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release/v1.2.0: updating version numbers
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‎cmdstanpy/_version.py

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"""PyPi Version"""
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__version__ = '1.1.0'
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__version__ = '1.2.0'

‎docs/_modules/cmdstanpy/cmdstan_args.html

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‎docs/_modules/cmdstanpy/compiler_opts.html ‎docs/_modules/cmdstanpy/compilation.html

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‎docs/_modules/cmdstanpy/stanfit/metadata.html

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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>cmdstanpy.stanfit.metadata &#8212; CmdStanPy 1.1.0 documentation</title>
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<title>cmdstanpy.stanfit.metadata &#8212; CmdStanPy 1.2.0 documentation</title>
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<!-- Loaded before other Sphinx assets -->
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<link href="../../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
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<div id="navbar-start">
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<!-- This will display the version of the docs -->
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<a class='navbar-brand' href='../../../index.html'>CmdStanPy 1.1.0</a>
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<a class='navbar-brand' href='../../../index.html'>CmdStanPy 1.2.0</a>
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</div>
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@@ -170,12 +170,12 @@ <h1>Source code for cmdstanpy.stanfit.metadata</h1><div class="highlight"><pre>
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<span></span><span class="sd">&quot;&quot;&quot;Container for metadata parsed from the output of a CmdStan run&quot;&quot;&quot;</span>
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<span class="kn">import</span> <span class="nn">copy</span>
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<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Tuple</span>
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<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Dict</span>
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<span class="kn">from</span> <span class="nn">cmdstanpy.utils</span> <span class="kn">import</span> <span class="n">BaseType</span><span class="p">,</span> <span class="n">parse_method_vars</span><span class="p">,</span> <span class="n">parse_stan_vars</span>
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<span class="kn">import</span> <span class="nn">stanio</span>
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<div class="viewcode-block" id="InferenceMetadata"><a class="viewcode-back" href="../../../internal_api.html#cmdstanpy.InferenceMetadata">[docs]</a><span class="k">class</span> <span class="nc">InferenceMetadata</span><span class="p">:</span>
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<div class="viewcode-block" id="InferenceMetadata"><a class="viewcode-back" href="../../../internal_api.html#cmdstanpy.stanfit.InferenceMetadata">[docs]</a><span class="k">class</span> <span class="nc">InferenceMetadata</span><span class="p">:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd"> CmdStan configuration and contents of output file parsed out of</span>
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<span class="sd"> the Stan CSV file header comments and column headers.</span>
@@ -185,13 +185,14 @@ <h1>Source code for cmdstanpy.stanfit.metadata</h1><div class="highlight"><pre>
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<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config</span><span class="p">:</span> <span class="n">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="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Initialize object from CSV headers&quot;&quot;&quot;</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_cmdstan_config</span> <span class="o">=</span> <span class="n">config</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_method_vars_cols</span> <span class="o">=</span> <span class="n">parse_method_vars</span><span class="p">(</span><span class="n">names</span><span class="o">=</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;column_names&#39;</span><span class="p">])</span>
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<span class="n">stan_vars_dims</span><span class="p">,</span> <span class="n">stan_vars_cols</span><span class="p">,</span> <span class="n">stan_vars_types</span> <span class="o">=</span> <span class="n">parse_stan_vars</span><span class="p">(</span>
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<span class="n">names</span><span class="o">=</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;column_names&#39;</span><span class="p">]</span>
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<span class="p">)</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_dims</span> <span class="o">=</span> <span class="n">stan_vars_dims</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_cols</span> <span class="o">=</span> <span class="n">stan_vars_cols</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_types</span> <span class="o">=</span> <span class="n">stan_vars_types</span>
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<span class="nb">vars</span> <span class="o">=</span> <span class="n">stanio</span><span class="o">.</span><span class="n">parse_header</span><span class="p">(</span><span class="n">config</span><span class="p">[</span><span class="s1">&#39;raw_header&#39;</span><span class="p">])</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_method_vars</span> <span class="o">=</span> <span class="p">{</span>
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<span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">vars</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;__&#39;</span><span class="p">)</span>
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<span class="p">}</span>
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<span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars</span> <span class="o">=</span> <span class="p">{</span>
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<span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">vars</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;__&#39;</span><span class="p">)</span>
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<span class="p">}</span>
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<span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
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<span class="k">return</span> <span class="s1">&#39;Metadata:</span><span class="se">\n</span><span class="si">{}</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cmdstan_config</span><span class="p">)</span>
@@ -207,43 +208,18 @@ <h1>Source code for cmdstanpy.stanfit.metadata</h1><div class="highlight"><pre>
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<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_cmdstan_config</span><span class="p">)</span>
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<span class="nd">@property</span>
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<span class="k">def</span> <span class="nf">method_vars_cols</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="o">...</span><span class="p">]]:</span>
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<span class="k">def</span> <span class="nf">method_vars</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">stanio</span><span class="o">.</span><span class="n">Variable</span><span class="p">]:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd"> Returns a map from a Stan inference method variable to</span>
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<span class="sd"> a tuple of column indices in inference engine&#39;s output array.</span>
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<span class="sd"> Method variable names always end in `__`, e.g. `lp__`.</span>
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<span class="sd"> Uses deepcopy for immutability.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_method_vars_cols</span><span class="p">)</span>
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<span class="nd">@property</span>
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<span class="k">def</span> <span class="nf">stan_vars_cols</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="o">...</span><span class="p">]]:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd"> Returns a map from a Stan program variable name to a</span>
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<span class="sd"> tuple of the column indices in the vector or matrix of</span>
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<span class="sd"> estimates produced by a CmdStan inference method.</span>
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<span class="sd"> Uses deepcopy for immutability.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_cols</span><span class="p">)</span>
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_method_vars</span>
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<span class="nd">@property</span>
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<span class="k">def</span> <span class="nf">stan_vars_dims</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="o">...</span><span class="p">]]:</span>
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<span class="k">def</span> <span class="nf">stan_vars</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">stanio</span><span class="o">.</span><span class="n">Variable</span><span class="p">]:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd"> Returns map from Stan program variable names to variable dimensions.</span>
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<span class="sd"> Scalar types are mapped to the empty tuple, e.g.,</span>
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<span class="sd"> program variable ``int foo`` has dimension ``()`` and</span>
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<span class="sd"> program variable ``vector[10] bar`` has single dimension ``(10)``.</span>
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<span class="sd"> Uses deepcopy for immutability.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_dims</span><span class="p">)</span>
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<span class="nd">@property</span>
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<span class="k">def</span> <span class="nf">stan_vars_types</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">BaseType</span><span class="p">]:</span>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd"> Returns map from Stan program variable names to variable base type.</span>
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<span class="sd"> Uses deepcopy for immutability.</span>
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<span class="sd"> These are the user-defined variables in the Stan program.</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars_types</span><span class="p">)</span></div>
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars</span></div>
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</pre></div>
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</div>
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<div class="footer-item">
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<p class="copyright">
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&copy; Copyright 2022, Stan Development Team.<br>
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&copy; Copyright 2023, Stan Development Team.<br>
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</p>
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</div>
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