deploy: 28bfbbc

.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: a4ddb4b1ee677e2944e527df7fecdbe0
+config: a3784d844b5c9a0de36a926f4b21a8bb
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_autosummary/regdiffusion.GRN.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -382,12 +382,12 @@ <h1>GRN<a class="headerlink" href="#grn" title="Link to this heading">#</a></h1>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>adj_matrix</strong> (<em>np.ndarray</em>) – A 2D adjacency matrix to save.</p></li>
 <li><p><strong>gene_names</strong> (<em>np.ndarray</em>) – A 1D numpy array with all the target gene</p></li>
-<li><p><strong>names.</strong> – </p></li>
+<li><p><strong>names.</strong></p></li>
 <li><p><strong>tf_names</strong> (<em>np.ndarray</em><em>, </em><em>optional</em>) – A 1D numpy array with all the TF gene</p></li>
-<li><p><strong>names.</strong> – </p></li>
+<li><p><strong>names.</strong></p></li>
 <li><p><strong>top_gene_percentile</strong> (<em>int</em>) – If this value is set, only the top k absolute</p></li>
-<li><p><strong>values</strong> (<em>values in the adjacency matrix will be kept. All the other</em>) – </p></li>
-<li><p><strong>zero.</strong> (<em>will be set to</em>) – </p></li>
+<li><p><strong>values</strong> (<em>values in the adjacency matrix will be kept. All the other</em>)</p></li>
+<li><p><strong>zero.</strong> (<em>will be set to</em>)</p></li>
 </ul>
 </dd>
 </dl>
@@ -405,7 +405,7 @@ <h1>GRN<a class="headerlink" href="#grn" title="Link to this heading">#</a></h1>
 <li><p><strong>genes</strong> (<em>str</em><em>, </em><em>List</em><em>(</em><em>str</em><em>)</em>) – A single gene or a list of genes to inspect.</p></li>
 <li><p><strong>k</strong> (<em>int</em>) – Top-k edges to inspect on each node. If k=-1, export all</p></li>
 <li><p><strong>hops</strong> (<em>str</em>) – Number of hops to explore. We can either do a “2.5” or</p></li>
-<li><p><strong>&quot;2.5&quot;.</strong> (<em>&quot;1.5&quot; hop travesal around selected genes. Default is</em>) – </p></li>
+<li><p><strong>&quot;2.5&quot;.</strong> (<em>&quot;1.5&quot; hop travesal around selected genes. Default is</em>)</p></li>
 </ul>
 </dd>
 </dl>
@@ -546,11 +546,11 @@ <h1>GRN<a class="headerlink" href="#grn" title="Link to this heading">#</a></h1>
 <li><p><strong>genes</strong> (<em>str</em><em>, </em><em>List</em><em>(</em><em>str</em><em>)</em>) – A single gene or a list of genes to inspect.</p></li>
 <li><p><strong>k</strong> (<em>int</em>) – Top-k edges to inspect on each node. If k=-1, export all.</p></li>
 <li><p><strong>hops</strong> (<em>str</em>) – Number of hops of the neighborhood to explore. Default</p></li>
-<li><p><strong>&quot;2.5&quot;.</strong> (<em>is</em>) – </p></li>
+<li><p><strong>&quot;2.5&quot;.</strong> (<em>is</em>)</p></li>
 <li><p><strong>edge_widths</strong> (<em>List</em>) – The widths for edges for different edge width</p></li>
-<li><p><strong>levels.</strong> – </p></li>
+<li><p><strong>levels.</strong></p></li>
 <li><p><strong>plot_engine</strong> (<em>str</em>) – Choose which network plot engine to use. Default</p></li>
-<li><p><strong>&quot;pyvis&quot;.</strong> (<em>is</em>) – </p></li>
+<li><p><strong>&quot;pyvis&quot;.</strong> (<em>is</em>)</p></li>
 <li><p><strong>**kwargs</strong> – Keyword arguments to be passed to <code class="docutils literal notranslate"><span class="pre">plot_pyvis</span></code>.</p></li>
 </ul>
 </dd>

_autosummary/regdiffusion.GRNEvaluator.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>

_autosummary/regdiffusion.RegDiffusionTrainer.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -425,7 +425,7 @@ <h1>RegDiffusionTrainer<a class="headerlink" href="#regdiffusiontrainer" title="
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>x_0</strong> (<em>torch.FloatTensor</em>) – Torch tensor for expression data. Rows are</p></li>
-<li><p><strong>genes</strong> (<em>cells and columns are</em>) – </p></li>
+<li><p><strong>genes</strong> (<em>cells and columns are</em>)</p></li>
 <li><p><strong>t</strong> (<em>torch.LongTensor</em>) – Torch tensor for diffusion time steps.</p></li>
 </ul>
 </dd>

_autosummary/regdiffusion.data.load_atlas_microglia.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -358,9 +358,9 @@ <h1>regdiffusion.data.load_atlas_microglia<a class="headerlink" href="#regdiffus
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>data_dir</strong> (<em>str</em>) – Parent directory to save and load the data. If the path</p></li>
-<li><p><strong>exist</strong> (<em>does not</em>) – </p></li>
-<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>) – </p></li>
-<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>) – </p></li>
+<li><p><strong>exist</strong> (<em>does not</em>)</p></li>
+<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>)</p></li>
+<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>)</p></li>
 </ul>
 </dd>
 </dl>

_autosummary/regdiffusion.data.load_beeline.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -356,20 +356,20 @@ <h1>regdiffusion.data.load_beeline<a class="headerlink" href="#regdiffusion-data
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>data_dir</strong> (<em>str</em>) – Parent directory to save and load the data. If the path</p></li>
-<li><p><strong>exist</strong> (<em>does not</em>) – </p></li>
-<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>) – </p></li>
-<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>) – </p></li>
+<li><p><strong>exist</strong> (<em>does not</em>)</p></li>
+<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>)</p></li>
+<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>)</p></li>
 <li><p><strong>benchmark_data</strong> (<em>str</em>) – Benchmark datasets. Choose among “hESC”, “hHep”,</p></li>
-<li><p><strong>&quot;mDC&quot;</strong> – </p></li>
-<li><p><strong>&quot;mESC&quot;</strong> – </p></li>
-<li><p><strong>&quot;mHSC&quot;</strong> – </p></li>
-<li><p><strong>&quot;mHSC-GM&quot;</strong> – </p></li>
-<li><p><strong>&quot;mHSC-L&quot;.</strong> (<em>and</em>) – </p></li>
+<li><p><strong>&quot;mDC&quot;</strong></p></li>
+<li><p><strong>&quot;mESC&quot;</strong></p></li>
+<li><p><strong>&quot;mHSC&quot;</strong></p></li>
+<li><p><strong>&quot;mHSC-GM&quot;</strong></p></li>
+<li><p><strong>&quot;mHSC-L&quot;.</strong> (<em>and</em>)</p></li>
 <li><p><strong>benchmark_setting</strong> (<em>str</em>) – Benchmark settings. Choose among “500_STRING”,</p></li>
-<li><p><strong>&quot;1000_STRING&quot;</strong> – </p></li>
-<li><p><strong>&quot;500_Non-ChIP&quot;</strong> – </p></li>
-<li><p><strong>&quot;1000_Non-ChIP&quot;</strong> – </p></li>
-<li><p><strong>&quot;500_ChIP-seq&quot;</strong> – </p></li>
+<li><p><strong>&quot;1000_STRING&quot;</strong></p></li>
+<li><p><strong>&quot;500_Non-ChIP&quot;</strong></p></li>
+<li><p><strong>&quot;1000_Non-ChIP&quot;</strong></p></li>
+<li><p><strong>&quot;500_ChIP-seq&quot;</strong></p></li>
 </ul>
 </dd>
 </dl>

_autosummary/regdiffusion.data.load_hammond_microglia.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -364,9 +364,9 @@ <h1>regdiffusion.data.load_hammond_microglia<a class="headerlink" href="#regdiff
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>data_dir</strong> (<em>str</em>) – Parent directory to save and load the data. If the path</p></li>
-<li><p><strong>exist</strong> (<em>does not</em>) – </p></li>
-<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>) – </p></li>
-<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>) – </p></li>
+<li><p><strong>exist</strong> (<em>does not</em>)</p></li>
+<li><p><strong>a</strong> (<em>it will be created. Data will be saved in</em>)</p></li>
+<li><p><strong>path.</strong> (<em>subdirectory under the provided</em>)</p></li>
 </ul>
 </dd>
 </dl>

_autosummary/regdiffusion.models.RegDiffusion.html

@@ -38,7 +38,7 @@
   <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script src="../_static/documentation_options.js?v=6424ca4d"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=4ea706d9"></script>
@@ -401,16 +401,16 @@ <h1>RegDiffusion<a class="headerlink" href="#regdiffusion" title="Link to this h
 <li><p><strong>n_genes</strong> (<em>int</em>) – Number of Genes</p></li>
 <li><p><strong>time_dim</strong> (<em>int</em>) – Dimension of time step embedding</p></li>
 <li><p><strong>n_celltype</strong> (<em>int</em>) – Number of expected cell types. If it is not provided,</p></li>
-<li><p><strong>None.</strong> (<em>there would be no celltype embedding. Default is</em>) – </p></li>
+<li><p><strong>None.</strong> (<em>there would be no celltype embedding. Default is</em>)</p></li>
 <li><p><strong>celltype_dim</strong> (<em>int</em>) – Dimension of cell types</p></li>
 <li><p><strong>hidden_dims</strong> (<em>list</em><em>[</em><em>int</em><em>]</em>) – List of integer for the dimensions of the</p></li>
-<li><p><strong>size</strong> (<em>hidden layers. The first hidden dimension will be used as the</em>) – </p></li>
-<li><p><strong>embedding.</strong> (<em>for gene</em>) – </p></li>
+<li><p><strong>size</strong> (<em>hidden layers. The first hidden dimension will be used as the</em>)</p></li>
+<li><p><strong>embedding.</strong> (<em>for gene</em>)</p></li>
 <li><p><strong>adj_dropout</strong> (<em>float</em>) – A single number between 0 and 1 specifying the</p></li>
-<li><p><strong>dropped</strong> (<em>percentage</em><em> of </em><em>values in the adjacency matrix that are</em>) – </p></li>
-<li><p><strong>training.</strong> (<em>during</em>) – </p></li>
+<li><p><strong>dropped</strong> (<em>percentage</em><em> of </em><em>values in the adjacency matrix that are</em>)</p></li>
+<li><p><strong>training.</strong> (<em>during</em>)</p></li>
 <li><p><strong>init_coef</strong> (<em>int</em>) – Coefficient to multiply with gene regulation norm</p></li>
-<li><p><strong>(</strong><strong>1/</strong> (<em>n_gene - 1</em><em>)</em>) – </p></li>
+<li><p><strong>(</strong><strong>1/</strong> (<em>n_gene - 1</em><em>)</em>)</p></li>
 </ul>
 </dd>
 </dl>
@@ -834,7 +834,8 @@ <h1>RegDiffusion<a class="headerlink" href="#regdiffusion" title="Link to this h
 <div class="admonition warning">
 <p class="admonition-title">Warning</p>
 <p>If <code class="xref py py-attr docutils literal notranslate"><span class="pre">assign</span></code> is <code class="docutils literal notranslate"><span class="pre">True</span></code> the optimizer must be created after
-the call to <a class="reference internal" href="#regdiffusion.models.RegDiffusion.load_state_dict" title="regdiffusion.models.RegDiffusion.load_state_dict"><code class="xref py py-attr docutils literal notranslate"><span class="pre">load_state_dict</span></code></a>.</p>
+the call to <a class="reference internal" href="#regdiffusion.models.RegDiffusion.load_state_dict" title="regdiffusion.models.RegDiffusion.load_state_dict"><code class="xref py py-attr docutils literal notranslate"><span class="pre">load_state_dict</span></code></a> unless
+<code class="xref py py-func docutils literal notranslate"><span class="pre">get_swap_module_params_on_conversion()</span></code> is <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p>
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -844,13 +845,11 @@ <h1>RegDiffusion<a class="headerlink" href="#regdiffusion" title="Link to this h
 <li><p><strong>strict</strong> (<em>bool</em><em>, </em><em>optional</em>) – whether to strictly enforce that the keys
 in <a class="reference internal" href="#regdiffusion.models.RegDiffusion.state_dict" title="regdiffusion.models.RegDiffusion.state_dict"><code class="xref py py-attr docutils literal notranslate"><span class="pre">state_dict</span></code></a> match the keys returned by this module’s
 <code class="xref py py-meth docutils literal notranslate"><span class="pre">state_dict()</span></code> function. Default: <code class="docutils literal notranslate"><span class="pre">True</span></code></p></li>
-<li><p><strong>assign</strong> (<em>bool</em><em>, </em><em>optional</em>) – whether to assign items in the state
-dictionary to their corresponding keys in the module instead
-of copying them inplace into the module’s current parameters and buffers.
-When <code class="docutils literal notranslate"><span class="pre">False</span></code>, the properties of the tensors in the current
-module are preserved while when <code class="docutils literal notranslate"><span class="pre">True</span></code>, the properties of the
-Tensors in the state dict are preserved.
-Default: <code class="docutils literal notranslate"><span class="pre">False</span></code></p></li>
+<li><p><strong>assign</strong> (<em>bool</em><em>, </em><em>optional</em>) – When <code class="docutils literal notranslate"><span class="pre">False</span></code>, the properties of the tensors
+in the current module are preserved while when <code class="docutils literal notranslate"><span class="pre">True</span></code>, the
+properties of the Tensors in the state dict are preserved. The only
+exception is the <code class="docutils literal notranslate"><span class="pre">requires_grad</span></code> field of <code class="xref py py-class docutils literal notranslate">
+<span class="pre">Default:</span> <span class="pre">``False`</span></code></p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
@@ -1342,7 +1341,7 @@ <h1>RegDiffusion<a class="headerlink" href="#regdiffusion" title="Link to this h
 <dl class="py method">
 <dt class="sig sig-object py" id="regdiffusion.models.RegDiffusion.register_state_dict_pre_hook">
 <span class="sig-name descname"><span class="pre">register_state_dict_pre_hook</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hook</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#regdiffusion.models.RegDiffusion.register_state_dict_pre_hook" title="Link to this definition">#</a></dt>
-<dd><p>Register a pre-hook for the <code class="xref py py-meth docutils literal notranslate"><span class="pre">load_state_dict()</span></code> method.</p>
+<dd><p>Register a pre-hook for the <code class="xref py py-meth docutils literal notranslate"><span class="pre">state_dict()</span></code> method.</p>
 <p>These hooks will be called with arguments: <code class="docutils literal notranslate"><span class="pre">self</span></code>, <code class="docutils literal notranslate"><span class="pre">prefix</span></code>,
 and <code class="docutils literal notranslate"><span class="pre">keep_vars</span></code> before calling <code class="docutils literal notranslate"><span class="pre">state_dict</span></code> on <code class="docutils literal notranslate"><span class="pre">self</span></code>. The registered
 hooks can be used to perform pre-processing before the <code class="docutils literal notranslate"><span class="pre">state_dict</span></code>
@@ -1375,7 +1374,7 @@ <h1>RegDiffusion<a class="headerlink" href="#regdiffusion" title="Link to this h
 
 <dl class="py method">
 <dt class="sig sig-object py" id="regdiffusion.models.RegDiffusion.set_extra_state">
-<span class="sig-name descname"><span class="pre">set_extra_state</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">state</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#regdiffusion.models.RegDiffusion.set_extra_state" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">set_extra_state</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">state</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</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="#regdiffusion.models.RegDiffusion.set_extra_state" title="Link to this definition">#</a></dt>
 <dd><p>Set extra state contained in the loaded <cite>state_dict</cite>.</p>
 <p>This function is called from <a class="reference internal" href="#regdiffusion.models.RegDiffusion.load_state_dict" title="regdiffusion.models.RegDiffusion.load_state_dict"><code class="xref py py-func docutils literal notranslate"><span class="pre">load_state_dict()</span></code></a> to handle any extra state
 found within the <cite>state_dict</cite>. Implement this function and a corresponding