Deploying to gh-pages from @ 0c19f7f 🚀

Author: fsoubelet

_modules/omc3/correction/response_io.html

@@ -344,7 +344,7 @@ <h1>Source code for omc3.correction.response_io</h1><div class="highlight"><pre>
     <span class="n">groups</span> <span class="o">=</span> <span class="n">_main_store_groups</span><span class="p">(</span><span class="n">store</span><span class="p">)</span>
     <span class="n">not_found</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">keys</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">]</span>
     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">not_found</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;The following keys could not be found in </span><span class="si">{</span><span class="n">file_id</span><span class="si">}</span><span class="s2"> file:&quot;</span> <span class="sa">f</span><span class="s2">&quot; </span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">not_found</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;The following keys could not be found in </span><span class="si">{</span><span class="n">file_id</span><span class="si">}</span><span class="s2"> file: </span><span class="si">{</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">not_found</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
 
 <span class="k">def</span><span class="w"> </span><span class="nf">_main_store_groups</span><span class="p">(</span><span class="n">store</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">HDFStore</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>

_modules/omc3/correction/response_madx.html

@@ -229,7 +229,8 @@ <h1>Source code for omc3.harpy.handler</h1><div class="highlight"><pre>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">__future__</span><span class="w"> </span><span class="kn">import</span> <span class="n">annotations</span>
 
-<span class="kn">from</span><span class="w"> </span><span class="nn">os.path</span><span class="w"> </span><span class="kn">import</span> <span class="n">basename</span><span class="p">,</span> <span class="n">join</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">TYPE_CHECKING</span>
 
 <span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
@@ -255,14 +256,19 @@ <h1>Source code for omc3.harpy.handler</h1><div class="highlight"><pre>
 <span class="kn">from</span><span class="w"> </span><span class="nn">omc3.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">logging_tools</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">omc3.utils.contexts</span><span class="w"> </span><span class="kn">import</span> <span class="n">timeit</span>
 
+<span class="k">if</span> <span class="n">TYPE_CHECKING</span><span class="p">:</span>
+    <span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Any</span>
+
+    <span class="kn">from</span><span class="w"> </span><span class="nn">turn_by_turn</span><span class="w"> </span><span class="kn">import</span> <span class="n">TbtData</span>
+
 <span class="n">LOGGER</span> <span class="o">=</span> <span class="n">logging_tools</span><span class="o">.</span><span class="n">get_logger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
 <span class="n">ALL_PLANES</span> <span class="o">=</span> <span class="p">(</span><span class="o">*</span><span class="n">PLANES</span><span class="p">,</span> <span class="s2">&quot;Z&quot;</span><span class="p">)</span>
 <span class="n">PLANE_TO_NUM</span> <span class="o">=</span> <span class="p">{</span><span class="o">**</span><span class="n">P2N</span><span class="p">,</span> <span class="s2">&quot;Z&quot;</span><span class="p">:</span> <span class="mi">3</span><span class="p">}</span>
 
 
 <div class="viewcode-block" id="run_per_bunch">
 <a class="viewcode-back" href="../../../modules/harpy.html#omc3.harpy.handler.run_per_bunch">[docs]</a>
-<span class="k">def</span><span class="w"> </span><span class="nf">run_per_bunch</span><span class="p">(</span><span class="n">tbt_data</span><span class="p">,</span> <span class="n">harpy_input</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">run_per_bunch</span><span class="p">(</span><span class="n">tbt_data</span><span class="p">:</span> <span class="n">TbtData</span><span class="p">,</span> <span class="n">harpy_input</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Cleans data, analyses frequencies and searches for resonances.</span>
 
@@ -275,7 +281,7 @@ <h1>Source code for omc3.harpy.handler</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">model</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">harpy_input</span><span class="o">.</span><span class="n">model</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">tfs</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">harpy_input</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="n">COL_NAME</span><span class="p">)</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span> <span class="s1">&#39;S&#39;</span><span class="p">]</span>
     <span class="n">bpm_datas</span><span class="p">,</span> <span class="n">usvs</span><span class="p">,</span> <span class="n">lins</span><span class="p">,</span> <span class="n">bad_bpms</span> <span class="o">=</span> <span class="p">{},</span> <span class="p">{},</span> <span class="p">{},</span> <span class="p">{}</span>
-    <span class="n">output_file_path</span> <span class="o">=</span> <span class="n">_get_output_path_without_suffix</span><span class="p">(</span><span class="n">harpy_input</span><span class="o">.</span><span class="n">outputdir</span><span class="p">,</span> <span class="n">harpy_input</span><span class="o">.</span><span class="n">files</span><span class="p">)</span>
+    <span class="n">output_file_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">_get_output_path_without_suffix</span><span class="p">(</span><span class="n">harpy_input</span><span class="o">.</span><span class="n">outputdir</span><span class="p">,</span> <span class="n">harpy_input</span><span class="o">.</span><span class="n">files</span><span class="p">)</span>
     <span class="k">for</span> <span class="n">plane</span> <span class="ow">in</span> <span class="n">PLANES</span><span class="p">:</span>
         <span class="n">bpm_data</span> <span class="o">=</span> <span class="n">_get_cut_tbt_matrix</span><span class="p">(</span><span class="n">tbt_data</span><span class="p">,</span> <span class="n">harpy_input</span><span class="o">.</span><span class="n">turns</span><span class="p">,</span> <span class="n">plane</span><span class="p">)</span>
         <span class="n">bpm_data</span> <span class="o">=</span> <span class="n">_scale_to_meters</span><span class="p">(</span><span class="n">bpm_data</span><span class="p">,</span> <span class="n">harpy_input</span><span class="o">.</span><span class="n">unit</span><span class="p">)</span>
@@ -404,23 +410,22 @@ <h1>Source code for omc3.harpy.handler</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">headers</span>
 
 
-<span class="k">def</span><span class="w"> </span><span class="nf">_write_bad_bpms</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">,</span> <span class="n">plane</span><span class="p">,</span> <span class="n">bad_bpms_with_reasons</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">output_path_without_suffix</span><span class="si">}</span><span class="s2">.bad_bpms_</span><span class="si">{</span><span class="n">plane</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">bad_bpms_file</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">bad_bpms_with_reasons</span><span class="p">:</span>
-            <span class="n">bad_bpms_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">line</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_write_bad_bpms</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="nb">str</span><span class="p">,</span> <span class="n">plane</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">bad_bpms_with_reasons</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+    <span class="n">bad_bpms_file</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">output_path_without_suffix</span><span class="si">}</span><span class="s2">.bad_bpms_</span><span class="si">{</span><span class="n">plane</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+    <span class="n">bad_bpms_file</span><span class="o">.</span><span class="n">write_text</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bad_bpms_with_reasons</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
 
 
-<span class="k">def</span><span class="w"> </span><span class="nf">_write_spectrum</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">,</span> <span class="n">plane</span><span class="p">,</span> <span class="n">spectra</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_write_spectrum</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="nb">str</span><span class="p">,</span> <span class="n">plane</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">spectra</span><span class="p">:</span> <span class="n">tfs</span><span class="o">.</span><span class="n">TfsDataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
     <span class="n">tfs</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">output_path_without_suffix</span><span class="si">}{</span><span class="n">FILE_AMPS_EXT</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">plane</span><span class="o">=</span><span class="n">plane</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">spectra</span><span class="p">[</span><span class="s2">&quot;COEFFS&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">abs</span><span class="p">()</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>
     <span class="n">tfs</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">output_path_without_suffix</span><span class="si">}{</span><span class="n">FILE_FREQS_EXT</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">plane</span><span class="o">=</span><span class="n">plane</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">spectra</span><span class="p">[</span><span class="s2">&quot;FREQS&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">T</span><span class="p">)</span>
 
 
-<span class="k">def</span><span class="w"> </span><span class="nf">_write_lin_tfs</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">,</span> <span class="n">plane</span><span class="p">,</span> <span class="n">lin_frame</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_write_lin_tfs</span><span class="p">(</span><span class="n">output_path_without_suffix</span><span class="p">:</span> <span class="n">Path</span> <span class="o">|</span> <span class="nb">str</span><span class="p">,</span> <span class="n">plane</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">lin_frame</span><span class="p">:</span> <span class="n">tfs</span><span class="o">.</span><span class="n">TfsDataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
     <span class="n">tfs</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">output_path_without_suffix</span><span class="si">}{</span><span class="n">FILE_LIN_EXT</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">plane</span><span class="o">=</span><span class="n">plane</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">lin_frame</span><span class="p">)</span>
 
 
-<span class="k">def</span><span class="w"> </span><span class="nf">_get_output_path_without_suffix</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">file_path</span><span class="p">):</span>
-    <span class="k">return</span> <span class="n">join</span><span class="p">(</span><span class="n">output_dir</span><span class="p">,</span> <span class="n">basename</span><span class="p">(</span><span class="n">file_path</span><span class="p">))</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">_get_output_path_without_suffix</span><span class="p">(</span><span class="n">output_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">file_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Path</span><span class="p">:</span>
+    <span class="k">return</span> <span class="n">Path</span><span class="p">(</span><span class="n">output_dir</span><span class="p">)</span> <span class="o">/</span> <span class="n">Path</span><span class="p">(</span><span class="n">file_path</span><span class="p">)</span><span class="o">.</span><span class="n">name</span>
 
 
 <span class="k">def</span><span class="w"> </span><span class="nf">_rescale_amps_to_main_line_and_compute_noise</span><span class="p">(</span><span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">plane</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>