doc updates [skip ci]

dev/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 7b1c5c2ed764786850c39b03e1a32d96
+config: 6510663d1723231992ef825375bdb39e
 tags: 645f666f9bcd5a90fca523b33c5a78b7

dev/_modules/hnn_core/params.html

@@ -794,13 +794,7 @@ <h1>Source code for hnn_core.params</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">d1</span>
 
 
-<span class="k">def</span> <span class="nf">_convert_to_path</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-        <span class="n">value</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">value</span>
-
-
-<span class="k">def</span> <span class="nf">convert_to_hdf5</span><span class="p">(</span><span class="n">params_fname</span><span class="p">,</span> <span class="n">out_fname</span><span class="p">,</span>
+<span class="k">def</span> <span class="nf">convert_to_hdf5</span><span class="p">(</span><span class="n">params_fname</span><span class="p">,</span> <span class="n">out_fname</span><span class="p">,</span> <span class="n">include_drives</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
                     <span class="n">overwrite</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">write_output</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Converts json or param format to hdf5</span>
 
@@ -810,6 +804,8 @@ <h1>Source code for hnn_core.params</h1><div class="highlight"><pre>
 <span class="sd">        Path to file</span>
 <span class="sd">    out_fname: str</span>
 <span class="sd">        Path to output</span>
+<span class="sd">    include_drives: bool, default=True</span>
+<span class="sd">        Include drives from params file</span>
 <span class="sd">    overwrite: bool, default=True</span>
 <span class="sd">        Overwrite file</span>
 <span class="sd">    write_output: bool, default=False</span>
@@ -819,18 +815,26 @@ <h1>Source code for hnn_core.params</h1><div class="highlight"><pre>
 <span class="sd">    None</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="kn">from</span> <span class="nn">.network</span> <span class="kn">import</span> <span class="n">Network</span>
-
+    <span class="c1"># Validate inputs</span>
     <span class="n">_validate_type</span><span class="p">(</span><span class="n">params_fname</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">Path</span><span class="p">),</span> <span class="s1">&#39;params_fname&#39;</span><span class="p">)</span>
     <span class="n">_validate_type</span><span class="p">(</span><span class="n">out_fname</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">Path</span><span class="p">),</span> <span class="s1">&#39;out_fname&#39;</span><span class="p">)</span>
+    <span class="c1"># Convert to Path</span>
+    <span class="n">params_fname</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">params_fname</span><span class="p">)</span>
+    <span class="n">out_fname</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">out_fname</span><span class="p">)</span>
+    <span class="n">params_suffix</span> <span class="o">=</span> <span class="n">params_fname</span><span class="o">.</span><span class="n">suffix</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
 
-    <span class="n">params_fname</span> <span class="o">=</span> <span class="n">_convert_to_path</span><span class="p">(</span><span class="n">params_fname</span><span class="p">)</span>
-    <span class="n">out_fname</span> <span class="o">=</span> <span class="n">_convert_to_path</span><span class="p">(</span><span class="n">out_fname</span><span class="p">)</span>
+    <span class="c1"># Add suffix if not supplied</span>
     <span class="k">if</span> <span class="n">out_fname</span><span class="o">.</span><span class="n">suffix</span> <span class="o">!=</span> <span class="s1">&#39;.hdf5&#39;</span><span class="p">:</span>
         <span class="n">out_fname</span> <span class="o">=</span> <span class="n">out_fname</span><span class="o">.</span><span class="n">with_suffix</span><span class="p">(</span><span class="s1">&#39;.hdf5&#39;</span><span class="p">)</span>
 
-    <span class="n">params</span> <span class="o">=</span> <span class="n">read_params</span><span class="p">(</span><span class="n">params_fname</span><span class="p">)</span>
-    <span class="n">net</span> <span class="o">=</span> <span class="n">Network</span><span class="p">(</span><span class="n">params</span><span class="p">)</span>
-    <span class="n">net</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">out_fname</span><span class="p">,</span> <span class="n">overwrite</span><span class="p">,</span> <span class="n">write_output</span><span class="p">)</span>
+    <span class="n">net</span> <span class="o">=</span> <span class="n">Network</span><span class="p">(</span><span class="n">params</span><span class="o">=</span><span class="n">read_params</span><span class="p">(</span><span class="n">params_fname</span><span class="p">),</span>
+                  <span class="n">add_drives_from_params</span><span class="o">=</span><span class="n">include_drives</span><span class="p">,</span>
+                  <span class="n">legacy_mode</span><span class="o">=</span><span class="kc">True</span> <span class="k">if</span> <span class="n">params_suffix</span> <span class="o">==</span> <span class="s1">&#39;param&#39;</span> <span class="k">else</span> <span class="kc">False</span><span class="p">,</span>
+                  <span class="p">)</span>
+    <span class="n">net</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">fname</span><span class="o">=</span><span class="n">out_fname</span><span class="p">,</span>
+              <span class="n">overwrite</span><span class="o">=</span><span class="n">overwrite</span><span class="p">,</span>
+              <span class="n">write_output</span><span class="o">=</span><span class="n">write_output</span><span class="p">,</span>
+              <span class="p">)</span>
     <span class="k">return</span>
 
 

dev/generated/hnn_core.extracellular.ExtracellularArray.html

@@ -305,7 +305,7 @@ <h1>hnn_core.extracellular.ExtracellularArray<a class="headerlink" href="#hnn-co
 standard color strings may be used (e.g., ‘b’ for blue). A color
 can also be defined as an RGBA-quadruplet, or an array of
 RGBA-values (one for each electrode contact trace to plot). An
-instance of <a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.ListedColormap.html#matplotlib.colors.ListedColormap" title="(in Matplotlib v3.8.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ListedColormap</span></code></a> may also be
+instance of <a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.ListedColormap.html#matplotlib.colors.ListedColormap" title="(in Matplotlib v3.8.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ListedColormap</span></code></a> may also be
 provided.</p>
 </dd>
 <dt><strong>voltage_offset</strong><span class="classifier">float | None (optional)</span></dt><dd><p>Amount to offset traces by on the voltage-axis. Useful for plotting

dev/generated/hnn_core.viz.plot_laminar_lfp.html

@@ -173,7 +173,7 @@ <h1>hnn_core.viz.plot_laminar_lfp<a class="headerlink" href="#hnn-core-viz-plot-
 colormap strings may be used (e.g., ‘jetblue’). A color can also be
 defined as an RGBA-quadruplet, or an array of RGBA-values (one for each
 electrode contact trace to plot). An instance of
-<a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.ListedColormap.html#matplotlib.colors.ListedColormap" title="(in Matplotlib v3.8.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ListedColormap</span></code></a> may also be provided.</p>
+<a class="reference external" href="https://matplotlib.org/stable/api/_as_gen/matplotlib.colors.ListedColormap.html#matplotlib.colors.ListedColormap" title="(in Matplotlib v3.8.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ListedColormap</span></code></a> may also be provided.</p>
 </dd>
 <dt><strong>voltage_offset</strong><span class="classifier">float | None (optional)</span></dt><dd><p>Amount to offset traces by on the voltage-axis. Useful for plotting
 laminar arrays.</p>