release/v1.2.1: updating version numbers

stan-dev · Feb 5, 2024 · 9a59a1a · 9a59a1a
1 parent a83ec63
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diff --git a/cmdstanpy/_version.py b/cmdstanpy/_version.py
@@ -1,3 +1,3 @@
 """PyPi Version"""
 
-__version__ = '1.2.0'
+__version__ = '1.2.1'
diff --git a/docs/_modules/cmdstanpy/cmdstan_args.html b/docs/_modules/cmdstanpy/cmdstan_args.html
@@ -1,51 +1,55 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.cmdstan_args &#8212; CmdStanPy 1.2.0 documentation</title>
+    <title>cmdstanpy.cmdstan_args &#8212; CmdStanPy 1.2.1 documentation</title>
 
-  <!-- Loaded before other Sphinx assets -->
-  <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+    <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
 <link href="../../_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
-
+
+
+    <link rel="stylesheet"
+      href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
+
+
+
+
 
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-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
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+
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     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
+    <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
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+    <script src="../../_static/sphinx_highlight.js"></script>
     <script src="../../_static/clipboard.min.js"></script>
     <script src="../../_static/copybutton.js"></script>
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     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
     <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
+    <meta name="docsearch:language" content="en">
 
 
     <!-- Google Analytics -->
 
 <link rel="stylesheet" href="_static/basic.css" type="text/css" />
 
   </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="60">
+  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
 
     <div class="container-fluid" id="banner"></div>
 
@@ -56,7 +60,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='../../index.html'>CmdStanPy 1.2.0</a>
+<a class='navbar-brand' href='../../index.html'>CmdStanPy 1.2.1</a>
 
   </div>
 
@@ -176,7 +180,7 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
 <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">List</span><span class="p">,</span> <span class="n">Mapping</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Union</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">numpy.random</span> <span class="kn">import</span> <span class="n">RandomState</span>
+<span class="kn">from</span> <span class="nn">numpy.random</span> <span class="kn">import</span> <span class="n">default_rng</span>
 
 <span class="kn">from</span> <span class="nn">cmdstanpy</span> <span class="kn">import</span> <span class="n">_TMPDIR</span>
 <span class="kn">from</span> <span class="nn">cmdstanpy.utils</span> <span class="kn">import</span> <span class="p">(</span>
@@ -308,10 +312,9 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
                     <span class="s1">&#39;Value for iter_warmup must be a non-negative integer,&#39;</span>
                     <span class="s1">&#39; found </span><span class="si">{}</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">iter_warmup</span><span class="p">)</span>
                 <span class="p">)</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_warmup</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">adapt_engaged</span><span class="p">:</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_warmup</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">adapt_engaged</span><span class="p">:</span>
                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                    <span class="s1">&#39;Argument &quot;adapt_engaged&quot; is False, &#39;</span>
-                    <span class="s1">&#39;cannot specify warmup iterations.&#39;</span>
+                    <span class="s1">&#39;Must specify iter_warmup &gt; 0 when adapt_engaged=True.&#39;</span>
                 <span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_sampling</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_sampling</span> <span class="o">&lt;</span> <span class="mi">0</span> <span class="ow">or</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span>
@@ -710,6 +713,8 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
         <span class="n">num_draws</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <span class="n">num_elbo_draws</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
         <span class="n">save_single_paths</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">psis_resample</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">calculate_lp</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">init_alpha</span> <span class="o">=</span> <span class="n">init_alpha</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">tol_obj</span> <span class="o">=</span> <span class="n">tol_obj</span>
@@ -726,6 +731,8 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">num_elbo_draws</span> <span class="o">=</span> <span class="n">num_elbo_draws</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">save_single_paths</span> <span class="o">=</span> <span class="n">save_single_paths</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">psis_resample</span> <span class="o">=</span> <span class="n">psis_resample</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">calculate_lp</span> <span class="o">=</span> <span class="n">calculate_lp</span>
 
 <div class="viewcode-block" id="PathfinderArgs.validate"><a class="viewcode-back" href="../../internal_api.html#cmdstanpy.cmdstan_args.PathfinderArgs.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_chains</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
@@ -778,6 +785,12 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">save_single_paths</span><span class="p">:</span>
             <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;save_single_paths=1&#39;</span><span class="p">)</span>
 
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">psis_resample</span><span class="p">:</span>
+            <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;psis_resample=0&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">calculate_lp</span><span class="p">:</span>
+            <span class="n">cmd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;calculate_lp=0&#39;</span><span class="p">)</span>
+
         <span class="k">return</span> <span class="n">cmd</span></div></div>
 
 
@@ -1037,8 +1050,8 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
                 <span class="p">)</span>
 
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seed</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="n">rng</span> <span class="o">=</span> <span class="n">RandomState</span><span class="p">()</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">seed</span> <span class="o">=</span> <span class="n">rng</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">99999</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="n">rng</span> <span class="o">=</span> <span class="n">default_rng</span><span class="p">()</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seed</span> <span class="o">=</span> <span class="n">rng</span><span class="o">.</span><span class="n">integers</span><span class="p">(</span><span class="n">low</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">high</span><span class="o">=</span><span class="mi">99999</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">item</span><span class="p">()</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seed</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">list</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">integer</span><span class="p">)):</span>
                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
@@ -1177,9 +1190,8 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
       </div>
     </div>
 
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+    <script src="../../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
+  <footer class="footer mt-5 mt-md-0">
   <div class="container">
 
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@@ -1190,7 +1202,7 @@ <h1>Source code for cmdstanpy.cmdstan_args</h1><div class="highlight"><pre>
 
     <div class="footer-item">
       <p class="sphinx-version">
-Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.<br>
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 </p>
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diff --git a/docs/_modules/cmdstanpy/compilation.html b/docs/_modules/cmdstanpy/compilation.html
@@ -1,51 +1,55 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.compilation &#8212; CmdStanPy 1.2.0 documentation</title>
+    <title>cmdstanpy.compilation &#8212; CmdStanPy 1.2.1 documentation</title>
 
-  <!-- Loaded before other Sphinx assets -->
-  <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+    <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
 <link href="../../_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
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+
+    <link rel="stylesheet"
+      href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
+
+
+
+
 
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-    href="../../_static/vendor/fontawesome/5.13.0/css/all.min.css">
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-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="../../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
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+
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     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
+    <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
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+    <script src="../../_static/sphinx_highlight.js"></script>
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     <script src="../../_static/copybutton.js"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 
     <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="None">
+    <meta name="docsearch:language" content="en">
 
 
     <!-- Google Analytics -->
 
 <link rel="stylesheet" href="_static/basic.css" type="text/css" />
 
   </head>
-  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="60">
+  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
 
     <div class="container-fluid" id="banner"></div>
 
@@ -56,7 +60,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='../../index.html'>CmdStanPy 1.2.0</a>
+<a class='navbar-brand' href='../../index.html'>CmdStanPy 1.2.1</a>
 
   </div>
 
@@ -660,9 +664,8 @@ <h1>Source code for cmdstanpy.compilation</h1><div class="highlight"><pre>
       </div>
     </div>
 
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-  <script src="../../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
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+    <script src="../../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
+  <footer class="footer mt-5 mt-md-0">
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@@ -673,7 +676,7 @@ <h1>Source code for cmdstanpy.compilation</h1><div class="highlight"><pre>
 
     <div class="footer-item">
       <p class="sphinx-version">
-Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.5.0.<br>
+Created using <a href="http://sphinx-doc.org/">Sphinx</a> 5.3.0.<br>
 </p>
     </div>