Skip to content

Commit 2197480

Browse files
github-actions[bot]github-actions[bot]
committed
release/v1.2.0: updating version numbers
1 parent 4c5d3d5 commit 2197480

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

72 files changed

+7394
-6105
lines changed

‎cmdstanpy/_version.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
"""PyPi Version"""
22

3-
__version__ = '1.1.0'
3+
__version__ = '1.2.0'

‎docs/_modules/cmdstanpy/cmdstan_args.html‎

Lines changed: 269 additions & 219 deletions
Large diffs are not rendered by default.

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

Lines changed: 193 additions & 19 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/model.html‎

Lines changed: 587 additions & 223 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/stanfit.html‎

Lines changed: 53 additions & 5 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/stanfit/gq.html‎

Lines changed: 106 additions & 114 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/stanfit/laplace.html‎

Lines changed: 509 additions & 0 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/stanfit/mcmc.html‎

Lines changed: 62 additions & 55 deletions
Large diffs are not rendered by default.

‎docs/_modules/cmdstanpy/stanfit/metadata.html‎

Lines changed: 19 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<head>
66
<meta charset="utf-8" />
77
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
8-
<title>cmdstanpy.stanfit.metadata &#8212; CmdStanPy 1.1.0 documentation</title>
8+
<title>cmdstanpy.stanfit.metadata &#8212; CmdStanPy 1.2.0 documentation</title>
99

1010
<!-- Loaded before other Sphinx assets -->
1111
<link href="../../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
5656
<div id="navbar-start">
5757

5858
<!-- This will display the version of the docs -->
59-
<a class='navbar-brand' href='../../../index.html'>CmdStanPy 1.1.0</a>
59+
<a class='navbar-brand' href='../../../index.html'>CmdStanPy 1.2.0</a>
6060

6161
</div>
6262

@@ -170,12 +170,12 @@ <h1>Source code for cmdstanpy.stanfit.metadata</h1><div class="highlight"><pre>
170170
<span></span><span class="sd">&quot;&quot;&quot;Container for metadata parsed from the output of a CmdStan run&quot;&quot;&quot;</span>
171171

172172
<span class="kn">import</span> <span class="nn">copy</span>
173-
<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>
173+
<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>
174174

175-
<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>
175+
<span class="kn">import</span> <span class="nn">stanio</span>
176176

177177

178-
<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>
178+
<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>
179179
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
180180
<span class="sd"> CmdStan configuration and contents of output file parsed out of</span>
181181
<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>
185185
<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>
186186
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Initialize object from CSV headers&quot;&quot;&quot;</span>
187187
<span class="bp">self</span><span class="o">.</span><span class="n">_cmdstan_config</span> <span class="o">=</span> <span class="n">config</span>
188-
<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>
189-
<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>
190-
<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>
191-
<span class="p">)</span>
192-
<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>
193-
<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>
194-
<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>
188+
<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>
189+
190+
<span class="bp">self</span><span class="o">.</span><span class="n">_method_vars</span> <span class="o">=</span> <span class="p">{</span>
191+
<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>
192+
<span class="p">}</span>
193+
<span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars</span> <span class="o">=</span> <span class="p">{</span>
194+
<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>
195+
<span class="p">}</span>
195196

196197
<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>
197198
<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>
207208
<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>
208209

209210
<span class="nd">@property</span>
210-
<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>
211+
<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>
211212
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
212-
<span class="sd"> Returns a map from a Stan inference method variable to</span>
213-
<span class="sd"> a tuple of column indices in inference engine&#39;s output array.</span>
214213
<span class="sd"> Method variable names always end in `__`, e.g. `lp__`.</span>
215-
<span class="sd"> Uses deepcopy for immutability.</span>
216-
<span class="sd"> &quot;&quot;&quot;</span>
217-
<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>
218-
219-
<span class="nd">@property</span>
220-
<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>
221-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
222-
<span class="sd"> Returns a map from a Stan program variable name to a</span>
223-
<span class="sd"> tuple of the column indices in the vector or matrix of</span>
224-
<span class="sd"> estimates produced by a CmdStan inference method.</span>
225-
<span class="sd"> Uses deepcopy for immutability.</span>
226214
<span class="sd"> &quot;&quot;&quot;</span>
227-
<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>
215+
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_method_vars</span>
228216

229217
<span class="nd">@property</span>
230-
<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>
218+
<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>
231219
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
232-
<span class="sd"> Returns map from Stan program variable names to variable dimensions.</span>
233-
<span class="sd"> Scalar types are mapped to the empty tuple, e.g.,</span>
234-
<span class="sd"> program variable ``int foo`` has dimension ``()`` and</span>
235-
<span class="sd"> program variable ``vector[10] bar`` has single dimension ``(10)``.</span>
236-
<span class="sd"> Uses deepcopy for immutability.</span>
237-
<span class="sd"> &quot;&quot;&quot;</span>
238-
<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>
239-
240-
<span class="nd">@property</span>
241-
<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>
242-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
243-
<span class="sd"> Returns map from Stan program variable names to variable base type.</span>
244-
<span class="sd"> Uses deepcopy for immutability.</span>
220+
<span class="sd"> These are the user-defined variables in the Stan program.</span>
245221
<span class="sd"> &quot;&quot;&quot;</span>
246-
<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>
222+
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stan_vars</span></div>
247223
</pre></div>
248224

249225
</div>
@@ -266,7 +242,7 @@ <h1>Source code for cmdstanpy.stanfit.metadata</h1><div class="highlight"><pre>
266242

267243
<div class="footer-item">
268244
<p class="copyright">
269-
&copy; Copyright 2022, Stan Development Team.<br>
245+
&copy; Copyright 2023, Stan Development Team.<br>
270246
</p>
271247
</div>
272248

0 commit comments

Comments
 (0)