Merge pull request #14 from MachineLearningLifeScience/feature-updating-to-new-interface

Updates the documentation to new poli interface

Author: miguelgondu

docs/poli-docs/_autosummary/poli.tests.docs_examples.test_objective_functions.rst

@@ -16,8 +16,13 @@
       test_aloha_example
       test_dockstring_example
       test_drd3_docking_example
+      test_foldx_sasa
+      test_foldx_stability
       test_logp_example
+      test_penalized_logp_lambo
       test_qed_example
+      test_rasp_example
+      test_sa_tdc_example
       test_toy_continuous_example
       test_white_noise_example
 

docs/poli-docs/_autosummary/poli.tests.registry.chemistry.test_chemistry_objectives.rst

@@ -16,13 +16,9 @@
       test_force_registering_logp
       test_force_registering_qed
       test_force_registering_qed_with_context_manager
-      test_logp_is_available
       test_penalized_logp_lambo
-      test_qed_is_available
       test_querying_dockstring_using_selfies
       test_querying_dockstring_using_smiles
-      test_registering_logp
-      test_registering_qed
 
 
 

docs/poli-docs/_autosummary/poli.tests.registry.rst

@@ -1,4 +1,4 @@
-poli.tests.registry
+poli.tests.registry
 ===================
 
 .. automodule:: poli.tests.registry
@@ -34,6 +34,7 @@ poli.tests.registry
    poli.tests.registry.test_black_box_instancing
    poli.tests.registry.test_force_isolation
    poli.tests.registry.test_instancing_black_boxes_alone
+   poli.tests.registry.test_multi_objective_and_negative
    poli.tests.registry.test_passing_array_of_strings
    poli.tests.registry.toy_continuous_problems
 

docs/poli-docs/_autosummary/poli.tests.registry.test_black_box_instancing.rst

@@ -0,0 +1,29 @@
+poli.tests.registry.test\_black\_box\_instancing
+================================================
+
+.. automodule:: poli.tests.registry.test_black_box_instancing
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_instancing_a_black_box_both_ways_matches
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/poli-docs/_autosummary/poli.tests.registry.test_multi_objective_and_negative.rst

@@ -0,0 +1,30 @@
+poli.tests.registry.test\_multi\_objective\_and\_negative
+=========================================================
+
+.. automodule:: poli.tests.registry.test_multi_objective_and_negative
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_multi_objective_instantiation
+      test_negative_black_boxes
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/poli-docs/_autosummary/poli.tests.registry.test_passing_array_of_strings.rst

@@ -1,4 +1,4 @@
-poli.tests.registry.test\_passing\_array\_of\_strings
+poli.tests.registry.test\_passing\_array\_of\_strings
 =====================================================
 
 .. automodule:: poli.tests.registry.test_passing_array_of_strings

docs/poli-docs/_autosummary/poli.tests.test_core_promises.rst

@@ -0,0 +1,31 @@
+poli.tests.test\_core\_promises
+===============================
+
+.. automodule:: poli.tests.test_core_promises
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_creating_a_problem
+      test_creating_an_instance_of_a_black_box
+      test_instancing_a_black_box_that_requires_isolation
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/poli-docs/_build/.doctrees/_autosummary/poli.core.multi_objective_black_box.MultiObjectiveBlackBox.doctree

@@ -576,14 +576,13 @@ <h1>poli.core.multi_objective_black_box.MultiObjectiveBlackBox</h1>
 <h1>poli.core.multi_objective_black_box.MultiObjectiveBlackBox<a class="headerlink" href="#poli-core-multi-objective-black-box-multiobjectiveblackbox" title="Permalink to this heading">#</a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="poli.core.multi_objective_black_box.MultiObjectiveBlackBox">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">poli.core.multi_objective_black_box.</span></span><span class="sig-name descname"><span class="pre">MultiObjectiveBlackBox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="poli.core.problem_setup_information.ProblemSetupInformation.html#poli.core.problem_setup_information.ProblemSetupInformation" title="poli.core.problem_setup_information.ProblemSetupInformation"><span class="pre">ProblemSetupInformation</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">objective_functions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><span class="pre">AbstractBlackBox</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox" title="Permalink to this definition">#</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">poli.core.multi_objective_black_box.</span></span><span class="sig-name descname"><span class="pre">MultiObjectiveBlackBox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">objective_functions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><span class="pre">AbstractBlackBox</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox" title="Permalink to this definition">#</a></dt>
 <dd><p>This class implements a multi-objective black box function
 by concatenating the results of evaluating individual
 objective functions.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>info</strong> (<a class="reference internal" href="poli.core.problem_setup_information.ProblemSetupInformation.html#poli.core.problem_setup_information.ProblemSetupInformation" title="poli.core.problem_setup_information.ProblemSetupInformation"><em>ProblemSetupInformation</em></a>) – The problem setup information.</p></li>
 <li><p><strong>batch_size</strong> (<em>int</em><em>, </em><em>optional</em>) – The batch size for evaluating the black box function. Defaults to None.</p></li>
 <li><p><strong>objective_functions</strong> (<em>List</em><em>[</em><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><em>AbstractBlackBox</em></a><em>]</em><em>, </em><em>required</em>) – The list of objective functions to be evaluated. Defaults to None.</p></li>
 </ul>
@@ -614,12 +613,11 @@ <h1>poli.core.multi_objective_black_box.MultiObjectiveBlackBox<a class="headerli
 </dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="poli.core.problem_setup_information.ProblemSetupInformation.html#poli.core.problem_setup_information.ProblemSetupInformation" title="poli.core.problem_setup_information.ProblemSetupInformation"><span class="pre">ProblemSetupInformation</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">objective_functions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><span class="pre">AbstractBlackBox</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</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="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__" title="Permalink to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">objective_functions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><span class="pre">AbstractBlackBox</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</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="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__" title="Permalink to this definition">#</a></dt>
 <dd><p>Initialize the MultiObjectiveBlackBox class.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>info</strong> (<a class="reference internal" href="poli.core.problem_setup_information.ProblemSetupInformation.html#poli.core.problem_setup_information.ProblemSetupInformation" title="poli.core.problem_setup_information.ProblemSetupInformation"><em>ProblemSetupInformation</em></a>) – The problem setup information.</p></li>
 <li><p><strong>objective_functions</strong> (<em>List</em><em>[</em><a class="reference internal" href="poli.core.abstract_black_box.AbstractBlackBox.html#poli.core.abstract_black_box.AbstractBlackBox" title="poli.core.abstract_black_box.AbstractBlackBox"><em>AbstractBlackBox</em></a><em>]</em>) – The list of objective functions.</p></li>
 <li><p><strong>batch_size</strong> (<em>int</em><em>, </em><em>optional</em>) – The batch size. Defaults to None.</p></li>
 </ul>
@@ -637,7 +635,7 @@ <h1>poli.core.multi_objective_black_box.MultiObjectiveBlackBox<a class="headerli
 <col style="width: 90%" />
 </colgroup>
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__" title="poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(info, objective_functions[, batch_size])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__" title="poli.core.multi_objective_black_box.MultiObjectiveBlackBox.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(objective_functions[, batch_size])</p></td>
 <td><p>Initialize the MultiObjectiveBlackBox class.</p></td>
 </tr>
 <tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset_evaluation_budget</span></code>()</p></td>

docs/poli-docs/_build/.doctrees/_autosummary/poli.core.multi_objective_black_box.doctree

@@ -584,7 +584,7 @@ <h1>poli.core.multi_objective_black_box</h1>
 <col style="width: 90%" />
 </colgroup>
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="poli.core.multi_objective_black_box.MultiObjectiveBlackBox.html#poli.core.multi_objective_black_box.MultiObjectiveBlackBox" title="poli.core.multi_objective_black_box.MultiObjectiveBlackBox"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MultiObjectiveBlackBox</span></code></a>(info, objective_functions)</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="poli.core.multi_objective_black_box.MultiObjectiveBlackBox.html#poli.core.multi_objective_black_box.MultiObjectiveBlackBox" title="poli.core.multi_objective_black_box.MultiObjectiveBlackBox"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MultiObjectiveBlackBox</span></code></a>(objective_functions)</p></td>
 <td><p>This class implements a multi-objective black box function by concatenating the results of evaluating individual objective functions.</p></td>
 </tr>
 </tbody>