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asogaard committed Sep 25, 2023
1 parent d8eec16 commit e8bb3dc
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11 changes: 8 additions & 3 deletions _modules/graphnet/data/dataset/dataset.html
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Expand Up @@ -351,7 +351,7 @@ <h1 id="modules-graphnet-data-dataset-dataset--page-root">Source code for graphn
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">Configurable</span><span class="p">,</span>
<span class="n">DatasetConfig</span><span class="p">,</span>
<span class="n">save_dataset_config</span><span class="p">,</span>
<span class="n">DatasetConfigSaverABCMeta</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config.parsing</span> <span class="kn">import</span> <span class="n">traverse_and_apply</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.logging</span> <span class="kn">import</span> <span class="n">Logger</span>
Expand Down Expand Up @@ -420,7 +420,13 @@ <h1 id="modules-graphnet-data-dataset-dataset--page-root">Source code for graphn

<div class="viewcode-block" id="Dataset">
<a class="viewcode-back" href="../../../../api/graphnet.data.dataset.dataset.html#graphnet.data.dataset.dataset.Dataset">[docs]</a>
<span class="k">class</span> <span class="nc">Dataset</span><span class="p">(</span><span class="n">Logger</span><span class="p">,</span> <span class="n">Configurable</span><span class="p">,</span> <span class="n">torch</span><span class="o">.</span><span class="n">utils</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">Dataset</span><span class="p">,</span> <span class="n">ABC</span><span class="p">):</span>
<span class="k">class</span> <span class="nc">Dataset</span><span class="p">(</span>
<span class="n">Logger</span><span class="p">,</span>
<span class="n">Configurable</span><span class="p">,</span>
<span class="n">torch</span><span class="o">.</span><span class="n">utils</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">Dataset</span><span class="p">,</span>
<span class="n">ABC</span><span class="p">,</span>
<span class="n">metaclass</span><span class="o">=</span><span class="n">DatasetConfigSaverABCMeta</span><span class="p">,</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">"""Base Dataset class for reading from any intermediate file format."""</span>

<span class="c1"># Class method(s)</span>
Expand Down Expand Up @@ -529,7 +535,6 @@ <h1 id="modules-graphnet-data-dataset-dataset--page-root">Source code for graphn
<span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"$</span><span class="si">{GRAPHNET}</span><span class="s2">"</span><span class="p">,</span> <span class="n">GRAPHNET_ROOT_DIR</span><span class="p">)</span>
<span class="p">)</span>

<span class="nd">@save_dataset_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">path</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]],</span>
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515 changes: 0 additions & 515 deletions _modules/graphnet/data/dataset/sqlite/sqlite_dataset_perturbed.html

This file was deleted.

3 changes: 0 additions & 3 deletions _modules/graphnet/models/coarsening.html
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Expand Up @@ -346,7 +346,6 @@ <h1 id="modules-graphnet-models-coarsening--page-root">Source code for graphnet.
<span class="n">std_pool_x</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">graphnet.models</span> <span class="kn">import</span> <span class="n">Model</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>

<span class="c1"># Utility method(s)</span>
<span class="kn">from</span> <span class="nn">torch_geometric.utils</span> <span class="kn">import</span> <span class="n">degree</span>
Expand Down Expand Up @@ -392,7 +391,6 @@ <h1 id="modules-graphnet-models-coarsening--page-root">Source code for graphnet.
<span class="s2">"sum"</span><span class="p">:</span> <span class="p">(</span><span class="n">sum_pool</span><span class="p">,</span> <span class="n">sum_pool_x</span><span class="p">),</span>
<span class="p">}</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">reduce</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"avg"</span><span class="p">,</span>
Expand Down Expand Up @@ -533,7 +531,6 @@ <h1 id="modules-graphnet-models-coarsening--page-root">Source code for graphnet.
<span class="k">class</span> <span class="nc">AttributeCoarsening</span><span class="p">(</span><span class="n">Coarsening</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""Coarsen pulses based on specified attributes."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">attributes</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
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2 changes: 0 additions & 2 deletions _modules/graphnet/models/detector/detector.html
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Expand Up @@ -332,15 +332,13 @@ <h1 id="modules-graphnet-models-detector-detector--page-root">Source code for gr

<span class="kn">from</span> <span class="nn">graphnet.models</span> <span class="kn">import</span> <span class="n">Model</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.decorators</span> <span class="kn">import</span> <span class="n">final</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>


<div class="viewcode-block" id="Detector">
<a class="viewcode-back" href="../../../../api/graphnet.models.detector.detector.html#graphnet.models.detector.detector.Detector">[docs]</a>
<span class="k">class</span> <span class="nc">Detector</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""Base class for all detector-specific read-ins in graphnet."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">"""Construct `Detector`."""</span>
<span class="c1"># Base class constructor</span>
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2 changes: 0 additions & 2 deletions _modules/graphnet/models/gnn/convnet.html
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Expand Up @@ -334,7 +334,6 @@ <h1 id="modules-graphnet-models-gnn-convnet--page-root">Source code for graphnet
<span class="kn">from</span> <span class="nn">torch_geometric.nn</span> <span class="kn">import</span> <span class="n">TAGConv</span><span class="p">,</span> <span class="n">global_add_pool</span><span class="p">,</span> <span class="n">global_max_pool</span>
<span class="kn">from</span> <span class="nn">torch_geometric.data</span> <span class="kn">import</span> <span class="n">Data</span>

<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>
<span class="kn">from</span> <span class="nn">graphnet.models.gnn.gnn</span> <span class="kn">import</span> <span class="n">GNN</span>


Expand All @@ -343,7 +342,6 @@ <h1 id="modules-graphnet-models-gnn-convnet--page-root">Source code for graphnet
<span class="k">class</span> <span class="nc">ConvNet</span><span class="p">(</span><span class="n">GNN</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""ConvNet (convolutional network) model."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">nb_inputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
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2 changes: 0 additions & 2 deletions _modules/graphnet/models/gnn/dynedge.html
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Expand Up @@ -331,7 +331,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge--page-root">Source code for graphnet
<span class="kn">from</span> <span class="nn">torch_scatter</span> <span class="kn">import</span> <span class="n">scatter_max</span><span class="p">,</span> <span class="n">scatter_mean</span><span class="p">,</span> <span class="n">scatter_min</span><span class="p">,</span> <span class="n">scatter_sum</span>

<span class="kn">from</span> <span class="nn">graphnet.models.components.layers</span> <span class="kn">import</span> <span class="n">DynEdgeConv</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>
<span class="kn">from</span> <span class="nn">graphnet.models.gnn.gnn</span> <span class="kn">import</span> <span class="n">GNN</span>
<span class="kn">from</span> <span class="nn">graphnet.models.utils</span> <span class="kn">import</span> <span class="n">calculate_xyzt_homophily</span>

Expand All @@ -348,7 +347,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge--page-root">Source code for graphnet
<span class="k">class</span> <span class="nc">DynEdge</span><span class="p">(</span><span class="n">GNN</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""DynEdge (dynamical edge convolutional) model."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">nb_inputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand Down
2 changes: 0 additions & 2 deletions _modules/graphnet/models/gnn/dynedge_jinst.html
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Expand Up @@ -334,7 +334,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge-jinst--page-root">Source code for gr
<span class="kn">from</span> <span class="nn">torch_scatter</span> <span class="kn">import</span> <span class="n">scatter_max</span><span class="p">,</span> <span class="n">scatter_mean</span><span class="p">,</span> <span class="n">scatter_min</span><span class="p">,</span> <span class="n">scatter_sum</span>

<span class="kn">from</span> <span class="nn">graphnet.models.components.layers</span> <span class="kn">import</span> <span class="n">DynEdgeConv</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>
<span class="kn">from</span> <span class="nn">graphnet.models.gnn.gnn</span> <span class="kn">import</span> <span class="n">GNN</span>
<span class="kn">from</span> <span class="nn">graphnet.models.utils</span> <span class="kn">import</span> <span class="n">calculate_xyzt_homophily</span>

Expand All @@ -344,7 +343,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge-jinst--page-root">Source code for gr
<span class="k">class</span> <span class="nc">DynEdgeJINST</span><span class="p">(</span><span class="n">GNN</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""DynEdge (dynamical edge convolutional) model used in [2209.03042]."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">nb_inputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand Down
2 changes: 0 additions & 2 deletions _modules/graphnet/models/gnn/dynedge_kaggle_tito.html
Original file line number Diff line number Diff line change
Expand Up @@ -342,7 +342,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge-kaggle-tito--page-root">Source code
<span class="kn">from</span> <span class="nn">torch_scatter</span> <span class="kn">import</span> <span class="n">scatter_max</span><span class="p">,</span> <span class="n">scatter_mean</span><span class="p">,</span> <span class="n">scatter_min</span><span class="p">,</span> <span class="n">scatter_sum</span>

<span class="kn">from</span> <span class="nn">graphnet.models.components.layers</span> <span class="kn">import</span> <span class="n">DynTrans</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>
<span class="kn">from</span> <span class="nn">graphnet.models.gnn.gnn</span> <span class="kn">import</span> <span class="n">GNN</span>
<span class="kn">from</span> <span class="nn">graphnet.models.utils</span> <span class="kn">import</span> <span class="n">calculate_xyzt_homophily</span>

Expand All @@ -359,7 +358,6 @@ <h1 id="modules-graphnet-models-gnn-dynedge-kaggle-tito--page-root">Source code
<span class="k">class</span> <span class="nc">DynEdgeTITO</span><span class="p">(</span><span class="n">GNN</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""DynEdge (dynamical edge convolutional) model."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">nb_inputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand Down
2 changes: 0 additions & 2 deletions _modules/graphnet/models/gnn/gnn.html
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Expand Up @@ -330,15 +330,13 @@ <h1 id="modules-graphnet-models-gnn-gnn--page-root">Source code for graphnet.mod
<span class="kn">from</span> <span class="nn">torch_geometric.data</span> <span class="kn">import</span> <span class="n">Data</span>

<span class="kn">from</span> <span class="nn">graphnet.models</span> <span class="kn">import</span> <span class="n">Model</span>
<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>


<div class="viewcode-block" id="GNN">
<a class="viewcode-back" href="../../../../api/graphnet.models.gnn.gnn.html#graphnet.models.gnn.gnn.GNN">[docs]</a>
<span class="k">class</span> <span class="nc">GNN</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""Base class for all core GNN models in graphnet."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nb_inputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">nb_outputs</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
<span class="w"> </span><span class="sd">"""Construct `GNN`."""</span>
<span class="c1"># Base class constructor</span>
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4 changes: 0 additions & 4 deletions _modules/graphnet/models/graphs/edges/edges.html
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Expand Up @@ -331,7 +331,6 @@ <h1 id="modules-graphnet-models-graphs-edges-edges--page-root">Source code for g
<span class="kn">from</span> <span class="nn">torch_geometric.nn</span> <span class="kn">import</span> <span class="n">knn_graph</span><span class="p">,</span> <span class="n">radius_graph</span>
<span class="kn">from</span> <span class="nn">torch_geometric.data</span> <span class="kn">import</span> <span class="n">Data</span>

<span class="kn">from</span> <span class="nn">graphnet.utilities.config</span> <span class="kn">import</span> <span class="n">save_model_config</span>
<span class="kn">from</span> <span class="nn">graphnet.models.utils</span> <span class="kn">import</span> <span class="n">calculate_distance_matrix</span>
<span class="kn">from</span> <span class="nn">graphnet.models</span> <span class="kn">import</span> <span class="n">Model</span>

Expand Down Expand Up @@ -380,7 +379,6 @@ <h1 id="modules-graphnet-models-graphs-edges-edges--page-root">Source code for g
<span class="k">class</span> <span class="nc">KNNEdges</span><span class="p">(</span><span class="n">EdgeDefinition</span><span class="p">):</span> <span class="c1"># pylint: disable=too-few-public-methods</span>
<span class="w"> </span><span class="sd">"""Builds edges from the k-nearest neighbours."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">nb_nearest_neighbours</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
Expand Down Expand Up @@ -420,7 +418,6 @@ <h1 id="modules-graphnet-models-graphs-edges-edges--page-root">Source code for g
<span class="k">class</span> <span class="nc">RadialEdges</span><span class="p">(</span><span class="n">EdgeDefinition</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""Builds graph from a sphere of chosen radius centred at each node."""</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">radius</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
Expand Down Expand Up @@ -464,7 +461,6 @@ <h1 id="modules-graphnet-models-graphs-edges-edges--page-root">Source code for g
<span class="sd"> See https://arxiv.org/pdf/1809.06166.pdf.</span>
<span class="sd"> """</span>

<span class="nd">@save_model_config</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
<span class="n">sigma</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
Expand Down
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