Making FAIR the docs figures

docs/_sources/examples.rst.txt

@@ -62,6 +62,13 @@ Below are some of the figures generated inside the postprocessing folder:
     hello_world_sensor_pressure_over_time.png, hello_world_summary_BHP_site_reference.png, and 
     hello_world_distance_from_border.png respectively
 
+.. tip::
+
+    All previous commands can be executed as (`docs_hello_world.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_hello_world.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_hello_world.sh
 
 Layered model
 -------------
@@ -130,13 +137,21 @@ not by pressure values. If you run that test, then using plopm:
 
 .. code-block:: bash
 
-    plopm -i 'tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM' -v rpr:3
+    plopm -i 'tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM' -v rpr:3 -step 1
 
 .. figure:: figs/regional_rpr3.png
 
     Comparison of the different functionality to map the dynamic boundary conditions. Here, rpr:3 (fipnum equal to 3) corresponds to the top part of the sandwich (three layers with the middel layer inactive) 
     in the regional model, while to the bottom part in the site model.
 
+.. tip::
+
+    All previous commands can be executed as (`docs_regular_boundaries.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_regular_boundaries.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_regular_boundaries.sh
+
 Non-regular boundaries
 ----------------------
 
@@ -183,4 +198,12 @@ For the following figure, it is necessary to include in the REGIONS section of t
 .. figure:: figs/expreccs_opernum_i,j,1_t0.png
 
     In the regional model (left), **expreccs** writes the location of the overlapping cells with the site model in the OPERNUM variable, while in the 
-    site model this variable is used to label the ij direction of the boundary conditions.
+    site model this variable is used to label the ij direction of the boundary conditions.
+
+.. tip::
+
+    All previous commands can be executed as (`docs_non-regular_boundaries.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_non-regular_boundaries.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_non-regular_boundaries.sh

docs/examples.html

@@ -154,6 +154,13 @@ <h2>Via configuration files<a class="headerlink" href="#via-configuration-files"
 hello_world_distance_from_border.png respectively</span><a class="headerlink" href="#id4" title="Link to this image"></a></p>
 </figcaption>
 </figure>
+<div class="admonition tip">
+<p class="admonition-title">Tip</p>
+<p>All previous commands can be executed as (<a class="reference external" href="https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_hello_world.sh">docs_hello_world.sh</a>):</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>.<span class="w"> </span>./tests/scripts/docs_hello_world.sh
+</pre></div>
+</div>
+</div>
 </section>
 <section id="layered-model">
 <h3>Layered model<a class="headerlink" href="#layered-model" title="Link to this heading"></a></h3>
@@ -209,7 +216,7 @@ <h3>Regular boundaries<a class="headerlink" href="#regular-boundaries" title="Li
 the functionality to select if the bc mappings are written per fipnums, i.e., if there is an offset between the site and regional models along the z direction, then
 using <strong>-z 1</strong> builds the interpolators per corresponding fipnums in the regional and site models. In addition, the flag <strong>-e 0</strong> set the interpolators to be defined by pressure increase and
 not by pressure values. If you run that test, then using plopm:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span><span class="s1">&#39;tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM&#39;</span><span class="w"> </span>-v<span class="w"> </span>rpr:3
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span><span class="s1">&#39;tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM&#39;</span><span class="w"> </span>-v<span class="w"> </span>rpr:3<span class="w"> </span>-step<span class="w"> </span><span class="m">1</span>
 </pre></div>
 </div>
 <figure class="align-default" id="id6">
@@ -219,6 +226,13 @@ <h3>Regular boundaries<a class="headerlink" href="#regular-boundaries" title="Li
 in the regional model, while to the bottom part in the site model.</span><a class="headerlink" href="#id6" title="Link to this image"></a></p>
 </figcaption>
 </figure>
+<div class="admonition tip">
+<p class="admonition-title">Tip</p>
+<p>All previous commands can be executed as (<a class="reference external" href="https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_regular_boundaries.sh">docs_regular_boundaries.sh</a>):</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>.<span class="w"> </span>./tests/scripts/docs_regular_boundaries.sh
+</pre></div>
+</div>
+</div>
 </section>
 <section id="non-regular-boundaries">
 <h3>Non-regular boundaries<a class="headerlink" href="#non-regular-boundaries" title="Link to this heading"></a></h3>
@@ -259,6 +273,13 @@ <h3>Non-regular boundaries<a class="headerlink" href="#non-regular-boundaries" t
 site model this variable is used to label the ij direction of the boundary conditions.</span><a class="headerlink" href="#id7" title="Link to this image"></a></p>
 </figcaption>
 </figure>
+<div class="admonition tip">
+<p class="admonition-title">Tip</p>
+<p>All previous commands can be executed as (<a class="reference external" href="https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_non-regular_boundaries.sh">docs_non-regular_boundaries.sh</a>):</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>.<span class="w"> </span>./tests/scripts/docs_non-regular_boundaries.sh
+</pre></div>
+</div>
+</div>
 </section>
 </section>
 </section>

docs/expreccs.core.expreccs.html

@@ -90,8 +90,20 @@
 <p>Main script for expreccs</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="expreccs.core.expreccs.check_cmdargs">
-<span class="sig-prename descclassname"><span class="pre">expreccs.core.expreccs.</span></span><span class="sig-name descname"><span class="pre">check_cmdargs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmdargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#expreccs.core.expreccs.check_cmdargs" title="Link to this definition"></a></dt>
-<dd><p>Check for invalid combinations of command arguments</p>
+<span class="sig-prename descclassname"><span class="pre">expreccs.core.expreccs.</span></span><span class="sig-name descname"><span class="pre">check_cmdargs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmdargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="headerlink" href="#expreccs.core.expreccs.check_cmdargs" title="Link to this definition"></a></dt>
+<dd><p>Validate command-line arguments and incompatible operations.</p>
+<p>The checks cover configuration and model-folder inputs, output names,
+boundary specifications, frequency and time-discretization values,
+rotations, comparison mode, workflow-specific options, and operations
+requiring the subfolder structure.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>cmdargs</strong> – Parsed arguments returned by <a class="reference internal" href="#expreccs.core.expreccs.load_parser" title="expreccs.core.expreccs.load_parser"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_parser()</span></code></a>.</p>
+</dd>
+<dt class="field-even">Raises<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>SystemExit</strong> – If an argument is invalid or an incompatible combination is requested.</p>
+</dd>
+</dl>
 </dd></dl>
 
 <dl class="py function">

docs/text/examples.rst

@@ -62,6 +62,13 @@ Below are some of the figures generated inside the postprocessing folder:
     hello_world_sensor_pressure_over_time.png, hello_world_summary_BHP_site_reference.png, and 
     hello_world_distance_from_border.png respectively
 
+.. tip::
+
+    All previous commands can be executed as (`docs_hello_world.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_hello_world.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_hello_world.sh
 
 Layered model
 -------------
@@ -130,13 +137,21 @@ not by pressure values. If you run that test, then using plopm:
 
 .. code-block:: bash
 
-    plopm -i 'tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM' -v rpr:3
+    plopm -i 'tests/regional/REGIONAL tests/expreccs/EXPRECCS tests/expreccs_dpincrease/EXPRECCS_DPINCREASE tests/expreccs_perfipnum/EXPRECCS_PERFIPNUM' -v rpr:3 -step 1
 
 .. figure:: figs/regional_rpr3.png
 
     Comparison of the different functionality to map the dynamic boundary conditions. Here, rpr:3 (fipnum equal to 3) corresponds to the top part of the sandwich (three layers with the middel layer inactive) 
     in the regional model, while to the bottom part in the site model.
 
+.. tip::
+
+    All previous commands can be executed as (`docs_regular_boundaries.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_regular_boundaries.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_regular_boundaries.sh
+
 Non-regular boundaries
 ----------------------
 
@@ -183,4 +198,12 @@ For the following figure, it is necessary to include in the REGIONS section of t
 .. figure:: figs/expreccs_opernum_i,j,1_t0.png
 
     In the regional model (left), **expreccs** writes the location of the overlapping cells with the site model in the OPERNUM variable, while in the 
-    site model this variable is used to label the ij direction of the boundary conditions.
+    site model this variable is used to label the ij direction of the boundary conditions.
+
+.. tip::
+
+    All previous commands can be executed as (`docs_non-regular_boundaries.sh <https://github.com/cssr-tools/expreccs/blob/main/tests/scripts/docs_non-regular_boundaries.sh>`_):
+
+    .. code-block:: bash
+
+        . ./tests/scripts/docs_non-regular_boundaries.sh

publications/ecmor2026/results_2d_synthetic_model/figure3_table1.py

@@ -515,7 +515,7 @@ def plot_error_extremes(model, case, order):
         "-grid",
         "black,1e-2",
         "-cbsfax",
-        "-1,0.0,0.0,0.0",
+        "empty",
         "-remove",
         "1,1,0,0",
         "-d",