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Documentation updated
This commit is contained in:
fjosw
parent
2d72c1ef6a
commit
3f977c264b
3 changed files with 20 additions and 38 deletions
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@ -213,7 +213,7 @@
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<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
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<span class="kn">import</span> <span class="nn">scipy.linalg</span>
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<span class="kn">from</span> <span class="nn">.obs</span> <span class="kn">import</span> <span class="n">Obs</span><span class="p">,</span> <span class="n">reweight</span><span class="p">,</span> <span class="n">correlate</span><span class="p">,</span> <span class="n">CObs</span>
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<span class="kn">from</span> <span class="nn">.misc</span> <span class="kn">import</span> <span class="n">dump_object</span>
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<span class="kn">from</span> <span class="nn">.misc</span> <span class="kn">import</span> <span class="n">dump_object</span><span class="p">,</span> <span class="n">_assert_equal_properties</span>
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<span class="kn">from</span> <span class="nn">.fits</span> <span class="kn">import</span> <span class="n">least_squares</span>
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<span class="kn">from</span> <span class="nn">.linalg</span> <span class="kn">import</span> <span class="n">eigh</span><span class="p">,</span> <span class="n">inv</span><span class="p">,</span> <span class="n">cholesky</span>
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<span class="kn">from</span> <span class="nn">.roots</span> <span class="kn">import</span> <span class="n">find_root</span>
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@ -251,10 +251,8 @@
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_input</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'Corr__init__ expects a list of timeslices.'</span><span class="p">)</span>
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<span class="c1"># data_input can have multiple shapes. The simplest one is a list of Obs.</span>
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<span class="c1"># We check, if this is the case</span>
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<span class="k">if</span> <span class="nb">all</span><span class="p">([(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">CObs</span><span class="p">))</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]):</span>
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<span class="n">_assert_equal_properties</span><span class="p">(</span><span class="n">data_input</span><span class="p">)</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">content</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">item</span><span class="p">])</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">N</span> <span class="o">=</span> <span class="mi">1</span>
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@ -1236,10 +1234,8 @@
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_input</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'Corr__init__ expects a list of timeslices.'</span><span class="p">)</span>
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<span class="c1"># data_input can have multiple shapes. The simplest one is a list of Obs.</span>
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<span class="c1"># We check, if this is the case</span>
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<span class="k">if</span> <span class="nb">all</span><span class="p">([(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">CObs</span><span class="p">))</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]):</span>
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<span class="n">_assert_equal_properties</span><span class="p">(</span><span class="n">data_input</span><span class="p">)</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">content</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">item</span><span class="p">])</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">N</span> <span class="o">=</span> <span class="mi">1</span>
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@ -2170,10 +2166,8 @@ smearing matrix at every timeslice. Other dependency (eg. spatial) are not suppo
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_input</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'Corr__init__ expects a list of timeslices.'</span><span class="p">)</span>
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<span class="c1"># data_input can have multiple shapes. The simplest one is a list of Obs.</span>
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<span class="c1"># We check, if this is the case</span>
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<span class="k">if</span> <span class="nb">all</span><span class="p">([(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">Obs</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">CObs</span><span class="p">))</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]):</span>
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<span class="n">_assert_equal_properties</span><span class="p">(</span><span class="n">data_input</span><span class="p">)</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">content</span> <span class="o">=</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">item</span><span class="p">])</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">data_input</span><span class="p">]</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">N</span> <span class="o">=</span> <span class="mi">1</span>
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@ -89,6 +89,7 @@
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<span class="kn">from</span> <span class="nn">..obs</span> <span class="kn">import</span> <span class="n">Obs</span>
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<span class="kn">from</span> <span class="nn">..covobs</span> <span class="kn">import</span> <span class="n">Covobs</span>
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<span class="kn">from</span> <span class="nn">..correlators</span> <span class="kn">import</span> <span class="n">Corr</span>
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<span class="kn">from</span> <span class="nn">..misc</span> <span class="kn">import</span> <span class="n">_assert_equal_properties</span>
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<span class="kn">from</span> <span class="nn">..</span> <span class="kn">import</span> <span class="n">version</span> <span class="k">as</span> <span class="n">pyerrorsversion</span>
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@ -184,20 +185,6 @@
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<span class="n">dl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ed</span><span class="p">)</span>
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<span class="k">return</span> <span class="n">dl</span>
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<span class="k">def</span> <span class="nf">_assert_equal_properties</span><span class="p">(</span><span class="n">ol</span><span class="p">,</span> <span class="n">otype</span><span class="o">=</span><span class="n">Obs</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">otype</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Wrong data type in list."</span><span class="p">)</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">is_merged</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">is_merged</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reweighted</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">reweighted</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to have the same property 'reweighted'."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">e_content</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">e_content</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idl</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">idl</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configurations."</span><span class="p">)</span>
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<span class="k">def</span> <span class="nf">write_Obs_to_dict</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
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<span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
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<span class="n">d</span><span class="p">[</span><span class="s1">'type'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'Obs'</span>
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@ -675,20 +662,6 @@
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<span class="n">dl</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ed</span><span class="p">)</span>
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<span class="k">return</span> <span class="n">dl</span>
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<span class="k">def</span> <span class="nf">_assert_equal_properties</span><span class="p">(</span><span class="n">ol</span><span class="p">,</span> <span class="n">otype</span><span class="o">=</span><span class="n">Obs</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">otype</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Wrong data type in list."</span><span class="p">)</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">is_merged</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">is_merged</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reweighted</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">reweighted</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to have the same property 'reweighted'."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">e_content</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">e_content</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idl</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">idl</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configurations."</span><span class="p">)</span>
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<span class="k">def</span> <span class="nf">write_Obs_to_dict</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
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<span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
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<span class="n">d</span><span class="p">[</span><span class="s1">'type'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'Obs'</span>
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@ -147,6 +147,21 @@
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<span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">a</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">rand</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">a</span> <span class="o">*</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
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<span class="n">corr_data</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">data</span><span class="p">)</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">means</span>
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<span class="k">return</span> <span class="p">[</span><span class="n">Obs</span><span class="p">([</span><span class="n">dat</span><span class="p">],</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">corr_data</span><span class="o">.</span><span class="n">T</span><span class="p">]</span>
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<span class="k">def</span> <span class="nf">_assert_equal_properties</span><span class="p">(</span><span class="n">ol</span><span class="p">,</span> <span class="n">otype</span><span class="o">=</span><span class="n">Obs</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="n">otype</span><span class="p">):</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Wrong data type in list."</span><span class="p">)</span>
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<span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">ol</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">is_merged</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">is_merged</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">reweighted</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">reweighted</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to have the same property 'reweighted'."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">e_content</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">e_content</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configs."</span><span class="p">)</span>
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<span class="k">if</span> <span class="ow">not</span> <span class="n">ol</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">idl</span> <span class="o">==</span> <span class="n">o</span><span class="o">.</span><span class="n">idl</span><span class="p">:</span>
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<span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"All Obs in list have to be defined on the same set of configurations."</span><span class="p">)</span>
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</pre></div>
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</details>
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