Updates Rasp and random mutations. Will wait until we update poli-baselines as well

Author: miguelgondu

docs/poli-docs/_build/.doctrees/environment.pickle

@@ -19,21 +19,19 @@ Assuming you have [`3ned.pdb`](https://www.rcsb.org/structure/3ned) in the same
 
 ```python
 from pathlib import Path
-    from poli.objective_repository import RaspBlackBox, RaspProblemFactory
+from poli.objective_repository import RaspBlackBox, RaspProblemFactory
 
-    wildtype_pdb_path = (
-        Path(__file__).parent.parent / "static_files_for_tests" / "3ned.pdb"
-    )
+wildtype_pdb_path = Path(__file__).parent  / "3ned.pdb"
 
-    # Creating the black box
-    f = RaspBlackBox(wildtype_pdb_path=[wildtype_pdb_path])
+# Creating the black box
+f = RaspBlackBox(wildtype_pdb_path=[wildtype_pdb_path])
 
-    # Creating a problem
-    problem = RaspProblemFactory().create(wildtype_pdb_path=[wildtype_pdb_path])
-    f, x0 = problem.black_box, problem.x0
+# Creating a problem
+problem = RaspProblemFactory().create(wildtype_pdb_path=[wildtype_pdb_path])
+f, x0 = problem.black_box, problem.x0
 
-    # Querying:
-    print(f(x0))
+# Querying:
+print(f(x0))
 ```
 
 ## Warnings

docs/poli-docs/_build/.doctrees/using_poli/objective_repository/RaSP.doctree

@@ -17,7 +17,9 @@ from poli_baselines.solvers import RandomMutation
 
 problem_factory = AlohaProblemFactory()
 
-f, x0, y0 = problem_factory.create()
+problem = problem_factory.create()
+f, x0 = problem.black_box, problem.x0
+y0 = f(x0)
 
 solver = RandomMutation(
     black_box=f,

docs/poli-docs/_build/.doctrees/using_poli_baselines/random_mutations.doctree

@@ -602,21 +602,19 @@ <h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to
 <h2>How to run<a class="headerlink" href="#how-to-run" title="Permalink to this heading">#</a></h2>
 <p>Assuming you have <a class="reference external" href="https://www.rcsb.org/structure/3ned"><code class="docutils literal notranslate"><span class="pre">3ned.pdb</span></code></a> in the same directory as this script:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
-    <span class="kn">from</span> <span class="nn">poli.objective_repository</span> <span class="kn">import</span> <span class="n">RaspBlackBox</span><span class="p">,</span> <span class="n">RaspProblemFactory</span>
+<span class="kn">from</span> <span class="nn">poli.objective_repository</span> <span class="kn">import</span> <span class="n">RaspBlackBox</span><span class="p">,</span> <span class="n">RaspProblemFactory</span>
 
-    <span class="n">wildtype_pdb_path</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">parent</span> <span class="o">/</span> <span class="s2">&quot;static_files_for_tests&quot;</span> <span class="o">/</span> <span class="s2">&quot;3ned.pdb&quot;</span>
-    <span class="p">)</span>
+<span class="n">wildtype_pdb_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="vm">__file__</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span>  <span class="o">/</span> <span class="s2">&quot;3ned.pdb&quot;</span>
 
-    <span class="c1"># Creating the black box</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="n">RaspBlackBox</span><span class="p">(</span><span class="n">wildtype_pdb_path</span><span class="o">=</span><span class="p">[</span><span class="n">wildtype_pdb_path</span><span class="p">])</span>
+<span class="c1"># Creating the black box</span>
+<span class="n">f</span> <span class="o">=</span> <span class="n">RaspBlackBox</span><span class="p">(</span><span class="n">wildtype_pdb_path</span><span class="o">=</span><span class="p">[</span><span class="n">wildtype_pdb_path</span><span class="p">])</span>
 
-    <span class="c1"># Creating a problem</span>
-    <span class="n">problem</span> <span class="o">=</span> <span class="n">RaspProblemFactory</span><span class="p">()</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">wildtype_pdb_path</span><span class="o">=</span><span class="p">[</span><span class="n">wildtype_pdb_path</span><span class="p">])</span>
-    <span class="n">f</span><span class="p">,</span> <span class="n">x0</span> <span class="o">=</span> <span class="n">problem</span><span class="o">.</span><span class="n">black_box</span><span class="p">,</span> <span class="n">problem</span><span class="o">.</span><span class="n">x0</span>
+<span class="c1"># Creating a problem</span>
+<span class="n">problem</span> <span class="o">=</span> <span class="n">RaspProblemFactory</span><span class="p">()</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">wildtype_pdb_path</span><span class="o">=</span><span class="p">[</span><span class="n">wildtype_pdb_path</span><span class="p">])</span>
+<span class="n">f</span><span class="p">,</span> <span class="n">x0</span> <span class="o">=</span> <span class="n">problem</span><span class="o">.</span><span class="n">black_box</span><span class="p">,</span> <span class="n">problem</span><span class="o">.</span><span class="n">x0</span>
 
-    <span class="c1"># Querying:</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="p">(</span><span class="n">x0</span><span class="p">))</span>
+<span class="c1"># Querying:</span>
+<span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="p">(</span><span class="n">x0</span><span class="p">))</span>
 </pre></div>
 </div>
 </section>

docs/poli-docs/_build/.jupyter_cache/global.db

@@ -600,7 +600,9 @@ <h2>How to run<a class="headerlink" href="#how-to-run" title="Permalink to this
 
 <span class="n">problem_factory</span> <span class="o">=</span> <span class="n">AlohaProblemFactory</span><span class="p">()</span>
 
-<span class="n">f</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">y0</span> <span class="o">=</span> <span class="n">problem_factory</span><span class="o">.</span><span class="n">create</span><span class="p">()</span>
+<span class="n">problem</span> <span class="o">=</span> <span class="n">problem_factory</span><span class="o">.</span><span class="n">create</span><span class="p">()</span>
+<span class="n">f</span><span class="p">,</span> <span class="n">x0</span> <span class="o">=</span> <span class="n">problem</span><span class="o">.</span><span class="n">black_box</span><span class="p">,</span> <span class="n">problem</span><span class="o">.</span><span class="n">x0</span>
+<span class="n">y0</span> <span class="o">=</span> <span class="n">f</span><span class="p">(</span><span class="n">x0</span><span class="p">)</span>
 
 <span class="n">solver</span> <span class="o">=</span> <span class="n">RandomMutation</span><span class="p">(</span>
     <span class="n">black_box</span><span class="o">=</span><span class="n">f</span><span class="p">,</span>

docs/poli-docs/_build/html/_sources/using_poli/objective_repository/RaSP.md

@@ -17,7 +17,9 @@ from poli_baselines.solvers import RandomMutation
 
 problem_factory = AlohaProblemFactory()
 
-f, x0, y0 = problem_factory.create()
+problem = problem_factory.create()
+f, x0 = problem.black_box, problem.x0
+y0 = f(x0)
 
 solver = RandomMutation(
     black_box=f,