Updating the docs

.github/workflows/CI.yml

@@ -9,23 +9,17 @@ on:
 jobs:
   run-pofff-local:
     timeout-minutes: 30
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.12']
-        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 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.12
 
     - name: Install Flow Simulator
       run: |
@@ -58,7 +52,7 @@ jobs:
 
     - name: Run the tests
       run: |
-        pytest --cov=pofff --cov-report term-missing tests/
+        pytest -x --cov=pofff --cov-report term-missing tests/
 
     - name: Build documentation
       run: |

docs/_sources/examples.rst.txt

@@ -22,8 +22,7 @@ Adding your results
 ===================
 
 The `publication <https://github.com/cssr-tools/pofff/blob/main/publication>`_ folder contains the configuration files used for the results in the
-`pofff paper <https://arxiv.org/abs/2510.20614>`_ (see :doc:`publication <./publication>` for details in the steps to reproduce the figures in the paper). 
-For example, running inside that folder:
+`pofff paper <https://arxiv.org/abs/2510.20614>`_ (see :doc:`publication <./publication>` for details in the steps to reproduce the figures in the paper).
 
 .. code-block:: bash
 
@@ -77,3 +76,36 @@ see/run the scripts in the `tests <https://github.com/OPM/pyopmspe11/blob/main/t
     After the runs, one can always use pofff to postprocess the data and generate the figures, running with the flag **-m none** (see the 
     `profiling.py <https://github.com/cssr-tools/pofff/blob/main/publication/sprofiling.py>`_ for an example of splitting the generation of the files, running of everest, and postprocessing).
     Please raise an issue for missing keywords in the toml configuration files that you would like to be added.
+
+=============
+Visualization
+=============
+To postprocess the data, `plopm <https://github.com/cssr-tools/plopm>`_ can be used. 
+
+.. tip::
+    You can install `plopm <https://github.com/cssr-tools/plopm>`_ by executing in the terminal:
+
+    .. code-block:: bash
+
+        pip install git+https://github.com/cssr-tools/plopm.git
+
+For example, if you run the `appendixb.toml <https://github.com/cssr-tools/pofff/blob/main/publication/appendixb.toml>`_ configuration file and change the 'inj' variable in line 17 to:
+
+.. code-block:: bash
+
+    inj=[[8100, 300, 3E-7, 0], 
+    [10200, 300, 3E-7, 3E-7],
+    [3300, 300, 0, 0], 
+    [64800, 3600, 0, 0], 
+    [345600, 21600, 0, 0]]
+
+Then the following GIF is generated by:
+
+    .. code-block:: bash
+
+        pofff -i appendixb.toml -o plopm -m single -c '5e-2' -f none
+        plopm -v xco2l -i plopm/PLOPM -d 8,2.5 -mask satnum -m gif -dpi 1000 -f 12 -loop 1 -cformat .2f -cbsfax 0.30,0.01,0.4,0.02 -remove 0,0,1,0 -interval 437.5 -maskthr 1e-5 -tunits h
+
+.. image:: ./figs/plopm_xco2l.gif
+
+See the `plopm online docmunetation <https://cssr-tools.github.io/plopm/>`_ for additional information of supported flag parameters to generate customized PNGs and GIFs.

docs/_sources/installation.rst.txt

@@ -7,6 +7,18 @@ While using package managers such as Anaconda, Miniforge, or Mamba might work, t
 update the documentation when Python 3.14 is supported (e.g., the ert Python package is not yet available
 via pip install in Python 3.14).
 
+`ResInsight <https://resinsight.org>`_ and `plopm <https://github.com/cssr-tools/plopm>`_ can be used for the visualization of the results.
+
+.. note::
+
+    There are binary packages for Linux and Windows to install Resinsight, see the `ResInsight Documentation <https://resinsight.org/releases/>`_. For macOS users, you could try to install it using `brew <https://brew.sh>`_ by executing:
+
+    .. code-block:: bash
+
+        brew install cssr-tools/opm/resinsight
+
+    Then, you should be able to open resinsight by typing in the terminal **resinsight**.
+
 .. _vpofff:
 
 Python package
@@ -44,6 +56,14 @@ install the Python requirements in a virtual environment with the following comm
 
     Typing **git tag -l** writes all available specific versions.
 
+.. note::
+
+    For not macOS users, to install the (optional but recommended) dependencies used for the figure's LaTeX formatting, execute 
+
+    **sudo apt-get install texlive-fonts-recommended texlive-fonts-extra dvipng cm-super**
+
+    For macOS users, the LaTeX dependency can be installed from https://www.tug.org/mactex/
+
 .. _opmflow:
 
 OPM Flow
@@ -52,6 +72,13 @@ You also need to install:
 
 * OPM Flow (https://opm-project.org, Release 2025.10 or current master branches)
 
+Binary packages
++++++++++++++++
+
+See the `downloading and installing <https://opm-project.org/?page_id=36>`_ OPM Flow online documentation for 
+instructions to install the binary packages in Ubuntu and Red Hat Enterprise Linux, and for other platforms which are
+supported either via source builds or through running a virtual machine.
+
 .. tip::
 
     See the `CI.yml <https://github.com/cssr-tools/pofff/blob/main/.github/workflows/CI.yml>`_ script 
@@ -89,30 +116,40 @@ in the terminal the following lines (which in turn should build flow in the fold
 
 .. _macOS:
 
+Brew formula for macOS
+++++++++++++++++++++++
+For macOS, there are no available binary packages, so OPM Flow needs to be built from source. Recently, a formula to build flow using brew has
+been added in `https://github.com/cssr-tools/homebrew-opm <https://github.com/cssr-tools/homebrew-opm>`_. 
+Then, you can try to install flow (v2025.10) by simply typing:
+
+.. code-block:: console
+
+    brew install cssr-tools/opm/opm-simulators
+
+You can check if the installation of OPM Flow succeded by typing in the terminal **flow \-\-help**.
+
+.. tip::
+    See the actions in the `cssr-tools/homebrew-opm <https://github.com/cssr-tools/homebrew-opm/actions>`_ repository.
+
 Source build in macOS
 +++++++++++++++++++++
-For macOS, there are no available binary packages, so OPM Flow needs to be built from source, in addition to the dune libraries 
-(see the `prerequisites <https://opm-project.org/?page_id=239>`_, which can be installed using macports or brew). For example,
-with brew the prerequisites can be installed by:
+If you would like to build the latest OPM Flow from the master branch, then you can first install the prerequisites using brew:
 
 .. code-block:: console
 
     brew install boost cmake openblas suite-sparse python@3.13
 
 In addition, it is recommended to upgrade and update your macOS to the latest available versions (the following steps have 
 worked for macOS Tahoe 26.1 with Apple clang version 17.0.0).
-After the prerequisites are installed and the vpofff Python environment is created (see :ref:`vpofff`), 
-then building OPM Flow and the opm Python package can be achieved with the following lines:
+After the prerequisites are installed, then building OPM Flow can be achieved with the following lines:
 
 .. code-block:: console
 
     CURRENT_DIRECTORY="$PWD"
 
-    deactivate
-    source vpofff/bin/activate
-
     for module in common geometry grid istl
-    do   git clone https://gitlab.dune-project.org/core/dune-$module.git --branch v2.9.1
+    do  git clone https://gitlab.dune-project.org/core/dune-$module.git
+        cd dune-$module && git checkout v2.10.0 && cd ..
         ./dune-common/bin/dunecontrol --only=dune-$module cmake -DCMAKE_DISABLE_FIND_PACKAGE_MPI=1
         ./dune-common/bin/dunecontrol --only=dune-$module make -j5
     done
@@ -121,9 +158,8 @@ then building OPM Flow and the opm Python package can be achieved with the follo
 
     for repo in common grid simulators
     do  git clone https://github.com/OPM/opm-$repo.git
-        mkdir build/opm-$repo
-        cd build/opm-$repo
-        cmake -DWITH_NDEBUG=1 -DUSE_MPI=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
+        mkdir build/opm-$repo && cd build/opm-$repo
+        cmake -DUSE_MPI=0 -DWITH_NDEBUG=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$CURRENT_DIRECTORY/dune-common/build-cmake;$CURRENT_DIRECTORY/dune-grid/build-cmake;$CURRENT_DIRECTORY/dune-geometry/build-cmake;$CURRENT_DIRECTORY/dune-istl/build-cmake;$CURRENT_DIRECTORY/build/opm-common;$CURRENT_DIRECTORY/build/opm-grid" $CURRENT_DIRECTORY/opm-$repo
         if [[ $repo == simulators ]]; then
             make -j5 flow
         else
@@ -132,15 +168,11 @@ then building OPM Flow and the opm Python package can be achieved with the follo
         cd ../..
     done
 
-    echo "export PATH=\$PATH:$CURRENT_DIRECTORY/build/opm-simulators/bin" >> $CURRENT_DIRECTORY/vpofff/bin/activate
+    echo "export PATH=\$PATH:$CURRENT_DIRECTORY/build/opm-simulators/bin" >> ~/.zprofile
+    source ~/.zprofile
 
-    deactivate
-    source vpofff/bin/activate
-
-This builds OPM Flow, and it exports the path to the flow executable (i.e., executing in the terminal **which flow** should print the path).
+This builds OPM Flow, and it exports the path to the flow executable. You can check if the installation of OPM Flow succeded by typing in the terminal **flow \-\-help**.
 
 .. tip::
     See `this repository <https://github.com/daavid00/OPM-Flow_macOS>`_ dedicated to build OPM Flow from source in the latest macOS (GitHub actions).
     If you still face problems, raise an issue in the GitHub repository, or you could also send an email to the maintainers.
-
-For macOS, the LaTeX dependency can be installed from https://www.tug.org/mactex/.

docs/_sources/publication.rst.txt

@@ -23,7 +23,7 @@ Figure 3:
     plopm -i figure3/FIGURE3 -v 'multx * 1.75' -grid 'black,1e-2' -remove 1,1,0,1 -d 20,15 -clabel 'Thickness map [cm]' -cformat .2f -cnum 5 -f 20 -o figure3 -save figure3b
 
 Figure 4 requires running the SPE11A cases using `pyopmspe11 <https://github.com/OPM/pyopmspe11>`_, which uses the simulation grid. You might need to edit the configuration files to
-adjust the computational resources to your machine (e.g., `r3_cp_1cmish_capmax2500Pa.txt <https://github.com/OPM/pyopmspe11/blob/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.txt>`_ is run with 32 cpus).
+adjust the computational resources to your machine (e.g., `r3_cp_1cmish_capmax2500Pa.toml <https://github.com/OPM/pyopmspe11/blob/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.toml>`_ is run with 32 cpus).
 
 .. tip::
     You can install `pyopmspe11 <https://github.com/OPM/pyopmspe11>`_ by executing in the terminal:
@@ -35,18 +35,18 @@ adjust the computational resources to your machine (e.g., `r3_cp_1cmish_capmax25
 .. code-block:: bash
 
     mkdir figure4 && cd figure4
-    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.txt
-    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.txt
-    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r4_Cart_1mm_capmax2500Pa.txt
-    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r5_Cart_1mm_capmax2500Pa_strictol.txt
-    pyopmspe11 -i r2_Cart_1cm_capmax2500Pa.txt -o r2_Cart_1cm_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
-    pyopmspe11 -i r3_cp_1cmish_capmax2500Pa.txt -o r3_cp_1cmish_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
-    pyopmspe11 -i r4_Cart_1mm_capmax2500Pa.txt -o r4_Cart_1mm_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
-    pyopmspe11 -i r5_Cart_1mm_capmax2500Pa_strictol.txt -o r5_Cart_1mm_capmax2500Pa_strictol -t 1 -r 280,1,120 -w 0.16666666666666666
+    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.toml
+    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r3_cp_1cmish_capmax2500Pa.toml
+    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r4_Cart_1mm_capmax2500Pa.toml
+    curl -O https://raw.githubusercontent.com/OPM/pyopmspe11/refs/heads/main/benchmark/spe11a/r5_Cart_1mm_capmax2500Pa_strictol.toml
+    pyopmspe11 -i r2_Cart_1cm_capmax2500Pa.toml -o r2_Cart_1cm_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
+    pyopmspe11 -i r3_cp_1cmish_capmax2500Pa.toml -o r3_cp_1cmish_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
+    pyopmspe11 -i r4_Cart_1mm_capmax2500Pa.toml -o r4_Cart_1mm_capmax2500Pa -t 1 -r 280,1,120 -w 0.16666666666666666
+    pyopmspe11 -i r5_Cart_1mm_capmax2500Pa_strictol.toml -o r5_Cart_1mm_capmax2500Pa_strictol -t 1 -r 280,1,120 -w 0.16666666666666666
     plopm -v xco2l -r 53 -mask satnum -maskthr 7e-5 -i 'r2_Cart_1cm_capmax2500Pa/flow/R2_CART_1CM_CAPMAX2500PA r3_cp_1cmish_capmax2500Pa/flow/R3_CP_1CMISH_CAPMAX2500PA r4_Cart_1mm_capmax2500Pa/flow/R4_CART_1MM_CAPMAX2500PA r5_Cart_1mm_capmax2500Pa_strictol/flow/R5_CART_1MM_CAPMAX2500PA_STRICTOL' -cnum 3 -xlnum 8 -clabel 'OPM results for SPE11A: CO$_2$ mass fraction (liquid phase) after 2 days' -d 16,6.5 -t "(a) Cartesian grid 1cm  (b) Corner-point grid 1cmish  (c) Cartesian grid 1mm  (d) Cartesian grid 1mm stricter tolerances" -yunits cm -xunits cm -yformat .0f -xformat .0f -f 16 -save figure4 -cformat .2e -suptitle 0 -subfigs 2,2 -cbsfax 0.35,0.97,0.3,0.02 -delax 1 -c '#9ca245 #9da347 #9fa44a #a0a64d #a2a750 #a3a953 #a5aa56 #a6ac59 #a8ad5c #a9af5f #abb062 #adb164 #aeb367 #b0b46a #b1b66d #b3b770 #b4b973 #b6ba76 #b7bc79 #b9bd7c #babf7f #bcc082 #bec184 #bfc387 #c1c48a #c2c68d #c4c790 #c5c993 #c7ca96 #c8cc99 #cacd9c #cbcf9f #cdd0a2 #cfd1a4 #d0d3a7 #d2d4aa #d3d6ad #d5d7b0 #d6d9b3 #d8dab6 #d9dcb9 #dbddbc #dcdfbf #dee0c1 #e0e1c4 #e1e3c7 #e3e4ca #e4e6cd #e6e7d0 #e7e9d3 #e9ead6 #eaecd9 #eceddc #edefdf #eff0e1 #f1f1e4 #f2f3e7 #f4f4ea #f5f6ed #f7f7f0 #f8f9f3 #fafaf6 #fbfcf9 #fdfdfc #ffffff #fefbfb #fdf7f7 #fcf3f3 #fbefef #faebeb #f9e7e7 #f8e3e3 #f7e0e0 #f6dcdc #f5d8d8 #f4d4d4 #f3d0d0 #f2cccc #f1c8c8 #f0c5c5 #efc1c1 #eebdbd #edb9b9 #ecb5b5 #ebb1b1 #eaadad #e9aaaa #e8a6a6 #e7a2a2 #e69e9e #e59a9a #e49696 #e39292 #e28f8f #e18b8b #e08787 #df8383 #de7f7f #dd7b7b #dc7777 #db7474 #da7070 #d96c6c #d86868 #d76464 #d66060 #d55c5c #d45959 #d35555 #d25151 #d14d4d #d04949 #cf4545 #ce4141 #cd3e3e #cc3a3a #cb3636 #ca3232 #c92e2e #c82a2a #c72626 #c62323 #c51f1f #c41b1b #c31717 #c21313 #c10f0f #c00b0b'
 
 A similar figure without the need of running the simulations (not showing the sands in the background and using the reporting grid) can be obtained by downloading the SPE11A benchmark data in csv format available at 
-`this website <https://darus.uni-stuttgart.de/dataset.xhtml?persistentId=doi:10.18419/DARUS-4750>`_ (the submitted benchmark data does not include the `r5_Cart_1mm_capmax2500Pa_strictol.txt <https://github.com/OPM/pyopmspe11/blob/main/benchmark/spe11a/r5_Cart_1mm_capmax2500Pa_strictol.txt>`_ results):
+`this website <https://darus.uni-stuttgart.de/dataset.xhtml?persistentId=doi:10.18419/DARUS-4750>`_ (the submitted benchmark data does not include the `r5_Cart_1mm_capmax2500Pa_strictol.toml <https://github.com/OPM/pyopmspe11/blob/main/benchmark/spe11a/r5_Cart_1mm_capmax2500Pa_strictol.toml>`_ results):
 
 .. code-block:: bash
 

docs/about.html

@@ -98,7 +98,7 @@ <h1>About pofff<a class="headerlink" href="#about-pofff" title="Link to this hea
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2025, NORCE Research AS.</p>
+    <p>&#169; Copyright 2025-2026, NORCE Research AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/api.html

@@ -149,7 +149,7 @@ <h2>pofff<a class="headerlink" href="#pofff" title="Link to this heading"></a
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2025, NORCE Research AS.</p>
+    <p>&#169; Copyright 2025-2026, NORCE Research AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/configuration_file.html

@@ -138,7 +138,7 @@ <h1>Configuration file<a class="headerlink" href="#configuration-file" title="Li
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2025, NORCE Research AS.</p>
+    <p>&#169; Copyright 2025-2026, NORCE Research AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

docs/contributing.html

@@ -157,7 +157,7 @@ <h2>Seek support<a class="headerlink" href="#seek-support" title="Link to this h
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2025, NORCE Research AS.</p>
+    <p>&#169; Copyright 2025-2026, NORCE Research AS.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a