openfoam14

.github/workflows/CI.yml

@@ -1,13 +1,13 @@
 name: Run pymm
 
 on:
- push:
-   branches:
-     - main
  pull_request:
 
 jobs:
   run-pymm-local:
+    permissions:
+      contents: read
+      pull-requests: write
     timeout-minutes: 30
     runs-on: ubuntu-latest
 
@@ -26,7 +26,7 @@ jobs:
         sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key > /etc/apt/trusted.gpg.d/openfoam.asc"
         sudo add-apt-repository http://dl.openfoam.org/ubuntu
         sudo apt-get update
-        sudo apt -y install openfoam13
+        sudo apt -y install openfoam14
 
     - name: Install gmsh
       run: |
@@ -44,17 +44,17 @@ jobs:
 
     - name: Check code style and linting 
       run: |
-        black --target-version py312 --check src/ tests/
+        black --target-version py312 src/ tests/ --check
         pylint src/ tests/
         ruff check src/ tests/
         mypy --ignore-missing-imports src/ tests/
 
     - name: Run the tests
       run: |
         set +e
-        source /opt/openfoam13/etc/bashrc
+        source /opt/openfoam14/etc/bashrc
         set -e
-        pytest --cov=pymm --exitfirst --cov-report term-missing --basetemp=test_outputs tests/
+        pytest --cov=pymm --cov-report term-missing --basetemp=test_outputs tests/ --exitfirst
 
     - name: Build documentation
       run: |

README.md

@@ -9,11 +9,11 @@
 <img src="docs/text/figs/pymm.gif" width="830" height="700">
 
 ## Main feature
-Creation of [_OpenFOAM_](https://www.openfoam.com) simulation models from given input images using [_Gmsh_](https://gmsh.info).
+Creation of [_OpenFOAM_](https://openfoam.org) simulation models from given input images using [_Gmsh_](https://gmsh.info).
 
 ## Installation
 You will first need to install
-* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-13)
+* OpenFOAM (https://openfoam.org) (tested with OpenFOAM-14)
 * Gmsh (https://gmsh.info) (tested with Gmsh 4.15.2)
 
 To install the _pymm_ executable from the development version: 
@@ -43,7 +43,7 @@ pip install -e .
 pip install -r dev-requirements.txt
 ```
 
-See the [_OpenFOAM page_](https://openfoam.org/download/13-ubuntu/), where from OpenFOAM-12 the simulator is available via apt get, and OpenFOAM-13 is the latest release. 
+See the [_OpenFOAM page_](https://openfoam.org/download/14-ubuntu/), where from OpenFOAM-12 the simulator is available via apt get, and OpenFOAM-14 is the latest release. 
 
 ## Running pymm
 You can run _pymm_ as a single command line:

docs/_sources/installation.rst.txt

@@ -46,11 +46,11 @@ OpenFOAM
 --------
 
 See the `OpenFOAM page <https://openfoam.org/download/13-ubuntu/>`_, where from OpenFOAM-12 the simulator is available via apt get,
-and OpenFOAM-13 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:
+and OpenFOAM-14 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:
 
 .. code-block:: console
 
-    source /opt/openfoam13/etc/bashrc    
+    source /opt/openfoam14/etc/bashrc    
     foamRun -help
 
 Gmsh
@@ -62,4 +62,4 @@ See the `Gmsh page <https://gmsh.info/#Download>`_.
 .. tip::
 
     See the `CI.yml <https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml>`_ script 
-    for installation of pymm, gmsh, and OpenFOAM-13 in Ubuntu using Python 3.14.
+    for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu using Python 3.14.

docs/_sources/introduction.rst.txt

@@ -12,7 +12,7 @@ Description
 The **pymm** tool relies on Python packages (e.g., `skimage <https://scikit-image.org>`_) to generate the spatial domains for the simulations from
 the microsystem images, and `Gmsh <https://gmsh.info>`_ as a mesh generator. 
 The numerical simulations for the water flow and tracer are performed using 
-the `OpenFOAM <https://www.openfoam.com>`_ simulator. This framework could be applied to general images and 
+the `OpenFOAM <https://openfoam.org>`_ simulator. This framework could be applied to general images and 
 the current implementation could be ('easily') extended to consider further 
 geometry of devices and solvers in OpenFOAM.
 

docs/_sources/output_folder.rst.txt

@@ -10,7 +10,7 @@ executing **pymm**.
     Generated files after executing **pymm**.
 
 The simulation results are saved in the VTK_flowSTokes and VTK_tracerTransport folders, and
-`paraview <https://www.paraview.orgs>`_ is used for the visualization.
+`paraview <https://www.paraview.org>`_ is used for the visualization.
 Then after running **pymm**, one could modify the generated OpenFOAM related files and 
 run directly the simulations calling the OpenFOAM solvers, e.g., to change additional 
 tolerances that are not currently included in the parameters.toml file and/or to change 

docs/installation.html

@@ -124,8 +124,8 @@ <h2>Python package<a class="headerlink" href="#python-package" title="Link to th
 <section id="openfoam">
 <h2>OpenFOAM<a class="headerlink" href="#openfoam" title="Link to this heading"></a></h2>
 <p>See the <a class="reference external" href="https://openfoam.org/download/13-ubuntu/">OpenFOAM page</a>, where from OpenFOAM-12 the simulator is available via apt get,
-and OpenFOAM-13 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">source /opt/openfoam13/etc/bashrc</span>
+and OpenFOAM-14 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:</p>
+<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">source /opt/openfoam14/etc/bashrc</span>
 <span class="go">foamRun -help</span>
 </pre></div>
 </div>
@@ -136,7 +136,7 @@ <h2>Gmsh<a class="headerlink" href="#gmsh" title="Link to this heading"></a><
 <div class="admonition tip">
 <p class="admonition-title">Tip</p>
 <p>See the <a class="reference external" href="https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml">CI.yml</a> script
-for installation of pymm, gmsh, and OpenFOAM-13 in Ubuntu using Python 3.14.</p>
+for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu using Python 3.14.</p>
 </div>
 </section>
 </section>

docs/introduction.html

@@ -93,7 +93,7 @@ <h2>Description<a class="headerlink" href="#description" title="Link to this hea
 <p>The <strong>pymm</strong> tool relies on Python packages (e.g., <a class="reference external" href="https://scikit-image.org">skimage</a>) to generate the spatial domains for the simulations from
 the microsystem images, and <a class="reference external" href="https://gmsh.info">Gmsh</a> as a mesh generator.
 The numerical simulations for the water flow and tracer are performed using
-the <a class="reference external" href="https://www.openfoam.com">OpenFOAM</a> simulator. This framework could be applied to general images and
+the <a class="reference external" href="https://openfoam.org">OpenFOAM</a> simulator. This framework could be applied to general images and
 the current implementation could be (‘easily’) extended to consider further
 geometry of devices and solvers in OpenFOAM.</p>
 </section>

docs/output_folder.html

@@ -91,7 +91,7 @@ <h1>Output folder<a class="headerlink" href="#output-folder" title="Link to this
 </figcaption>
 </figure>
 <p>The simulation results are saved in the VTK_flowSTokes and VTK_tracerTransport folders, and
-<a class="reference external" href="https://www.paraview.orgs">paraview</a> is used for the visualization.
+<a class="reference external" href="https://www.paraview.org">paraview</a> is used for the visualization.
 Then after running <strong>pymm</strong>, one could modify the generated OpenFOAM related files and
 run directly the simulations calling the OpenFOAM solvers, e.g., to change additional
 tolerances that are not currently included in the parameters.toml file and/or to change