Merge pull request #1 from cssr-tools/development

Updating to cssr-tools
cssr-tools · Feb 16, 2024 · 4bc488b · 4bc488b
2 parents 34b8678 + 95149ee
commit 4bc488b
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diff --git a/.gitignore b/.gitignore
@@ -133,6 +133,7 @@ dmypy.json
 
 # Extra folders
 vpymm
+cssr
 debugging
 developing
 tests/configs/files

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://github.com/daavid00/pymm/actions/workflows/CI.yml/badge.svg)](https://github.com/daavid00/pymm/actions/workflows/CI.yml)
+[![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>
 [![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)
@@ -18,7 +18,7 @@ You will first need to install
 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/daavid00/pymm.git
+git clone https://github.com/cssr-tools/pymm.git
 # Get inside the folder
 cd pymm
 # Create virtual environment
@@ -32,7 +32,7 @@ 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:
+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
@@ -51,7 +51,7 @@ 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://daavid00.github.io/pymm/introduction.html). 
+See 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:

diff --git a/docs/_images/contents.png b/docs/_images/contents.png
diff --git a/docs/_images/pyopmcsp11.gif → docs/_images/pyopmspe11.gif b/docs/_images/pyopmcsp11.gif → docs/_images/pyopmspe11.gif
diff --git a/docs/_sources/image.rst.txt b/docs/_sources/image.rst.txt
@@ -5,7 +5,7 @@ Image
 In this example we consider the micromodel described in the
 :doc:`configuration file<./configuration_file>` section.
 
-The image is available in the examples folder in the `Github page <https://github.com/daavid00/pymm>`_
+The image is available in the examples folder in the `Github page <https://github.com/cssr-tools/pymm>`_
 with the default name 'microsystem.png'. The configuration file corresponds to the one in the 
 :doc:`configuration file<./configuration_file>` section and it is saved as 'parameters.txt' 
 (the default name for the configuration file). Since 'image' is the default entry for the simulation

diff --git a/docs/_sources/introduction.rst.txt b/docs/_sources/introduction.rst.txt
@@ -34,4 +34,4 @@ where
 Installation
 ------------
 
-See the `Github page <https://github.com/daavid00/pymm>`_.
+See the `Github page <https://github.com/cssr-tools/pymm>`_.
diff --git a/docs/_sources/related.rst.txt b/docs/_sources/related.rst.txt
@@ -6,13 +6,13 @@ Below are some packages following the same configuration-file-to-postprocessing-
 check them out :).
 
 **********
-pyopmcsp11
+pyopmspe11
 **********
 
-.. image:: ./figs/pyopmcsp11.gif
+.. image:: ./figs/pyopmspe11.gif
     :scale: 50%
 
-`A Python framework using OPM Flow for the CSP11 benchmark project <https://github.com/daavid00/pyopmcsp11>`_.
+`A Python framework using OPM Flow for the CSP SPE11 benchmark project <https://github.com/OPM/pyopmspe11>`_.
 
 *************
 pyopmnearwell

diff --git a/docs/about.html b/docs/about.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>About pymm &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -96,7 +98,7 @@ <h1>About pymm<a class="headerlink" href="#about-pymm" title="Link to this headi
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/api.html b/docs/api.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>pymm Python API &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -126,7 +128,7 @@ <h2>pymm<a class="headerlink" href="#pymm" title="Link to this heading"></a><
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/configuration_file.html b/docs/configuration_file.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Configuration file &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -206,7 +208,7 @@ <h2>Remaining parameters<a class="headerlink" href="#remaining-parameters" title
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/device.html b/docs/device.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Device &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -109,7 +111,7 @@ <h1>Device<a class="headerlink" href="#device" title="Link to this heading"><
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/examples.html b/docs/examples.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Examples &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -89,7 +91,7 @@ <h1>Examples<a class="headerlink" href="#examples" title="Link to this heading">
 <h2>Image<a class="headerlink" href="#image" title="Link to this heading"></a></h2>
 <p>In this example we consider the micromodel described in the
 <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> section.</p>
-<p>The image is available in the examples folder in the <a class="reference external" href="https://github.com/daavid00/pymm">Github page</a>
+<p>The image is available in the examples folder in the <a class="reference external" href="https://github.com/cssr-tools/pymm">Github page</a>
 with the default name ‘microsystem.png’. The configuration file corresponds to the one in the
 <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> section and it is saved as ‘parameters.txt’
 (the default name for the configuration file). Since ‘image’ is the default entry for the simulation
@@ -199,7 +201,7 @@ <h2>Online<a class="headerlink" href="#online" title="Link to this heading"><
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -1,11 +1,13 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -202,7 +204,7 @@ <h2 id="W">W</h2>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/image.html b/docs/image.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Image &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -80,7 +82,7 @@
 <h1>Image<a class="headerlink" href="#image" title="Link to this heading"></a></h1>
 <p>In this example we consider the micromodel described in the
 <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> section.</p>
-<p>The image is available in the examples folder in the <a class="reference external" href="https://github.com/daavid00/pymm">Github page</a>
+<p>The image is available in the examples folder in the <a class="reference external" href="https://github.com/cssr-tools/pymm">Github page</a>
 with the default name ‘microsystem.png’. The configuration file corresponds to the one in the
 <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> section and it is saved as ‘parameters.txt’
 (the default name for the configuration file). Since ‘image’ is the default entry for the simulation
@@ -113,7 +115,7 @@ <h1>Image<a class="headerlink" href="#image" title="Link to this heading"></a
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/index.html b/docs/index.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Welcome to pymm’s documentation! &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -112,7 +114,7 @@ <h1>Welcome to pymm’s documentation!<a class="headerlink" href="#welcome-to-py
 </li>
 <li class="toctree-l1"><a class="reference internal" href="output_folder.html">Output folder</a></li>
 <li class="toctree-l1"><a class="reference internal" href="related.html">Related</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="related.html#pyopmcsp11">pyopmcsp11</a></li>
+<li class="toctree-l2"><a class="reference internal" href="related.html#pyopmspe11">pyopmspe11</a></li>
 <li class="toctree-l2"><a class="reference internal" href="related.html#pyopmnearwell">pyopmnearwell</a></li>
 <li class="toctree-l2"><a class="reference internal" href="related.html#ad-micp">ad-micp</a></li>
 <li class="toctree-l2"><a class="reference internal" href="related.html#expreccs">expreccs</a></li>
@@ -141,7 +143,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/introduction.html b/docs/introduction.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Introduction &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -111,7 +113,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
 </section>
 <section id="installation">
 <h2>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h2>
-<p>See the <a class="reference external" href="https://github.com/daavid00/pymm">Github page</a>.</p>
+<p>See the <a class="reference external" href="https://github.com/cssr-tools/pymm">Github page</a>.</p>
 </section>
 </section>
 
@@ -126,7 +128,7 @@ <h2>Installation<a class="headerlink" href="#installation" title="Link to this h
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/modules.html b/docs/modules.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>pymm &mdash; pymm  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -104,7 +106,7 @@ <h1>pymm<a class="headerlink" href="#pymm" title="Link to this heading"></a><
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022-2023, NORCE Norwegian Research Centre AS.</p>
+    <p>&#169; Copyright 2022-2024, NORCE Norwegian Research Centre AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a