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daavid00 merged 1 commit into from
Jan 3, 2026
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Running OpenFOAM in the tests via CI.yml #15

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22 changes: 13 additions & 9 deletions .github/workflows/CI.yml
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Expand Up @@ -9,23 +9,24 @@ on:
jobs:
run-pymm-local:
timeout-minutes: 30
strategy:
fail-fast: false
matrix:
python-version: ['3.13']
os: [ubuntu-latest]

runs-on: ${{ matrix.os }}
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0

- name: Set up Python ${{ matrix.python-version }}
- name: Set up Python 3.13
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
python-version: 3.13

- name: Install OpenFOAM
run: |
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

- name: Install gmsh
run: |
Expand All @@ -50,6 +51,9 @@ jobs:

- name: Run the tests
run: |
set +e
source /opt/openfoam13/etc/bashrc
set -e
pytest --cov=pymm --cov-report term-missing tests/

- name: Build documentation
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -137,4 +137,4 @@ cssr
debugging
developing
playground
**/tests/configs/*/
tests/output
7 changes: 3 additions & 4 deletions CITATION.cff
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Expand Up @@ -4,9 +4,8 @@ authors:
- family-names: Landa-Marbán
given-names: David
orcid: "https://orcid.org/0000-0002-3343-1005"
title: "py-micp: An Open-Source Simulation Workflow for Field-Scale Application of
Microbially Induced Calcite Precipitation Technology for Leakage Remediation"
version: "2025.10"
year: 2025
title: "pymm: An open-source image-based framework for CFD in microsystems"
version: "2023.10"
year: 2023
doi: 10.5281/zenodo.8430988
url: "https://github.com/cssr-tools/pymm"
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -56,7 +56,7 @@ Run `pymm --help` to see all possible command line argument options. Inside the
See the [_examples_](https://cssr-tools.github.io/pymm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pymm/introduction.html).

## Citing
* Landa-Marbán, D. 2023. An open-source image-based framework for CFD in microsystems. https://doi.org/10.5281/zenodo.8430988.
* Landa-Marbán, D. 2023. pymm: An open-source image-based framework for CFD in microsystems. https://doi.org/10.5281/zenodo.8430988.

## Journal papers using pymm
The following is a list of journal papers in which _pymm_ is used:
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7 changes: 3 additions & 4 deletions docs/_sources/installation.rst.txt
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Expand Up @@ -4,8 +4,7 @@ Installation

The following steps work installing the dependencies in Linux via apt-get.
While using package managers such as Anaconda, Miniforge, or Mamba might work, these are not tested.
The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported
(e.g., the porespy Python package is not yet available via pip install in Python 3.14).
The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported.

Python package
--------------
Expand Down Expand Up @@ -55,7 +54,7 @@ and OpenFOAM-13 is the latest release. To test if OpenFoam is installed and work

.. code-block:: console

. /opt/openfoam13/etc/bashrc
source /opt/openfoam13/etc/bashrc
foamRun -help

Gmsh
Expand All @@ -67,4 +66,4 @@ 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 in Ubuntu using Python 3.13.
for installation of pymm, gmsh, and OpenFOAM-13 in Ubuntu using Python 3.13.
2 changes: 1 addition & 1 deletion docs/about.html
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Expand Up @@ -100,7 +100,7 @@ <h1>About pymm<a class="headerlink" href="#about-pymm" title="Link to this headi
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/api.html
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Expand Up @@ -128,7 +128,7 @@ <h2>pymm<a class="headerlink" href="#pymm" title="Link to this heading"></a><
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/configuration_file.html
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Expand Up @@ -208,7 +208,7 @@ <h2>Remaining parameters<a class="headerlink" href="#remaining-parameters" title
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/contributing.html
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Expand Up @@ -154,7 +154,7 @@ <h2>Seek support<a class="headerlink" href="#seek-support" title="Link to this h
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/examples.html
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Expand Up @@ -202,7 +202,7 @@ <h2>Online<a class="headerlink" href="#online" title="Link to this heading"><
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/genindex.html
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Expand Up @@ -202,7 +202,7 @@ <h2 id="W">W</h2>
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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Expand Up @@ -159,7 +159,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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9 changes: 4 additions & 5 deletions docs/installation.html
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Expand Up @@ -89,8 +89,7 @@
<h1>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h1>
<p>The following steps work installing the dependencies in Linux via apt-get.
While using package managers such as Anaconda, Miniforge, or Mamba might work, these are not tested.
The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported
(e.g., the porespy Python package is not yet available via pip install in Python 3.14).</p>
The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported.</p>
<section id="python-package">
<h2>Python package<a class="headerlink" href="#python-package" title="Link to this heading"></a></h2>
<p>To install the <strong>pymm</strong> executable from the development version:</p>
Expand Down Expand Up @@ -131,7 +130,7 @@ <h2>Python package<a class="headerlink" href="#python-package" title="Link to th
<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">. /opt/openfoam13/etc/bashrc</span>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">source /opt/openfoam13/etc/bashrc</span>
<span class="go">foamRun -help</span>
</pre></div>
</div>
Expand All @@ -142,7 +141,7 @@ <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 in Ubuntu using Python 3.13.</p>
for installation of pymm, gmsh, and OpenFOAM-13 in Ubuntu using Python 3.13.</p>
</div>
</section>
</section>
Expand All @@ -158,7 +157,7 @@ <h2>Gmsh<a class="headerlink" href="#gmsh" title="Link to this heading"></a><
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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2 changes: 1 addition & 1 deletion docs/introduction.html
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Expand Up @@ -127,7 +127,7 @@ <h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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2 changes: 1 addition & 1 deletion docs/modules.html
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Expand Up @@ -106,7 +106,7 @@ <h1>pymm<a class="headerlink" href="#pymm" title="Link to this heading"></a><
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/output_folder.html
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Expand Up @@ -110,7 +110,7 @@ <h1>Output folder<a class="headerlink" href="#output-folder" title="Link to this
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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2 changes: 1 addition & 1 deletion docs/py-modindex.html
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Expand Up @@ -116,7 +116,7 @@ <h1>Python Module Index</h1>
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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Expand Up @@ -122,7 +122,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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Expand Up @@ -225,7 +225,7 @@
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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Expand Up @@ -129,7 +129,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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Expand Up @@ -145,7 +145,7 @@ <h2>ad-micp<a class="headerlink" href="#ad-micp" title="Link to this heading">
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

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Expand Up @@ -99,7 +99,7 @@
<hr/>

<div role="contentinfo">
<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
</div>

Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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