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Merge pull request #15 from daavid00/dev
Running OpenFOAM in the tests via CI.yml
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‎.github/workflows/CI.yml‎

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jobs:
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run-pymm-local:
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timeout-minutes: 30
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.13']
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os: [ubuntu-latest]
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runs-on: ${{ matrix.os }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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- name: Set up Python 3.13
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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python-version: 3.13
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- name: Install OpenFOAM
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run: |
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sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key > /etc/apt/trusted.gpg.d/openfoam.asc"
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sudo add-apt-repository http://dl.openfoam.org/ubuntu
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sudo apt-get update
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sudo apt -y install openfoam13
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- name: Install gmsh
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run: |
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- name: Run the tests
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run: |
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set +e
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source /opt/openfoam13/etc/bashrc
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set -e
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pytest --cov=pymm --cov-report term-missing tests/
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- name: Build documentation

‎.gitignore‎

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debugging
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developing
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playground
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**/tests/configs/*/
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tests/output

‎CITATION.cff‎

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- family-names: Landa-Marbán
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given-names: David
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orcid: "https://orcid.org/0000-0002-3343-1005"
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title: "py-micp: An Open-Source Simulation Workflow for Field-Scale Application of
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Microbially Induced Calcite Precipitation Technology for Leakage Remediation"
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version: "2025.10"
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year: 2025
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title: "pymm: An open-source image-based framework for CFD in microsystems"
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version: "2023.10"
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year: 2023
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doi: 10.5281/zenodo.8430988
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url: "https://github.com/cssr-tools/pymm"

‎README.md‎

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See the [_examples_](https://cssr-tools.github.io/pymm/examples.html) in the [_documentation_](https://cssr-tools.github.io/pymm/introduction.html).
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## Citing
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* Landa-Marbán, D. 2023. An open-source image-based framework for CFD in microsystems. https://doi.org/10.5281/zenodo.8430988.
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* Landa-Marbán, D. 2023. pymm: An open-source image-based framework for CFD in microsystems. https://doi.org/10.5281/zenodo.8430988.
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## Journal papers using pymm
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The following is a list of journal papers in which _pymm_ is used:

‎docs/_sources/installation.rst.txt‎

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The following steps work installing the dependencies in Linux via apt-get.
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While using package managers such as Anaconda, Miniforge, or Mamba might work, these are not tested.
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The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported
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(e.g., the porespy Python package is not yet available via pip install in Python 3.14).
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The supported Python versions are 3.12 and 3.13. We will update the documentation when Python3.14 is supported.
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Python package
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--------------
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.. code-block:: console
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. /opt/openfoam13/etc/bashrc
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source /opt/openfoam13/etc/bashrc
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foamRun -help
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Gmsh
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.. tip::
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See the `CI.yml <https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml>`_ script
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for installation of pymm in Ubuntu using Python 3.13.
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for installation of pymm, gmsh, and OpenFOAM-13 in Ubuntu using Python 3.13.

‎docs/about.html‎

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

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<hr/>
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<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
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<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
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‎docs/configuration_file.html‎

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<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
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<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
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‎docs/contributing.html‎

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<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
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<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
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‎docs/examples.html‎

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<p>&#169; Copyright 2022-2025, NORCE Research AS.</p>
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<p>&#169; Copyright 2022-2026, NORCE Research AS.</p>
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