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github-actions[bot] committed Nov 21, 2024
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2 changes: 1 addition & 1 deletion dev/reference/connect/index.html
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Expand Up @@ -1719,7 +1719,7 @@ <h3 id="jaxley.connect.sparse_connect" class="doc doc-heading">
<span class="n">post_rows</span> <span class="o">=</span> <span class="n">post_cell_view</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">global_post_indices</span><span class="p">]</span>

<span class="c1"># Pre-synapse is at the zero-eth branch and zero-eth compartment.</span>
<span class="n">global_pre_indices</span> <span class="o">=</span> <span class="n">pre_cell_view</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">_cumsum_nseg_per_cell</span><span class="p">[</span><span class="n">pre_syn_neurons</span><span class="p">]</span>
<span class="n">global_pre_indices</span> <span class="o">=</span> <span class="n">pre_cell_view</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">_cumsum_ncomp_per_cell</span><span class="p">[</span><span class="n">pre_syn_neurons</span><span class="p">]</span>
<span class="n">pre_rows</span> <span class="o">=</span> <span class="n">pre_cell_view</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">global_pre_indices</span><span class="p">]</span>

<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pre_rows</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
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14 changes: 7 additions & 7 deletions dev/reference/integration/index.html
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Expand Up @@ -2520,7 +2520,7 @@ <h3 id="jaxley.solver_gate.solve_inf_gate_exponential" class="doc doc-heading">


<h3 id="jaxley.solver_voltage.step_voltage_explicit" class="doc doc-heading">
<code class=" language-python"><span class="n">step_voltage_explicit</span><span class="p">(</span><span class="n">voltages</span><span class="p">,</span> <span class="n">voltage_terms</span><span class="p">,</span> <span class="n">constant_terms</span><span class="p">,</span> <span class="n">axial_conductances</span><span class="p">,</span> <span class="n">internal_node_inds</span><span class="p">,</span> <span class="n">sinks</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">nseg_per_branch</span><span class="p">,</span> <span class="n">par_inds</span><span class="p">,</span> <span class="n">child_inds</span><span class="p">,</span> <span class="n">nbranches</span><span class="p">,</span> <span class="n">solver</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="n">idx</span><span class="p">,</span> <span class="n">debug_states</span><span class="p">)</span></code>
<code class=" language-python"><span class="n">step_voltage_explicit</span><span class="p">(</span><span class="n">voltages</span><span class="p">,</span> <span class="n">voltage_terms</span><span class="p">,</span> <span class="n">constant_terms</span><span class="p">,</span> <span class="n">axial_conductances</span><span class="p">,</span> <span class="n">internal_node_inds</span><span class="p">,</span> <span class="n">sinks</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">ncomp_per_branch</span><span class="p">,</span> <span class="n">par_inds</span><span class="p">,</span> <span class="n">child_inds</span><span class="p">,</span> <span class="n">nbranches</span><span class="p">,</span> <span class="n">solver</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="n">idx</span><span class="p">,</span> <span class="n">debug_states</span><span class="p">)</span></code>

<a href="#jaxley.solver_voltage.step_voltage_explicit" class="headerlink" title="Permanent link">&para;</a></h3>

Expand Down Expand Up @@ -2580,7 +2580,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_explicit" class="doc doc-heading">
<span class="n">sinks</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">sources</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">types</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">nseg_per_branch</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">ncomp_per_branch</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">par_inds</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">child_inds</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">nbranches</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand Down Expand Up @@ -2622,7 +2622,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_explicit" class="doc doc-heading">


<h3 id="jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="doc doc-heading">
<code class=" language-python"><span class="n">step_voltage_implicit_with_jaxley_spsolve</span><span class="p">(</span><span class="n">voltages</span><span class="p">,</span> <span class="n">voltage_terms</span><span class="p">,</span> <span class="n">constant_terms</span><span class="p">,</span> <span class="n">axial_conductances</span><span class="p">,</span> <span class="n">internal_node_inds</span><span class="p">,</span> <span class="n">sinks</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">nseg_per_branch</span><span class="p">,</span> <span class="n">par_inds</span><span class="p">,</span> <span class="n">child_inds</span><span class="p">,</span> <span class="n">nbranches</span><span class="p">,</span> <span class="n">solver</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="n">idx</span><span class="p">,</span> <span class="n">debug_states</span><span class="p">)</span></code>
<code class=" language-python"><span class="n">step_voltage_implicit_with_jaxley_spsolve</span><span class="p">(</span><span class="n">voltages</span><span class="p">,</span> <span class="n">voltage_terms</span><span class="p">,</span> <span class="n">constant_terms</span><span class="p">,</span> <span class="n">axial_conductances</span><span class="p">,</span> <span class="n">internal_node_inds</span><span class="p">,</span> <span class="n">sinks</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">ncomp_per_branch</span><span class="p">,</span> <span class="n">par_inds</span><span class="p">,</span> <span class="n">child_inds</span><span class="p">,</span> <span class="n">nbranches</span><span class="p">,</span> <span class="n">solver</span><span class="p">,</span> <span class="n">delta_t</span><span class="p">,</span> <span class="n">idx</span><span class="p">,</span> <span class="n">debug_states</span><span class="p">)</span></code>

<a href="#jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="headerlink" title="Permanent link">&para;</a></h3>

Expand Down Expand Up @@ -2793,7 +2793,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="
<span class="n">sinks</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">sources</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">types</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">nseg_per_branch</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">ncomp_per_branch</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">par_inds</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">child_inds</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
<span class="n">nbranches</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand All @@ -2805,7 +2805,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Solve one timestep of branched nerve equations with implicit (backward) Euler.&quot;&quot;&quot;</span>
<span class="c1"># Build diagonals.</span>
<span class="n">c2c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">types</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span>
<span class="n">total_ncomp</span> <span class="o">=</span> <span class="n">idx</span><span class="o">.</span><span class="n">cumsum_nseg</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">total_ncomp</span> <span class="o">=</span> <span class="n">idx</span><span class="o">.</span><span class="n">cumsum_ncomp</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">diags</span> <span class="o">=</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">total_ncomp</span><span class="p">)</span>

<span class="c1"># if-case needed because `.at` does not allow empty inputs, but the input is</span>
Expand Down Expand Up @@ -2906,7 +2906,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="
<span class="n">branchpoint_diags</span><span class="p">,</span>
<span class="n">branchpoint_solves</span><span class="p">,</span>
<span class="n">solver</span><span class="p">,</span>
<span class="n">nseg_per_branch</span><span class="p">,</span>
<span class="n">ncomp_per_branch</span><span class="p">,</span>
<span class="n">idx</span><span class="p">,</span>
<span class="n">debug_states</span><span class="p">,</span>
<span class="p">)</span>
Expand All @@ -2931,7 +2931,7 @@ <h3 id="jaxley.solver_voltage.step_voltage_implicit_with_jaxley_spsolve" class="
<span class="n">branchpoint_diags</span><span class="p">,</span>
<span class="n">branchpoint_solves</span><span class="p">,</span>
<span class="n">solver</span><span class="p">,</span>
<span class="n">nseg_per_branch</span><span class="p">,</span>
<span class="n">ncomp_per_branch</span><span class="p">,</span>
<span class="n">idx</span><span class="p">,</span>
<span class="n">debug_states</span><span class="p">,</span>
<span class="p">)</span>
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