Merge pull request #158 from daavid00/dev

Adding check_cmdargs for illegal CLI combinations and making FAIR the docs

Author: daavid00

docs/_sources/examples.rst.txt

@@ -54,21 +54,29 @@ The following are some of the figures generated in the compare folder:
 
     The immiscible and isothermal simulations run faster since they have less dof.
 
-The `plopm <https://github.com/cssr-tools/plopm>`_ tool facilitates the visualization of selected results, and can be installed by:
+.. note::
 
-.. code-block:: bash
-    
-    pip install git+https://github.com/cssr-tools/plopm.git
+    `plopm <https://github.com/cssr-tools/plopm>`_ facilitates the visualization of selected results, and can be installed by:
+
+    .. code-block:: bash
+        
+        pip install git+https://github.com/cssr-tools/plopm.git
 
-For example, the following figures are generated with the commands:
+For example, the following figures are generated using `plopm <https://github.com/cssr-tools/plopm>`_ with the commands:
 
 .. code-block:: bash
 
     plopm -i isothermal/flow/ISOTHERMAL -v sgas -t 'Isothermal simulation (end of simulation)'
-    plopm -i 'immiscible/data/spe11b_time_series convective/data/spe11b_time_series' -csv 1,4 -labels "Immiscible  Convective" -tunits y -ylabel 'mobA [kg]' -xformat .0f -x '[0,25]' -xlnum 6 -f 20 -d 10,5 -yformat .1e -e 'solid,solid' -lw 4
+    plopm -i 'immiscible/data/spe11b_time_series convective/data/spe11b_time_series' -csv 1,4 -labels "Immiscible  Convective" -tunits y -ylabel 'mobA [kg]' -xformat .0f -x '[0,25]' -xlnum 6 -f 20 -d 10,5 -yformat .1e -e 'solid,solid' -lw 4 -step 1
 
 .. figure:: figs/plopm_hello_world.png
 
+All previous commands can be executed from the main repository location as (`docs_hello_world.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_hello_world.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_hello_world.sh
+
 .. tip::
 
     `This example <https://cssr-tools.github.io/plopm/examples.html#reading-from-csv-files>`_ shows how to use `plopm <https://github.com/cssr-tools/plopm>`_ to
@@ -91,6 +99,12 @@ saving the configuration file as spe11b_11-levels.toml, running them (we add the
 
 .. image:: ./figs/11_levels_dz_i,1,k_t5.png
 
+All previous commands can be executed from the main repository location as (`docs_cp_grids.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_cp_grids.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_cp_grids.sh
+
 ======================
 Localized lower domain
 ======================
@@ -103,4 +117,10 @@ The flag **-n lower** results in the generation of files for the lower part (low
 
 .. image:: ./figs/lower_domain_pvtnum-1-satnum_i,14,k_t5.png
 
+All previous commands can be executed from the main repository location as (`docs_localized_lower_domain.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_localized_lower_domain.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_localized_lower_domain.sh
+
 See the :doc:`convergence <./convergence>` for using the localized domain in the SPE11B corner-point grid case.

docs/examples.html

@@ -128,24 +128,31 @@ <h2>Hello world<a class="headerlink" href="#hello-world" title="Link to this hea
 <figure class="align-default">
 <img alt="_images/spe11b_sparse_data.png" src="_images/spe11b_sparse_data.png" />
 </figure>
-<figure class="align-default" id="id3">
+<figure class="align-default" id="id4">
 <img alt="_images/spe11b_performance.png" src="_images/spe11b_performance.png" />
 <figcaption>
-<p><span class="caption-text">The immiscible and isothermal simulations run faster since they have less dof.</span><a class="headerlink" href="#id3" title="Link to this image"></a></p>
+<p><span class="caption-text">The immiscible and isothermal simulations run faster since they have less dof.</span><a class="headerlink" href="#id4" title="Link to this image"></a></p>
 </figcaption>
 </figure>
-<p>The <a class="reference external" href="https://github.com/cssr-tools/plopm">plopm</a> tool facilitates the visualization of selected results, and can be installed by:</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p><a class="reference external" href="https://github.com/cssr-tools/plopm">plopm</a> facilitates the visualization of selected results, and can be installed by:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>git+https://github.com/cssr-tools/plopm.git
 </pre></div>
 </div>
-<p>For example, the following figures are generated with the commands:</p>
+</div>
+<p>For example, the following figures are generated using <a class="reference external" href="https://github.com/cssr-tools/plopm">plopm</a> with the commands:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>plopm<span class="w"> </span>-i<span class="w"> </span>isothermal/flow/ISOTHERMAL<span class="w"> </span>-v<span class="w"> </span>sgas<span class="w"> </span>-t<span class="w"> </span><span class="s1">&#39;Isothermal simulation (end of simulation)&#39;</span>
-plopm<span class="w"> </span>-i<span class="w"> </span><span class="s1">&#39;immiscible/data/spe11b_time_series convective/data/spe11b_time_series&#39;</span><span class="w"> </span>-csv<span class="w"> </span><span class="m">1</span>,4<span class="w"> </span>-labels<span class="w"> </span><span class="s2">&quot;Immiscible  Convective&quot;</span><span class="w"> </span>-tunits<span class="w"> </span>y<span class="w"> </span>-ylabel<span class="w"> </span><span class="s1">&#39;mobA [kg]&#39;</span><span class="w"> </span>-xformat<span class="w"> </span>.0f<span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,25]&#39;</span><span class="w"> </span>-xlnum<span class="w"> </span><span class="m">6</span><span class="w"> </span>-f<span class="w"> </span><span class="m">20</span><span class="w"> </span>-d<span class="w"> </span><span class="m">10</span>,5<span class="w"> </span>-yformat<span class="w"> </span>.1e<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;solid,solid&#39;</span><span class="w"> </span>-lw<span class="w"> </span><span class="m">4</span>
+plopm<span class="w"> </span>-i<span class="w"> </span><span class="s1">&#39;immiscible/data/spe11b_time_series convective/data/spe11b_time_series&#39;</span><span class="w"> </span>-csv<span class="w"> </span><span class="m">1</span>,4<span class="w"> </span>-labels<span class="w"> </span><span class="s2">&quot;Immiscible  Convective&quot;</span><span class="w"> </span>-tunits<span class="w"> </span>y<span class="w"> </span>-ylabel<span class="w"> </span><span class="s1">&#39;mobA [kg]&#39;</span><span class="w"> </span>-xformat<span class="w"> </span>.0f<span class="w"> </span>-x<span class="w"> </span><span class="s1">&#39;[0,25]&#39;</span><span class="w"> </span>-xlnum<span class="w"> </span><span class="m">6</span><span class="w"> </span>-f<span class="w"> </span><span class="m">20</span><span class="w"> </span>-d<span class="w"> </span><span class="m">10</span>,5<span class="w"> </span>-yformat<span class="w"> </span>.1e<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;solid,solid&#39;</span><span class="w"> </span>-lw<span class="w"> </span><span class="m">4</span><span class="w"> </span>-step<span class="w"> </span><span class="m">1</span>
 </pre></div>
 </div>
 <figure class="align-default">
 <img alt="_images/plopm_hello_world.png" src="_images/plopm_hello_world.png" />
 </figure>
+<p>All previous commands can be executed from the main repository location as (<a class="reference external" href="https://github.com/OPM/pyopmspe11/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 class="admonition tip">
 <p class="admonition-title">Tip</p>
 <p><a class="reference external" href="https://cssr-tools.github.io/plopm/examples.html#reading-from-csv-files">This example</a> shows how to use <a class="reference external" href="https://github.com/cssr-tools/plopm">plopm</a> to
@@ -165,6 +172,10 @@ <h2>Cp grids (11 and 18 levels)<a class="headerlink" href="#cp-grids-11-and-18-l
 </pre></div>
 </div>
 <img alt="_images/11_levels_dz_i%2C1%2Ck_t5.png" src="_images/11_levels_dz_i%2C1%2Ck_t5.png" />
+<p>All previous commands can be executed from the main repository location as (<a class="reference external" href="https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_cp_grids.sh">docs_cp_grids.sh</a>):</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>.<span class="w"> </span>./tests/scripts/docs_cp_grids.sh
+</pre></div>
+</div>
 </section>
 <section id="localized-lower-domain">
 <h2>Localized lower domain<a class="headerlink" href="#localized-lower-domain" title="Link to this heading"></a></h2>
@@ -174,6 +185,10 @@ <h2>Localized lower domain<a class="headerlink" href="#localized-lower-domain" t
 </pre></div>
 </div>
 <img alt="_images/lower_domain_pvtnum-1-satnum_i%2C14%2Ck_t5.png" src="_images/lower_domain_pvtnum-1-satnum_i%2C14%2Ck_t5.png" />
+<p>All previous commands can be executed from the main repository location as (<a class="reference external" href="https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_localized_lower_domain.sh">docs_localized_lower_domain.sh</a>):</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>.<span class="w"> </span>./tests/scripts/docs_localized_lower_domain.sh
+</pre></div>
+</div>
 <p>See the <a class="reference internal" href="convergence.html"><span class="doc">convergence</span></a> for using the localized domain in the SPE11B corner-point grid case.</p>
 </section>
 </section>

docs/genindex.html

@@ -176,6 +176,8 @@ <h2 id="C">C</h2>
 </li>
       </ul></li>
       <li><a href="pyopmspe11.visualization.plotting.html#pyopmspe11.visualization.plotting.CaseConfig">CaseConfig (class in pyopmspe11.visualization.plotting)</a>
+</li>
+      <li><a href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.check_cmdargs">check_cmdargs() (in module pyopmspe11.core.pyopmspe11)</a>
 </li>
       <li><a href="pyopmspe11.utils.inputvalues.html#pyopmspe11.utils.inputvalues.check_deck">check_deck() (in module pyopmspe11.utils.inputvalues)</a>
 </li>

docs/objects.inv

@@ -91,6 +91,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html">pyopmspe11.core.pyopmspe11 module</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.check_cmdargs"><code class="docutils literal notranslate"><span class="pre">check_cmdargs()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.load_parser"><code class="docutils literal notranslate"><span class="pre">load_parser()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.make_dir"><code class="docutils literal notranslate"><span class="pre">make_dir()</span></code></a></li>

docs/pyopmspe11.core.html

@@ -88,6 +88,23 @@
   <section id="module-pyopmspe11.core.pyopmspe11">
 <span id="pyopmspe11-core-pyopmspe11-module"></span><h1>pyopmspe11.core.pyopmspe11 module<a class="headerlink" href="#module-pyopmspe11.core.pyopmspe11" title="Link to this heading"></a></h1>
 <p>Main script for pyopmspe11</p>
+<dl class="py function">
+<dt class="sig sig-object py" id="pyopmspe11.core.pyopmspe11.check_cmdargs">
+<span class="sig-prename descclassname"><span class="pre">pyopmspe11.core.pyopmspe11.</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="#pyopmspe11.core.pyopmspe11.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 output names, spatial resolution,
+reporting times and intervals, comparison mode, and options restricted
+to data-generation workflows.</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="#pyopmspe11.core.pyopmspe11.load_parser" title="pyopmspe11.core.pyopmspe11.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">
 <dt class="sig sig-object py" id="pyopmspe11.core.pyopmspe11.load_parser">
 <span class="sig-prename descclassname"><span class="pre">pyopmspe11.core.pyopmspe11.</span></span><span class="sig-name descname"><span class="pre">load_parser</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">argv</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</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="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</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">dict</span></span></span><a class="headerlink" href="#pyopmspe11.core.pyopmspe11.load_parser" title="Link to this definition"></a></dt>

docs/pyopmspe11.core.pyopmspe11.html

@@ -103,6 +103,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l1"><a class="reference internal" href="pyopmspe11.core.html">pyopmspe11.core package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="pyopmspe11.core.html#submodules">Submodules</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html">pyopmspe11.core.pyopmspe11 module</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.check_cmdargs"><code class="docutils literal notranslate"><span class="pre">check_cmdargs()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.load_parser"><code class="docutils literal notranslate"><span class="pre">load_parser()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="pyopmspe11.core.pyopmspe11.html#pyopmspe11.core.pyopmspe11.make_dir"><code class="docutils literal notranslate"><span class="pre">make_dir()</span></code></a></li>

docs/pyopmspe11.html

@@ -54,21 +54,29 @@ The following are some of the figures generated in the compare folder:
 
     The immiscible and isothermal simulations run faster since they have less dof.
 
-The `plopm <https://github.com/cssr-tools/plopm>`_ tool facilitates the visualization of selected results, and can be installed by:
+.. note::
 
-.. code-block:: bash
-    
-    pip install git+https://github.com/cssr-tools/plopm.git
+    `plopm <https://github.com/cssr-tools/plopm>`_ facilitates the visualization of selected results, and can be installed by:
+
+    .. code-block:: bash
+        
+        pip install git+https://github.com/cssr-tools/plopm.git
 
-For example, the following figures are generated with the commands:
+For example, the following figures are generated using `plopm <https://github.com/cssr-tools/plopm>`_ with the commands:
 
 .. code-block:: bash
 
     plopm -i isothermal/flow/ISOTHERMAL -v sgas -t 'Isothermal simulation (end of simulation)'
-    plopm -i 'immiscible/data/spe11b_time_series convective/data/spe11b_time_series' -csv 1,4 -labels "Immiscible  Convective" -tunits y -ylabel 'mobA [kg]' -xformat .0f -x '[0,25]' -xlnum 6 -f 20 -d 10,5 -yformat .1e -e 'solid,solid' -lw 4
+    plopm -i 'immiscible/data/spe11b_time_series convective/data/spe11b_time_series' -csv 1,4 -labels "Immiscible  Convective" -tunits y -ylabel 'mobA [kg]' -xformat .0f -x '[0,25]' -xlnum 6 -f 20 -d 10,5 -yformat .1e -e 'solid,solid' -lw 4 -step 1
 
 .. figure:: figs/plopm_hello_world.png
 
+All previous commands can be executed from the main repository location as (`docs_hello_world.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_hello_world.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_hello_world.sh
+
 .. tip::
 
     `This example <https://cssr-tools.github.io/plopm/examples.html#reading-from-csv-files>`_ shows how to use `plopm <https://github.com/cssr-tools/plopm>`_ to
@@ -91,6 +99,12 @@ saving the configuration file as spe11b_11-levels.toml, running them (we add the
 
 .. image:: ./figs/11_levels_dz_i,1,k_t5.png
 
+All previous commands can be executed from the main repository location as (`docs_cp_grids.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_cp_grids.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_cp_grids.sh
+
 ======================
 Localized lower domain
 ======================
@@ -103,4 +117,10 @@ The flag **-n lower** results in the generation of files for the lower part (low
 
 .. image:: ./figs/lower_domain_pvtnum-1-satnum_i,14,k_t5.png
 
+All previous commands can be executed from the main repository location as (`docs_localized_lower_domain.sh <https://github.com/OPM/pyopmspe11/blob/main/tests/scripts/docs_localized_lower_domain.sh>`_):
+
+.. code-block:: bash
+
+    . ./tests/scripts/docs_localized_lower_domain.sh
+
 See the :doc:`convergence <./convergence>` for using the localized domain in the SPE11B corner-point grid case.

docs/searchindex.js

@@ -1,5 +1,5 @@
 # SPDX-FileCopyrightText: 2023-2026 NORCE Research AS
-# SPDX-License-Identifier: GPL-3.0
+# SPDX-License-Identifier: MIT
 # pylint: disable=C0103, R0902
 
 """Central configuration models for pyopmspe11"""