deploy: 8af3efe

CONTRIBUTE.html

@@ -55,6 +55,7 @@
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#branching-strategy">Branching strategy</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#developing-code">Developing code</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#formatting-code">Formatting code</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#adding-dependencies">Adding dependencies</a></li>
 </ul>
 </li>
@@ -183,6 +184,16 @@ <h2>Developing code<a class="headerlink" href="#developing-code" title="Permalin
 <li><p>If you’re adding code that should be tested, add tests</p></li>
 <li><p>If you’re adding or modifying examples, make sure to add them to <code class="docutils literal notranslate"><span class="pre">test_examples.py</span></code></p></li>
 </ul>
+<div class="section" id="formatting-code">
+<h3>Formatting code<a class="headerlink" href="#formatting-code" title="Permalink to this headline"></a></h3>
+<ul class="simple">
+<li><p>MALA uses <a class="reference external" href="https://github.com/psf/black"><code class="docutils literal notranslate"><span class="pre">black</span></code></a> for code formatting</p></li>
+<li><p>The <code class="docutils literal notranslate"><span class="pre">black</span></code> configuration is located in <code class="docutils literal notranslate"><span class="pre">pyproject.toml</span></code></p></li>
+<li><p>Currently, no automatic code reformatting will be done in the CI, thus
+please ensure that your code is properly formatted before creating a pull
+request</p></li>
+</ul>
+</div>
 <div class="section" id="adding-dependencies">
 <h3>Adding dependencies<a class="headerlink" href="#adding-dependencies" title="Permalink to this headline"></a></h3>
 <p>If you add additional dependencies, make sure to add them to <code class="docutils literal notranslate"><span class="pre">requirements.txt</span></code>

_modules/mala/common/check_modules.html

@@ -75,47 +75,70 @@
 
   <h1>Source code for mala.common.check_modules</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;Function to check module availability in MALA.&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">importlib</span>
 
 
 <div class="viewcode-block" id="check_modules"><a class="viewcode-back" href="../../../api/mala.common.check_modules.html#mala.common.check_modules.check_modules">[docs]</a><span class="k">def</span> <span class="nf">check_modules</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Check whether/which optional modules MALA can access.&quot;&quot;&quot;</span>
     <span class="c1"># The optional libs in MALA.</span>
     <span class="n">optional_libs</span> <span class="o">=</span> <span class="p">{</span>
-        <span class="s2">&quot;mpi4py&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                   <span class="s2">&quot;Enables inference parallelization.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;horovod&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                    <span class="s2">&quot;Enables training parallelization.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;lammps&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                   <span class="s2">&quot;Enables descriptor calculation for data preprocessing &quot;</span>
-                   <span class="s2">&quot;and inference.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;oapackage&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                      <span class="s2">&quot;Enables usage of OAT method for hyperparameter &quot;</span>
-                      <span class="s2">&quot;optimization.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;total_energy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                         <span class="s2">&quot;Enables calculation of total energy.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;asap3&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                  <span class="s2">&quot;Enables trajectory analysis.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;dftpy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-                  <span class="s2">&quot;Enables OF-DFT-MD initialization.&quot;</span><span class="p">},</span>
-        <span class="s2">&quot;minterpy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;description&quot;</span><span class="p">:</span>
-            <span class="s2">&quot;Enables minterpy descriptor calculation for data preprocessing.&quot;</span><span class="p">}</span>
+        <span class="s2">&quot;mpi4py&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables inference parallelization.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;horovod&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables training parallelization.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;lammps&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables descriptor calculation for data preprocessing &quot;</span>
+            <span class="s2">&quot;and inference.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;oapackage&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables usage of OAT method for hyperparameter &quot;</span>
+            <span class="s2">&quot;optimization.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;total_energy&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables calculation of total energy.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;asap3&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables trajectory analysis.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;dftpy&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables OF-DFT-MD initialization.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;minterpy&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;available&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s2">&quot;description&quot;</span><span class="p">:</span> <span class="s2">&quot;Enables minterpy descriptor calculation for data preprocessing.&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
     <span class="p">}</span>
 
     <span class="c1"># Find out if libs are available.</span>
     <span class="k">for</span> <span class="n">lib</span> <span class="ow">in</span> <span class="n">optional_libs</span><span class="p">:</span>
-        <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">importlib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">find_spec</span><span class="p">(</span><span class="n">lib</span><span class="p">)</span> \
-                                          <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+        <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">importlib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">find_spec</span><span class="p">(</span><span class="n">lib</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+        <span class="p">)</span>
 
     <span class="c1"># Print info about libs.</span>
     <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;The following optional modules are available in MALA:&quot;</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">lib</span> <span class="ow">in</span> <span class="n">optional_libs</span><span class="p">:</span>
-        <span class="n">available_string</span> <span class="o">=</span> <span class="s2">&quot;installed&quot;</span> <span class="k">if</span> <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> \
-            <span class="k">else</span> <span class="s2">&quot;not installed&quot;</span>
-        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{0}</span><span class="s2">: </span><span class="se">\t</span><span class="s2"> </span><span class="si">{1}</span><span class="s2"> </span><span class="se">\t</span><span class="s2"> </span><span class="si">{2}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">lib</span><span class="p">,</span> <span class="n">available_string</span><span class="p">,</span>
-                                          <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;description&quot;</span><span class="p">]))</span>
-        <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> <span class="o">=</span> \
-            <span class="n">importlib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">find_spec</span><span class="p">(</span><span class="n">lib</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span></div>
+        <span class="n">available_string</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s2">&quot;installed&quot;</span> <span class="k">if</span> <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> <span class="k">else</span> <span class="s2">&quot;not installed&quot;</span>
+        <span class="p">)</span>
+        <span class="nb">print</span><span class="p">(</span>
+            <span class="s2">&quot;</span><span class="si">{0}</span><span class="s2">: </span><span class="se">\t</span><span class="s2"> </span><span class="si">{1}</span><span class="s2"> </span><span class="se">\t</span><span class="s2"> </span><span class="si">{2}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+                <span class="n">lib</span><span class="p">,</span> <span class="n">available_string</span><span class="p">,</span> <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;description&quot;</span><span class="p">]</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">optional_libs</span><span class="p">[</span><span class="n">lib</span><span class="p">][</span><span class="s2">&quot;available&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">importlib</span><span class="o">.</span><span class="n">util</span><span class="o">.</span><span class="n">find_spec</span><span class="p">(</span><span class="n">lib</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+        <span class="p">)</span></div>
 </pre></div>
 
            </div>

_modules/mala/common/json_serializable.html

@@ -124,14 +124,14 @@ <h1>Source code for mala.common.json_serializable</h1><div class="highlight"><pr
 
     <span class="k">def</span> <span class="nf">_standard_serializer</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
-        <span class="n">members</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
-                                     <span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="ow">not</span> <span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">isroutine</span><span class="p">(</span><span class="n">a</span><span class="p">)))</span>
+        <span class="n">members</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="ow">not</span> <span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">isroutine</span><span class="p">(</span><span class="n">a</span><span class="p">))</span>
+        <span class="p">)</span>
         <span class="k">for</span> <span class="n">member</span> <span class="ow">in</span> <span class="n">members</span><span class="p">:</span>
             <span class="c1"># Filter out all private members, builtins, etc.</span>
             <span class="k">if</span> <span class="n">member</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">&quot;_&quot;</span><span class="p">:</span>
                 <span class="n">data</span><span class="p">[</span><span class="n">member</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">member</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-        <span class="n">json_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;object&quot;</span><span class="p">:</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
-                     <span class="s2">&quot;data&quot;</span><span class="p">:</span> <span class="n">data</span><span class="p">}</span>
+        <span class="n">json_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;object&quot;</span><span class="p">:</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s2">&quot;data&quot;</span><span class="p">:</span> <span class="n">data</span><span class="p">}</span>
         <span class="k">return</span> <span class="n">json_dict</span>
 
     <span class="nd">@classmethod</span>