deploy: 8acdf74

_modules/pisa/stages/absorption/earth_absorption.html

@@ -86,7 +86,6 @@ <h1>Source code for pisa.stages.absorption.earth_absorption</h1><div class="high
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">import</span> <span class="nn">math</span>
 
 <span class="kn">from</span> <span class="nn">numba</span> <span class="kn">import</span> <span class="n">guvectorize</span>
 
@@ -129,7 +128,7 @@ <h1>Source code for pisa.stages.absorption.earth_absorption</h1><div class="high
 
 <div class="viewcode-block" id="earth_absorption">
 <a class="viewcode-back" href="../../../../pisa.stages.absorption.html#pisa.stages.absorption.earth_absorption.earth_absorption">[docs]</a>
-<span class="k">class</span> <span class="nc">earth_absorption</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">earth_absorption</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    earth absorption PISA Pi class</span>
 
@@ -200,7 +199,7 @@ <h1>Source code for pisa.stages.absorption.earth_absorption</h1><div class="high
             <span class="n">container</span><span class="p">[</span><span class="s1">&#39;densities&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">density</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="n">container</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">max_layers</span><span class="p">))</span>
             <span class="n">container</span><span class="p">[</span><span class="s1">&#39;distances&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">distance</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="n">container</span><span class="o">.</span><span class="n">size</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">max_layers</span><span class="p">))</span>
             <span class="n">container</span><span class="p">[</span><span class="s1">&#39;rho_int&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="n">container</span><span class="o">.</span><span class="n">size</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="n">FTYPE</span><span class="p">)</span>
-            
+
             <span class="n">container</span><span class="o">.</span><span class="n">mark_changed</span><span class="p">(</span><span class="s1">&#39;densities&#39;</span><span class="p">)</span>
             <span class="n">container</span><span class="o">.</span><span class="n">mark_changed</span><span class="p">(</span><span class="s1">&#39;distances&#39;</span><span class="p">)</span>
             <span class="n">container</span><span class="o">.</span><span class="n">mark_changed</span><span class="p">(</span><span class="s1">&#39;rho_int&#39;</span><span class="p">)</span>

_modules/pisa/stages/aeff/aeff.html

@@ -80,7 +80,6 @@ <h1>Source code for pisa.stages.aeff.aeff</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
 
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils</span> <span class="kn">import</span> <span class="n">vectorizer</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
 
 

_modules/pisa/stages/aeff/weight.html

@@ -80,7 +80,6 @@ <h1>Source code for pisa.stages.aeff.weight</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
 
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils</span> <span class="kn">import</span> <span class="n">vectorizer</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
 
 

_modules/pisa/stages/background/atm_muons.html

@@ -73,32 +73,29 @@
            <div itemprop="articleBody">
 
   <h1>Source code for pisa.stages.background.atm_muons</h1><div class="highlight"><pre>
-<span></span><span class="c1"># pylint: disable=not-callable</span>
+<span></span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">A stage to handle atmospheric muon background systematics.</span>
+<span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
 
-<span class="kn">import</span> <span class="nn">math</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">interp1d</span>
-<span class="kn">from</span> <span class="nn">numba</span> <span class="kn">import</span> <span class="n">guvectorize</span><span class="p">,</span> <span class="n">cuda</span>
 
-<span class="kn">from</span> <span class="nn">pisa</span> <span class="kn">import</span> <span class="n">FTYPE</span><span class="p">,</span> <span class="n">TARGET</span>
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.resources</span> <span class="kn">import</span> <span class="n">open_resource</span>
-<span class="kn">from</span> <span class="nn">pisa.utils.log</span> <span class="kn">import</span> <span class="n">logging</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
-<span class="kn">from</span> <span class="nn">pisa.utils.numba_tools</span> <span class="kn">import</span> <span class="n">WHERE</span><span class="p">,</span> <span class="n">myjit</span><span class="p">,</span> <span class="n">ftype</span>
 
 <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;atm_muons&quot;</span><span class="p">]</span>
 
 <span class="n">__author__</span> <span class="o">=</span> <span class="s1">&#39;T. Stuttard, S. Wren, S. Mandalia&#39;</span>
 
 <div class="viewcode-block" id="atm_muons">
 <a class="viewcode-back" href="../../../../pisa.stages.background.html#pisa.stages.background.atm_muons.atm_muons">[docs]</a>
-<span class="k">class</span> <span class="nc">atm_muons</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">atm_muons</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Stage to handle atmospheric muon background systematics.</span>
-<span class="sd">    Typically this is used with muons generated by MuonGun, but should be </span>
+<span class="sd">    PISA stage to apply atmospheric muon background systematics.</span>
+<span class="sd">    Typically this is used with muons generated by MuonGun, but should be</span>
 <span class="sd">    generic to other generators.</span>
 <span class="sd">    Note that this stage only modifies an weights based on the systematics,</span>
 <span class="sd">    it does not determine the nominal flux (this is assumed to either already</span>

_modules/pisa/stages/data/csv_data_hist.html

@@ -79,20 +79,17 @@ <h1>Source code for pisa.stages.data.csv_data_hist</h1><div class="highlight"><p
 
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
 
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
 
 <span class="kn">from</span> <span class="nn">pisa</span> <span class="kn">import</span> <span class="n">FTYPE</span>
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.resources</span> <span class="kn">import</span> <span class="n">find_resource</span>
 <span class="kn">from</span> <span class="nn">pisa.core.container</span> <span class="kn">import</span> <span class="n">Container</span>
-<span class="kn">from</span> <span class="nn">pisa.core.events_pi</span> <span class="kn">import</span> <span class="n">EventsPi</span>
 
 
 <div class="viewcode-block" id="csv_data_hist">
 <a class="viewcode-back" href="../../../../pisa.stages.data.html#pisa.stages.data.csv_data_hist.csv_data_hist">[docs]</a>
-<span class="k">class</span> <span class="nc">csv_data_hist</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">csv_data_hist</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    CSV file loader PISA Pi class</span>
 
@@ -131,7 +128,7 @@ <h1>Source code for pisa.stages.data.csv_data_hist</h1><div class="highlight"><p
         <span class="n">container</span><span class="p">[</span><span class="s1">&#39;weights&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">events</span><span class="p">[</span><span class="s1">&#39;count&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">FTYPE</span><span class="p">)</span>
         <span class="n">container</span><span class="p">[</span><span class="s1">&#39;reco_energy&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">events</span><span class="p">[</span><span class="s1">&#39;reco_energy&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">FTYPE</span><span class="p">)</span>
         <span class="n">container</span><span class="p">[</span><span class="s1">&#39;reco_coszen&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">events</span><span class="p">[</span><span class="s1">&#39;reco_coszen&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">FTYPE</span><span class="p">)</span>
-        <span class="n">container</span><span class="p">[</span><span class="s1">&#39;pid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">events</span><span class="p">[</span><span class="s1">&#39;pid&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">FTYPE</span><span class="p">)</span> 
+        <span class="n">container</span><span class="p">[</span><span class="s1">&#39;pid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">events</span><span class="p">[</span><span class="s1">&#39;pid&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">FTYPE</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">add_container</span><span class="p">(</span><span class="n">container</span><span class="p">)</span>
 

_modules/pisa/stages/data/csv_icc_hist.html

@@ -84,15 +84,13 @@ <h1>Source code for pisa.stages.data.csv_icc_hist</h1><div class="highlight"><pr
 
 <span class="kn">from</span> <span class="nn">pisa</span> <span class="kn">import</span> <span class="n">FTYPE</span>
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils</span> <span class="kn">import</span> <span class="n">vectorizer</span>
-<span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.resources</span> <span class="kn">import</span> <span class="n">find_resource</span>
 <span class="kn">from</span> <span class="nn">pisa.core.container</span> <span class="kn">import</span> <span class="n">Container</span>
 
 
 <div class="viewcode-block" id="csv_icc_hist">
 <a class="viewcode-back" href="../../../../pisa.stages.data.html#pisa.stages.data.csv_icc_hist.csv_icc_hist">[docs]</a>
-<span class="k">class</span> <span class="nc">csv_icc_hist</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">csv_icc_hist</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    CSV file loader PISA class</span>
 

_modules/pisa/stages/data/csv_loader.html

@@ -84,15 +84,13 @@ <h1>Source code for pisa.stages.data.csv_loader</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">pisa</span> <span class="kn">import</span> <span class="n">FTYPE</span>
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils</span> <span class="kn">import</span> <span class="n">vectorizer</span>
 <span class="kn">from</span> <span class="nn">pisa.utils.resources</span> <span class="kn">import</span> <span class="n">find_resource</span>
-<span class="kn">from</span> <span class="nn">pisa.utils.profiler</span> <span class="kn">import</span> <span class="n">profile</span>
 <span class="kn">from</span> <span class="nn">pisa.core.container</span> <span class="kn">import</span> <span class="n">Container</span>
 
 
 <div class="viewcode-block" id="csv_loader">
 <a class="viewcode-back" href="../../../../pisa.stages.data.html#pisa.stages.data.csv_loader.csv_loader">[docs]</a>
-<span class="k">class</span> <span class="nc">csv_loader</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">csv_loader</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    CSV file loader PISA Pi class</span>
 
@@ -141,6 +139,7 @@ <h1>Source code for pisa.stages.data.csv_loader</h1><div class="highlight"><pre>
             <span class="k">if</span> <span class="s1">&#39;tau&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
                 <span class="n">flav</span> <span class="o">=</span> <span class="mi">2</span>
 
+
             <span class="c1"># cut out right part</span>
             <span class="n">pdg</span> <span class="o">=</span> <span class="n">nubar</span> <span class="o">*</span> <span class="p">(</span><span class="mi">12</span> <span class="o">+</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">flav</span><span class="p">)</span>
 

_modules/pisa/stages/data/freedom_hdf5_loader.html

@@ -105,7 +105,7 @@ <h1>Source code for pisa.stages.data.freedom_hdf5_loader</h1><div class="highlig
 
 <div class="viewcode-block" id="freedom_hdf5_loader">
 <a class="viewcode-back" href="../../../../pisa.stages.data.html#pisa.stages.data.freedom_hdf5_loader.freedom_hdf5_loader">[docs]</a>
-<span class="k">class</span> <span class="nc">freedom_hdf5_loader</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">freedom_hdf5_loader</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    FreeDOM hdf5 file loader</span>
 

_modules/pisa/stages/data/grid.html

@@ -82,13 +82,12 @@ <h1>Source code for pisa.stages.data.grid</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">pisa</span> <span class="kn">import</span> <span class="n">FTYPE</span>
 <span class="kn">from</span> <span class="nn">pisa.core.stage</span> <span class="kn">import</span> <span class="n">Stage</span>
-<span class="kn">from</span> <span class="nn">pisa.utils</span> <span class="kn">import</span> <span class="n">vectorizer</span>
 <span class="kn">from</span> <span class="nn">pisa.core.container</span> <span class="kn">import</span> <span class="n">Container</span>
 
 
 <div class="viewcode-block" id="grid">
 <a class="viewcode-back" href="../../../../pisa.stages.data.html#pisa.stages.data.grid.grid">[docs]</a>
-<span class="k">class</span> <span class="nc">grid</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>
+<span class="k">class</span> <span class="nc">grid</span><span class="p">(</span><span class="n">Stage</span><span class="p">):</span>  <span class="c1"># pylint: disable=invalid-name</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Create a grid of events</span>