benjamc: Fix #662 (#772)

development/_modules/smac/runhistory/runhistory2epm.html

@@ -348,8 +348,8 @@ <h1>Source code for smac.runhistory.runhistory2epm</h1><div class="highlight"><p
 <span class="sd">        num_params : int</span>
 <span class="sd">            number of parameters in config space</span>
 <span class="sd">        success_states: list, optional</span>
-<span class="sd">            List of states considered as successful (such as StatusType.SUCCESS)</span>
-<span class="sd">            If None, set to [StatusType.SUCCESS, ]</span>
+<span class="sd">            List of states considered as successful (such as StatusType.SUCCESS).</span>
+<span class="sd">            If None, raise TypeError.</span>
 <span class="sd">        impute_censored_data: bool, optional</span>
 <span class="sd">            Should we impute data?</span>
 <span class="sd">        consider_for_higher_budgets_state: list, optional</span>
@@ -359,12 +359,14 @@ <h1>Source code for smac.runhistory.runhistory2epm</h1><div class="highlight"><p
 <span class="sd">        impute_state: list, optional</span>
 <span class="sd">            List of states that mark censored data (such as StatusType.TIMEOUT)</span>
 <span class="sd">            in combination with runtime &lt; cutoff_time</span>
-<span class="sd">            If None, set to [StatusType.CAPPED, ]</span>
+<span class="sd">            If None, set to empty list [].</span>
+<span class="sd">            If None and impute_censored_data is True, raise TypeError.</span>
 <span class="sd">        scale_perc: int</span>
 <span class="sd">            scaled y-transformation use a percentile to estimate distance to optimum;</span>
 <span class="sd">            only used by some subclasses of AbstractRunHistory2EPM</span>
 <span class="sd">        rng : numpy.random.RandomState</span>
-<span class="sd">            only used for reshuffling data after imputation</span>
+<span class="sd">            Only used for reshuffling data after imputation.</span>
+<span class="sd">            If None, use np.random.RandomState(seed=1).</span>
 <span class="sd">        &quot;&quot;&quot;</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span>

development/_sources/examples/SMAC4BB/SMAC4BB_rosenbrock_example.rst.txt

@@ -95,7 +95,7 @@ Using the black-box optimization interface of SMAC
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  21.098 seconds)
+   **Total running time of the script:** ( 0 minutes  21.141 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4BB_SMAC4BB_rosenbrock_example.py:

development/_sources/examples/SMAC4BB/sg_execution_times.rst.txt

@@ -5,8 +5,8 @@
 
 Computation times
 =================
-**00:21.098** total execution time for **examples_SMAC4BB** files:
+**00:21.141** total execution time for **examples_SMAC4BB** files:
 
 +----------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4BB_SMAC4BB_rosenbrock_example.py` (``SMAC4BB_rosenbrock_example.py``) | 00:21.098 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4BB_SMAC4BB_rosenbrock_example.py` (``SMAC4BB_rosenbrock_example.py``) | 00:21.141 | 0.0 MB |
 +----------------------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/SMAC4HPO/SMAC4HPO_acq_rosenbrock_example.rst.txt

@@ -109,7 +109,7 @@ Changing the acquisition function
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  3.484 seconds)
+   **Total running time of the script:** ( 0 minutes  3.470 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4HPO_SMAC4HPO_acq_rosenbrock_example.py:

development/_sources/examples/SMAC4HPO/SMAC4HPO_gradientboosting_example.rst.txt

@@ -118,7 +118,7 @@ We optimize a GradientBoosting on an artificially created binary classification
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 2 minutes  13.068 seconds)
+   **Total running time of the script:** ( 2 minutes  10.994 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4HPO_SMAC4HPO_gradientboosting_example.py:

development/_sources/examples/SMAC4HPO/SMAC4HPO_rosenbrock_example.rst.txt

@@ -96,7 +96,7 @@ Using SMAC tuned for HPO for black-box optimization
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  3.910 seconds)
+   **Total running time of the script:** ( 0 minutes  3.847 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4HPO_SMAC4HPO_rosenbrock_example.py:

development/_sources/examples/SMAC4HPO/SMAC4HPO_svm_example.rst.txt

@@ -163,7 +163,7 @@ Note: SMAC-documentation uses linenumbers to generate docs from this file.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  26.483 seconds)
+   **Total running time of the script:** ( 0 minutes  26.790 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4HPO_SMAC4HPO_svm_example.py:

development/_sources/examples/SMAC4HPO/sg_execution_times.rst.txt

@@ -5,14 +5,14 @@
 
 Computation times
 =================
-**02:46.945** total execution time for **examples_SMAC4HPO** files:
+**02:45.101** total execution time for **examples_SMAC4HPO** files:
 
 +-------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_gradientboosting_example.py` (``SMAC4HPO_gradientboosting_example.py``) | 02:13.068 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_gradientboosting_example.py` (``SMAC4HPO_gradientboosting_example.py``) | 02:10.994 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_svm_example.py` (``SMAC4HPO_svm_example.py``)                           | 00:26.483 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_svm_example.py` (``SMAC4HPO_svm_example.py``)                           | 00:26.790 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_rosenbrock_example.py` (``SMAC4HPO_rosenbrock_example.py``)             | 00:03.910 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_rosenbrock_example.py` (``SMAC4HPO_rosenbrock_example.py``)             | 00:03.847 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_acq_rosenbrock_example.py` (``SMAC4HPO_acq_rosenbrock_example.py``)     | 00:03.484 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4HPO_SMAC4HPO_acq_rosenbrock_example.py` (``SMAC4HPO_acq_rosenbrock_example.py``)     | 00:03.470 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/SMAC4MF/SMAC4MF_mlp_example.rst.txt

@@ -187,7 +187,7 @@ optimize the average accuracy on a 5-fold cross validation.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 1 minutes  53.036 seconds)
+   **Total running time of the script:** ( 1 minutes  53.123 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4MF_SMAC4MF_mlp_example.py:

development/_sources/examples/SMAC4MF/SMAC4MF_sgd_example.rst.txt

@@ -119,7 +119,9 @@ digit-2 vs digit-3.
       warnings.warn("{} is intended to be used "
     /home/runner/work/SMAC3/SMAC3/doc/../smac/intensification/parallel_scheduling.py:152: UserWarning: Hyperband is intended to be used with more than 1 worker but num_workers=1
       warnings.warn("{} is intended to be used "
-    Optimized Value: 0.0038
+    /home/runner/work/SMAC3/SMAC3/doc/../smac/intensification/parallel_scheduling.py:152: UserWarning: Hyperband is intended to be used with more than 1 worker but num_workers=1
+      warnings.warn("{} is intended to be used "
+    Optimized Value: 0.0042
 
 
 
@@ -274,7 +276,7 @@ digit-2 vs digit-3.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 1 minutes  47.518 seconds)
+   **Total running time of the script:** ( 1 minutes  48.154 seconds)
 
 
 .. _sphx_glr_download_examples_SMAC4MF_SMAC4MF_sgd_example.py:

development/_sources/examples/SMAC4MF/sg_execution_times.rst.txt

@@ -5,10 +5,10 @@
 
 Computation times
 =================
-**03:40.553** total execution time for **examples_SMAC4MF** files:
+**03:41.277** total execution time for **examples_SMAC4MF** files:
 
 +--------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4MF_SMAC4MF_mlp_example.py` (``SMAC4MF_mlp_example.py``) | 01:53.036 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4MF_SMAC4MF_mlp_example.py` (``SMAC4MF_mlp_example.py``) | 01:53.123 | 0.0 MB |
 +--------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_SMAC4MF_SMAC4MF_sgd_example.py` (``SMAC4MF_sgd_example.py``) | 01:47.518 | 0.0 MB |
+| :ref:`sphx_glr_examples_SMAC4MF_SMAC4MF_sgd_example.py` (``SMAC4MF_sgd_example.py``) | 01:48.154 | 0.0 MB |
 +--------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/function_minimization/fmin_rosenbrock_example.rst.txt

@@ -20,7 +20,7 @@ scipy-style fmin interface
 
  .. code-block:: none
 
-    INFO:smac.utils.io.cmd_reader.CMDReader:Output to smac3-output_2021-08-26_08:03:43_223636
+    INFO:smac.utils.io.cmd_reader.CMDReader:Output to smac3-output_2021-09-09_12:06:54_210770
     INFO:smac.facade.smac_hpo_facade.SMAC4HPO:Optimizing a deterministic scenario for quality without a tuner timeout - will make SMAC deterministic and only evaluate one configuration per iteration!
     INFO:smac.initial_design.sobol_design.SobolDesign:Running initial design for 2 configurations
     INFO:smac.facade.smac_hpo_facade.SMAC4HPO:<class 'smac.facade.smac_hpo_facade.SMAC4HPO'>
@@ -38,8 +38,8 @@ scipy-style fmin interface
     INFO:smac.stats.stats.Stats:#Submitted target algorithm runs: 10 / 10.0
     INFO:smac.stats.stats.Stats:#Finished target algorithm runs: 10 / 10.0
     INFO:smac.stats.stats.Stats:#Configurations: 10
-    INFO:smac.stats.stats.Stats:Used wallclock time: 3.25 / inf sec 
-    INFO:smac.stats.stats.Stats:Used target algorithm runtime: 0.06 / inf sec
+    INFO:smac.stats.stats.Stats:Used wallclock time: 3.26 / inf sec 
+    INFO:smac.stats.stats.Stats:Used target algorithm runtime: 0.07 / inf sec
     INFO:smac.stats.stats.Stats:##########################################################
     INFO:smac.facade.smac_hpo_facade.SMAC4HPO:Final Incumbent: Configuration:
       x1, Value: -1.345753380449037
@@ -97,7 +97,7 @@ scipy-style fmin interface
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  3.264 seconds)
+   **Total running time of the script:** ( 0 minutes  3.268 seconds)
 
 
 .. _sphx_glr_download_examples_function_minimization_fmin_rosenbrock_example.py:

development/_sources/examples/function_minimization/sg_execution_times.rst.txt

@@ -5,8 +5,8 @@
 
 Computation times
 =================
-**00:03.264** total execution time for **examples_function_minimization** files:
+**00:03.268** total execution time for **examples_function_minimization** files:
 
 +------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_function_minimization_fmin_rosenbrock_example.py` (``fmin_rosenbrock_example.py``) | 00:03.264 | 0.0 MB |
+| :ref:`sphx_glr_examples_function_minimization_fmin_rosenbrock_example.py` (``fmin_rosenbrock_example.py``) | 00:03.268 | 0.0 MB |
 +------------------------------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/hyperband/hyperband_mlp_example.rst.txt

@@ -190,7 +190,7 @@ optimize the average accuracy on a 5-fold cross validation.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 2 minutes  0.629 seconds)
+   **Total running time of the script:** ( 2 minutes  0.677 seconds)
 
 
 .. _sphx_glr_download_examples_hyperband_hyperband_mlp_example.py:

development/_sources/examples/hyperband/sg_execution_times.rst.txt

@@ -5,8 +5,8 @@
 
 Computation times
 =================
-**02:00.629** total execution time for **examples_hyperband** files:
+**02:00.677** total execution time for **examples_hyperband** files:
 
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_hyperband_hyperband_mlp_example.py` (``hyperband_mlp_example.py``) | 02:00.629 | 0.0 MB |
+| :ref:`sphx_glr_examples_hyperband_hyperband_mlp_example.py` (``hyperband_mlp_example.py``) | 02:00.677 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/parallel/fmin_rosenbrock_parallel_example.rst.txt

@@ -25,7 +25,7 @@ launch parallel configurations via n_workers
 
     /opt/hostedtoolcache/Python/3.8.11/x64/lib/python3.8/site-packages/scipy/stats/_qmc.py:1078: UserWarning: The balance properties of Sobol' points require n to be a power of 2.
       warnings.warn("The balance properties of Sobol' points require"
-    Best x: [-0.7883424   0.83818718]; with cost: 7.894206
+    Best x: [ 0.04405074 -0.22701279]; with cost: 6.155798
 
 
 
@@ -83,7 +83,7 @@ launch parallel configurations via n_workers
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  30.818 seconds)
+   **Total running time of the script:** ( 0 minutes  31.011 seconds)
 
 
 .. _sphx_glr_download_examples_parallel_fmin_rosenbrock_parallel_example.py:

development/_sources/examples/parallel/parallel_sh_mlp_example.rst.txt

@@ -129,7 +129,7 @@ advantage of the idle resources.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 1 minutes  48.841 seconds)
+   **Total running time of the script:** ( 1 minutes  48.459 seconds)
 
 
 .. _sphx_glr_download_examples_parallel_parallel_sh_mlp_example.py:

development/_sources/examples/parallel/sg_execution_times.rst.txt

@@ -5,10 +5,10 @@
 
 Computation times
 =================
-**02:19.659** total execution time for **examples_parallel** files:
+**02:19.470** total execution time for **examples_parallel** files:
 
 +-----------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_parallel_parallel_sh_mlp_example.py` (``parallel_sh_mlp_example.py``)                   | 01:48.841 | 0.0 MB |
+| :ref:`sphx_glr_examples_parallel_parallel_sh_mlp_example.py` (``parallel_sh_mlp_example.py``)                   | 01:48.459 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_parallel_fmin_rosenbrock_parallel_example.py` (``fmin_rosenbrock_parallel_example.py``) | 00:30.818 | 0.0 MB |
+| :ref:`sphx_glr_examples_parallel_fmin_rosenbrock_parallel_example.py` (``fmin_rosenbrock_parallel_example.py``) | 00:31.011 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------------------------+-----------+--------+

development/_sources/examples/quickstart/quickstart_example.rst.txt

@@ -453,7 +453,7 @@ We can also validate our results (though this makes a lot more sense with instan
 
     Specified 100 repetitions, but fixing to 1, because algorithm is deterministic.
 
-    <smac.runhistory.runhistory.RunHistory object at 0x7fe5f2a3cf70>
+    <smac.runhistory.runhistory.RunHistory object at 0x7f8028317760>
 
 
 
@@ -655,7 +655,7 @@ The resulting portfolio can be used with any algorithm selector such as
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  5.009 seconds)
+   **Total running time of the script:** ( 0 minutes  5.018 seconds)
 
 
 .. _sphx_glr_download_examples_quickstart_quickstart_example.py:

development/_sources/examples/quickstart/sg_execution_times.rst.txt

@@ -5,8 +5,8 @@
 
 Computation times
 =================
-**00:05.009** total execution time for **examples_quickstart** files:
+**00:05.018** total execution time for **examples_quickstart** files:
 
 +---------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_examples_quickstart_quickstart_example.py` (``quickstart_example.py``) | 00:05.009 | 0.0 MB |
+| :ref:`sphx_glr_examples_quickstart_quickstart_example.py` (``quickstart_example.py``) | 00:05.018 | 0.0 MB |
 +---------------------------------------------------------------------------------------+-----------+--------+

development/_sources/smac_options.rst.txt

@@ -9,7 +9,7 @@
 :limit_resources: If true, *SMAC* will use pynisher to limit time and memory for the target algorithm. Allows SMAC to use all resources available. Applicable only to func TAEs. Set to 'True' by default. (Use with caution!) Default: True.
 :maxR: Maximum number of calls per configuration. Default: 2000.
 :minR: Minimum number of calls per configuration. Default: 1.
-:output_dir: Specifies the output-directory for all emerging files, such as logging and results. Default: smac3-output_2021-08-26_08:03:34_823009.
+:output_dir: Specifies the output-directory for all emerging files, such as logging and results. Default: smac3-output_2021-09-09_12:06:44_178810.
 :rand_prob: probablity to run a random configuration instead of configuration optimized on the acquisition function Default: 0.5.
 :random_configuration_chooser: path to a python module containing a class`RandomConfigurationChooserImpl` implementingthe interface of `RandomConfigurationChooser`
 :rf_do_bootstrapping: Use bootstraping in random forest. Default: True.