last commit for v0.3.0

CONTRIBUTING.rst

@@ -56,8 +56,7 @@ Ready to contribute? Here's how to set up `pudu` for local development.
 
         $ git clone [email protected]:your_name_here/pudu.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up
-your fork for local development::
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
 
         $ mkvirtualenv pudu
         $ cd pudu/
@@ -67,8 +66,7 @@ your fork for local development::
 
         $ git checkout -b name-of-your-bugfix-or-feature
 
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python
-versions with tox::
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
 
         $ flake8 pudu tests
         $ pytest
@@ -97,6 +95,5 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests. Coverage should not go below 70% with `Codecov`.
 2. CodeQL should pass.
-3. If the pull request adds functionality, the docs should be updated. Add useful
-documentation to your functionality so it is included in the `docs`.
+3. If the pull request adds functionality, the docs should be updated. Add useful documentation to your functionality so it is included in the `docs`.
 4. The pull request should work for Python 3.6 through 3.10.

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022, Institut de Recerca en Energia de Catalunya
+Copyright (c) 2023, Institut de Recerca en Energia de Catalunya
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """Enric Tomas Grau-Luque"""
 __email__ = '[email protected]'
-__version__ = '0.2.0'
+__version__ = '0.3.0'

docs/_modules/pudu.html

@@ -195,12 +195,6 @@ <h1>Source code for pudu</h1><div class="highlight"><pre>
 
                     <span class="n">temp</span><span class="p">,</span> <span class="n">temp2</span> <span class="o">=</span> <span class="n">perturbation</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="n">x_copy</span><span class="p">,</span> <span class="n">row</span><span class="p">,</span> <span class="n">col</span><span class="p">,</span> <span class="n">window</span><span class="p">,</span> <span class="n">bias</span><span class="p">)</span>
 
-                    <span class="c1"># print(np.shape(temp[0,:,:,0]), np.shape(self.x[0,:,:,0]))</span>
-                    <span class="c1"># plt.plot(temp[0,0,:,0])</span>
-                    <span class="c1"># plt.plot(self.x[0,0,:,0])</span>
-                    <span class="c1"># plt.show()</span>
-                    <span class="c1"># exit()</span>
-
                     <span class="k">if</span> <span class="n">temp2</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                         <span class="n">val</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pf</span><span class="p">(</span><span class="n">temp</span><span class="p">)</span> <span class="o">-</span> <span class="n">p0</span>
                     <span class="k">else</span><span class="p">:</span>
@@ -620,23 +614,15 @@ <h1>Source code for pudu</h1><div class="highlight"><pre>
         <span class="n">s_x</span><span class="p">,</span> <span class="n">s_y</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span>
 
         <span class="n">master</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="c1"># master = np.array()</span>
         <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">s_x</span><span class="p">,</span> <span class="n">s_y</span><span class="p">):</span>
             <span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">expand_dims</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">y</span> <span class="o">=</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span>
 
             <span class="n">feats</span><span class="p">,</span> <span class="n">units</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactivations</span><span class="p">(</span><span class="n">layer</span><span class="p">,</span> <span class="n">slope</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">window</span><span class="p">,</span> <span class="n">scope</span><span class="p">,</span> <span class="n">bias</span><span class="p">,</span> <span class="n">padding</span><span class="p">,</span>
-                                            <span class="n">perturbation</span><span class="o">=</span><span class="n">perturbation</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="n">mask</span><span class="p">)</span>
+                                                <span class="n">perturbation</span><span class="p">,</span> <span class="n">mask</span><span class="p">)</span>
 
             <span class="n">master</span><span class="o">.</span><span class="n">extend</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">feats</span><span class="p">,</span> <span class="n">units</span><span class="p">))</span>
 
-            <span class="n">feats</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">feats</span><span class="p">)</span>
-            <span class="n">units</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">units</span><span class="p">)</span>
-            <span class="n">master</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">column_stack</span><span class="p">((</span><span class="n">feats</span><span class="p">,</span> <span class="n">units</span><span class="p">))</span>
-
-            <span class="n">master</span> <span class="o">=</span> <span class="n">master</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
-
-        <span class="n">master</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span> <span class="k">for</span> <span class="n">arr</span> <span class="ow">in</span> <span class="n">master</span><span class="p">]</span>
         <span class="n">counts</span> <span class="o">=</span> <span class="n">Counter</span><span class="p">(</span><span class="n">master</span><span class="p">)</span>
         <span class="n">result</span> <span class="o">=</span> <span class="p">[[</span><span class="n">j</span><span class="p">,</span> <span class="n">count</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">),</span> <span class="n">count</span> <span class="ow">in</span> <span class="n">counts</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span>
         <span class="n">result</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>

docs/_sources/examples.rst.txt

@@ -8,44 +8,50 @@ Example 1: PC-LDA with Scikit-learn for classification of spectroscopic data
     :linenos: 
 
 
-Examples 2: Regression for predicition of open circuit voltage of solar cells with RBFN
+Example 2: Regression for predicition of open circuit voltage of solar cells with RBFN
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_rbnf.py
     :language: python
 
 
-Examples 3: Handwritten numbers recognition using CNN with Keras and Mnist
+Example 3: Handwritten numbers recognition using CNN with Keras and Mnist
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_cnn_mnist.py
     :language: python
 
 
-Examples 4: How to call different masks 
+Example 4: How to call different masks 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_masking.py
     :language: python
 
 
-Examples 5: How to call different perturbations 
+Example 5: How to call different perturbations 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_perturbation.py
     :language: python
 
 
-Examples 6: Re-activations with 1-D CNN 
+Example 6: Re-activations with 1-D CNN 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_activations_1d.py
     :language: python
 
 
-Examples 7: Re-activations with 2-D CNN 
+Example 7: Re-activations with 2-D CNN 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. literalinclude:: ../examples/example_activations_2d.py
     :language: python
-
+
+
+Example 8: SEelcting specific sections to evaluate
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. literalinclude:: ../examples/example_specific_sections.py
+    :language: python

docs/contributions.html

@@ -136,29 +136,25 @@ <h2>Get Started!<a class="headerlink" href="#get-started" title="Permalink to th
 </pre></div>
 </div>
 </li>
-</ol>
-<p>3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up
-your fork for local development:</p>
+<li><p>Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ mkvirtualenv pudu
 $ cd pudu/
 $ python setup.py develop
 </pre></div>
 </div>
-<ol class="arabic" start="4">
+</li>
 <li><p>Create a branch for local development to make changes locally:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ git checkout -b name-of-your-bugfix-or-feature
 </pre></div>
 </div>
 </li>
-</ol>
-<p>5. When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python
-versions with tox:</p>
+<li><p>When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ flake8 pudu tests
 $ pytest
 $ tox
 </pre></div>
 </div>
-<ol class="arabic" start="6">
+</li>
 <li><p>Run unittest, check the test coverage, and create a coverage report in the <cite>tests</cite> folder:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ coverage run -m unittest test_pudu.py
 $ coverage xml
@@ -185,10 +181,9 @@ <h2>Pull Request Guidelines<a class="headerlink" href="#pull-request-guidelines"
 <ol class="arabic simple">
 <li><p>The pull request should include tests. Coverage should not go below 70% with <cite>Codecov</cite>.</p></li>
 <li><p>CodeQL should pass.</p></li>
+<li><p>If the pull request adds functionality, the docs should be updated. Add useful documentation to your functionality so it is included in the <cite>docs</cite>.</p></li>
+<li><p>The pull request should work for Python 3.6 through 3.10.</p></li>
 </ol>
-<p>3. If the pull request adds functionality, the docs should be updated. Add useful
-documentation to your functionality so it is included in the <cite>docs</cite>.
-4. The pull request should work for Python 3.6 through 3.10.</p>
 </section>
 </section>