From 3a1e1c6d346a5e8b0ae0ff487904e903a91e3f14 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 25 Aug 2022 13:30:24 +0000 Subject: [PATCH] release/v1.0.7: updating version numbers --- cmdstanpy/_version.py | 2 +- docs/_modules/cmdstanpy/cmdstan_args.html | 4 +- docs/_modules/cmdstanpy/compiler_opts.html | 4 +- docs/_modules/cmdstanpy/model.html | 4 +- docs/_modules/cmdstanpy/stanfit.html | 4 +- docs/_modules/cmdstanpy/stanfit/gq.html | 15 +- docs/_modules/cmdstanpy/stanfit/mcmc.html | 13 +- docs/_modules/cmdstanpy/stanfit/metadata.html | 4 +- docs/_modules/cmdstanpy/stanfit/mle.html | 15 +- docs/_modules/cmdstanpy/stanfit/runset.html | 4 +- docs/_modules/cmdstanpy/stanfit/vb.html | 15 +- docs/_modules/cmdstanpy/utils.html | 4 +- docs/_modules/cmdstanpy/utils/cmdstan.html | 4 +- docs/_modules/cmdstanpy/utils/json.html | 4 +- docs/_modules/index.html | 4 +- docs/_sources/changes.rst.txt | 4 + docs/_static/documentation_options.js | 2 +- docs/api.html | 4 +- docs/changes.html | 15 +- docs/community.html | 4 +- docs/genindex.html | 4 +- docs/index.html | 5 +- docs/installation.html | 4 +- docs/internal_api.html | 4 +- docs/objects.inv | Bin 5057 -> 5064 bytes docs/py-modindex.html | 4 +- docs/search.html | 4 +- docs/searchindex.js | 2 +- docs/users-guide.html | 4 +- docs/users-guide/examples.html | 4 +- docs/users-guide/examples/MCMC Sampling.html | 4 +- .../Maximum Likelihood Estimation.html | 12 +- .../Maximum Likelihood Estimation.ipynb | 20 +- .../examples/Run Generated Quantities.html | 140 +++++------ .../examples/Run Generated Quantities.ipynb | 224 +++++++++--------- .../examples/Using External C++.html | 4 +- .../examples/VI as Sampler Inits.html | 81 ++++--- .../examples/VI as Sampler Inits.ipynb | 214 ++++++++--------- .../examples/Variational Inference.html | 28 +-- .../examples/Variational Inference.ipynb | 80 +++---- docs/users-guide/hello_world.html | 56 ++--- docs/users-guide/outputs.html | 98 ++++---- docs/users-guide/overview.html | 4 +- docs/users-guide/workflow.html | 4 +- 44 files changed, 586 insertions(+), 547 deletions(-) diff --git a/cmdstanpy/_version.py b/cmdstanpy/_version.py index 6092f239..cb8406c9 100644 --- a/cmdstanpy/_version.py +++ b/cmdstanpy/_version.py @@ -1,3 +1,3 @@ """PyPi Version""" -__version__ = '1.0.6' +__version__ = '1.0.7' diff --git a/docs/_modules/cmdstanpy/cmdstan_args.html b/docs/_modules/cmdstanpy/cmdstan_args.html index d1b4ea17..c711184b 100644 --- a/docs/_modules/cmdstanpy/cmdstan_args.html +++ b/docs/_modules/cmdstanpy/cmdstan_args.html @@ -5,7 +5,7 @@ - cmdstanpy.cmdstan_args — CmdStanPy 1.0.6 documentation + cmdstanpy.cmdstan_args — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ diff --git a/docs/_modules/cmdstanpy/compiler_opts.html b/docs/_modules/cmdstanpy/compiler_opts.html index d7042b9a..0a7ba706 100644 --- a/docs/_modules/cmdstanpy/compiler_opts.html +++ b/docs/_modules/cmdstanpy/compiler_opts.html @@ -5,7 +5,7 @@ - cmdstanpy.compiler_opts — CmdStanPy 1.0.6 documentation + cmdstanpy.compiler_opts — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ diff --git a/docs/_modules/cmdstanpy/model.html b/docs/_modules/cmdstanpy/model.html index bfe08cdd..8c8304c4 100644 --- a/docs/_modules/cmdstanpy/model.html +++ b/docs/_modules/cmdstanpy/model.html @@ -5,7 +5,7 @@ - cmdstanpy.model — CmdStanPy 1.0.6 documentation + cmdstanpy.model — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ diff --git a/docs/_modules/cmdstanpy/stanfit.html b/docs/_modules/cmdstanpy/stanfit.html index 04c0bd3c..a012160f 100644 --- a/docs/_modules/cmdstanpy/stanfit.html +++ b/docs/_modules/cmdstanpy/stanfit.html @@ -5,7 +5,7 @@ - cmdstanpy.stanfit — CmdStanPy 1.0.6 documentation + cmdstanpy.stanfit — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ diff --git a/docs/_modules/cmdstanpy/stanfit/gq.html b/docs/_modules/cmdstanpy/stanfit/gq.html index 231410c2..08a9ff7c 100644 --- a/docs/_modules/cmdstanpy/stanfit/gq.html +++ b/docs/_modules/cmdstanpy/stanfit/gq.html @@ -5,7 +5,7 @@ - cmdstanpy.stanfit.gq — CmdStanPy 1.0.6 documentation + cmdstanpy.stanfit.gq — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ @@ -692,10 +692,15 @@

Source code for cmdstanpy.stanfit.gq

             col_idxs = self._metadata.stan_vars_cols[var]
             if len(col_idxs) > 0:
                 dims.extend(self._metadata.stan_vars_dims[var])
-            # pylint: disable=redundant-keyword-arg
-            draws = self._draws[draw1:, :, col_idxs].reshape(dims, order='F')
+
+            draws = self._draws[draw1:, :, col_idxs]
+
             if self._metadata.stan_vars_types[var] == BaseType.COMPLEX:
-                draws = draws[..., 0] + 1j * draws[..., 1]
+                draws = draws[..., ::2] + 1j * draws[..., 1::2]
+                dims = dims[:-1]
+
+            draws = draws.reshape(dims, order='F')
+
             return draws
[docs] def stan_variables(self, inc_warmup: bool = False) -> Dict[str, np.ndarray]: diff --git a/docs/_modules/cmdstanpy/stanfit/mcmc.html b/docs/_modules/cmdstanpy/stanfit/mcmc.html index 344d0d1e..8e4c0593 100644 --- a/docs/_modules/cmdstanpy/stanfit/mcmc.html +++ b/docs/_modules/cmdstanpy/stanfit/mcmc.html @@ -5,7 +5,7 @@ - cmdstanpy.stanfit.mcmc — CmdStanPy 1.0.6 documentation + cmdstanpy.stanfit.mcmc — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ @@ -916,9 +916,14 @@

Source code for cmdstanpy.stanfit.mcmc

         col_idxs = self._metadata.stan_vars_cols[var]
         if len(col_idxs) > 0:
             dims.extend(self._metadata.stan_vars_dims[var])
-        draws = self._draws[draw1:, :, col_idxs].reshape(dims, order='F')
+        draws = self._draws[draw1:, :, col_idxs]
+
         if self._metadata.stan_vars_types[var] == BaseType.COMPLEX:
-            draws = draws[..., 0] + 1j * draws[..., 1]
+            draws = draws[..., ::2] + 1j * draws[..., 1::2]
+            dims = dims[:-1]
+
+        draws = draws.reshape(dims, order='F')
+
         return draws
[docs] def stan_variables(self) -> Dict[str, np.ndarray]: diff --git a/docs/_modules/cmdstanpy/stanfit/metadata.html b/docs/_modules/cmdstanpy/stanfit/metadata.html index ed0a1dcb..bf171b8b 100644 --- a/docs/_modules/cmdstanpy/stanfit/metadata.html +++ b/docs/_modules/cmdstanpy/stanfit/metadata.html @@ -5,7 +5,7 @@ - cmdstanpy.stanfit.metadata — CmdStanPy 1.0.6 documentation + cmdstanpy.stanfit.metadata — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ diff --git a/docs/_modules/cmdstanpy/stanfit/mle.html b/docs/_modules/cmdstanpy/stanfit/mle.html index 91e3197d..6d94f7ee 100644 --- a/docs/_modules/cmdstanpy/stanfit/mle.html +++ b/docs/_modules/cmdstanpy/stanfit/mle.html @@ -5,7 +5,7 @@ - cmdstanpy.stanfit.mle — CmdStanPy 1.0.6 documentation + cmdstanpy.stanfit.mle — CmdStanPy 1.0.7 documentation @@ -56,7 +56,7 @@ @@ -387,12 +387,17 @@

Source code for cmdstanpy.stanfit.mle

             dims = (num_rows,) + self._metadata.stan_vars_dims[var]
             # pylint: disable=redundant-keyword-arg
             if num_rows > 1:
-                result = self._all_iters[:, col_idxs].reshape(dims, order='F')
+                result = self._all_iters[:, col_idxs]
             else:
-                result = self._mle[col_idxs].reshape(dims[1:], order="F")
+                result = self._mle[col_idxs]
+                dims = dims[1:]
 
             if self._metadata.stan_vars_types[var] == BaseType.COMPLEX:
-                result = result[..., 0] + 1j * result[..., 1]
+                result = result[..., ::2] + 1j * result[..., 1::2]
+                dims = dims[:-1]
+
+            result = result.reshape(dims, order='F')
+
             return result
 
         else:  # scalar var
diff --git a/docs/_modules/cmdstanpy/stanfit/runset.html b/docs/_modules/cmdstanpy/stanfit/runset.html
index 176aabc5..68721c48 100644
--- a/docs/_modules/cmdstanpy/stanfit/runset.html
+++ b/docs/_modules/cmdstanpy/stanfit/runset.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.runset — CmdStanPy 1.0.6 documentation
+    cmdstanpy.stanfit.runset — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/vb.html b/docs/_modules/cmdstanpy/stanfit/vb.html
index 29d88043..0a0a265c 100644
--- a/docs/_modules/cmdstanpy/stanfit/vb.html
+++ b/docs/_modules/cmdstanpy/stanfit/vb.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.vb — CmdStanPy 1.0.6 documentation
+    cmdstanpy.stanfit.vb — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
@@ -312,12 +312,13 @@ 
Source code for cmdstanpy.stanfit.vb
         shape: Tuple[int, ...] = ()
         if len(col_idxs) > 1:
             shape = self._metadata.stan_vars_dims[var]
-            result: np.ndarray = np.asarray(self._variational_mean)[
-                col_idxs
-            ].reshape(shape, order="F")
-
+            result: np.ndarray = np.asarray(self._variational_mean)[col_idxs]
             if self._metadata.stan_vars_types[var] == BaseType.COMPLEX:
-                result = result[..., 0] + 1j * result[..., 1]
+                result = result[..., ::2] + 1j * result[..., 1::2]
+                shape = shape[:-1]
+
+            result = result.reshape(shape, order="F")
+
             return result
         else:
             return float(self._variational_mean[col_idxs[0]])

diff --git a/docs/_modules/cmdstanpy/utils.html b/docs/_modules/cmdstanpy/utils.html
index 71a549df..11cd7f23 100644
--- a/docs/_modules/cmdstanpy/utils.html
+++ b/docs/_modules/cmdstanpy/utils.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.utils — CmdStanPy 1.0.6 documentation
+    cmdstanpy.utils — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/utils/cmdstan.html b/docs/_modules/cmdstanpy/utils/cmdstan.html
index de97e43e..b6096524 100644
--- a/docs/_modules/cmdstanpy/utils/cmdstan.html
+++ b/docs/_modules/cmdstanpy/utils/cmdstan.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.utils.cmdstan — CmdStanPy 1.0.6 documentation
+    cmdstanpy.utils.cmdstan — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/utils/json.html b/docs/_modules/cmdstanpy/utils/json.html
index cc6ea3de..fb5cd55d 100644
--- a/docs/_modules/cmdstanpy/utils/json.html
+++ b/docs/_modules/cmdstanpy/utils/json.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.utils.json — CmdStanPy 1.0.6 documentation
+    cmdstanpy.utils.json — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index d46fa65b..56befbea 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -5,7 +5,7 @@
   
     
     
-    Overview: module code — CmdStanPy 1.0.6 documentation
+    Overview: module code — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/_sources/changes.rst.txt b/docs/_sources/changes.rst.txt
index 6752fd88..68f2b558 100644
--- a/docs/_sources/changes.rst.txt
+++ b/docs/_sources/changes.rst.txt
@@ -7,6 +7,10 @@ What's New
 
 For full changes, see the `Releases page `__ on GitHub.
 
+CmdStanPy 1.0.6
+---------------
+
+- Fixed an issue where complex number containers in Stan program outputs were not being read in properly by CmdStanPy. The output would have the correct shape, but the values would be mixed up.
 
 CmdStanPy 1.0.6
 ---------------
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 047e8de6..f3b2e8ff 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.6',
+    VERSION: '1.0.7',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/api.html b/docs/api.html
index 5ff59067..e52e6089 100644
--- a/docs/api.html
+++ b/docs/api.html
@@ -6,7 +6,7 @@
     
     
 
-    API Reference — CmdStanPy 1.0.6 documentation
+    API Reference — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/changes.html b/docs/changes.html
index 509219f6..1eab93fd 100644
--- a/docs/changes.html
+++ b/docs/changes.html
@@ -6,7 +6,7 @@
     
     
 
-    What’s New — CmdStanPy 1.0.6 documentation
+    What’s New — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
@@ -172,6 +172,11 @@
    CmdStanPy 1.0.6
   
  
+ 
  • 
+  
+   CmdStanPy 1.0.6
+  
+ 
    • 
  
  • 
   
    CmdStanPy 1.0.5
@@ -236,6 +241,12 @@ 
    What’s New
 
    CmdStanPy 1.0.6#
    
 
      
+
    • Fixed an issue where complex number containers in Stan program outputs were not being read in properly by CmdStanPy. The output would have the correct shape, but the values would be mixed up.
      • 
+
    
+
+
    
+
    CmdStanPy 1.0.6#
    
+
      
 
    • Fixed a build error in the documentation
      • 
 
    • Improved messages when model fails to compile due to C++ errors.
      • 
 
    
diff --git a/docs/community.html b/docs/community.html
index 5786d3fe..e5469a8b 100644
--- a/docs/community.html
+++ b/docs/community.html
@@ -6,7 +6,7 @@
     
     
 
-    Community — CmdStanPy 1.0.6 documentation
+    Community — CmdStanPy 1.0.7 documentation
     
   
   
@@ -58,7 +58,7 @@
   
 
diff --git a/docs/genindex.html b/docs/genindex.html
index b7a08361..74adcd0f 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,7 +5,7 @@
   
     
     
-    Index — CmdStanPy 1.0.6 documentation
+    Index — CmdStanPy 1.0.7 documentation
     
   
   
@@ -56,7 +56,7 @@
   
 
diff --git a/docs/index.html b/docs/index.html
index 93b64465..d1d14af5 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
     
     
 
-    cmdstanpy – Python interface to CmdStan — CmdStanPy 1.0.6 documentation
+    cmdstanpy – Python interface to CmdStan — CmdStanPy 1.0.7 documentation
     
   
   
@@ -58,7 +58,7 @@
   
 
@@ -294,6 +294,7 @@
 
    • 
 
  • What’s New
      
 
    • CmdStanPy 1.0.6
      • 
+
    • CmdStanPy 1.0.6
      • 
 
    • CmdStanPy 1.0.5
      • 
 
    • CmdStanPy 1.0.4
      • 
 
    • CmdStanPy 1.0.3
      • 
diff --git a/docs/installation.html b/docs/installation.html
index 8da2ca49..2a748896 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -6,7 +6,7 @@
     
     
 
-    Installation — CmdStanPy 1.0.6 documentation
+    Installation — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/internal_api.html b/docs/internal_api.html
index 7d87e939..2813a0a6 100644
--- a/docs/internal_api.html
+++ b/docs/internal_api.html
@@ -6,7 +6,7 @@
     
     
 
-    Internal API Reference — CmdStanPy 1.0.6 documentation
+    Internal API Reference — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/objects.inv b/docs/objects.inv
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\ No newline at end of file
diff --git a/docs/users-guide.html b/docs/users-guide.html
index ab07faff..23aec2b0 100644
--- a/docs/users-guide.html
+++ b/docs/users-guide.html
@@ -6,7 +6,7 @@
     
     
 
-    User’s Guide — CmdStanPy 1.0.6 documentation
+    User’s Guide — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/users-guide/examples.html b/docs/users-guide/examples.html
index 77ae407c..5e23f081 100644
--- a/docs/users-guide/examples.html
+++ b/docs/users-guide/examples.html
@@ -6,7 +6,7 @@
     
     
 
-    CmdStanPy Examples — CmdStanPy 1.0.6 documentation
+    CmdStanPy Examples — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/users-guide/examples/MCMC Sampling.html b/docs/users-guide/examples/MCMC Sampling.html
index 08b0d412..0e567773 100644
--- a/docs/users-guide/examples/MCMC Sampling.html	
+++ b/docs/users-guide/examples/MCMC Sampling.html	
@@ -6,7 +6,7 @@
     
     
 
-    MCMC Sampling — CmdStanPy 1.0.6 documentation
+    MCMC Sampling — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
diff --git a/docs/users-guide/examples/Maximum Likelihood Estimation.html b/docs/users-guide/examples/Maximum Likelihood Estimation.html
index cffe8e55..d1a687af 100644
--- a/docs/users-guide/examples/Maximum Likelihood Estimation.html	
+++ b/docs/users-guide/examples/Maximum Likelihood Estimation.html	
@@ -6,7 +6,7 @@
     
     
 
-    Maximum Likelihood Estimation — CmdStanPy 1.0.6 documentation
+    Maximum Likelihood Estimation — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
@@ -551,8 +551,8 @@ 
      Maximum Likelihood Estimation
       /opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
   from .autonotebook import tqdm as notebook_tqdm
-18:58:31 - cmdstanpy - INFO - Chain [1] start processing
-18:58:31 - cmdstanpy - INFO - Chain [1] done processing
+13:29:25 - cmdstanpy - INFO - Chain [1] start processing
+13:29:25 - cmdstanpy - INFO - Chain [1] done processing
    • @@ -561,7 +561,7 @@

    Maximum Likelihood Estimation 
     ('lp__', 'theta')
-OrderedDict([('lp__', -5.00402), ('theta', 0.2)])
+OrderedDict([('lp__', -5.00402), ('theta', 0.200006)])

    @@ -595,7 +595,7 @@

    Maximum Likelihood Estimation\n", " 0\n", " -5.00402\n", - " 0.2\n", + " 0.200006\n", " \n", " \n", "\n", "

    " ], "text/plain": [ - " lp__ theta\n", - "0 -5.00402 0.2" + " lp__ theta\n", + "0 -5.00402 0.200006" ] }, "execution_count": 1, diff --git a/docs/users-guide/examples/Run Generated Quantities.html b/docs/users-guide/examples/Run Generated Quantities.html index cd426d13..d046d580 100644 --- a/docs/users-guide/examples/Run Generated Quantities.html +++ b/docs/users-guide/examples/Run Generated Quantities.html @@ -6,7 +6,7 @@ - Generating new quantities of interest. — CmdStanPy 1.0.6 documentation + Generating new quantities of interest. — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@ @@ -625,7 +625,7 @@

    Example: add posterior predictive checks to 
    -18:58:33 - cmdstanpy - INFO - CmdStan start processing
+13:29:28 - cmdstanpy - INFO - CmdStan start processing
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@@ -652,7 +652,7 @@ 
    Example: add posterior predictive checks to 
 
     
-18:58:33 - cmdstanpy - INFO - CmdStan done processing.
+13:29:28 - cmdstanpy - INFO - CmdStan done processing.
    @@ -709,27 +709,27 @@

    Example: add posterior predictive checks to 
    -18:58:33 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc
-18:58:41 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc
+13:29:28 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc
+13:29:37 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc

    @@ -795,14 +795,14 @@

    Example: add posterior predictive checks to 
    -18:58:41 - cmdstanpy - INFO - Chain [1] start processing
-18:58:41 - cmdstanpy - INFO - Chain [1] done processing
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-18:58:41 - cmdstanpy - INFO - Chain [3] done processing
-18:58:41 - cmdstanpy - INFO - Chain [4] start processing
-18:58:41 - cmdstanpy - INFO - Chain [4] done processing
+13:29:38 - cmdstanpy - INFO - Chain [1] start processing
+13:29:38 - cmdstanpy - INFO - Chain [1] done processing
+13:29:38 - cmdstanpy - INFO - Chain [2] start processing
+13:29:38 - cmdstanpy - INFO - Chain [2] done processing
+13:29:38 - cmdstanpy - INFO - Chain [3] start processing
+13:29:38 - cmdstanpy - INFO - Chain [3] done processing
+13:29:38 - cmdstanpy - INFO - Chain [4] start processing
+13:29:38 - cmdstanpy - INFO - Chain [4] done processing

    The generate_quantities method returns a CmdStanGQ object which contains the values for all variables in the generated quantitites block of the program bernoulli_ppc.stan. Unlike the output from the sample method, it doesn’t contain any information on the joint log probability density, sampler state, or parameters or transformed parameter values.

    @@ -823,18 +823,18 @@

    Example: add posterior predictive checks to 
     (1000, 4, 10) ('y_rep[1]', 'y_rep[2]', 'y_rep[3]', 'y_rep[4]', 'y_rep[5]', 'y_rep[6]', 'y_rep[7]', 'y_rep[8]', 'y_rep[9]', 'y_rep[10]')
-[[0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]
- [0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]
- [0. 0. 0. 1. 0. 1. 0. 1. 0. 0.]
- [0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]]
+[[1. 1. 1. 0. 1. 0. 0. 0. 0. 0.]
+ [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]
+ [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]
+ [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]]
+[[1. 1. 1. 0. 0. 0. 1. 0. 1. 1.]
+ [1. 0. 1. 0. 0. 0. 1. 0. 0. 0.]
+ [1. 0. 1. 0. 0. 0. 0. 0. 0. 0.]
+ [1. 1. 1. 0. 0. 0. 1. 0. 1. 1.]]
 [[0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
- [0. 0. 0. 0. 0. 0. 1. 0. 0. 0.]
- [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]
- [0. 0. 0. 0. 0. 0. 1. 0. 0. 0.]]
-[[0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]
- [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]
- [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]
- [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]]
+ [0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
+ [0. 0. 0. 1. 0. 0. 0. 0. 1. 0.]
+ [0. 0. 0. 1. 0. 0. 0. 0. 1. 0.]]

    We can also use draws_pd(inc_sample=True) to get a pandas DataFrame which combines the input drawset with the generated quantities.

    @@ -903,65 +903,65 @@

    Example: add posterior predictive checks to \n", " \n", " lp__\n", - " -7.272190\n", - " 0.020193\n", - " 0.759561\n", - " -8.739310\n", - " -6.98950\n", - " -6.750100\n", - " 1414.94\n", - " 34510.6\n", - " 1.00527\n", + " -7.281860\n", + " 0.020178\n", + " 0.750850\n", + " -8.966000\n", + " -6.980410\n", + " -6.749890\n", + " 1384.73\n", + " 32203.1\n", + " 1.00237\n", " \n", " \n", " theta\n", - " 0.253475\n", - " 0.003270\n", - " 0.120090\n", - " 0.081312\n", - " 0.23948\n", - " 0.475314\n", - " 1349.00\n", - " 32902.4\n", - " 1.00439\n", + " 0.251858\n", + " 0.003258\n", + " 0.121122\n", + " 0.074654\n", + " 0.238443\n", + " 0.473461\n", + " 1381.77\n", + " 32134.2\n", + " 1.00304\n", " \n", " \n", "\n", "" ], "text/plain": [ - " Mean MCSE StdDev 5% 50% 95% N_Eff \\\n", - "lp__ -7.272190 0.020193 0.759561 -8.739310 -6.98950 -6.750100 1414.94 \n", - "theta 0.253475 0.003270 0.120090 0.081312 0.23948 0.475314 1349.00 \n", + " Mean MCSE StdDev 5% 50% 95% N_Eff \\\n", + "lp__ -7.281860 0.020178 0.750850 -8.966000 -6.980410 -6.749890 1384.73 \n", + "theta 0.251858 0.003258 0.121122 0.074654 0.238443 0.473461 1381.77 \n", "\n", " N_Eff/s R_hat \n", - "lp__ 34510.6 1.00527 \n", - "theta 32902.4 1.00439 " + "lp__ 32203.1 1.00237 \n", + "theta 32134.2 1.00304 " ] }, "execution_count": 4, @@ -426,10 +426,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:33.420954Z", - "iopub.status.busy": "2022-08-23T18:58:33.420715Z", - "iopub.status.idle": "2022-08-23T18:58:41.344977Z", - "shell.execute_reply": "2022-08-23T18:58:41.343853Z" + "iopub.execute_input": "2022-08-25T13:29:28.322277Z", + "iopub.status.busy": "2022-08-25T13:29:28.321772Z", + "iopub.status.idle": "2022-08-25T13:29:37.996776Z", + "shell.execute_reply": "2022-08-25T13:29:37.995958Z" } }, "outputs": [ @@ -437,14 +437,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "18:58:33 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n" + "13:29:28 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n" + "13:29:37 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n" ] }, { @@ -494,10 +494,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:41.348938Z", - "iopub.status.busy": "2022-08-23T18:58:41.348305Z", - "iopub.status.idle": "2022-08-23T18:58:41.447133Z", - "shell.execute_reply": "2022-08-23T18:58:41.446206Z" + "iopub.execute_input": "2022-08-25T13:29:38.001015Z", + "iopub.status.busy": "2022-08-25T13:29:38.000298Z", + "iopub.status.idle": "2022-08-25T13:29:38.114089Z", + "shell.execute_reply": "2022-08-25T13:29:38.113297Z" } }, "outputs": [ @@ -505,56 +505,56 @@ "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [1] start processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [1] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [1] done processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [1] done processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [2] start processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [2] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [2] done processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [2] done processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [3] start processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [3] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [3] done processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [3] done processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [4] start processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [4] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:41 - cmdstanpy - INFO - Chain [4] done processing\n" + "13:29:38 - cmdstanpy - INFO - Chain [4] done processing\n" ] } ], @@ -576,10 +576,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:41.450802Z", - "iopub.status.busy": "2022-08-23T18:58:41.450404Z", - "iopub.status.idle": "2022-08-23T18:58:41.479041Z", - "shell.execute_reply": "2022-08-23T18:58:41.477816Z" + "iopub.execute_input": "2022-08-25T13:29:38.118453Z", + "iopub.status.busy": "2022-08-25T13:29:38.117860Z", + "iopub.status.idle": "2022-08-25T13:29:38.144565Z", + "shell.execute_reply": "2022-08-25T13:29:38.143726Z" } }, "outputs": [ @@ -588,18 +588,18 @@ "output_type": "stream", "text": [ "(1000, 4, 10) ('y_rep[1]', 'y_rep[2]', 'y_rep[3]', 'y_rep[4]', 'y_rep[5]', 'y_rep[6]', 'y_rep[7]', 'y_rep[8]', 'y_rep[9]', 'y_rep[10]')\n", - "[[0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]\n", - " [0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]\n", - " [0. 0. 0. 1. 0. 1. 0. 1. 0. 0.]\n", - " [0. 0. 0. 0. 0. 0. 0. 1. 0. 0.]]\n", + "[[1. 1. 1. 0. 1. 0. 0. 0. 0. 0.]\n", + " [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]\n", + " [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]\n", + " [1. 1. 1. 0. 0. 0. 0. 0. 0. 0.]]\n", + "[[1. 1. 1. 0. 0. 0. 1. 0. 1. 1.]\n", + " [1. 0. 1. 0. 0. 0. 1. 0. 0. 0.]\n", + " [1. 0. 1. 0. 0. 0. 0. 0. 0. 0.]\n", + " [1. 1. 1. 0. 0. 0. 1. 0. 1. 1.]]\n", "[[0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]\n", - " [0. 0. 0. 0. 0. 0. 1. 0. 0. 0.]\n", - " [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]\n", - " [0. 0. 0. 0. 0. 0. 1. 0. 0. 0.]]\n", - "[[0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]\n", - " [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]\n", - " [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]\n", - " [0. 1. 0. 1. 0. 0. 0. 0. 1. 0.]]\n" + " [0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]\n", + " [0. 0. 0. 1. 0. 0. 0. 0. 1. 0.]\n", + " [0. 0. 0. 1. 0. 0. 0. 0. 1. 0.]]\n" ] } ], @@ -621,10 +621,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:41.482546Z", - "iopub.status.busy": "2022-08-23T18:58:41.482102Z", - "iopub.status.idle": "2022-08-23T18:58:41.507144Z", - "shell.execute_reply": "2022-08-23T18:58:41.505767Z" + "iopub.execute_input": "2022-08-25T13:29:38.148105Z", + "iopub.status.busy": "2022-08-25T13:29:38.147688Z", + "iopub.status.idle": "2022-08-25T13:29:38.170916Z", + "shell.execute_reply": "2022-08-25T13:29:38.170035Z" } }, "outputs": [ @@ -679,65 +679,65 @@ " \n", " \n", " 0\n", - " -7.29072\n", - " 0.913481\n", - " 1.18093\n", + " -9.13552\n", + " 0.940254\n", + " 0.836793\n", " 1.0\n", " 1.0\n", " 0.0\n", - " 7.29639\n", - " 0.136884\n", - " 0.0\n", - " 0.0\n", + " 9.68264\n", + " 0.560479\n", + " 1.0\n", + " 1.0\n", + " 1.0\n", " 0.0\n", + " 1.0\n", " 0.0\n", " 0.0\n", " 0.0\n", " 0.0\n", - " 1.0\n", - " 0.0\n", " 0.0\n", " \n", " \n", " 1\n", - " -7.22814\n", + " -8.78559\n", " 1.000000\n", - " 1.18093\n", + " 0.836793\n", " 1.0\n", " 1.0\n", " 0.0\n", - " 7.38664\n", - " 0.142567\n", - " 0.0\n", - " 0.0\n", - " 0.0\n", - " 0.0\n", - " 0.0\n", - " 0.0\n", + " 9.52300\n", + " 0.536282\n", + " 1.0\n", + " 1.0\n", + " 1.0\n", " 0.0\n", " 0.0\n", " 0.0\n", + " 1.0\n", " 0.0\n", + " 1.0\n", + " 1.0\n", " \n", " \n", " 2\n", - " -6.96068\n", + " -8.59408\n", " 1.000000\n", - " 1.18093\n", + " 0.836793\n", " 2.0\n", - " 3.0\n", + " 7.0\n", + " 0.0\n", + " 8.69180\n", + " 0.071122\n", + " 0.0\n", + " 0.0\n", " 0.0\n", - " 7.18040\n", - " 0.174933\n", " 0.0\n", - " 1.0\n", " 0.0\n", - " 1.0\n", " 0.0\n", " 0.0\n", " 0.0\n", " 0.0\n", - " 1.0\n", " 0.0\n", " \n", " \n", @@ -745,15 +745,15 @@ "" ], "text/plain": [ - " 0 1 2 3 4 5 6 7 8 9 \\\n", - "0 -7.29072 0.913481 1.18093 1.0 1.0 0.0 7.29639 0.136884 0.0 0.0 \n", - "1 -7.22814 1.000000 1.18093 1.0 1.0 0.0 7.38664 0.142567 0.0 0.0 \n", - "2 -6.96068 1.000000 1.18093 2.0 3.0 0.0 7.18040 0.174933 0.0 1.0 \n", + " 0 1 2 3 4 5 6 7 8 9 \\\n", + "0 -9.13552 0.940254 0.836793 1.0 1.0 0.0 9.68264 0.560479 1.0 1.0 \n", + "1 -8.78559 1.000000 0.836793 1.0 1.0 0.0 9.52300 0.536282 1.0 1.0 \n", + "2 -8.59408 1.000000 0.836793 2.0 7.0 0.0 8.69180 0.071122 0.0 0.0 \n", "\n", " 10 11 12 13 14 15 16 17 \n", - "0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 \n", - "1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n", - "2 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 " + "0 1.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 \n", + "1 1.0 0.0 0.0 0.0 1.0 0.0 1.0 1.0 \n", + "2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 " ] }, "execution_count": 8, diff --git a/docs/users-guide/examples/Using External C++.html b/docs/users-guide/examples/Using External C++.html index c81f41b9..6ec6697e 100644 --- a/docs/users-guide/examples/Using External C++.html +++ b/docs/users-guide/examples/Using External C++.html @@ -6,7 +6,7 @@ - Advanced Topic: Using External C++ Functions — CmdStanPy 1.0.6 documentation + Advanced Topic: Using External C++ Functions — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@ diff --git a/docs/users-guide/examples/VI as Sampler Inits.html b/docs/users-guide/examples/VI as Sampler Inits.html index 14cae937..2a76626f 100644 --- a/docs/users-guide/examples/VI as Sampler Inits.html +++ b/docs/users-guide/examples/VI as Sampler Inits.html @@ -6,7 +6,7 @@ - Using Variational Estimates to Initialize the NUTS-HMC Sampler — CmdStanPy 1.0.6 documentation + Using Variational Estimates to Initialize the NUTS-HMC Sampler — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@ @@ -556,8 +556,8 @@

    Model and data
     /opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
   from .autonotebook import tqdm as notebook_tqdm
-18:58:44 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr
-18:58:54 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr
+13:29:41 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr
+13:29:52 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr
    @@ -603,9 +603,9 @@

    Run Stan’s variational inference algorithm, obtain fitted estimates 
    -18:58:54 - cmdstanpy - INFO - Chain [1] start processing
-18:58:54 - cmdstanpy - INFO - Chain [1] done processing
-18:58:54 - cmdstanpy - WARNING - The algorithm may not have converged.
+13:29:52 - cmdstanpy - INFO - Chain [1] start processing
+13:29:52 - cmdstanpy - INFO - Chain [1] done processing
+13:29:52 - cmdstanpy - WARNING - The algorithm may not have converged.
 Proceeding because require_converged is set to False

    @@ -647,7 +647,7 @@

    Run Stan’s variational inference algorithm, obtain fitted estimates 
    -18:58:54 - cmdstanpy - INFO - CmdStan start processing
+13:29:52 - cmdstanpy - INFO - CmdStan start processing
 chain 1 |          | 00:00 Status
 chain 2 |          | 00:00 Status
 
@@ -685,8 +685,8 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates
 
     
-18:58:55 - cmdstanpy - INFO - CmdStan done processing.
-18:58:55 - cmdstanpy - WARNING - Non-fatal error during sampling:
+13:29:53 - cmdstanpy - INFO - CmdStan done processing.
+13:29:53 - cmdstanpy - WARNING - Non-fatal error during sampling:
 Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)
 Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)
 Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)
@@ -754,7 +754,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates-156.532000
       -154.64600
       938.42000
-      2085.380000
+      2035.620000
       1.001480
     
     
@@ -766,7 +766,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates0.999461
       1.00107
       4863.49000
-      10807.800000
+      10549.900000
       1.000320
     
     
@@ -778,7 +778,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.000210
       1.00210
       4344.92000
-      9655.380000
+      9424.990000
       0.999725
     
     
@@ -790,7 +790,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.000430
       1.00200
       4385.54000
-      9745.650000
+      9513.100000
       0.999669
     
     
@@ -802,7 +802,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.001150
       1.00292
       4664.71000
-      10366.000000
+      10118.700000
       0.999536
     
     
@@ -814,7 +814,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.001540
       1.00321
       4786.98000
-      10637.700000
+      10383.900000
       0.999197
     
     
@@ -826,7 +826,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates0.961783
       1.09259
       256.47117
-      569.935933
+      556.336594
       1.011019
     
   
@@ -847,7 +847,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates
 
    
 
    -Processing csv files: /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_1.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_2.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_3.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_4.csv
+Processing csv files: /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_1.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_2.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_3.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_4.csv
 
 Checking sampler transitions treedepth.
 Treedepth satisfactory for all transitions.
@@ -880,7 +880,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates
 
    
 
    -18:58:55 - cmdstanpy - INFO - CmdStan start processing
+13:29:53 - cmdstanpy - INFO - CmdStan start processing
 chain 1 |          | 00:00 Status
 chain 2 |          | 00:00 Status
 
@@ -888,14 +888,14 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates          | 00:00 Status
+chain 2 |████████▎ | 00:00 Iteration:  775 / 1075 [ 72%]  (Sampling)
+
+
 chain 1 |██████████| 00:00 Sampling completed
 chain 2 |██████████| 00:00 Sampling completed
 
 
 chain 3 |██████████| 00:00 Sampling completed
-
-
-
 chain 4 |██████████| 00:00 Sampling completed
 
    
 
    
@@ -913,20 +913,27 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates
 
     
-18:58:55 - cmdstanpy - INFO - CmdStan done processing.
-18:58:55 - cmdstanpy - WARNING - Some chains may have failed to converge.
-        Chain 1 had 161 divergent transitions (16.1%)
-        Chain 3 had 147 divergent transitions (14.7%)
-        Chain 4 had 244 divergent transitions (24.4%)
-        Use function "diagnose()" to see further information.
+13:29:53 - cmdstanpy - INFO - CmdStan done processing.
 
    
 
    
-
    
+
    
 
    
 
    
 
    
 
     
+
    
+
    
+
    
+
    
+
    
+
    
+
    +13:29:53 - cmdstanpy - WARNING - Some chains may have failed to converge.
+        Chain 1 had 161 divergent transitions (16.1%)
+        Chain 3 had 147 divergent transitions (14.7%)
+        Chain 4 had 244 divergent transitions (24.4%)
+        Use function "diagnose()" to see further information.
 
    
 
    
 
    
@@ -981,7 +988,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates-165.541000
       -154.33900
       2.03097
-      13.10310
+      12.08910
       11.37150
     
     
@@ -993,7 +1000,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates0.999494
       1.00252
       232.18100
-      1497.94000
+      1382.03000
       1.01286
     
     
@@ -1005,7 +1012,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.000410
       1.00459
       110.88200
-      715.37000
+      660.01400
       1.04571
     
     
@@ -1017,7 +1024,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.000480
       1.00442
       62.47110
-      403.03900
+      371.85200
       1.04607
     
     
@@ -1029,7 +1036,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.001690
       1.00512
       103.34500
-      666.74000
+      615.14700
       1.09049
     
     
@@ -1041,7 +1048,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates1.001290
       1.00443
       180.70500
-      1165.84000
+      1075.63000
       1.03165
     
     
@@ -1053,7 +1060,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates2.708830
       3.17346
       2.03514
-      13.12994
+      12.11393
       10.50420
     
   
@@ -1073,7 +1080,7 @@ 
    Run Stan’s variational inference algorithm, obtain fitted estimates
 
    
 
    -Processing csv files: /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_1.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_2.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_3.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_4.csv
+Processing csv files: /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_1.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_2.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_3.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_4.csv
 
 Checking sampler transitions treedepth.
 Treedepth satisfactory for all transitions.
diff --git a/docs/users-guide/examples/VI as Sampler Inits.ipynb b/docs/users-guide/examples/VI as Sampler Inits.ipynb
index 643dbc42..8e85b05a 100644
--- a/docs/users-guide/examples/VI as Sampler Inits.ipynb	
+++ b/docs/users-guide/examples/VI as Sampler Inits.ipynb	
@@ -26,10 +26,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:44.319367Z",
-     "iopub.status.busy": "2022-08-23T18:58:44.319061Z",
-     "iopub.status.idle": "2022-08-23T18:58:54.682098Z",
-     "shell.execute_reply": "2022-08-23T18:58:54.681286Z"
+     "iopub.execute_input": "2022-08-25T13:29:41.587631Z",
+     "iopub.status.busy": "2022-08-25T13:29:41.587309Z",
+     "iopub.status.idle": "2022-08-25T13:29:52.713679Z",
+     "shell.execute_reply": "2022-08-25T13:29:52.712928Z"
     }
    },
    "outputs": [
@@ -45,14 +45,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:44 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr\n"
+      "13:29:41 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:54 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr\n"
+      "13:29:52 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr\n"
      ]
     },
     {
@@ -108,10 +108,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:54.685938Z",
-     "iopub.status.busy": "2022-08-23T18:58:54.685503Z",
-     "iopub.status.idle": "2022-08-23T18:58:54.785390Z",
-     "shell.execute_reply": "2022-08-23T18:58:54.784678Z"
+     "iopub.execute_input": "2022-08-25T13:29:52.718078Z",
+     "iopub.status.busy": "2022-08-25T13:29:52.717630Z",
+     "iopub.status.idle": "2022-08-25T13:29:52.820872Z",
+     "shell.execute_reply": "2022-08-25T13:29:52.820138Z"
     }
    },
    "outputs": [
@@ -119,21 +119,21 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:54 - cmdstanpy - INFO - Chain [1] start processing\n"
+      "13:29:52 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:54 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "13:29:52 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:54 - cmdstanpy - WARNING - The algorithm may not have converged.\n",
+      "13:29:52 - cmdstanpy - WARNING - The algorithm may not have converged.\n",
       "Proceeding because require_converged is set to False\n"
      ]
     }
@@ -157,10 +157,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:54.788944Z",
-     "iopub.status.busy": "2022-08-23T18:58:54.788459Z",
-     "iopub.status.idle": "2022-08-23T18:58:54.794200Z",
-     "shell.execute_reply": "2022-08-23T18:58:54.793547Z"
+     "iopub.execute_input": "2022-08-25T13:29:52.824561Z",
+     "iopub.status.busy": "2022-08-25T13:29:52.824061Z",
+     "iopub.status.idle": "2022-08-25T13:29:52.830029Z",
+     "shell.execute_reply": "2022-08-25T13:29:52.829337Z"
     }
    },
    "outputs": [
@@ -192,10 +192,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:54.797236Z",
-     "iopub.status.busy": "2022-08-23T18:58:54.796816Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.133334Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.132579Z"
+     "iopub.execute_input": "2022-08-25T13:29:52.833146Z",
+     "iopub.status.busy": "2022-08-25T13:29:52.832908Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.182640Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.181426Z"
     }
    },
    "outputs": [
@@ -203,7 +203,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:54 - cmdstanpy - INFO - CmdStan start processing\n"
+      "13:29:52 - cmdstanpy - INFO - CmdStan start processing\n"
      ]
     },
     {
@@ -295,7 +295,7 @@
      "output_type": "stream",
      "text": [
       "\r",
-      "chain 2 |\u001b[34m████████▎ \u001b[0m| 00:00 Iteration:  775 / 1075 [ 72%]  (Sampling)"
+      "chain 2 |\u001b[34m███████▌  \u001b[0m| 00:00 Iteration:  675 / 1075 [ 62%]  (Sampling)"
      ]
     },
     {
@@ -397,7 +397,7 @@
      "output_type": "stream",
      "text": [
       "\r",
-      "chain 4 |\u001b[34m████████▎ \u001b[0m| 00:00 Iteration:  775 / 1075 [ 72%]  (Sampling)"
+      "chain 4 |\u001b[34m█████████▏\u001b[0m| 00:00 Iteration:  875 / 1075 [ 81%]  (Sampling)"
      ]
     },
     {
@@ -475,14 +475,14 @@
      "output_type": "stream",
      "text": [
       "\n",
-      "18:58:55 - cmdstanpy - INFO - CmdStan done processing.\n"
+      "13:29:53 - cmdstanpy - INFO - CmdStan done processing.\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:55 - cmdstanpy - WARNING - Non-fatal error during sampling:\n",
+      "13:29:53 - cmdstanpy - WARNING - Non-fatal error during sampling:\n",
       "Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)\n",
       "Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)\n",
       "Exception: normal_lpdf: Scale parameter is 0, but must be positive! (in '/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/blr.stan', line 16, column 2 to column 45)\n",
@@ -510,10 +510,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:55.136660Z",
-     "iopub.status.busy": "2022-08-23T18:58:55.136253Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.229132Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.228368Z"
+     "iopub.execute_input": "2022-08-25T13:29:53.186592Z",
+     "iopub.status.busy": "2022-08-25T13:29:53.186110Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.283248Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.282370Z"
     }
    },
    "outputs": [
@@ -559,7 +559,7 @@
        "      -156.532000\n",
        "      -154.64600\n",
        "      938.42000\n",
-       "      2085.380000\n",
+       "      2035.620000\n",
        "      1.001480\n",
        "    \n",
        "    \n",
@@ -571,7 +571,7 @@
        "      0.999461\n",
        "      1.00107\n",
        "      4863.49000\n",
-       "      10807.800000\n",
+       "      10549.900000\n",
        "      1.000320\n",
        "    \n",
        "    \n",
@@ -583,7 +583,7 @@
        "      1.000210\n",
        "      1.00210\n",
        "      4344.92000\n",
-       "      9655.380000\n",
+       "      9424.990000\n",
        "      0.999725\n",
        "    \n",
        "    \n",
@@ -595,7 +595,7 @@
        "      1.000430\n",
        "      1.00200\n",
        "      4385.54000\n",
-       "      9745.650000\n",
+       "      9513.100000\n",
        "      0.999669\n",
        "    \n",
        "    \n",
@@ -607,7 +607,7 @@
        "      1.001150\n",
        "      1.00292\n",
        "      4664.71000\n",
-       "      10366.000000\n",
+       "      10118.700000\n",
        "      0.999536\n",
        "    \n",
        "    \n",
@@ -619,7 +619,7 @@
        "      1.001540\n",
        "      1.00321\n",
        "      4786.98000\n",
-       "      10637.700000\n",
+       "      10383.900000\n",
        "      0.999197\n",
        "    \n",
        "    \n",
@@ -631,7 +631,7 @@
        "      0.961783\n",
        "      1.09259\n",
        "      256.47117\n",
-       "      569.935933\n",
+       "      556.336594\n",
        "      1.011019\n",
        "    \n",
        "  \n",
@@ -649,13 +649,13 @@
        "sigma      0.963840  0.004465  0.071505    0.849600    0.961783    1.09259   \n",
        "\n",
        "              N_Eff       N_Eff/s     R_hat  \n",
-       "lp__      938.42000   2085.380000  1.001480  \n",
-       "beta[1]  4863.49000  10807.800000  1.000320  \n",
-       "beta[2]  4344.92000   9655.380000  0.999725  \n",
-       "beta[3]  4385.54000   9745.650000  0.999669  \n",
-       "beta[4]  4664.71000  10366.000000  0.999536  \n",
-       "beta[5]  4786.98000  10637.700000  0.999197  \n",
-       "sigma     256.47117    569.935933  1.011019  "
+       "lp__      938.42000   2035.620000  1.001480  \n",
+       "beta[1]  4863.49000  10549.900000  1.000320  \n",
+       "beta[2]  4344.92000   9424.990000  0.999725  \n",
+       "beta[3]  4385.54000   9513.100000  0.999669  \n",
+       "beta[4]  4664.71000  10118.700000  0.999536  \n",
+       "beta[5]  4786.98000  10383.900000  0.999197  \n",
+       "sigma     256.47117    556.336594  1.011019  "
       ]
      },
      "execution_count": 5,
@@ -679,10 +679,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:55.232537Z",
-     "iopub.status.busy": "2022-08-23T18:58:55.232080Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.291013Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.290247Z"
+     "iopub.execute_input": "2022-08-25T13:29:53.287418Z",
+     "iopub.status.busy": "2022-08-25T13:29:53.286667Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.347367Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.346371Z"
     }
    },
    "outputs": [
@@ -690,7 +690,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Processing csv files: /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_1.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_2.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_3.csv, /tmp/tmpkher3kfz/blrlaeynh9b/blr-20220823185854_4.csv\n",
+      "Processing csv files: /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_1.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_2.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_3.csv, /tmp/tmpyvkgpyxk/blrty52urby/blr-20220825132952_4.csv\n",
       "\n",
       "Checking sampler transitions treedepth.\n",
       "Treedepth satisfactory for all transitions.\n",
@@ -726,10 +726,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:55.294521Z",
-     "iopub.status.busy": "2022-08-23T18:58:55.294276Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.475518Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.474727Z"
+     "iopub.execute_input": "2022-08-25T13:29:53.351563Z",
+     "iopub.status.busy": "2022-08-25T13:29:53.351229Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.552085Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.551207Z"
     }
    },
    "outputs": [
@@ -737,7 +737,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "18:58:55 - cmdstanpy - INFO - CmdStan start processing\n"
+      "13:29:53 - cmdstanpy - INFO - CmdStan start processing\n"
      ]
     },
     {
@@ -843,8 +843,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
-      "chain 1 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "\n",
+      "\n",
+      "\n"
      ]
     },
     {
@@ -852,25 +853,22 @@
      "output_type": "stream",
      "text": [
       "\r",
-      "chain 1 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "chain 4 |\u001b[34m█▋        \u001b[0m| 00:00 Iteration:    1 / 1075 [  0%]  (Warmup)"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n",
-      "\r",
-      "chain 2 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed                       "
+      "\u001b[A\u001b[A\u001b[A"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n",
-      "\n",
-      "\n"
+      "\r",
+      "chain 1 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
      ]
     },
     {
@@ -878,55 +876,57 @@
      "output_type": "stream",
      "text": [
       "\r",
-      "chain 3 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "chain 1 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[A\u001b[A"
+      "\n",
+      "\r",
+      "chain 2 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed                       "
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
-      "chain 3 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "\n",
+      "\n",
+      "\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n",
-      "\n",
-      "\n",
-      "\n"
+      "\r",
+      "chain 3 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
-      "chain 4 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "\u001b[A\u001b[A"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[A\u001b[A\u001b[A"
+      "\r",
+      "chain 3 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
+      "\n",
       "\r",
-      "chain 4 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
+      "chain 4 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed                     "
      ]
     },
     {
@@ -962,25 +962,25 @@
      "output_type": "stream",
      "text": [
       "\n",
-      "18:58:55 - cmdstanpy - INFO - CmdStan done processing.\n"
+      "13:29:53 - cmdstanpy - INFO - CmdStan done processing.\n"
      ]
     },
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
-      "18:58:55 - cmdstanpy - WARNING - Some chains may have failed to converge.\n",
-      "\tChain 1 had 161 divergent transitions (16.1%)\n",
-      "\tChain 3 had 147 divergent transitions (14.7%)\n",
-      "\tChain 4 had 244 divergent transitions (24.4%)\n",
-      "\tUse function \"diagnose()\" to see further information.\n"
+      "\n"
      ]
     },
     {
-     "name": "stdout",
+     "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n"
+      "13:29:53 - cmdstanpy - WARNING - Some chains may have failed to converge.\n",
+      "\tChain 1 had 161 divergent transitions (16.1%)\n",
+      "\tChain 3 had 147 divergent transitions (14.7%)\n",
+      "\tChain 4 had 244 divergent transitions (24.4%)\n",
+      "\tUse function \"diagnose()\" to see further information.\n"
      ]
     }
    ],
@@ -993,10 +993,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:55.479074Z",
-     "iopub.status.busy": "2022-08-23T18:58:55.478734Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.564131Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.563367Z"
+     "iopub.execute_input": "2022-08-25T13:29:53.555931Z",
+     "iopub.status.busy": "2022-08-25T13:29:53.555455Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.644358Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.643482Z"
     }
    },
    "outputs": [
@@ -1042,7 +1042,7 @@
        "      -165.541000\n",
        "      -154.33900\n",
        "      2.03097\n",
-       "      13.10310\n",
+       "      12.08910\n",
        "      11.37150\n",
        "    \n",
        "    \n",
@@ -1054,7 +1054,7 @@
        "      0.999494\n",
        "      1.00252\n",
        "      232.18100\n",
-       "      1497.94000\n",
+       "      1382.03000\n",
        "      1.01286\n",
        "    \n",
        "    \n",
@@ -1066,7 +1066,7 @@
        "      1.000410\n",
        "      1.00459\n",
        "      110.88200\n",
-       "      715.37000\n",
+       "      660.01400\n",
        "      1.04571\n",
        "    \n",
        "    \n",
@@ -1078,7 +1078,7 @@
        "      1.000480\n",
        "      1.00442\n",
        "      62.47110\n",
-       "      403.03900\n",
+       "      371.85200\n",
        "      1.04607\n",
        "    \n",
        "    \n",
@@ -1090,7 +1090,7 @@
        "      1.001690\n",
        "      1.00512\n",
        "      103.34500\n",
-       "      666.74000\n",
+       "      615.14700\n",
        "      1.09049\n",
        "    \n",
        "    \n",
@@ -1102,7 +1102,7 @@
        "      1.001290\n",
        "      1.00443\n",
        "      180.70500\n",
-       "      1165.84000\n",
+       "      1075.63000\n",
        "      1.03165\n",
        "    \n",
        "    \n",
@@ -1114,7 +1114,7 @@
        "      2.708830\n",
        "      3.17346\n",
        "      2.03514\n",
-       "      13.12994\n",
+       "      12.11393\n",
        "      10.50420\n",
        "    \n",
        "  \n",
@@ -1132,13 +1132,13 @@
        "sigma      1.962000   0.725020   1.034300    0.907470    2.708830    3.17346   \n",
        "\n",
        "             N_Eff     N_Eff/s     R_hat  \n",
-       "lp__       2.03097    13.10310  11.37150  \n",
-       "beta[1]  232.18100  1497.94000   1.01286  \n",
-       "beta[2]  110.88200   715.37000   1.04571  \n",
-       "beta[3]   62.47110   403.03900   1.04607  \n",
-       "beta[4]  103.34500   666.74000   1.09049  \n",
-       "beta[5]  180.70500  1165.84000   1.03165  \n",
-       "sigma      2.03514    13.12994  10.50420  "
+       "lp__       2.03097    12.08910  11.37150  \n",
+       "beta[1]  232.18100  1382.03000   1.01286  \n",
+       "beta[2]  110.88200   660.01400   1.04571  \n",
+       "beta[3]   62.47110   371.85200   1.04607  \n",
+       "beta[4]  103.34500   615.14700   1.09049  \n",
+       "beta[5]  180.70500  1075.63000   1.03165  \n",
+       "sigma      2.03514    12.11393  10.50420  "
       ]
      },
      "execution_count": 8,
@@ -1155,10 +1155,10 @@
    "execution_count": 9,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2022-08-23T18:58:55.567401Z",
-     "iopub.status.busy": "2022-08-23T18:58:55.567035Z",
-     "iopub.status.idle": "2022-08-23T18:58:55.625001Z",
-     "shell.execute_reply": "2022-08-23T18:58:55.624211Z"
+     "iopub.execute_input": "2022-08-25T13:29:53.648058Z",
+     "iopub.status.busy": "2022-08-25T13:29:53.647552Z",
+     "iopub.status.idle": "2022-08-25T13:29:53.711136Z",
+     "shell.execute_reply": "2022-08-25T13:29:53.710090Z"
     }
    },
    "outputs": [
@@ -1166,7 +1166,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Processing csv files: /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_1.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_2.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_3.csv, /tmp/tmpkher3kfz/blrux5anwjl/blr-20220823185855_4.csv\n",
+      "Processing csv files: /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_1.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_2.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_3.csv, /tmp/tmpyvkgpyxk/blr2u04w073/blr-20220825132953_4.csv\n",
       "\n",
       "Checking sampler transitions treedepth.\n",
       "Treedepth satisfactory for all transitions.\n",
diff --git a/docs/users-guide/examples/Variational Inference.html b/docs/users-guide/examples/Variational Inference.html
index 1fac03a4..bc5f9f26 100644
--- a/docs/users-guide/examples/Variational Inference.html	
+++ b/docs/users-guide/examples/Variational Inference.html	
@@ -6,7 +6,7 @@
     
     
 
-    Variational Inference in Stan — CmdStanPy 1.0.6 documentation
+    Variational Inference in Stan — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
@@ -558,8 +558,8 @@ 
    Example: variational inference for model 
     /opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
   from .autonotebook import tqdm as notebook_tqdm
-18:58:57 - cmdstanpy - INFO - Chain [1] start processing
-18:58:57 - cmdstanpy - INFO - Chain [1] done processing
+13:29:56 - cmdstanpy - INFO - Chain [1] start processing
+13:29:56 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
    
 
    The class `CmdStanVB <https://cmdstanpy.readthedocs.io/en/latest/api.html#stanvariational>`__ provides the following properties to access information about the parameter names, estimated means, and the sample: + column_names + variational_params_dict + variational_params_np + variational_params_pd + variational_sample
    
@@ -592,7 +592,7 @@ 
    Example: variational inference for model 
 
    -0.230433
+0.230342
    @@ -626,10 +626,10 @@

    Example: variational inference for model 
    -18:58:57 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
-18:59:08 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
-18:59:08 - cmdstanpy - INFO - Chain [1] start processing
-18:59:08 - cmdstanpy - INFO - Chain [1] done processing
+13:29:56 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
+13:30:08 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
+13:30:08 - cmdstanpy - INFO - Chain [1] start processing
+13:30:08 - cmdstanpy - INFO - Chain [1] done processing

    @@ -676,9 +676,9 @@

    Example: variational inference for model 
    -18:59:09 - cmdstanpy - INFO - Chain [1] start processing
-18:59:09 - cmdstanpy - INFO - Chain [1] done processing
-18:59:09 - cmdstanpy - WARNING - The algorithm may not have converged.
+13:30:08 - cmdstanpy - INFO - Chain [1] start processing
+13:30:09 - cmdstanpy - INFO - Chain [1] done processing
+13:30:09 - cmdstanpy - WARNING - The algorithm may not have converged.
 Proceeding because require_converged is set to False

    @@ -700,8 +700,8 @@

    Example: variational inference for model api docs, section `CmdStanModel.variational <https://cmdstanpy.readthedocs.io/en/latest/api.html#cmdstanpy.CmdStanModel.variational>`__ for a full description of all arguments.

    diff --git a/docs/users-guide/examples/Variational Inference.ipynb b/docs/users-guide/examples/Variational Inference.ipynb index 4f7f27a6..00077efb 100644 --- a/docs/users-guide/examples/Variational Inference.ipynb +++ b/docs/users-guide/examples/Variational Inference.ipynb @@ -42,10 +42,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:57.378900Z", - "iopub.status.busy": "2022-08-23T18:58:57.378589Z", - "iopub.status.idle": "2022-08-23T18:58:57.757962Z", - "shell.execute_reply": "2022-08-23T18:58:57.757232Z" + "iopub.execute_input": "2022-08-25T13:29:55.906343Z", + "iopub.status.busy": "2022-08-25T13:29:55.906042Z", + "iopub.status.idle": "2022-08-25T13:29:56.328048Z", + "shell.execute_reply": "2022-08-25T13:29:56.327167Z" } }, "outputs": [ @@ -61,14 +61,14 @@ "name": "stderr", "output_type": "stream", "text": [ - "18:58:57 - cmdstanpy - INFO - Chain [1] start processing\n" + "13:29:56 - cmdstanpy - INFO - Chain [1] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:58:57 - cmdstanpy - INFO - Chain [1] done processing\n" + "13:29:56 - cmdstanpy - INFO - Chain [1] done processing\n" ] } ], @@ -103,10 +103,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:57.761692Z", - "iopub.status.busy": "2022-08-23T18:58:57.761443Z", - "iopub.status.idle": "2022-08-23T18:58:57.767438Z", - "shell.execute_reply": "2022-08-23T18:58:57.766262Z" + "iopub.execute_input": "2022-08-25T13:29:56.332562Z", + "iopub.status.busy": "2022-08-25T13:29:56.332190Z", + "iopub.status.idle": "2022-08-25T13:29:56.336354Z", + "shell.execute_reply": "2022-08-25T13:29:56.335826Z" }, "scrolled": true }, @@ -128,10 +128,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:57.770166Z", - "iopub.status.busy": "2022-08-23T18:58:57.769943Z", - "iopub.status.idle": "2022-08-23T18:58:57.775495Z", - "shell.execute_reply": "2022-08-23T18:58:57.774381Z" + "iopub.execute_input": "2022-08-25T13:29:56.339498Z", + "iopub.status.busy": "2022-08-25T13:29:56.339050Z", + "iopub.status.idle": "2022-08-25T13:29:56.346480Z", + "shell.execute_reply": "2022-08-25T13:29:56.345764Z" } }, "outputs": [ @@ -139,7 +139,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "0.230433\n" + "0.230342\n" ] } ], @@ -152,10 +152,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:57.778610Z", - "iopub.status.busy": "2022-08-23T18:58:57.778177Z", - "iopub.status.idle": "2022-08-23T18:58:57.784452Z", - "shell.execute_reply": "2022-08-23T18:58:57.783267Z" + "iopub.execute_input": "2022-08-25T13:29:56.350086Z", + "iopub.status.busy": "2022-08-25T13:29:56.349644Z", + "iopub.status.idle": "2022-08-25T13:29:56.355335Z", + "shell.execute_reply": "2022-08-25T13:29:56.354462Z" } }, "outputs": [ @@ -185,10 +185,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:58:57.787603Z", - "iopub.status.busy": "2022-08-23T18:58:57.787163Z", - "iopub.status.idle": "2022-08-23T18:59:09.729569Z", - "shell.execute_reply": "2022-08-23T18:59:09.728232Z" + "iopub.execute_input": "2022-08-25T13:29:56.359861Z", + "iopub.status.busy": "2022-08-25T13:29:56.359117Z", + "iopub.status.idle": "2022-08-25T13:30:08.954269Z", + "shell.execute_reply": "2022-08-25T13:30:08.953337Z" }, "tags": [ "raises-exception" @@ -199,28 +199,28 @@ "name": "stderr", "output_type": "stream", "text": [ - "18:58:57 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n" + "13:29:56 - cmdstanpy - INFO - compiling stan file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail.stan to exe file /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:59:08 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n" + "13:30:08 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:59:08 - cmdstanpy - INFO - Chain [1] start processing\n" + "13:30:08 - cmdstanpy - INFO - Chain [1] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:59:08 - cmdstanpy - INFO - Chain [1] done processing\n" + "13:30:08 - cmdstanpy - INFO - Chain [1] done processing\n" ] }, { @@ -253,10 +253,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:59:09.733252Z", - "iopub.status.busy": "2022-08-23T18:59:09.732823Z", - "iopub.status.idle": "2022-08-23T18:59:09.793025Z", - "shell.execute_reply": "2022-08-23T18:59:09.791750Z" + "iopub.execute_input": "2022-08-25T13:30:08.958204Z", + "iopub.status.busy": "2022-08-25T13:30:08.957951Z", + "iopub.status.idle": "2022-08-25T13:30:09.019084Z", + "shell.execute_reply": "2022-08-25T13:30:09.018340Z" } }, "outputs": [ @@ -264,21 +264,21 @@ "name": "stderr", "output_type": "stream", "text": [ - "18:59:09 - cmdstanpy - INFO - Chain [1] start processing\n" + "13:30:08 - cmdstanpy - INFO - Chain [1] start processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:59:09 - cmdstanpy - INFO - Chain [1] done processing\n" + "13:30:09 - cmdstanpy - INFO - Chain [1] done processing\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "18:59:09 - cmdstanpy - WARNING - The algorithm may not have converged.\n", + "13:30:09 - cmdstanpy - WARNING - The algorithm may not have converged.\n", "Proceeding because require_converged is set to False\n" ] } @@ -299,10 +299,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2022-08-23T18:59:09.796825Z", - "iopub.status.busy": "2022-08-23T18:59:09.796444Z", - "iopub.status.idle": "2022-08-23T18:59:09.806601Z", - "shell.execute_reply": "2022-08-23T18:59:09.806092Z" + "iopub.execute_input": "2022-08-25T13:30:09.022964Z", + "iopub.status.busy": "2022-08-25T13:30:09.022506Z", + "iopub.status.idle": "2022-08-25T13:30:09.033489Z", + "shell.execute_reply": "2022-08-25T13:30:09.032794Z" } }, "outputs": [ @@ -312,8 +312,8 @@ "OrderedDict([('lp__', 0.0),\n", " ('log_p__', 0.0),\n", " ('log_g__', 0.0),\n", - " ('mu[1]', 0.0640189),\n", - " ('mu[2]', 0.0211201)])" + " ('mu[1]', -0.0410882),\n", + " ('mu[2]', 0.0440459)])" ] }, "execution_count": 7, diff --git a/docs/users-guide/hello_world.html b/docs/users-guide/hello_world.html index 1224e5c4..378779d5 100644 --- a/docs/users-guide/hello_world.html +++ b/docs/users-guide/hello_world.html @@ -6,7 +6,7 @@ - “Hello, World!” — CmdStanPy 1.0.6 documentation + “Hello, World!” — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@ @@ -433,13 +433,13 @@

    Accessing the results 
    # access model variable by name
 In [9]: print(fit.stan_variable('theta'))
-[0.186233 0.143687 0.091574 ... 0.274911 0.133892 0.136057]
+[0.179125 0.204862 0.192807 ... 0.12798  0.286286 0.248383]
 
 In [10]: print(fit.draws_pd('theta')[:3])
       theta
-0  0.186233
-1  0.143687
-2  0.091574
+0  0.179125
+1  0.204862
+2  0.192807
 
 In [11]: print(fit.draws_xr('theta'))
 <xarray.Dataset>
@@ -448,7 +448,7 @@ 
    Accessing the results  * chain    (chain) int64 1 2 3 4
   * draw     (draw) int64 0 1 2 3 4 5 6 7 8 ... 992 993 994 995 996 997 998 999
 Data variables:
-    theta    (chain, draw) float64 0.1862 0.1437 0.09157 ... 0.1339 0.1361
+    theta    (chain, draw) float64 0.1791 0.2049 0.1928 ... 0.128 0.2863 0.2484
 Attributes:
     stan_version:        2.30.0
     model:               bernoulli_model
@@ -478,18 +478,18 @@ 
    Accessing the resultsIn [15]: fit.draws_pd()
 Out[15]: 
-          lp__  accept_stat__  stepsize__  ...  divergent__  energy__     theta
-0     -6.89700       0.947727    1.101290  ...          0.0   6.99652  0.186233
-1     -7.21642       0.924881    1.101290  ...          0.0   7.21940  0.143687
-2     -8.03620       0.857268    1.101290  ...          0.0   8.03760  0.091574
-3    -10.69590       0.932073    1.101290  ...          0.0  11.48940  0.647868
-4     -6.80160       1.000000    1.101290  ...          0.0   9.58406  0.210643
-...        ...            ...         ...  ...          ...       ...       ...
-3995  -7.37753       0.945035    0.888086  ...          0.0   7.37756  0.404115
-3996  -6.76707       0.947942    0.888086  ...          0.0   7.72180  0.274911
-3997  -6.76707       0.615003    0.888086  ...          0.0   8.90034  0.274911
-3998  -7.32588       0.832552    0.888086  ...          0.0   7.76475  0.133892
-3999  -7.30028       1.000000    0.888086  ...          0.0   7.41109  0.136057
+         lp__  accept_stat__  stepsize__  ...  divergent__  energy__     theta
+0    -6.93547       1.000000    1.017540  ...          0.0   7.02660  0.179125
+1    -6.81941       1.000000    1.017540  ...          0.0   6.90990  0.204862
+2    -6.86593       0.988312    1.017540  ...          0.0   6.87645  0.192807
+3    -7.39833       0.865988    1.017540  ...          0.0   7.69372  0.406802
+4    -6.75601       1.000000    1.017540  ...          0.0   7.20515  0.266019
+...       ...            ...         ...  ...          ...       ...       ...
+3995 -6.75089       1.000000    0.926829  ...          0.0   6.76236  0.240606
+3996 -7.14210       0.909684    0.926829  ...          0.0   7.22993  0.151280
+3997 -7.40014       0.955873    0.926829  ...          0.0   7.42595  0.127980
+3998 -6.78775       0.948321    0.926829  ...          0.0   7.63194  0.286286
+3999 -6.74811       0.999957    0.926829  ...          0.0   6.78531  0.248383
 
 [4000 rows x 8 columns]
    @@ -501,13 +501,13 @@

    Accessing the resultsdiag_e In [17]: print(fit.metric) -[[0.476924] - [0.352321] - [0.531111] - [0.530174]] +[[0.509565] + [0.600678] + [0.52729 ] + [0.5595 ]] In [18]: print(fit.step_size) -[1.10129 1.28151 0.962403 0.888086] +[1.01754 0.887862 1.03376 0.926829]

    The CmdStanMCMC object also provides access to metadata about the model and the sampler run.

    @@ -515,7 +515,7 @@

    Accessing the resultsbernoulli_model In [20]: print(fit.metadata.cmdstan_config['seed']) -28271 +79174 In [21]: print(fit.metadata.stan_vars_cols.keys()) dict_keys(['theta']) @@ -537,8 +537,8 @@

    CmdStan utilities: 
    In [23]: fit.summary()
 Out[23]: 
            Mean      MCSE    StdDev  ...    N_Eff  N_Eff/s    R_hat
-lp__  -7.261660  0.017316  0.702779  ...  1647.21  40175.9  1.00064
-theta  0.247289  0.003183  0.119199  ...  1402.33  34203.1  1.00006
+lp__  -7.298720  0.019946  0.753564  ...  1427.36  29736.6  1.00056
+theta  0.247262  0.003402  0.121020  ...  1265.31  26360.7  1.00227
 
 [2 rows x 9 columns]
    @@ -550,7 +550,7 @@

    CmdStan utilities: diagnose() method runs this utility and prints the output to the console.

    In [24]: print(fit.diagnose())
-Processing csv files: /tmp/tmpcmi54clh/bernoullik_gx5ac0/bernoulli-20220823185919_1.csv, /tmp/tmpcmi54clh/bernoullik_gx5ac0/bernoulli-20220823185919_2.csv, /tmp/tmpcmi54clh/bernoullik_gx5ac0/bernoulli-20220823185919_3.csv, /tmp/tmpcmi54clh/bernoullik_gx5ac0/bernoulli-20220823185919_4.csv
+Processing csv files: /tmp/tmpvmhl6e01/bernoulli_rnkfcga/bernoulli-20220825133019_1.csv, /tmp/tmpvmhl6e01/bernoulli_rnkfcga/bernoulli-20220825133019_2.csv, /tmp/tmpvmhl6e01/bernoulli_rnkfcga/bernoulli-20220825133019_3.csv, /tmp/tmpvmhl6e01/bernoulli_rnkfcga/bernoulli-20220825133019_4.csv
 
 Checking sampler transitions treedepth.
 Treedepth satisfactory for all transitions.
diff --git a/docs/users-guide/outputs.html b/docs/users-guide/outputs.html
index 22a50407..697bd167 100644
--- a/docs/users-guide/outputs.html
+++ b/docs/users-guide/outputs.html
@@ -6,7 +6,7 @@
     
     
 
-    Controlling Outputs — CmdStanPy 1.0.6 documentation
+    Controlling Outputs — CmdStanPy 1.0.7 documentation
     
   
   
@@ -59,7 +59,7 @@
   
 
@@ -297,15 +297,15 @@ 
    CSV File OutputsIn [7]: print(fit)
 CmdStanMCMC: model=bernoulli chains=4['method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
  csv_files:
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_1.csv
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_2.csv
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_3.csv
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_4.csv
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_1.csv
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_2.csv
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_3.csv
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_4.csv
  output_files:
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_0-stdout.txt
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_1-stdout.txt
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_2-stdout.txt
-	/tmp/tmpcmi54clh/bernoulli3m8g8fsb/bernoulli-20220823185919_3-stdout.txt
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_0-stdout.txt
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_1-stdout.txt
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_2-stdout.txt
+	/tmp/tmpvmhl6e01/bernoullil5w0sndq/bernoulli-20220825133019_3-stdout.txt

    The output_dir argument is an optional argument which specifies @@ -319,10 +319,10 @@

    CSV File OutputsINFO:cmdstanpy:CmdStan done processing. In [9]: !ls outputs/ -bernoulli-20220823185919_0-stdout.txt bernoulli-20220823185919_2.csv -bernoulli-20220823185919_1-stdout.txt bernoulli-20220823185919_3-stdout.txt -bernoulli-20220823185919_1.csv bernoulli-20220823185919_3.csv -bernoulli-20220823185919_2-stdout.txt bernoulli-20220823185919_4.csv +bernoulli-20220825133020_0-stdout.txt bernoulli-20220825133020_2.csv +bernoulli-20220825133020_1-stdout.txt bernoulli-20220825133020_3-stdout.txt +bernoulli-20220825133020_1.csv bernoulli-20220825133020_3.csv +bernoulli-20220825133020_2-stdout.txt bernoulli-20220825133020_4.csv

    Alternatively, the save_csvfiles() function moves the CSV files @@ -335,8 +335,8 @@

    CSV File OutputsIn [11]: fit.save_csvfiles(dir='some/path') In [12]: !ls some/path -bernoulli-20220823185920_1.csv bernoulli-20220823185920_3.csv -bernoulli-20220823185920_2.csv bernoulli-20220823185920_4.csv +bernoulli-20220825133020_1.csv bernoulli-20220825133020_3.csv +bernoulli-20220825133020_2.csv bernoulli-20220825133020_4.csv @@ -399,40 +399,40 @@

    Logging ....: for line in logs.readlines(): ....: print(line.strip()) ....: -18:59:20 - cmdstanpy - DEBUG - cmd: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli info +13:30:20 - cmdstanpy - DEBUG - cmd: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli info cwd: None -18:59:20 - cmdstanpy - INFO - CmdStan start processing -18:59:20 - cmdstanpy - DEBUG - idx 0 -18:59:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 -18:59:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=11847', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] -18:59:20 - cmdstanpy - INFO - Chain [1] start processing -18:59:20 - cmdstanpy - DEBUG - idx 1 -18:59:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 -18:59:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=2', 'random', 'seed=11847', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_2.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] -18:59:20 - cmdstanpy - INFO - Chain [2] start processing -18:59:20 - cmdstanpy - INFO - Chain [1] done processing -18:59:20 - cmdstanpy - DEBUG - idx 2 -18:59:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 -18:59:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=3', 'random', 'seed=11847', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_3.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] -18:59:20 - cmdstanpy - INFO - Chain [3] start processing -18:59:20 - cmdstanpy - INFO - Chain [2] done processing -18:59:20 - cmdstanpy - DEBUG - idx 3 -18:59:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 -18:59:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=4', 'random', 'seed=11847', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_4.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] -18:59:20 - cmdstanpy - INFO - Chain [4] start processing -18:59:20 - cmdstanpy - INFO - Chain [3] done processing -18:59:20 - cmdstanpy - INFO - Chain [4] done processing -18:59:20 - cmdstanpy - DEBUG - runset +13:30:20 - cmdstanpy - INFO - CmdStan start processing +13:30:20 - cmdstanpy - DEBUG - idx 0 +13:30:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 +13:30:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=46798', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] +13:30:20 - cmdstanpy - INFO - Chain [1] start processing +13:30:20 - cmdstanpy - DEBUG - idx 1 +13:30:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 +13:30:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=2', 'random', 'seed=46798', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_2.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] +13:30:20 - cmdstanpy - INFO - Chain [2] start processing +13:30:20 - cmdstanpy - INFO - Chain [1] done processing +13:30:20 - cmdstanpy - DEBUG - idx 2 +13:30:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 +13:30:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=3', 'random', 'seed=46798', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_3.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] +13:30:20 - cmdstanpy - INFO - Chain [3] start processing +13:30:20 - cmdstanpy - INFO - Chain [2] done processing +13:30:20 - cmdstanpy - DEBUG - idx 3 +13:30:20 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1 +13:30:20 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=4', 'random', 'seed=46798', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_4.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] +13:30:20 - cmdstanpy - INFO - Chain [4] start processing +13:30:20 - cmdstanpy - INFO - Chain [3] done processing +13:30:20 - cmdstanpy - INFO - Chain [4] done processing +13:30:20 - cmdstanpy - DEBUG - runset RunSet: chains=4, chain_ids=[1, 2, 3, 4], num_processes=4 cmd (chain 1): -['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=11847', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] +['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=46798', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1'] retcodes=[0, 0, 0, 0] per-chain output files (showing chain 1 only): csv_file: -/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_1.csv +/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_1.csv console_msgs (if any): -/tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_0-stdout.txt -18:59:20 - cmdstanpy - DEBUG - Chain 1 console: +/tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_0-stdout.txt +13:30:20 - cmdstanpy - DEBUG - Chain 1 console: method = sample (Default) sample num_samples = 1000 (Default) @@ -463,9 +463,9 @@

    Loggingfile = users-guide/examples/bernoulli.data.json init = 2 (Default) random -seed = 11847 +seed = 46798 output -file = /tmp/tmpcmi54clh/bernoullibaz_rbid/bernoulli-20220823185920_1.csv +file = /tmp/tmpvmhl6e01/bernoulliqddsdaoh/bernoulli-20220825133020_1.csv diagnostic_file = (Default) refresh = 100 (Default) sig_figs = -1 (Default) @@ -473,8 +473,8 @@

    Loggingnum_threads = 1 (Default) -Gradient evaluation took 2e-06 seconds -1000 transitions using 10 leapfrog steps per transition would take 0.02 seconds. +Gradient evaluation took 4e-06 seconds +1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds. Adjust your expectations accordingly! @@ -502,8 +502,8 @@

    LoggingIteration: 2000 / 2000 [100%] (Sampling) Elapsed Time: 0.004 seconds (Warm-up) -0.011 seconds (Sampling) -0.015 seconds (Total) +0.01 seconds (Sampling) +0.014 seconds (Total) diff --git a/docs/users-guide/overview.html b/docs/users-guide/overview.html index 30735402..6960556e 100644 --- a/docs/users-guide/overview.html +++ b/docs/users-guide/overview.html @@ -6,7 +6,7 @@ - Overview — CmdStanPy 1.0.6 documentation + Overview — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@ diff --git a/docs/users-guide/workflow.html b/docs/users-guide/workflow.html index 6d16d21a..f9c27536 100644 --- a/docs/users-guide/workflow.html +++ b/docs/users-guide/workflow.html @@ -6,7 +6,7 @@ - CmdStanPy Workflow — CmdStanPy 1.0.6 documentation + CmdStanPy Workflow — CmdStanPy 1.0.7 documentation @@ -59,7 +59,7 @@