Sarah Segel: Merge pull request #103 from automl/bugfix/api-examples

development/.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: cc40638524a75869b5752aca302f69f8
+config: 19058a216288311270b2d5b6ce1eaac4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

development/_downloads/486eb49d7cdf943097f599661017192d/parallel_coordinates.py

@@ -2,17 +2,18 @@
 Parallel Coordinates
 ^^^^^^^^^^^^^^^^^^^^
 
-This example shows how to use the plugin parallel coordinates.
+This example shows how to use the plugin Parallel Coordinates.
 Note that other plugins use the same interfaces and can be used in the same fashion.
 """
 
 from deepcave.plugins.objective.parallel_coordinates import ParallelCoordinates
 from deepcave.runs.converters.deepcave import DeepCAVERun
+from pathlib import Path
 
 
 if __name__ == "__main__":
     # Instantiate the run
-    run = DeepCAVERun.from_path("examples/record/logs/DeepCAVE/mlp/run_2")
+    run = DeepCAVERun.from_path(Path("logs/DeepCAVE/minimal/run_2"))
     objective_id = run.get_objective_ids()[0]
     budget_id = run.get_budget_ids()[-1]
 
@@ -22,12 +23,16 @@
         hyperparameter_names=run.configspace.get_hyperparameter_names(),
         objective_id=objective_id,
         budget_id=budget_id,
+        show_important_only=True,
+        show_unsuccessful=False,
+        hide_hps=False,
+        n_hps=3,
     )
     # Note: Filter variables are not considered.
     outputs = plugin.generate_outputs(run, inputs)
 
     # Finally, you can load the figure. Here, the filter variables play a role.
     # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.
     figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure
+    figure.write_image("examples/api/parallel_coordinates.png", scale=2.)
     # figure.show()
-    # figure.write_image("examples/api/test.png")

development/_downloads/99282791bd8a0f766c85ce43b212a6b7/pdp.ipynb

@@ -0,0 +1,43 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Partial Dependencies\n\nThis example shows how to use the plugin Partial Dependencies.\nNote that other plugins use the same interfaces and can be used in the same fashion.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from deepcave.plugins.hyperparameter.pdp import PartialDependencies\nfrom deepcave.runs.converters.deepcave import DeepCAVERun\nfrom pathlib import Path\n\n\nif __name__ == \"__main__\":\n    # Instantiate the run\n    run = DeepCAVERun.from_path(Path(\"logs/DeepCAVE/minimal/run_2\"))\n    objective_id = run.get_objective_ids()[0]\n    budget_id = run.get_budget_ids()[-1]\n\n    # Instantiate the plugin\n    plugin = PartialDependencies()\n    inputs = plugin.generate_inputs(\n        hyperparameter_name_1=\"alpha\",\n        hyperparameter_name_2=\"beta\",\n        objective_id=objective_id,\n        budget_id=budget_id,\n        show_confidence=False,\n        show_ice=True,\n    )\n    # Note: Filter variables are not considered.\n    outputs = plugin.generate_outputs(run, inputs)\n\n    # Finally, you can load the figure. Here, the filter variables play a role.\n    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.\n    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure\n    figure.write_image(\"examples/api/pdp.png\")\n    #figure.show()"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.9.18"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

development/_downloads/aabae18a223fa014a3ff3692699ee5e2/importances.ipynb

@@ -0,0 +1,43 @@
+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "\n# Importances\n\nThis example shows how to use the plugin Importances.\nNote that other plugins use the same interfaces and can be used in the same fashion.\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "from deepcave.plugins.hyperparameter.importances import Importances\nfrom deepcave.runs.converters.deepcave import DeepCAVERun\nfrom pathlib import Path\n\n\nif __name__ == \"__main__\":\n    # Instantiate the run\n    run = DeepCAVERun.from_path(Path(\"logs/DeepCAVE/minimal/run_2\"))\n\n    objective_id = run.get_objective_ids()[0]\n    budget_ids = run.get_budget_ids()\n\n    # Instantiate the plugin\n    plugin = Importances()\n    inputs = plugin.generate_inputs(\n        hyperparameter_names=run.configspace.get_hyperparameter_names(),\n        objective_id=objective_id,\n        budget_ids=budget_ids,\n        method=\"global\",\n        n_hps=3,\n        n_trees=10\n    )\n    # Note: Filter variables are not considered.\n    outputs = plugin.generate_outputs(run, inputs)\n\n    # Finally, you can load the figure. Here, the filter variables play a role.\n    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.\n    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure\n    figure.write_image(\"examples/api/importances.png\", scale=2.)\n    # figure.show()"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "codemirror_mode": {
+        "name": "ipython",
+        "version": 3
+      },
+      "file_extension": ".py",
+      "mimetype": "text/x-python",
+      "name": "python",
+      "nbconvert_exporter": "python",
+      "pygments_lexer": "ipython3",
+      "version": "3.9.18"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
+}

development/_downloads/e839af13aa37ae3d835848af3db8e085/pdp.py

@@ -0,0 +1,37 @@
+"""
+Partial Dependencies
+^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to use the plugin Partial Dependencies.
+Note that other plugins use the same interfaces and can be used in the same fashion.
+"""
+
+from deepcave.plugins.hyperparameter.pdp import PartialDependencies
+from deepcave.runs.converters.deepcave import DeepCAVERun
+from pathlib import Path
+
+
+if __name__ == "__main__":
+    # Instantiate the run
+    run = DeepCAVERun.from_path(Path("logs/DeepCAVE/minimal/run_2"))
+    objective_id = run.get_objective_ids()[0]
+    budget_id = run.get_budget_ids()[-1]
+
+    # Instantiate the plugin
+    plugin = PartialDependencies()
+    inputs = plugin.generate_inputs(
+        hyperparameter_name_1="alpha",
+        hyperparameter_name_2="beta",
+        objective_id=objective_id,
+        budget_id=budget_id,
+        show_confidence=False,
+        show_ice=True,
+    )
+    # Note: Filter variables are not considered.
+    outputs = plugin.generate_outputs(run, inputs)
+
+    # Finally, you can load the figure. Here, the filter variables play a role.
+    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.
+    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure
+    figure.write_image("examples/api/pdp.png")
+    #figure.show()

development/_downloads/e9c545ae14a903164c9a627d1b3a375a/parallel_coordinates.ipynb

@@ -4,7 +4,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Parallel Coordinates\n\nThis example shows how to use the plugin parallel coordinates.\nNote that other plugins use the same interfaces and can be used in the same fashion.\n"
+        "\n# Parallel Coordinates\n\nThis example shows how to use the plugin Parallel Coordinates.\nNote that other plugins use the same interfaces and can be used in the same fashion.\n"
       ]
     },
     {
@@ -15,7 +15,7 @@
       },
       "outputs": [],
       "source": [
-        "from deepcave.plugins.objective.parallel_coordinates import ParallelCoordinates\nfrom deepcave.runs.converters.deepcave import DeepCAVERun\n\n\nif __name__ == \"__main__\":\n    # Instantiate the run\n    run = DeepCAVERun.from_path(\"examples/record/logs/DeepCAVE/mlp/run_2\")\n    objective_id = run.get_objective_ids()[0]\n    budget_id = run.get_budget_ids()[-1]\n\n    # Instantiate the plugin\n    plugin = ParallelCoordinates()\n    inputs = plugin.generate_inputs(\n        hyperparameter_names=run.configspace.get_hyperparameter_names(),\n        objective_id=objective_id,\n        budget_id=budget_id,\n    )\n    # Note: Filter variables are not considered.\n    outputs = plugin.generate_outputs(run, inputs)\n\n    # Finally, you can load the figure. Here, the filter variables play a role.\n    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.\n    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure\n    # figure.show()\n    # figure.write_image(\"examples/api/test.png\")"
+        "from deepcave.plugins.objective.parallel_coordinates import ParallelCoordinates\nfrom deepcave.runs.converters.deepcave import DeepCAVERun\nfrom pathlib import Path\n\n\nif __name__ == \"__main__\":\n    # Instantiate the run\n    run = DeepCAVERun.from_path(Path(\"logs/DeepCAVE/minimal/run_2\"))\n    objective_id = run.get_objective_ids()[0]\n    budget_id = run.get_budget_ids()[-1]\n\n    # Instantiate the plugin\n    plugin = ParallelCoordinates()\n    inputs = plugin.generate_inputs(\n        hyperparameter_names=run.configspace.get_hyperparameter_names(),\n        objective_id=objective_id,\n        budget_id=budget_id,\n        show_important_only=True,\n        show_unsuccessful=False,\n        hide_hps=False,\n        n_hps=3,\n    )\n    # Note: Filter variables are not considered.\n    outputs = plugin.generate_outputs(run, inputs)\n\n    # Finally, you can load the figure. Here, the filter variables play a role.\n    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.\n    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure\n    figure.write_image(\"examples/api/parallel_coordinates.png\", scale=2.)\n    # figure.show()"
       ]
     }
   ],

development/_downloads/f0660e643860808c88e59e2b47bd432b/importances.py

@@ -0,0 +1,38 @@
+"""
+Importances
+^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to use the plugin Importances.
+Note that other plugins use the same interfaces and can be used in the same fashion.
+"""
+
+from deepcave.plugins.hyperparameter.importances import Importances
+from deepcave.runs.converters.deepcave import DeepCAVERun
+from pathlib import Path
+
+
+if __name__ == "__main__":
+    # Instantiate the run
+    run = DeepCAVERun.from_path(Path("logs/DeepCAVE/minimal/run_2"))
+
+    objective_id = run.get_objective_ids()[0]
+    budget_ids = run.get_budget_ids()
+
+    # Instantiate the plugin
+    plugin = Importances()
+    inputs = plugin.generate_inputs(
+        hyperparameter_names=run.configspace.get_hyperparameter_names(),
+        objective_id=objective_id,
+        budget_ids=budget_ids,
+        method="global",
+        n_hps=3,
+        n_trees=10
+    )
+    # Note: Filter variables are not considered.
+    outputs = plugin.generate_outputs(run, inputs)
+
+    # Finally, you can load the figure. Here, the filter variables play a role.
+    # Alternatively: Use the matplotlib output (`load_mpl_outputs`) if available.
+    figure = plugin.load_outputs(run, inputs, outputs)  # plotly.go figure
+    figure.write_image("examples/api/importances.png", scale=2.)
+    # figure.show()

development/_modules/deepcave/evaluators/epm/fanova_forest.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/evaluators/epm/random_forest_surrogate.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/evaluators/epm/utils.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/evaluators/fanova.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/layouts.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/layouts/not_found.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/layouts/sidebar.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates

development/_modules/deepcave/plugins.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../examples/api/parallel_coordinates.html">
        Parallel Coordinates
@@ -776,9 +786,9 @@ <h1>Source code for deepcave.plugins</h1><div class="highlight"><pre>
 <span class="sd">        str</span>
 <span class="sd">            Url for the plugin as string.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">deepcave</span> <span class="kn">import</span> <span class="n">config</span>
+        <span class="kn">from</span> <span class="nn">deepcave.config</span> <span class="kn">import</span> <span class="n">Config</span>
 
-        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;http://</span><span class="si">{</span><span class="n">config</span><span class="o">.</span><span class="n">DASH_ADDRESS</span><span class="si">}</span><span class="s2">:</span><span class="si">{</span><span class="n">config</span><span class="o">.</span><span class="n">DASH_PORT</span><span class="si">}</span><span class="s2">/plugins/</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2">&quot;</span></div>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;http://</span><span class="si">{</span><span class="n">Config</span><span class="o">.</span><span class="n">DASH_ADDRESS</span><span class="si">}</span><span class="s2">:</span><span class="si">{</span><span class="n">Config</span><span class="o">.</span><span class="n">DASH_PORT</span><span class="si">}</span><span class="s2">/plugins/</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2">&quot;</span></div>
 
 
 <div class="viewcode-block" id="Plugin.check_run_compatibility">

development/_modules/deepcave/plugins/dynamic.html

@@ -154,6 +154,16 @@
      </i>
     </label>
     <ul>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/pdp.html">
+       Partial Dependencies
+      </a>
+     </li>
+     <li class="toctree-l3">
+      <a class="reference internal" href="../../../examples/api/importances.html">
+       Importances
+      </a>
+     </li>
      <li class="toctree-l3">
       <a class="reference internal" href="../../../examples/api/parallel_coordinates.html">
        Parallel Coordinates