release/v1.0.3: updating version numbers

stan-dev · Jun 29, 2022 · 3fe0469 · 3fe0469
1 parent 8e021ef
commit 3fe0469
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Showing 38 changed files with 561 additions and 579 deletions.
diff --git a/cmdstanpy/_version.py b/cmdstanpy/_version.py
@@ -1,3 +1,3 @@
 """PyPi Version"""
 
-__version__ = '1.0.2'
+__version__ = '1.0.3'
diff --git a/docs/_modules/cmdstanpy/cmdstan_args.html b/docs/_modules/cmdstanpy/cmdstan_args.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.cmdstan_args &#8212; CmdStanPy 1.0.2 documentation</title>
+    <title>cmdstanpy.cmdstan_args &#8212; CmdStanPy 1.0.3 documentation</title>
 
   <!-- Loaded before other Sphinx assets -->
   <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.2</a>
+<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.3</a>
 
   </div>
 

diff --git a/docs/_modules/cmdstanpy/compiler_opts.html b/docs/_modules/cmdstanpy/compiler_opts.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.compiler_opts &#8212; CmdStanPy 1.0.2 documentation</title>
+    <title>cmdstanpy.compiler_opts &#8212; CmdStanPy 1.0.3 documentation</title>
 
   <!-- Loaded before other Sphinx assets -->
   <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.2</a>
+<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.3</a>
 
   </div>
 

diff --git a/docs/_modules/cmdstanpy/model.html b/docs/_modules/cmdstanpy/model.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.model &#8212; CmdStanPy 1.0.2 documentation</title>
+    <title>cmdstanpy.model &#8212; CmdStanPy 1.0.3 documentation</title>
 
   <!-- Loaded before other Sphinx assets -->
   <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.2</a>
+<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.3</a>
 
   </div>
 

diff --git a/docs/_modules/cmdstanpy/stanfit.html b/docs/_modules/cmdstanpy/stanfit.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.stanfit &#8212; CmdStanPy 1.0.2 documentation</title>
+    <title>cmdstanpy.stanfit &#8212; CmdStanPy 1.0.3 documentation</title>
 
   <!-- Loaded before other Sphinx assets -->
   <link href="../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.2</a>
+<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.3</a>
 
   </div>
 
@@ -197,7 +197,8 @@ <h1>Source code for cmdstanpy.stanfit</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="from_csv"><a class="viewcode-back" href="../../api.html#cmdstanpy.from_csv">[docs]</a><span class="k">def</span> <span class="nf">from_csv</span><span class="p">(</span>
-    <span class="n">path</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">method</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">path</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">os</span><span class="o">.</span><span class="n">PathLike</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">method</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">CmdStanMCMC</span><span class="p">,</span> <span class="n">CmdStanMLE</span><span class="p">,</span> <span class="n">CmdStanVB</span><span class="p">,</span> <span class="kc">None</span><span class="p">]:</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Instantiate a CmdStan object from a the Stan CSV files from a CmdStan run.</span>
@@ -229,22 +230,22 @@ <h1>Source code for cmdstanpy.stanfit</h1><div class="highlight"><pre>
     <span class="n">csvfiles</span> <span class="o">=</span> <span class="p">[]</span>
     <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
         <span class="n">csvfiles</span> <span class="o">=</span> <span class="n">path</span>
-    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-        <span class="k">if</span> <span class="s1">&#39;*&#39;</span> <span class="ow">in</span> <span class="n">path</span><span class="p">:</span>
-            <span class="n">splits</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">]</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="ow">not</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])):</span>
-                    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                        <span class="s1">&#39;Invalid path specification, </span><span class="si">{}</span><span class="s1"> &#39;</span>
-                        <span class="s1">&#39; unknown directory: </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="n">path</span><span class="p">,</span> <span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-                    <span class="p">)</span>
-            <span class="n">csvfiles</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
-        <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="s1">&#39;*&#39;</span> <span class="ow">in</span> <span class="n">path</span><span class="p">:</span>
+        <span class="n">splits</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">]</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="ow">not</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])):</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                    <span class="s1">&#39;Invalid path specification, </span><span class="si">{}</span><span class="s1"> &#39;</span>
+                    <span class="s1">&#39; unknown directory: </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="n">path</span><span class="p">,</span> <span class="n">splits</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+                <span class="p">)</span>
+        <span class="n">csvfiles</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">PathLike</span><span class="p">)):</span>
+        <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
             <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
-                <span class="k">if</span> <span class="n">file</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">&quot;.csv&quot;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">file</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;.csv&quot;</span><span class="p">:</span>
                     <span class="n">csvfiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">file</span><span class="p">))</span>
         <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
-            <span class="n">csvfiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+            <span class="n">csvfiles</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">path</span><span class="p">))</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Invalid path specification: </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="n">path</span><span class="p">))</span>
     <span class="k">else</span><span class="p">:</span>
@@ -253,7 +254,7 @@ <h1>Source code for cmdstanpy.stanfit</h1><div class="highlight"><pre>
     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">csvfiles</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;No CSV files found in directory </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="n">path</span><span class="p">))</span>
     <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csvfiles</span><span class="p">:</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">file</span><span class="p">)</span> <span class="ow">and</span> <span class="n">file</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;.csv&#39;</span><span class="p">)):</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">file</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">file</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;.csv&quot;</span><span class="p">):</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
                 <span class="s1">&#39;Bad CSV file path spec,&#39;</span>
                 <span class="s1">&#39; includes non-csv file: </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="n">file</span><span class="p">)</span>

diff --git a/docs/_modules/cmdstanpy/stanfit/mcmc.html b/docs/_modules/cmdstanpy/stanfit/mcmc.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>cmdstanpy.stanfit.mcmc &#8212; CmdStanPy 1.0.2 documentation</title>
+    <title>cmdstanpy.stanfit.mcmc &#8212; CmdStanPy 1.0.3 documentation</title>
 
   <!-- Loaded before other Sphinx assets -->
   <link href="../../../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
@@ -56,7 +56,7 @@
   <div id="navbar-start">
 
     <!-- This will display the version of the docs -->
-<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.2</a>
+<a class='navbar-brand' href='index.html'>CmdStanPy 1.0.3</a>
 
   </div>
 
@@ -211,6 +211,7 @@ <h1>Source code for cmdstanpy.stanfit.mcmc</h1><div class="highlight"><pre>
     <span class="n">get_logger</span><span class="p">,</span>
     <span class="n">scan_generated_quantities_csv</span><span class="p">,</span>
 <span class="p">)</span>
+
 <span class="kn">from</span> <span class="nn">.metadata</span> <span class="kn">import</span> <span class="n">InferenceMetadata</span>
 <span class="kn">from</span> <span class="nn">.runset</span> <span class="kn">import</span> <span class="n">RunSet</span>
 
@@ -290,6 +291,8 @@ <h1>Source code for cmdstanpy.stanfit.mcmc</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
         <span class="sd">&quot;&quot;&quot;Synonymous with ``fit.stan_variable(attr)&quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">attr</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Unknown variable name </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">stan_variable</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
         <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
@@ -1001,6 +1004,8 @@ <h1>Source code for cmdstanpy.stanfit.mcmc</h1><div class="highlight"><pre>
 
     <span class="k">def</span> <span class="fm">__getattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
         <span class="sd">&quot;&quot;&quot;Synonymous with ``fit.stan_variable(attr)&quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">attr</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">):</span>
+            <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Unknown variable name </span><span class="si">{</span><span class="n">attr</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">stan_variable</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
         <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>