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daavid00 merged 2 commits into from
Nov 3, 2025
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Preparing for the release 2025.10 #10

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d338af8
Preparing for the release 2025.10
daavid00 Nov 3, 2025
0238e07
Setting back scikit-image==0.25.2 for Python 3.13
daavid00 Nov 3, 2025
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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/configs/*/
4 changes: 2 additions & 2 deletions CONTRIBUTING.md
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Expand Up @@ -18,7 +18,7 @@ Contributions are more than welcome using the fork and pull request approach
1. **mypy --ignore-missing-imports src/ tests/** (this is a static checker, and might rise issues that need to be fixed before the pull request)
1. **pytest --cov=pymm --cov-report term-missing tests/** (this runs locally the tests, and might rise issues that need to be fixed before the pull request)
1. **pushd docs & make html** (this generates the documentation, and might rise issues that need to be fixed before the pull request; if the build succeeds and if the contribution changes the documentation, then copy all content from the docs/_build/html/ folder and replace the files in the [_docs_](https://github.com/cssr-tools/pymm/tree/main/docs) folder)
* Tip: See the [_CI.yml_](https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml) script and the [_Actions_](https://github.com/cssr-tools/pymm/actions) for installation of _pymm_, as well as the execution of the six previous steps in Ubuntu 24.10 using Python 3.12.
* Tip: See the [_CI.yml_](https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml) script and the [_Actions_](https://github.com/cssr-tools/pymm/actions) for installation of _pymm_, as well as the execution of the six previous steps in Ubuntu 24.04 using Python 3.12.
1. Squash your commits into a single commit (see this [_nice tutorial_](https://gist.github.com/lpranam/4ae996b0a4bc37448dc80356efbca7fa) if you are not familiar with this)
1. Push your commit and make a pull request
1. The maintainers will review the pull request, and if the contribution is accepted, then it will be merge to the main repo
Expand All @@ -32,4 +32,4 @@ Contributions are more than welcome using the fork and pull request approach

1. The preferred approach to seek support is to raise an Issue as described in the previous lines.
1. We will try to answer as soon as possible, but also any user is more than welcome to answer.
- An alternative approach is to send an email to any of the [_mantainers_](https://github.com/cssr-tools/pymm/blob/main/pyproject.toml).
- An alternative approach is to send an email to any of the [_mantainers_](https://github.com/cssr-tools/pymm/blob/main/pyproject.toml).
6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -14,7 +14,7 @@ Creation of [_OpenFOAM_](https://www.openfoam.com) simulation models from given
## Installation
You will first need to install
* OpenFOAM (https://www.openfoam.com) (tested with OpenFOAM-13)
* Gmsh (https://gmsh.info) (tested with Gmsh 4.14.0)
* Gmsh (https://gmsh.info) (tested with Gmsh 4.15.0)

To install the _pymm_ executable from the development version:

Expand Down Expand Up @@ -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.
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.

## Running pymm
You can run _pymm_ as a single command line:
Expand All @@ -67,4 +67,4 @@ The following is a list of journal papers in which _pymm_ is used:
## About pymm
_pymm_, an image-based Python package for computational fluid dynamics, is funded by [_Center for Sustainable Subsurface Resources_](https://cssr.no) [project no. 331841] and [_NORCE Research As_](https://www.norceresearch.no) [project number 101070].
Contributions are more than welcome using the fork and pull request approach.
For a new feature, please request this by raising an issue.
For a new feature, please request this by raising an issue.
2 changes: 1 addition & 1 deletion dev-requirements.txt
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Expand Up @@ -4,4 +4,4 @@ mypy
pylint
pytest-cov
sphinx
sphinx-rtd-theme
sphinx-rtd-theme
Binary file added docs/_images/pofff.png
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6 changes: 3 additions & 3 deletions docs/_sources/about.rst.txt
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Expand Up @@ -6,9 +6,9 @@ About pymm
:scale: 35%

The image-based Python package for computational fluid dynamics **pymm** is funded by
Center for Sustainable Subsurface Resources [project no. 331841] and NORCE Norwegian
Research Centre As [project number 101070].
Center for Sustainable Subsurface Resources [project no. 331841] and NORCE
Research As [project number 101070].

Contributions are more than welcome using the fork and pull request approach.

For a new feature, please request this raising an issue.
For a new feature, please request this raising an issue.
2 changes: 1 addition & 1 deletion docs/_sources/api.rst.txt
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Expand Up @@ -9,4 +9,4 @@ The templates folder contains mako files.

Files in the pymm package.

.. include:: modules.rst
.. include:: modules.rst
4 changes: 2 additions & 2 deletions docs/_sources/contributing.rst.txt
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Expand Up @@ -29,7 +29,7 @@ Contribute to the software
#. **pushd docs & make html** (this generates the documentation, and might rise issues that need to be fixed before the pull request; if the build succeeds and if the contribution changes the documentation, then copy all content from the docs/_build/html/ folder and replace the files in the `docs <https://github.com/cssr-tools/pymm/tree/main/docs>`_ folder)

.. tip::
See the `CI.yml <https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml>`_ script and the `Actions <https://github.com/cssr-tools/pymm/actions>`_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.10.
See the `CI.yml <https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml>`_ script and the `Actions <https://github.com/cssr-tools/pymm/actions>`_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.04.

#. Squash your commits into a single commit (see this `nice tutorial <https://gist.github.com/lpranam/4ae996b0a4bc37448dc80356efbca7fa>`_ if you are not familiar with this)
#. Push your commit and make a pull request
Expand All @@ -49,4 +49,4 @@ Seek support
#. The preferred approach to seek support is to raise an Issue as described in the previous lines.
#. We will try to answer as soon as possible, but also any user is more than welcome to answer.

- An alternative approach is to send an email to any of the `mantainers <https://github.com/cssr-tools/pymm/blob/main/pyproject.toml>`_.
- An alternative approach is to send an email to any of the `mantainers <https://github.com/cssr-tools/pymm/blob/main/pyproject.toml>`_.
2 changes: 1 addition & 1 deletion docs/_sources/examples.rst.txt
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Expand Up @@ -101,4 +101,4 @@ The execution time was ca. 15 minutes and the following are screenshots of the s
.. figure:: figs/online_velocity.png
.. figure:: figs/online_tracer.png

Simulation results of the (top) pressure, (middle) velocity, and (bottom) tracer concentration.
Simulation results of the (top) pressure, (middle) velocity, and (bottom) tracer concentration.
4 changes: 3 additions & 1 deletion docs/_sources/installation.rst.txt
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Expand Up @@ -4,6 +4,8 @@ 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).

Python package
--------------
Expand Down Expand Up @@ -65,4 +67,4 @@ 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 Python3.13.
for installation of pymm in Ubuntu using Python 3.13.
2 changes: 1 addition & 1 deletion docs/_sources/output_folder.rst.txt
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Expand Up @@ -15,4 +15,4 @@ Then after running **pymm**, one could modify the generated OpenFOAM related fil
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
the numerical schemes (see the OpenFOAM documentation
`here <https://www.openfoam.com/documentation/user-guide/6-solving/6.2-numerical-schemes>`_).
`here <https://www.openfoam.com/documentation/user-guide/6-solving/6.2-numerical-schemes>`_).
10 changes: 9 additions & 1 deletion docs/_sources/related.rst.txt
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Expand Up @@ -13,6 +13,14 @@ pyopmspe11

`A Python framework using OPM Flow for the CSP SPE11 benchmark project <https://github.com/OPM/pyopmspe11>`_.

*****
pofff
*****

.. image:: ./figs/pofff.png

`An image-based history-matching framework for the FluidFlower Benchmark using OPM Flow <https://github.com/cssr-tools/pofff>`_.

******
pycopm
******
Expand Down Expand Up @@ -55,4 +63,4 @@ 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>`_.
`A module to study CO2 leakage remediation by microbially induced calcite precipitation (MICP) <https://github.com/daavid00/ad-micp>`_.
4 changes: 2 additions & 2 deletions docs/about.html
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Expand Up @@ -84,8 +84,8 @@ <h1>About pymm<a class="headerlink" href="#about-pymm" title="Link to this headi
<a class="reference internal image-reference" href="_images/pymm_logo.png"><img alt="_images/pymm_logo.png" src="_images/pymm_logo.png" style="width: 259.0px; height: 259.0px;" />
</a>
<p>The image-based Python package for computational fluid dynamics <strong>pymm</strong> is funded by
Center for Sustainable Subsurface Resources [project no. 331841] and NORCE Norwegian
Research Centre As [project number 101070].</p>
Center for Sustainable Subsurface Resources [project no. 331841] and NORCE
Research As [project number 101070].</p>
<p>Contributions are more than welcome using the fork and pull request approach.</p>
<p>For a new feature, please request this raising an issue.</p>
</section>
Expand Down
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Expand Up @@ -115,7 +115,7 @@ <h2>Contribute to the software<a class="headerlink" href="#contribute-to-the-sof
</ol>
<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 and the <a class="reference external" href="https://github.com/cssr-tools/pymm/actions">Actions</a> for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.10.</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 and the <a class="reference external" href="https://github.com/cssr-tools/pymm/actions">Actions</a> for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.04.</p>
</div>
</div></blockquote>
</li>
Expand Down
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Expand Up @@ -128,6 +128,7 @@ <h1>Welcome to pymm’s documentation!<a class="headerlink" href="#welcome-to-py
</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#pyopmspe11">pyopmspe11</a></li>
<li class="toctree-l2"><a class="reference internal" href="related.html#pofff">pofff</a></li>
<li class="toctree-l2"><a class="reference internal" href="related.html#pycopm">pycopm</a></li>
<li class="toctree-l2"><a class="reference internal" href="related.html#plopm">plopm</a></li>
<li class="toctree-l2"><a class="reference internal" href="related.html#pyopmnearwell">pyopmnearwell</a></li>
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6 changes: 4 additions & 2 deletions docs/installation.html
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Expand Up @@ -88,7 +88,9 @@
<section id="installation">
<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.</p>
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>
<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 @@ -140,7 +142,7 @@ <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 Python3.13.</p>
for installation of pymm in Ubuntu using Python 3.13.</p>
</div>
</section>
</section>
Expand Down
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Expand Up @@ -54,6 +54,7 @@
<li class="toctree-l1"><a class="reference internal" href="contributing.html">Contributing</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Related</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#pyopmspe11">pyopmspe11</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pofff">pofff</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pycopm">pycopm</a></li>
<li class="toctree-l2"><a class="reference internal" href="#plopm">plopm</a></li>
<li class="toctree-l2"><a class="reference internal" href="#pyopmnearwell">pyopmnearwell</a></li>
Expand Down Expand Up @@ -97,6 +98,11 @@ <h2>pyopmspe11<a class="headerlink" href="#pyopmspe11" title="Link to this headi
</a>
<p><a class="reference external" href="https://github.com/OPM/pyopmspe11">A Python framework using OPM Flow for the CSP SPE11 benchmark project</a>.</p>
</section>
<section id="pofff">
<h2>pofff<a class="headerlink" href="#pofff" title="Link to this heading"></a></h2>
<img alt="_images/pofff.png" src="_images/pofff.png" />
<p><a class="reference external" href="https://github.com/cssr-tools/pofff">An image-based history-matching framework for the FluidFlower Benchmark using OPM Flow</a>.</p>
</section>
<section id="pycopm">
<h2>pycopm<a class="headerlink" href="#pycopm" title="Link to this heading"></a></h2>
<a class="reference internal image-reference" href="_images/pycopm.png"><img alt="_images/pycopm.png" src="_images/pycopm.png" style="width: 699.52px; height: 295.68px;" />
Expand Down
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