black --check src/ tests/ setup.py
-        pylint src/ tests/ setup.py
-        mypy --ignore-missing-imports src/ tests/ setup.py
+        black --check src/ tests/
+        pylint src/ tests/
+        mypy --ignore-missing-imports src/ tests/
       
     - name: Run the tests
       run: |

.gitignore

@@ -136,5 +136,6 @@ vpymm
 cssr
 debugging
 developing
+playgroud
 tests/configs/files
 tests/configs/output

README.md

@@ -1,5 +1,5 @@
 [![Build Status](https://github.com/cssr-tools/pymm/actions/workflows/CI.yml/badge.svg)](https://github.com/cssr-tools/pymm/actions/workflows/CI.yml)
-<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20|%203.9%20|%203.10-blue.svg"></a>
+<a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.8%20to%203.12-blue.svg"></a>
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8430989.svg)](https://doi.org/10.5281/zenodo.8430989)
@@ -12,10 +12,17 @@ This repository provides a workflow to perform computational fluid dynamics (CFD
 
 ## Installation
 You will first need to install
-* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-11)
-* Gmsh (https://gmsh.info) (tested with Gmsh 4.8.4) 
+* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-12)
+* Gmsh (https://gmsh.info) (tested with Gmsh 4.13.1)
+
+To install the _pymm_ executable in an existing Python environment: 
+
+```bash
+pip install git+https://github.com/cssr-tools/pymm.git
+```
+
+If you are interested in modifying the source code, then you can clone the repository and install the Python requirements in a virtual environment with the following commands:
 
-You will also need to install some Python packages, see ```requirements.txt``` for a complete list. You can install all the required Python packages in a virtual environment with the following commands:
 ```bash
 # Clone the repo
 git clone https://github.com/cssr-tools/pymm.git
@@ -27,21 +34,13 @@ python3 -m venv vpymm
 source vpymm/bin/activate
 # Upgrade pip, setuptools, and wheel
 pip install --upgrade pip setuptools wheel
-# Install the pymm package (in editable mode for contributions/modifications; otherwise, pip install .)
+# Install the pymm package
 pip install -e .
 # For contributions/testing/linting, install the dev-requirements
 pip install -r dev-requirements.txt
 ```
-Depending on the location where OpenFOAM is installed, then before running pymm (inside the vpymm Python environment), you need to enter the OpenFOAM environment:
-```bash
-# Check where openFOAM is installed
-echo $WM_PROJECT_DIR
-# The return value was /opt/openfoam11, then we activate the environment
-source /opt/openfoam11/etc/bashrc
-# Then, if everything went fine, typing 
-gmshToFoam
-# should print the argument flags for that OpenFOAM executable.
-```
+
+See the [_OpenFOAM page_](https://openfoam.org/download/12-ubuntu/), where from OpenFOAM-12 the simulator is available via apt get. 
 
 ## Running pymm
 You can run _pymm_ as a single command line:
@@ -51,7 +50,7 @@ pymm -i some_input_image.png -p some_input_parameters.txt -o some_output_folder
 Run `pymm --help` to see all possible command line argument options. Inside the `some_input_parameters.txt` file you provide the framework parameters such as the dimensions of the microsystem, mesh size, inlet pressure, and more. See the .txt files in the examples folder.
 
 ## Getting started
-See the [_documentation_](https://cssr-tools.github.io/pymm/introduction.html). 
+See the [_examples_](https://cssr-tools.github.io/pymm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pymm/introduction.html). 
 
 ## Journal papers using pymm
 The following is a list of journal papers in which _pymm_ is used:
@@ -61,5 +60,4 @@ The following is a list of journal papers in which _pymm_ is used:
 
 ## About pymm
 The image-based Python package for computational fluid dynamics pymm is funded by [_Center for Sustainable Subsurface Resources_](https://cssr.no) [project no. 331841] and [_NORCE Norwegian Research Centre As_](https://www.norceresearch.no) [project number 101070]. 
-
 Contributions are more than welcome using the fork and pull request approach.

dev-requirements.txt

@@ -1,6 +1,7 @@
 black
-pylint
+numpydoc
 mypy
+pylint
 pytest-cov
 sphinx
 sphinx-rtd-theme

docs/_sources/introduction.rst.txt

@@ -34,4 +34,8 @@ where
 Installation
 ------------
 
-See the `Github page <https://github.com/cssr-tools/pymm>`_.
+See the `Github page <https://github.com/cssr-tools/pymm>`_.
+
+.. tip::
+
+    See the `CI.yml <https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml>`_.

docs/_sources/related.rst.txt

@@ -2,8 +2,7 @@
 Related
 =======
 
-Below are some packages following the same configuration-file-to-postprocessing-folder approach; 
-check them out :).
+Below are some tools that might be of interest; check them out 🙂.
 
 **********
 pyopmspe11
@@ -23,14 +22,22 @@ pyopmnearwell
 
 `A framework to simulate near well dynamics using OPM Flow <https://github.com/daavid00/pyopmnearwell>`_.
 
-*******
-ad-micp
-*******
+******
+pycopm
+******
 
-.. image:: ./figs/ad-micp.gif
-    :scale: 40%
+.. image:: ./figs/pycopm.gif
+    :scale: 60%
+
+`Simplified and flexible framework for coarsening geological models <https://github.com/cssr-tools/pycopm>`_.
+
+*****
+plopm
+*****
+
+.. image:: ./figs/plopm.png
 
-`A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP) <https://github.com/daavid00/ad-micp>`_.
+`Quick generation of PNG figures from a simulation model given any 2D slide <https://github.com/cssr-tools/plopm>`_.
 
 ********
 expreccs
@@ -39,4 +46,13 @@ expreccs
 .. image:: ./figs/expreccs.gif
     :scale: 50%
 
-`Expansion of ResourCes for CO2 Storage on the Horda Platform <https://github.com/daavid00/expreccs>`_.
+`Expansion of ResourCes for CO2 Storage on the Horda Platform <https://github.com/daavid00/expreccs>`_.
+
+*******
+ad-micp
+*******
+
+.. image:: ./figs/ad-micp.gif
+    :scale: 40%
+
+`A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP) <https://github.com/daavid00/ad-micp>`_.

docs/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

docs/_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer