diff --git a/cmdstanpy/_version.py b/cmdstanpy/_version.py index d221d8be..06a2851d 100644 --- a/cmdstanpy/_version.py +++ b/cmdstanpy/_version.py @@ -1,3 +1,3 @@ """PyPi Version""" -__version__ = '1.2.1' +__version__ = '1.2.2' diff --git a/docs/_modules/cmdstanpy/cmdstan_args.html b/docs/_modules/cmdstanpy/cmdstan_args.html index 92a94c40..9df74f14 100644 --- a/docs/_modules/cmdstanpy/cmdstan_args.html +++ b/docs/_modules/cmdstanpy/cmdstan_args.html @@ -5,7 +5,7 @@ - cmdstanpy.cmdstan_args — CmdStanPy 1.2.1 documentation + cmdstanpy.cmdstan_args — CmdStanPy 1.2.2 documentation @@ -37,6 +37,7 @@ + @@ -60,7 +61,7 @@ @@ -1103,6 +1104,7 @@

Source code for cmdstanpy.cmdstan_args

                 if not (
                     isinstance(self.method_args, SamplerArgs)
                     and self.method_args.num_chains > 1
+                    or isinstance(self.method_args, PathfinderArgs)
                 ):
                     if not os.path.exists(self.inits):
                         raise ValueError('no such file {}'.format(self.inits))
diff --git a/docs/_modules/cmdstanpy/compilation.html b/docs/_modules/cmdstanpy/compilation.html
index fa38fe5e..69f84faf 100644
--- a/docs/_modules/cmdstanpy/compilation.html
+++ b/docs/_modules/cmdstanpy/compilation.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.compilation — CmdStanPy 1.2.1 documentation
+    cmdstanpy.compilation — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
@@ -182,11 +183,17 @@ 
Source code for cmdstanpy.compilation
 import shutil
 import subprocess
 from copy import copy
+from datetime import datetime
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional, Union
 
 from cmdstanpy.utils import get_logger
-from cmdstanpy.utils.cmdstan import EXTENSION, cmdstan_path
+from cmdstanpy.utils.cmdstan import (
+    EXTENSION,
+    cmdstan_path,
+    cmdstan_version,
+    cmdstan_version_before,
+)
 from cmdstanpy.utils.command import do_command
 from cmdstanpy.utils.filesystem import SanitizedOrTmpFilePath
 
@@ -234,7 +241,7 @@ 
Source code for cmdstanpy.compilation
 
 
 # TODO(2.0): can remove add function and other logic
-
[docs]class CompilerOptions:
+
[docs]class CompilerOptions:
     """
     User-specified flags for stanc and C++ compiler.
 
@@ -273,7 +280,7 @@ 
Source code for cmdstanpy.compilation
             and self._user_header == other.user_header
         )
 
-
[docs]    def is_empty(self) -> bool:
+
[docs]    def is_empty(self) -> bool:
         """True if no options specified."""
         return (
             self._stanc_options == {}
@@ -296,7 +303,7 @@ 
Source code for cmdstanpy.compilation
         """user header."""
         return self._user_header
 
-
[docs]    def validate(self) -> None:
+
[docs]    def validate(self) -> None:
         """
         Check compiler args.
         Raise ValueError if invalid options are found.
@@ -305,7 +312,7 @@ 
Source code for cmdstanpy.compilation
         self.validate_cpp_opts()
         self.validate_user_header()

 
-
[docs]    def validate_stanc_opts(self) -> None:
+
[docs]    def validate_stanc_opts(self) -> None:
         """
         Check stanc compiler args and consistency between stanc and C++ options.
         Raise ValueError if bad config is found.
@@ -378,7 +385,7 @@ 
Source code for cmdstanpy.compilation
                 os.path.abspath(os.path.expanduser(path)) for path in paths
             ]

 
-
[docs]    def validate_cpp_opts(self) -> None:
+
[docs]    def validate_cpp_opts(self) -> None:
         """
         Check cpp compiler args.
         Raise ValueError if bad config is found.
@@ -395,7 +402,7 @@ 
Source code for cmdstanpy.compilation
                         f' found {val}.'
                     )

 
-
[docs]    def validate_user_header(self) -> None:
+
[docs]    def validate_user_header(self) -> None:
         """
         User header exists.
         Raise ValueError if bad config is found.
@@ -433,7 +440,7 @@ 
Source code for cmdstanpy.compilation
 
             self._cpp_options['USER_HEADER'] = self._user_header

 
-
[docs]    def add(self, new_opts: "CompilerOptions") -> None:  # noqa: disable=Q000
+
[docs]    def add(self, new_opts: "CompilerOptions") -> None:  # noqa: disable=Q000
         """Adds options to existing set of compiler options."""
         if new_opts.stanc_options is not None:
             if self._stanc_options is None:
@@ -456,7 +463,7 @@ 
Source code for cmdstanpy.compilation
         if new_opts._user_header != '' and self._user_header == '':
             self._user_header = new_opts._user_header

 
-
[docs]    def add_include_path(self, path: str) -> None:
+
[docs]    def add_include_path(self, path: str) -> None:
         """Adds include path to existing set of compiler options."""
         path = os.path.abspath(os.path.expanduser(path))
         if 'include-paths' not in self._stanc_options:
@@ -488,7 +495,7 @@ 
Source code for cmdstanpy.compilation
                     opts.append(f'--{key}')
         return opts
 
-
[docs]    def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
+
[docs]    def compose(self, filename_in_msg: Optional[str] = None) -> List[str]:
         """
         Format makefile options as list of strings.
 
@@ -533,7 +540,7 @@ 
Source code for cmdstanpy.compilation
     return result
 
 
-def compile_stan_file(
+
[docs]def compile_stan_file(
     src: Union[str, Path],
     force: bool = False,
     stanc_options: Optional[Dict[str, Any]] = None,
@@ -648,7 +655,102 @@ 
Source code for cmdstanpy.compilation
             raise ValueError(
                 f"Failed to compile Stan model '{src}'. " f"Console:\n{console}"
             )
-        return str(exe_target)
+        return str(exe_target)

+
+
+
[docs]def format_stan_file(
+    stan_file: Union[str, os.PathLike],
+    *,
+    overwrite_file: bool = False,
+    canonicalize: Union[bool, str, Iterable[str]] = False,
+    max_line_length: int = 78,
+    backup: bool = True,
+    stanc_options: Optional[Dict[str, Any]] = None,
+) -> None:
+    """
+    Run stanc's auto-formatter on the model code. Either saves directly
+    back to the file or prints for inspection
+
+    :param stan_file: Path to Stan program file.
+    :param overwrite_file: If True, save the updated code to disk, rather
+        than printing it. By default False
+    :param canonicalize: Whether or not the compiler should 'canonicalize'
+        the Stan model, removing things like deprecated syntax. Default is
+        False. If True, all canonicalizations are run. If it is a list of
+        strings, those options are passed to stanc (new in Stan 2.29)
+    :param max_line_length: Set the wrapping point for the formatter. The
+        default value is 78, which wraps most lines by the 80th character.
+    :param backup: If True, create a stanfile.bak backup before
+        writing to the file. Only disable this if you're sure you have other
+        copies of the file or are using a version control system like Git.
+    :param stanc_options: Additional options to pass to the stanc compiler.
+    """
+    stan_file = Path(stan_file).resolve()
+
+    if not stan_file.exists():
+        raise ValueError(f'File does not exist: {stan_file}')
+
+    try:
+        cmd = (
+            [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
+            # handle include-paths, allow-undefined etc
+            + CompilerOptions(stanc_options=stanc_options).compose_stanc(None)
+            + [str(stan_file)]
+        )
+
+        if canonicalize:
+            if cmdstan_version_before(2, 29):
+                if isinstance(canonicalize, bool):
+                    cmd.append('--print-canonical')
+                else:
+                    raise ValueError(
+                        "Invalid arguments passed for current CmdStan"
+                        + " version({})\n".format(
+                            cmdstan_version() or "Unknown"
+                        )
+                        + "--canonicalize requires 2.29 or higher"
+                    )
+            else:
+                if isinstance(canonicalize, str):
+                    cmd.append('--canonicalize=' + canonicalize)
+                elif isinstance(canonicalize, Iterable):
+                    cmd.append('--canonicalize=' + ','.join(canonicalize))
+                else:
+                    cmd.append('--print-canonical')
+
+        # before 2.29, having both --print-canonical
+        # and --auto-format printed twice
+        if not (cmdstan_version_before(2, 29) and canonicalize):
+            cmd.append('--auto-format')
+
+        if not cmdstan_version_before(2, 29):
+            cmd.append(f'--max-line-length={max_line_length}')
+        elif max_line_length != 78:
+            raise ValueError(
+                "Invalid arguments passed for current CmdStan version"
+                + " ({})\n".format(cmdstan_version() or "Unknown")
+                + "--max-line-length requires 2.29 or higher"
+            )
+
+        out = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        if out.stderr:
+            get_logger().warning(out.stderr)
+        result = out.stdout
+        if overwrite_file:
+            if result:
+                if backup:
+                    shutil.copyfile(
+                        stan_file,
+                        str(stan_file)
+                        + '.bak-'
+                        + datetime.now().strftime("%Y%m%d%H%M%S"),
+                    )
+                stan_file.write_text(result)
+        else:
+            print(result)
+
+    except (ValueError, RuntimeError) as e:
+        raise RuntimeError("Stanc formatting failed") from e

 

 
               

diff --git a/docs/_modules/cmdstanpy/model.html b/docs/_modules/cmdstanpy/model.html
index 4f7ec869..8a75af9f 100644
--- a/docs/_modules/cmdstanpy/model.html
+++ b/docs/_modules/cmdstanpy/model.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.model — CmdStanPy 1.2.1 documentation
+    cmdstanpy.model — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
@@ -183,7 +184,6 @@ 
Source code for cmdstanpy.model
 import threading
 from collections import OrderedDict
 from concurrent.futures import ThreadPoolExecutor
-from datetime import datetime
 from io import StringIO
 from multiprocessing import cpu_count
 from typing import (
@@ -230,9 +230,7 @@ 
Source code for cmdstanpy.model
     from_csv,
 )
 from cmdstanpy.utils import (
-    EXTENSION,
     cmdstan_path,
-    cmdstan_version,
     cmdstan_version_before,
     do_command,
     get_logger,
@@ -493,6 +491,7 @@ 
Source code for cmdstanpy.model
             return {}
         return compilation.src_info(str(self.stan_file), self._compiler_options)

 
+    # TODO(2.0) remove
 
[docs]    def format(
         self,
         overwrite_file: bool = False,
@@ -502,6 +501,8 @@ 
Source code for cmdstanpy.model
         backup: bool = True,
     ) -> None:
         """
+        Deprecated: Use :func:`cmdstanpy.format_stan_file()` instead.
+
         Run stanc's auto-formatter on the model code. Either saves directly
         back to the file or prints for inspection
 
@@ -518,72 +519,24 @@ 
Source code for cmdstanpy.model
             writing to the file. Only disable this if you're sure you have other
             copies of the file or are using a version control system like Git.
         """
-        if self.stan_file is None or not os.path.isfile(self.stan_file):
-            raise ValueError("No Stan file found for this module")
-        try:
-            cmd = (
-                [os.path.join(cmdstan_path(), 'bin', 'stanc' + EXTENSION)]
-                # handle include-paths, allow-undefined etc
-                + self._compiler_options.compose_stanc(None)
-                + [str(self.stan_file)]
-            )
 
-            if canonicalize:
-                if cmdstan_version_before(2, 29):
-                    if isinstance(canonicalize, bool):
-                        cmd.append('--print-canonical')
-                    else:
-                        raise ValueError(
-                            "Invalid arguments passed for current CmdStan"
-                            + " version({})\n".format(
-                                cmdstan_version() or "Unknown"
-                            )
-                            + "--canonicalize requires 2.29 or higher"
-                        )
-                else:
-                    if isinstance(canonicalize, str):
-                        cmd.append('--canonicalize=' + canonicalize)
-                    elif isinstance(canonicalize, Iterable):
-                        cmd.append('--canonicalize=' + ','.join(canonicalize))
-                    else:
-                        cmd.append('--print-canonical')
-
-            # before 2.29, having both --print-canonical
-            # and --auto-format printed twice
-            if not (cmdstan_version_before(2, 29) and canonicalize):
-                cmd.append('--auto-format')
-
-            if not cmdstan_version_before(2, 29):
-                cmd.append(f'--max-line-length={max_line_length}')
-            elif max_line_length != 78:
-                raise ValueError(
-                    "Invalid arguments passed for current CmdStan version"
-                    + " ({})\n".format(cmdstan_version() or "Unknown")
-                    + "--max-line-length requires 2.29 or higher"
-                )
+        get_logger().warning(
+            "CmdStanModel.format() is deprecated and will be "
+            "removed in the next major version.\n"
+            "Use cmdstanpy.format_stan_file() instead."
+        )
 
-            out = subprocess.run(
-                cmd, capture_output=True, text=True, check=True
-            )
-            if out.stderr:
-                get_logger().warning(out.stderr)
-            result = out.stdout
-            if overwrite_file:
-                if result:
-                    if backup:
-                        shutil.copyfile(
-                            self.stan_file,
-                            str(self.stan_file)
-                            + '.bak-'
-                            + datetime.now().strftime("%Y%m%d%H%M%S"),
-                        )
-                    with open(self.stan_file, 'w') as file_handle:
-                        file_handle.write(result)
-            else:
-                print(result)
+        if self.stan_file is None:
+            raise ValueError("No Stan file found for this module")
 
-        except (ValueError, RuntimeError) as e:
-            raise RuntimeError("Stanc formatting failed") from e

+        compilation.format_stan_file(
+            self.stan_file,
+            overwrite_file=overwrite_file,
+            max_line_length=max_line_length,
+            canonicalize=canonicalize,
+            backup=backup,
+            stanc_options=self.stanc_options,
+        )

 
     @property
     def stanc_options(self) -> Dict[str, Union[bool, int, str]]:
@@ -1808,6 +1761,7 @@ 
Source code for cmdstanpy.model
         refresh: Optional[int] = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
+        num_threads: Optional[int] = None,
     ) -> CmdStanPathfinder:
         """
         Run CmdStan's Pathfinder variational inference algorithm.
@@ -1910,6 +1864,10 @@ 
Source code for cmdstanpy.model
         :param timeout: Duration at which Pathfinder times
             out in seconds. Defaults to None.
 
+        :param num_threads: Number of threads to request for parallel execution.
+            A number other than ``1`` requires the model to have been compiled
+            with STAN_THREADS=True.
+
         :return: A :class:`CmdStanPathfinder` object
 
         References
@@ -1936,6 +1894,17 @@ 
Source code for cmdstanpy.model
                 "available for CmdStan versions 2.34 and later"
             )
 
+        if num_threads is not None:
+            if (
+                num_threads != 1
+                and exe_info.get('STAN_THREADS', '').lower() != 'true'
+            ):
+                raise ValueError(
+                    "Model must be compiled with 'STAN_THREADS=true' to use"
+                    " 'num_threads' argument"
+                )
+            os.environ['STAN_NUM_THREADS'] = str(num_threads)
+
         if num_paths == 1:
             if num_single_draws is None:
                 num_single_draws = draws
diff --git a/docs/_modules/cmdstanpy/stanfit.html b/docs/_modules/cmdstanpy/stanfit.html
index dc6c6689..396b7a0f 100644
--- a/docs/_modules/cmdstanpy/stanfit.html
+++ b/docs/_modules/cmdstanpy/stanfit.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/gq.html b/docs/_modules/cmdstanpy/stanfit/gq.html
index af7303eb..f03cb89e 100644
--- a/docs/_modules/cmdstanpy/stanfit/gq.html
+++ b/docs/_modules/cmdstanpy/stanfit/gq.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.gq — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.gq — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/laplace.html b/docs/_modules/cmdstanpy/stanfit/laplace.html
index 73c13242..548c0131 100644
--- a/docs/_modules/cmdstanpy/stanfit/laplace.html
+++ b/docs/_modules/cmdstanpy/stanfit/laplace.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.laplace — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.laplace — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/mcmc.html b/docs/_modules/cmdstanpy/stanfit/mcmc.html
index e8b729b8..232c7e53 100644
--- a/docs/_modules/cmdstanpy/stanfit/mcmc.html
+++ b/docs/_modules/cmdstanpy/stanfit/mcmc.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.mcmc — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.mcmc — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/metadata.html b/docs/_modules/cmdstanpy/stanfit/metadata.html
index 53db7e9d..fb1340c7 100644
--- a/docs/_modules/cmdstanpy/stanfit/metadata.html
+++ b/docs/_modules/cmdstanpy/stanfit/metadata.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.metadata — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.metadata — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/mle.html b/docs/_modules/cmdstanpy/stanfit/mle.html
index dfeaedf2..929c124b 100644
--- a/docs/_modules/cmdstanpy/stanfit/mle.html
+++ b/docs/_modules/cmdstanpy/stanfit/mle.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.mle — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.mle — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/pathfinder.html b/docs/_modules/cmdstanpy/stanfit/pathfinder.html
index dfbcc6b7..0c1c486b 100644
--- a/docs/_modules/cmdstanpy/stanfit/pathfinder.html
+++ b/docs/_modules/cmdstanpy/stanfit/pathfinder.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.pathfinder — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.pathfinder — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/runset.html b/docs/_modules/cmdstanpy/stanfit/runset.html
index b7d975ec..2fc8301c 100644
--- a/docs/_modules/cmdstanpy/stanfit/runset.html
+++ b/docs/_modules/cmdstanpy/stanfit/runset.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.runset — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.runset — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/stanfit/vb.html b/docs/_modules/cmdstanpy/stanfit/vb.html
index fee5a8f5..49c5f0c0 100644
--- a/docs/_modules/cmdstanpy/stanfit/vb.html
+++ b/docs/_modules/cmdstanpy/stanfit/vb.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.stanfit.vb — CmdStanPy 1.2.1 documentation
+    cmdstanpy.stanfit.vb — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/utils.html b/docs/_modules/cmdstanpy/utils.html
index 74725c83..ea1958ef 100644
--- a/docs/_modules/cmdstanpy/utils.html
+++ b/docs/_modules/cmdstanpy/utils.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.utils — CmdStanPy 1.2.1 documentation
+    cmdstanpy.utils — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/cmdstanpy/utils/cmdstan.html b/docs/_modules/cmdstanpy/utils/cmdstan.html
index df7a23af..46683793 100644
--- a/docs/_modules/cmdstanpy/utils/cmdstan.html
+++ b/docs/_modules/cmdstanpy/utils/cmdstan.html
@@ -5,7 +5,7 @@
   
     
     
-    cmdstanpy.utils.cmdstan — CmdStanPy 1.2.1 documentation
+    cmdstanpy.utils.cmdstan — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 94648a23..f1dce97b 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -5,7 +5,7 @@
   
     
     
-    Overview: module code — CmdStanPy 1.2.1 documentation
+    Overview: module code — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
diff --git a/docs/_modules/stanio/json.html b/docs/_modules/stanio/json.html
index 5f89f624..551304fb 100644
--- a/docs/_modules/stanio/json.html
+++ b/docs/_modules/stanio/json.html
@@ -5,7 +5,7 @@
   
     
     
-    stanio.json — CmdStanPy 1.2.1 documentation
+    stanio.json — CmdStanPy 1.2.2 documentation
     
     
 
@@ -37,6 +37,7 @@
     
     
     
+    
     
     
 
@@ -60,7 +61,7 @@
   
 
@@ -174,7 +175,17 @@ 
Source code for stanio.json
 """
 Utilities for writing Stan Json files
 """
-import json
+try:
+    import ujson as json
+
+    uj_version = tuple(map(int, json.__version__.split(".")))
+    if uj_version < (5, 5, 0):
+        raise ImportError("ujson version too old")
+    UJSON_AVAILABLE = True
+except:
+    UJSON_AVAILABLE = False
+    import json
+
 from typing import Any, Mapping
 
 import numpy as np
@@ -204,7 +215,17 @@ 
Source code for stanio.json
         or "xarray" in original_module
         or "pandas" in original_module
     ):
-        return process_value(np.asanyarray(val).tolist())
+        numpy_val = np.asanyarray(val)
+        # fast paths for numeric types
+        if numpy_val.dtype.kind in "iuf":
+            return numpy_val.tolist()
+        if numpy_val.dtype.kind == "c":
+            return np.stack([numpy_val.real, numpy_val.imag], axis=-1).tolist()
+        if numpy_val.dtype.kind == "b":
+            return numpy_val.astype(int).tolist()
+
+        # should only be object arrays (tuples, etc)
+        return process_value(numpy_val.tolist())
 
     return val
 
@@ -248,8 +269,11 @@ 
Source code for stanio.json
         copied before type conversion, not modified
     """
     with open(path, "w") as fd:
-        for chunk in json.JSONEncoder().iterencode(process_dictionary(data)):
-            fd.write(chunk)

+        if UJSON_AVAILABLE:
+            json.dump(process_dictionary(data), fd)
+        else:
+            for chunk in json.JSONEncoder().iterencode(process_dictionary(data)):
+                fd.write(chunk)

 

 
               

diff --git a/docs/_sources/api.rst.txt b/docs/_sources/api.rst.txt
index 5ec5867c..f527f159 100644
--- a/docs/_sources/api.rst.txt
+++ b/docs/_sources/api.rst.txt
@@ -84,6 +84,17 @@ CmdStanGQ
 Functions
 *********
 
+compile_stan_file
+=================
+
+.. autofunction:: cmdstanpy.compile_stan_file
+
+
+format_stan_file
+================
+
+.. autofunction:: cmdstanpy.format_stan_file
+
 show_versions
 =============
 
diff --git a/docs/_sources/changes.rst.txt b/docs/_sources/changes.rst.txt
index cd179060..15feeb75 100644
--- a/docs/_sources/changes.rst.txt
+++ b/docs/_sources/changes.rst.txt
@@ -7,6 +7,19 @@ What's New
 
 For full changes, see the `Releases page `_ on GitHub.
 
+CmdStanPy 1.2.2
+---------------
+
+- Updated Community page to link to the ``bibat`` package.
+- Moved CmdStanPy's metadata to exclusively use the ``pyproject.toml`` file.
+- Fixed an issue where the deprecation of the ``compile=False`` argument to :class:`CmdStanModel` would
+  make it impossible to use the canonicalizer to update old models.
+  The new function :func:`cmdstanpy.format_stan_file` supports this use case.
+- Fixed a bug preventing multiple inits from being used with :meth:`CmdStanModel.pathfinder`.
+- Added a helper argument ``num_threads`` to :meth:`CmdStanModel.pathfinder`.
+
+Reminder: The next non-bugfix release of CmdStanPy will be version 2.0, which will remove all existing deprecations.
+
 CmdStanPy 1.2.1
 ---------------
 
diff --git a/docs/_sources/community.rst.txt b/docs/_sources/community.rst.txt
index 82ef9373..eabfd829 100644
--- a/docs/_sources/community.rst.txt
+++ b/docs/_sources/community.rst.txt
@@ -9,8 +9,8 @@ Project templates
 Templates are a great way to piggy back on other users' work, saving you time
 when you start a new project.
 
-- `cookiecutter-cmdstanpy-analysis `_
-  A cookiecutter template for cmdstanpy-based statistical analysis projects.
+- `bibat `_
+  A batteries-included template for Bayesian statistical analysis projects.
 
 - `cookiecutter-cmdstanpy-wrapper `_
   A cookiecutter template using Stan models in Python packages, including
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 744c587f..809835b6 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: '1.2.1',
+    VERSION: '1.2.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_static/images/logo_icon.png b/docs/_static/images/logo_icon.png
index a4be80e9..ca139697 100644
Binary files a/docs/_static/images/logo_icon.png and b/docs/_static/images/logo_icon.png differ
diff --git a/docs/_static/images/logo_tm.png b/docs/_static/images/logo_tm.png
index 4a4f06aa..72f17ec0 100644
Binary files a/docs/_static/images/logo_tm.png and b/docs/_static/images/logo_tm.png differ
diff --git a/docs/_static/logo_icon.png b/docs/_static/logo_icon.png
index a4be80e9..ca139697 100644
Binary files a/docs/_static/logo_icon.png and b/docs/_static/logo_icon.png differ
diff --git a/docs/api.html b/docs/api.html
index 3cf6e32b..3ca6aa91 100644
--- a/docs/api.html
+++ b/docs/api.html
@@ -6,7 +6,7 @@
     
     
 
-    API Reference — CmdStanPy 1.2.1 documentation
+    API Reference — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
@@ -1117,6 +1118,38 @@
    Functions
   
   
 
 
Returns:

@@ -2189,7 +2226,7 @@ 
CmdStanMCMCReturn type:
-
DataFrame

+
DataFrame

 

 
 

@@ -2212,7 +2249,7 @@ 
CmdStanMCMCReturn type:
-
Dataset

+
Dataset

 

 
 

@@ -2346,7 +2383,7 @@ 
CmdStanMCMC
pandas.DataFrame

 
 
Return type:

-
DataFrame

+
DataFrame

 

 
 
@@ -2548,7 +2585,7 @@ 
CmdStanMLE
 

-property optimized_iterations_pd: Optional[DataFrame]

+property optimized_iterations_pd: Optional[DataFrame]
 
Returns all saved iterations from the optimizer and final estimate
 as a pandas.DataFrame which contains all optimizer outputs, i.e.,
 the value for lp__ as well as all Stan program variables.

@@ -2571,7 +2608,7 @@ 
CmdStanMLE
 

-property optimized_params_pd: DataFrame

+property optimized_params_pd: DataFrame
 
Returns all final estimates from the optimizer as a pandas.DataFrame
 which contains all optimizer outputs, i.e., the value for lp__
 as well as all Stan program variables.

@@ -2615,7 +2652,7 @@ 
CmdStanLaplace
vars (Optional[Union[List[str], str]]) – optional list of variable names.

 

 
Return type:

-
Dataset

+
Dataset

 

 
 

@@ -3015,7 +3052,7 @@ 
CmdStanVB
 

-property variational_params_pd: DataFrame

+property variational_params_pd: DataFrame
 
Returns inferred parameter means as pandas DataFrame.

 

 
@@ -3027,7 +3064,7 @@ 
CmdStanVB
 

-property variational_sample_pd: DataFrame

+property variational_sample_pd: DataFrame
 
Returns the set of approximate posterior output draws as
 a pandas DataFrame.

 

@@ -3105,7 +3142,7 @@ 
CmdStanGQReturn type:
-
DataFrame

+
DataFrame

 

 
 

@@ -3118,7 +3155,7 @@ 
CmdStanGQ
 draws_xr(vars: Optional[Union[str, List[str]]] = None, inc_warmup: bool = False, inc_sample: bool = False) → NoReturn[source]
 

-draws_xr(vars: Optional[Union[str, List[str]]] = None, inc_warmup: bool = False, inc_sample: bool = False) → Dataset

+draws_xr(vars: Optional[Union[str, List[str]]] = None, inc_warmup: bool = False, inc_sample: bool = False) → Dataset
 
Returns the generated quantities draws as a xarray Dataset.

 
This method can only be called when the underlying fit was made
 through sampling, it cannot be used on MLE or VB outputs.

@@ -3258,6 +3295,70 @@ 
CmdStanGQ
 
Functions

+

+
compile_stan_file

+

+

+cmdstanpy.compile_stan_file(src, force=False, stanc_options=None, cpp_options=None, user_header=None)[source]

+
Compile the given Stan program file.  Translates the Stan code to
+C++, then calls the C++ compiler.

+
By default, this function compares the timestamps on the source and
+executable files; if the executable is newer than the source file, it
+will not recompile the file, unless argument force is True
+or unless the compiler options have been changed.

+

+
Parameters:

+
    
+
  • src (Union[str, Path]) – Path to Stan program file.
    • 
+
  • force (bool) – When True, always compile, even if the executable file
+is newer than the source file.  Used for Stan models which have
+#include directives in order to force recompilation when changes
+are made to the included files.
    • 
+
  • stanc_options (Optional[Dict[str, Any]]) – Options for stanc compiler.
    • 
+
  • cpp_options (Optional[Dict[str, Any]]) – Options for C++ compiler.
    • 
+
  • user_header (Optional[Union[str, PathLike]]) – A path to a header file to include during C++
+compilation.
    • 
+

+

+
Return type:

+
str

+

+

+

+
+

+

+
format_stan_file

+

+

+cmdstanpy.format_stan_file(stan_file, *, overwrite_file=False, canonicalize=False, max_line_length=78, backup=True, stanc_options=None)[source]

+
Run stanc’s auto-formatter on the model code. Either saves directly
+back to the file or prints for inspection

+

+
Parameters:

+
    
+
  • stan_file (Union[str, PathLike]) – Path to Stan program file.
    • 
+
  • overwrite_file (bool) – If True, save the updated code to disk, rather
+than printing it. By default False
    • 
+
  • canonicalize (Union[bool, str, Iterable[str]]) – Whether or not the compiler should ‘canonicalize’
+the Stan model, removing things like deprecated syntax. Default is
+False. If True, all canonicalizations are run. If it is a list of
+strings, those options are passed to stanc (new in Stan 2.29)
    • 
+
  • max_line_length (int) – Set the wrapping point for the formatter. The
+default value is 78, which wraps most lines by the 80th character.
    • 
+
  • backup (bool) – If True, create a stanfile.bak backup before
+writing to the file. Only disable this if you’re sure you have other
+copies of the file or are using a version control system like Git.
    • 
+
  • stanc_options (Optional[Dict[str, Any]]) – Additional options to pass to the stanc compiler.
    • 
+

+

+
Return type:

+
None

+

+

+

+
+

 

 
show_versions

 

@@ -3430,7 +3531,7 @@ 
write_stan_jsonnumpy.asarray(), e.g a
-pandas.Series.

+pandas.Series.

 
Produces a file compatible with the
 Json Format for Cmdstan

 

@@ -3439,7 +3540,7 @@ 
write_stan_jsonstr) – File path for the created json. Will be overwritten if
 already in existence.

 
  • data (Mapping[str, Any]) – A mapping from strings to values. This can be a dictionary
-or something more exotic like an xarray.Dataset. This will be
+or something more exotic like an xarray.Dataset. This will be
 copied before type conversion, not modified
    • 
 
 
    
diff --git a/docs/changes.html b/docs/changes.html
index 983ff693..41694480 100644
--- a/docs/changes.html
+++ b/docs/changes.html
@@ -6,7 +6,7 @@
     
     
 
-    What’s New — CmdStanPy 1.2.1 documentation
+    What’s New — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
@@ -171,6 +172,11 @@
 
 
    
 
    
 
    
@@ -312,15 +312,7 @@ 
    Maximum Likelihood Estimation
 
    -20:41:35 - cmdstanpy - INFO - Chain [1] start processing
-
    
-
    
-
    
-
    
-
    
-
    
-
    -20:41:35 - cmdstanpy - INFO - Chain [1] done processing
+16:29:42 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
    
 
    
@@ -329,7 +321,7 @@ 
    Maximum Likelihood Estimation
 
     ('lp__', 'theta')
-OrderedDict([('lp__', -5.00402), ('theta', 0.20001)])
+OrderedDict([('lp__', -5.00402), ('theta', 0.199999)])
 
    
 
    
 
    
@@ -363,7 +355,7 @@ 
    Maximum Likelihood Estimation\n",
        "      0\n",
        "      -5.00402\n",
-       "      0.20001\n",
+       "      0.199999\n",
        "    \n",
        "  \n",
        "\n",
        "
    "
       ],
       "text/plain": [
-       "      lp__    theta\n",
-       "0 -5.00402  0.20001"
+       "      lp__     theta\n",
+       "0 -5.00402  0.199999"
       ]
      },
      "execution_count": 1,
diff --git a/docs/users-guide/examples/Pathfinder.html b/docs/users-guide/examples/Pathfinder.html
index b2cd54ac..c0e27d42 100644
--- a/docs/users-guide/examples/Pathfinder.html
+++ b/docs/users-guide/examples/Pathfinder.html
@@ -6,7 +6,7 @@
     
     
 
-    Variational Inference using Pathfinder — CmdStanPy 1.2.1 documentation
+    Variational Inference using Pathfinder — CmdStanPy 1.2.2 documentation
     
     
 
@@ -39,6 +39,7 @@
     
     
     
+    
     
     
     
@@ -64,7 +65,7 @@
   
 
@@ -293,7 +294,7 @@ 
    Variational Inference using Pathfinderbernoulli.stan
    
 
    The CmdStanModel pathfinder method wraps the CmdStan pathfinder method.
    
 
    By default, CmdStanPy runs multi-path Pathfinder which returns an importance-resampled set of draws over the outputs of 4 independent single-path Pathfinders.
    
-
    
+
    
 
    [1]:
 
    
 
    
@@ -302,15 +303,6 @@ 
    Example: variational inference with Pathfinder for model 
-
    
-
    
-
    
-
    -/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/tqdm/auto.py:21: 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
-
    
-
    
 
    
 
    [2]:
 
    
@@ -330,7 +322,7 @@ 
    Example: variational inference with Pathfinder for model 
 
    -20:41:37 - cmdstanpy - INFO - Chain [1] start processing
+16:29:44 - cmdstanpy - INFO - Chain [1] start processing
 
    
 
    
 
    
@@ -338,7 +330,7 @@ 
    Example: variational inference with Pathfinder for model 
 
    -20:41:37 - cmdstanpy - INFO - Chain [1] done processing
+16:29:44 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
    
 
    
@@ -357,11 +349,11 @@ 
    Example: variational inference with Pathfinder for model 
     CmdStanPathfinder: model=bernoulli['method=pathfinder']
  csv_files:
-        /tmp/tmpar1gm37y/bernoulli3ctxpbm0/bernoulli-20240205204137.csv
+        /tmp/tmpimv2ege0/bernoullifbcxwakw/bernoulli-20240326162944.csv
  output_files:
-        /tmp/tmpar1gm37y/bernoulli3ctxpbm0/bernoulli-20240205204137_0-stdout.txt
+        /tmp/tmpimv2ege0/bernoullifbcxwakw/bernoulli-20240326162944_0-stdout.txt
 Metadata:
-{'stan_version_major': 2, 'stan_version_minor': 34, 'stan_version_patch': 1, 'model': 'bernoulli_model', 'start_datetime': '2024-02-05 20:41:37 UTC', 'method': 'pathfinder', 'init_alpha': 0.001, 'tol_obj': 1e-12, 'tol_rel_obj': 10000, 'tol_grad': 1e-08, 'tol_rel_grad': 10000000.0, 'tol_param': 1e-08, 'history_size': 5, 'num_psis_draws': 1000, 'num_paths': 4, 'save_single_paths': 0, 'psis_resample': 1, 'calculate_lp': 1, 'max_lbfgs_iters': 1000, 'num_draws': 1000, 'num_elbo_draws': 25, 'id': 1, 'data_file': '/home/runner/.cmdstan/cmdstan-2.34.1/examples/bernoulli/bernoulli.data.json', 'init': 2, 'seed': 1285, 'diagnostic_file': '', 'refresh': 100, 'sig_figs': -1, 'profile_file': 'profile.csv', 'save_cmdstan_config': 0, 'num_threads': 1, 'stanc_version': 'stanc3 v2.34.0', 'stancflags': '', 'raw_header': 'lp_approx__,lp__,theta', 'column_names': ('lp_approx__', 'lp__', 'theta')}
+{'stan_version_major': 2, 'stan_version_minor': 34, 'stan_version_patch': 1, 'model': 'bernoulli_model', 'start_datetime': '2024-03-26 16:29:44 UTC', 'method': 'pathfinder', 'init_alpha': 0.001, 'tol_obj': 1e-12, 'tol_rel_obj': 10000, 'tol_grad': 1e-08, 'tol_rel_grad': 10000000.0, 'tol_param': 1e-08, 'history_size': 5, 'num_psis_draws': 1000, 'num_paths': 4, 'save_single_paths': 0, 'psis_resample': 1, 'calculate_lp': 1, 'max_lbfgs_iters': 1000, 'num_draws': 1000, 'num_elbo_draws': 25, 'id': 1, 'data_file': '/home/runner/.cmdstan/cmdstan-2.34.1/examples/bernoulli/bernoulli.data.json', 'init': 2, 'seed': 50890, 'diagnostic_file': '', 'refresh': 100, 'sig_figs': -1, 'profile_file': 'profile.csv', 'save_cmdstan_config': 0, 'num_threads': 1, 'stanc_version': 'stanc3 v2.34.0', 'stancflags': '', 'raw_header': 'lp_approx__,lp__,theta', 'column_names': ('lp_approx__', 'lp__', 'theta')}
 
 
    
 
    
@@ -439,7 +431,7 @@ 
    Pathfinders as initialization for the MCMC sampler
 
    
 
    -[{'theta': array(0.335465)}, {'theta': array(0.370054)}, {'theta': array(0.327206)}, {'theta': array(0.220554)}]
+[{'theta': array(0.278046)}, {'theta': array(0.189515)}, {'theta': array(0.28219)}, {'theta': array(0.174821)}]
 
    
 
    
 
    The create_inits takes two arguments:
    
@@ -461,7 +453,7 @@ 
    Pathfinders as initialization for the MCMC sampler
 
    
 
    -[{'theta': array(0.190597)}, {'theta': array(0.268621)}, {'theta': array(0.227258)}]
+[{'theta': array(0.151519)}, {'theta': array(0.156614)}, {'theta': array(0.066908)}]
 
    
 
    
 
diff --git a/docs/users-guide/examples/Pathfinder.ipynb b/docs/users-guide/examples/Pathfinder.ipynb
index 2b97e57b..daeee884 100644
--- a/docs/users-guide/examples/Pathfinder.ipynb
+++ b/docs/users-guide/examples/Pathfinder.ipynb
@@ -42,22 +42,13 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:36.890695Z",
-     "iopub.status.busy": "2024-02-05T20:41:36.890218Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.188270Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.187699Z"
+     "iopub.execute_input": "2024-03-26T16:29:43.878098Z",
+     "iopub.status.busy": "2024-03-26T16:29:43.877555Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.225458Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.224871Z"
     }
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "from cmdstanpy.model import CmdStanModel, cmdstan_path"
@@ -68,10 +59,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:37.191153Z",
-     "iopub.status.busy": "2024-02-05T20:41:37.190684Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.276597Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.276028Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.228431Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.227964Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.313140Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.312554Z"
     }
    },
    "outputs": [
@@ -79,14 +70,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:37 - cmdstanpy - INFO - Chain [1] start processing\n"
+      "16:29:44 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:37 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "16:29:44 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     }
    ],
@@ -105,10 +96,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:37.279188Z",
-     "iopub.status.busy": "2024-02-05T20:41:37.278927Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.282778Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.282171Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.316072Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.315710Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.319485Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.318839Z"
     }
    },
    "outputs": [
@@ -118,11 +109,11 @@
      "text": [
       "CmdStanPathfinder: model=bernoulli['method=pathfinder']\n",
       " csv_files:\n",
-      "\t/tmp/tmpar1gm37y/bernoulli3ctxpbm0/bernoulli-20240205204137.csv\n",
+      "\t/tmp/tmpimv2ege0/bernoullifbcxwakw/bernoulli-20240326162944.csv\n",
       " output_files:\n",
-      "\t/tmp/tmpar1gm37y/bernoulli3ctxpbm0/bernoulli-20240205204137_0-stdout.txt\n",
+      "\t/tmp/tmpimv2ege0/bernoullifbcxwakw/bernoulli-20240326162944_0-stdout.txt\n",
       "Metadata:\n",
-      "{'stan_version_major': 2, 'stan_version_minor': 34, 'stan_version_patch': 1, 'model': 'bernoulli_model', 'start_datetime': '2024-02-05 20:41:37 UTC', 'method': 'pathfinder', 'init_alpha': 0.001, 'tol_obj': 1e-12, 'tol_rel_obj': 10000, 'tol_grad': 1e-08, 'tol_rel_grad': 10000000.0, 'tol_param': 1e-08, 'history_size': 5, 'num_psis_draws': 1000, 'num_paths': 4, 'save_single_paths': 0, 'psis_resample': 1, 'calculate_lp': 1, 'max_lbfgs_iters': 1000, 'num_draws': 1000, 'num_elbo_draws': 25, 'id': 1, 'data_file': '/home/runner/.cmdstan/cmdstan-2.34.1/examples/bernoulli/bernoulli.data.json', 'init': 2, 'seed': 1285, 'diagnostic_file': '', 'refresh': 100, 'sig_figs': -1, 'profile_file': 'profile.csv', 'save_cmdstan_config': 0, 'num_threads': 1, 'stanc_version': 'stanc3 v2.34.0', 'stancflags': '', 'raw_header': 'lp_approx__,lp__,theta', 'column_names': ('lp_approx__', 'lp__', 'theta')}\n",
+      "{'stan_version_major': 2, 'stan_version_minor': 34, 'stan_version_patch': 1, 'model': 'bernoulli_model', 'start_datetime': '2024-03-26 16:29:44 UTC', 'method': 'pathfinder', 'init_alpha': 0.001, 'tol_obj': 1e-12, 'tol_rel_obj': 10000, 'tol_grad': 1e-08, 'tol_rel_grad': 10000000.0, 'tol_param': 1e-08, 'history_size': 5, 'num_psis_draws': 1000, 'num_paths': 4, 'save_single_paths': 0, 'psis_resample': 1, 'calculate_lp': 1, 'max_lbfgs_iters': 1000, 'num_draws': 1000, 'num_elbo_draws': 25, 'id': 1, 'data_file': '/home/runner/.cmdstan/cmdstan-2.34.1/examples/bernoulli/bernoulli.data.json', 'init': 2, 'seed': 50890, 'diagnostic_file': '', 'refresh': 100, 'sig_figs': -1, 'profile_file': 'profile.csv', 'save_cmdstan_config': 0, 'num_threads': 1, 'stanc_version': 'stanc3 v2.34.0', 'stancflags': '', 'raw_header': 'lp_approx__,lp__,theta', 'column_names': ('lp_approx__', 'lp__', 'theta')}\n",
       "\n"
      ]
     }
@@ -154,10 +145,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
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-     "iopub.status.busy": "2024-02-05T20:41:37.284877Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.292194Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.291591Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.322023Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.321649Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.328711Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.328190Z"
     }
    },
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-     "shell.execute_reply": "2024-02-05T20:41:37.297809Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.331257Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.330886Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.335028Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.334351Z"
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-     "shell.execute_reply": "2024-02-05T20:41:37.303933Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.337482Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.337102Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.341146Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.340523Z"
     }
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@@ -244,10 +235,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
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-     "iopub.status.busy": "2024-02-05T20:41:37.306736Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.310810Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.310186Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.343774Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.343296Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.347590Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.346955Z"
     }
    },
    "outputs": [
@@ -255,7 +246,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'theta': array(0.335465)}, {'theta': array(0.370054)}, {'theta': array(0.327206)}, {'theta': array(0.220554)}]\n"
+      "[{'theta': array(0.278046)}, {'theta': array(0.189515)}, {'theta': array(0.28219)}, {'theta': array(0.174821)}]\n"
      ]
     }
    ],
@@ -279,10 +270,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:37.313029Z",
-     "iopub.status.busy": "2024-02-05T20:41:37.312846Z",
-     "iopub.status.idle": "2024-02-05T20:41:37.316790Z",
-     "shell.execute_reply": "2024-02-05T20:41:37.316156Z"
+     "iopub.execute_input": "2024-03-26T16:29:44.350084Z",
+     "iopub.status.busy": "2024-03-26T16:29:44.349681Z",
+     "iopub.status.idle": "2024-03-26T16:29:44.353504Z",
+     "shell.execute_reply": "2024-03-26T16:29:44.352850Z"
     }
    },
    "outputs": [
@@ -290,7 +281,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[{'theta': array(0.190597)}, {'theta': array(0.268621)}, {'theta': array(0.227258)}]\n"
+      "[{'theta': array(0.151519)}, {'theta': array(0.156614)}, {'theta': array(0.066908)}]\n"
      ]
     }
    ],
diff --git a/docs/users-guide/examples/Run Generated Quantities.html b/docs/users-guide/examples/Run Generated Quantities.html
index af2da5b4..fd0543f3 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 1.2.1 documentation
+    Generating new quantities of interest. — CmdStanPy 1.2.2 documentation
     
     
 
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+16:29:46 - 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
 
    
 
    
 
    
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    -20:41:53 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc
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    Example: add posterior predictive checks to 
 
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+16:30:00 - cmdstanpy - INFO - Chain [4] done processing
 
    
 
    
 
    The generate_quantities method returns a CmdStanGQ object which contains the values for all variables in the generated quantities 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.
    
@@ -833,7 +661,7 @@ 
    Example: add posterior predictive checks to 
 
    -20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
+16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
 
    
 
    
 
    
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+16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
 
    
 
    
 
    
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+16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
 
    
 
    
 
    
@@ -866,18 +694,18 @@ 
    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. 1. 1. 0. 0. 0. 0. 0.]
- [0. 0. 1. 1. 1. 0. 0. 0. 0. 1.]
- [0. 0. 1. 1. 1. 0. 0. 0. 0. 1.]
- [0. 0. 0. 1. 1. 0. 0. 0. 0. 0.]]
-[[0. 1. 0. 1. 0. 0. 1. 1. 0. 1.]
- [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]
- [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]
- [0. 1. 0. 0. 0. 0. 1. 0. 0. 0.]]
-[[1. 1. 0. 0. 0. 0. 0. 1. 0. 0.]
- [1. 1. 0. 0. 0. 0. 0. 1. 0. 0.]
- [1. 1. 0. 0. 0. 0. 0. 0. 0. 0.]
- [0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]]
+[[0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]
+ [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]
+ [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]
+ [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]]
+[[0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 1. 0. 0. 0. 0. 0. 1.]]
+[[0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]
+ [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]]
 
    
 
    
 
    We can also use draws_pd(inc_sample=True) to get a pandas DataFrame which combines the input drawset with the generated quantities.
    
@@ -897,7 +725,7 @@ 
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    -20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
+16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with "save_warmup=True".
 
    
 
    
 
    
@@ -957,75 +785,75 @@ 
    Example: add posterior predictive checks to 
    
 
    
 
    For models as simple as the bernoulli models here, it would be trivial to re-run the sampler and generate a new sample which contains both the estimate of the parameters theta as well as y_rep values. For models which are difficult to fit, i.e., when producing a sample is computationally expensive, the generate_quantities method is preferred.
    
-
+
 
 
 
diff --git a/docs/users-guide/examples/Run Generated Quantities.ipynb b/docs/users-guide/examples/Run Generated Quantities.ipynb
index b20af744..80477c75 100644
--- a/docs/users-guide/examples/Run Generated Quantities.ipynb	
+++ b/docs/users-guide/examples/Run Generated Quantities.ipynb	
@@ -42,21 +42,13 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:39.081240Z",
-     "iopub.status.busy": "2024-02-05T20:41:39.081047Z",
-     "iopub.status.idle": "2024-02-05T20:41:39.443810Z",
-     "shell.execute_reply": "2024-02-05T20:41:39.443074Z"
+     "iopub.execute_input": "2024-03-26T16:29:46.036648Z",
+     "iopub.status.busy": "2024-03-26T16:29:46.036452Z",
+     "iopub.status.idle": "2024-03-26T16:29:46.441221Z",
+     "shell.execute_reply": "2024-03-26T16:29:46.440481Z"
     }
    },
    "outputs": [
-    {
-     "name": "stderr",
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-      "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
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-     "shell.execute_reply": "2024-02-05T20:41:39.485729Z"
+     "iopub.execute_input": "2024-03-26T16:29:46.444455Z",
+     "iopub.status.busy": "2024-03-26T16:29:46.443867Z",
+     "iopub.status.idle": "2024-03-26T16:29:46.502957Z",
+     "shell.execute_reply": "2024-03-26T16:29:46.502392Z"
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-     "iopub.status.idle": "2024-02-05T20:41:39.624251Z",
-     "shell.execute_reply": "2024-02-05T20:41:39.623588Z"
+     "iopub.execute_input": "2024-03-26T16:29:46.505763Z",
+     "iopub.status.busy": "2024-03-26T16:29:46.505069Z",
+     "iopub.status.idle": "2024-03-26T16:29:46.709551Z",
+     "shell.execute_reply": "2024-03-26T16:29:46.708948Z"
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-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\r",
-      "chain 1 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
-     ]
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "d8220583290146688fa0dcd1925ad1e5",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "chain 1 |          | 00:00 Status"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     },
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\r",
-      "chain 2 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
-     ]
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "46749833be2f497f927fdb925199d231",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "chain 2 |          | 00:00 Status"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     },
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\r",
-      "chain 3 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
-     ]
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "f52d3bec872b4454b3ab4912a4ccd42a",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "chain 3 |          | 00:00 Status"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     },
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "\r",
-      "chain 4 |\u001b[34m██████████\u001b[0m| 00:00 Sampling completed"
-     ]
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "da5c161a59bc4cdaa557c3421c211f32",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "chain 4 |          | 00:00 Status"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     },
     {
      "name": "stdout",
@@ -298,8 +234,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\n",
-      "20:41:39 - cmdstanpy - INFO - CmdStan done processing.\n"
+      "16:29:46 - cmdstanpy - INFO - CmdStan done processing.\n"
      ]
     },
     {
@@ -327,10 +262,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:39.627092Z",
-     "iopub.status.busy": "2024-02-05T20:41:39.626692Z",
-     "iopub.status.idle": "2024-02-05T20:41:39.673685Z",
-     "shell.execute_reply": "2024-02-05T20:41:39.672907Z"
+     "iopub.execute_input": "2024-03-26T16:29:46.712397Z",
+     "iopub.status.busy": "2024-03-26T16:29:46.711862Z",
+     "iopub.status.idle": "2024-03-26T16:29:46.756228Z",
+     "shell.execute_reply": "2024-03-26T16:29:46.755501Z"
     }
    },
    "outputs": [
@@ -369,40 +304,40 @@
        "  \n",
        "    \n",
        "      lp__\n",
-       "      -7.273190\n",
-       "      0.024164\n",
-       "      0.755960\n",
-       "      -8.784640\n",
-       "      -6.98039\n",
-       "      -6.75028\n",
-       "      978.759\n",
-       "      22244.5\n",
-       "      1.00159\n",
+       "      -7.297320\n",
+       "      0.017912\n",
+       "      0.755274\n",
+       "      -8.851160\n",
+       "      -6.996700\n",
+       "      -6.750000\n",
+       "      1778.01\n",
+       "      36286.0\n",
+       "      1.00036\n",
        "    \n",
        "    \n",
        "      theta\n",
-       "      0.252528\n",
-       "      0.003132\n",
-       "      0.120077\n",
-       "      0.081241\n",
-       "      0.23811\n",
-       "      0.46955\n",
-       "      1469.970\n",
-       "      33408.4\n",
-       "      1.00101\n",
+       "      0.250792\n",
+       "      0.003315\n",
+       "      0.121648\n",
+       "      0.076211\n",
+       "      0.240263\n",
+       "      0.470491\n",
+       "      1346.53\n",
+       "      27480.2\n",
+       "      1.00109\n",
        "    \n",
        "  \n",
        "\n",
        "
    "
       ],
       "text/plain": [
-       "           Mean      MCSE    StdDev        5%      50%      95%     N_Eff  \\\n",
-       "lp__  -7.273190  0.024164  0.755960 -8.784640 -6.98039 -6.75028   978.759   \n",
-       "theta  0.252528  0.003132  0.120077  0.081241  0.23811  0.46955  1469.970   \n",
+       "           Mean      MCSE    StdDev        5%       50%       95%    N_Eff  \\\n",
+       "lp__  -7.297320  0.017912  0.755274 -8.851160 -6.996700 -6.750000  1778.01   \n",
+       "theta  0.250792  0.003315  0.121648  0.076211  0.240263  0.470491  1346.53   \n",
        "\n",
        "       N_Eff/s    R_hat  \n",
-       "lp__   22244.5  1.00159  \n",
-       "theta  33408.4  1.00101  "
+       "lp__   36286.0  1.00036  \n",
+       "theta  27480.2  1.00109  "
       ]
      },
      "execution_count": 4,
@@ -426,10 +361,10 @@
    "execution_count": 5,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:39.676525Z",
-     "iopub.status.busy": "2024-02-05T20:41:39.676108Z",
-     "iopub.status.idle": "2024-02-05T20:41:53.232238Z",
-     "shell.execute_reply": "2024-02-05T20:41:53.231630Z"
+     "iopub.execute_input": "2024-03-26T16:29:46.759240Z",
+     "iopub.status.busy": "2024-03-26T16:29:46.758703Z",
+     "iopub.status.idle": "2024-03-26T16:30:00.640995Z",
+     "shell.execute_reply": "2024-03-26T16:30:00.640392Z"
     }
    },
    "outputs": [
@@ -437,14 +372,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:39 - 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"
+      "16:29:46 - 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": [
-      "20:41:53 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n"
+      "16:30:00 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli_ppc\n"
      ]
     },
     {
@@ -495,10 +430,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:53.235249Z",
-     "iopub.status.busy": "2024-02-05T20:41:53.234750Z",
-     "iopub.status.idle": "2024-02-05T20:41:53.287981Z",
-     "shell.execute_reply": "2024-02-05T20:41:53.287436Z"
+     "iopub.execute_input": "2024-03-26T16:30:00.643833Z",
+     "iopub.status.busy": "2024-03-26T16:30:00.643524Z",
+     "iopub.status.idle": "2024-03-26T16:30:00.701815Z",
+     "shell.execute_reply": "2024-03-26T16:30:00.701030Z"
     }
    },
    "outputs": [
@@ -506,56 +441,56 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [1] start processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [2] start processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [2] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [3] start processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [3] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [2] done processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [2] done processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [4] start processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [4] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [3] done processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [3] done processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - INFO - Chain [4] done processing\n"
+      "16:30:00 - cmdstanpy - INFO - Chain [4] done processing\n"
      ]
     }
    ],
@@ -577,10 +512,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:53.290756Z",
-     "iopub.status.busy": "2024-02-05T20:41:53.290376Z",
-     "iopub.status.idle": "2024-02-05T20:41:53.313591Z",
-     "shell.execute_reply": "2024-02-05T20:41:53.312968Z"
+     "iopub.execute_input": "2024-03-26T16:30:00.704656Z",
+     "iopub.status.busy": "2024-03-26T16:30:00.704243Z",
+     "iopub.status.idle": "2024-03-26T16:30:00.728113Z",
+     "shell.execute_reply": "2024-03-26T16:30:00.727557Z"
     }
    },
    "outputs": [
@@ -588,28 +523,28 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
+      "16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
+      "16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
+      "16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
+      "16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
      ]
     },
     {
@@ -617,18 +552,18 @@
      "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. 1. 1. 0. 0. 0. 0. 0.]\n",
-      " [0. 0. 1. 1. 1. 0. 0. 0. 0. 1.]\n",
-      " [0. 0. 1. 1. 1. 0. 0. 0. 0. 1.]\n",
-      " [0. 0. 0. 1. 1. 0. 0. 0. 0. 0.]]\n",
-      "[[0. 1. 0. 1. 0. 0. 1. 1. 0. 1.]\n",
-      " [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]\n",
-      " [0. 1. 0. 1. 0. 0. 1. 0. 0. 0.]\n",
-      " [0. 1. 0. 0. 0. 0. 1. 0. 0. 0.]]\n",
-      "[[1. 1. 0. 0. 0. 0. 0. 1. 0. 0.]\n",
-      " [1. 1. 0. 0. 0. 0. 0. 1. 0. 0.]\n",
-      " [1. 1. 0. 0. 0. 0. 0. 0. 0. 0.]\n",
-      " [0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]]\n"
+      "[[0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]\n",
+      " [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]\n",
+      " [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]\n",
+      " [0. 0. 0. 0. 1. 1. 0. 0. 0. 0.]]\n",
+      "[[0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 1. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 1. 0. 0. 0. 0. 0. 1.]]\n",
+      "[[0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]\n",
+      " [0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]]\n"
      ]
     }
    ],
@@ -650,10 +585,10 @@
    "execution_count": 8,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:53.316211Z",
-     "iopub.status.busy": "2024-02-05T20:41:53.315860Z",
-     "iopub.status.idle": "2024-02-05T20:41:53.337714Z",
-     "shell.execute_reply": "2024-02-05T20:41:53.337056Z"
+     "iopub.execute_input": "2024-03-26T16:30:00.730757Z",
+     "iopub.status.busy": "2024-03-26T16:30:00.730373Z",
+     "iopub.status.idle": "2024-03-26T16:30:00.752951Z",
+     "shell.execute_reply": "2024-03-26T16:30:00.752316Z"
     }
    },
    "outputs": [
@@ -661,7 +596,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:53 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
+      "16:30:00 - cmdstanpy - WARNING - Sample doesn't contain draws from warmup iterations, rerun sampler with \"save_warmup=True\".\n"
      ]
     },
     {
@@ -718,75 +653,75 @@
        "  \n",
        "    \n",
        "      0\n",
-       "      -6.94949\n",
-       "      0.891339\n",
-       "      0.834473\n",
-       "      1.0\n",
+       "      -6.88937\n",
+       "      0.797647\n",
+       "      1.17203\n",
+       "      2.0\n",
        "      3.0\n",
        "      0.0\n",
-       "      7.75373\n",
-       "      0.176755\n",
+       "      7.55922\n",
+       "      0.320028\n",
        "      1.0\n",
        "      1.0\n",
        "      ...\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
+       "      0.0\n",
        "      1.0\n",
        "      1.0\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
-       "      0.0\n",
        "    \n",
        "    \n",
        "      1\n",
-       "      -7.04638\n",
-       "      0.988320\n",
-       "      0.834473\n",
-       "      2.0\n",
-       "      7.0\n",
+       "      -6.92103\n",
+       "      0.987890\n",
+       "      1.17203\n",
+       "      1.0\n",
+       "      1.0\n",
        "      0.0\n",
-       "      7.14451\n",
-       "      0.353708\n",
+       "      6.96935\n",
+       "      0.327844\n",
        "      1.0\n",
        "      2.0\n",
        "      ...\n",
        "      0.0\n",
-       "      1.0\n",
+       "      0.0\n",
        "      0.0\n",
        "      1.0\n",
        "      0.0\n",
        "      0.0\n",
-       "      1.0\n",
-       "      1.0\n",
        "      0.0\n",
+       "      0.0\n",
+       "      1.0\n",
        "      1.0\n",
        "    \n",
        "    \n",
        "      2\n",
-       "      -7.43716\n",
-       "      0.915396\n",
-       "      0.834473\n",
-       "      1.0\n",
-       "      1.0\n",
+       "      -6.77679\n",
+       "      0.998779\n",
+       "      1.17203\n",
+       "      2.0\n",
+       "      3.0\n",
        "      0.0\n",
-       "      7.44403\n",
-       "      0.411715\n",
+       "      6.94984\n",
+       "      0.220845\n",
        "      1.0\n",
        "      3.0\n",
        "      ...\n",
-       "      1.0\n",
-       "      1.0\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
        "      0.0\n",
-       "      1.0\n",
        "      0.0\n",
        "      0.0\n",
+       "      0.0\n",
+       "      1.0\n",
+       "      1.0\n",
        "    \n",
        "  \n",
        "\n",
@@ -795,19 +730,19 @@
       ],
       "text/plain": [
        "      lp__  accept_stat__  stepsize__  treedepth__  n_leapfrog__  divergent__  \\\n",
-       "0 -6.94949       0.891339    0.834473          1.0           3.0          0.0   \n",
-       "1 -7.04638       0.988320    0.834473          2.0           7.0          0.0   \n",
-       "2 -7.43716       0.915396    0.834473          1.0           1.0          0.0   \n",
+       "0 -6.88937       0.797647     1.17203          2.0           3.0          0.0   \n",
+       "1 -6.92103       0.987890     1.17203          1.0           1.0          0.0   \n",
+       "2 -6.77679       0.998779     1.17203          2.0           3.0          0.0   \n",
        "\n",
        "   energy__     theta  chain__  iter__  ...  y_rep[1]  y_rep[2]  y_rep[3]  \\\n",
-       "0   7.75373  0.176755      1.0     1.0  ...       0.0       0.0       0.0   \n",
-       "1   7.14451  0.353708      1.0     2.0  ...       0.0       1.0       0.0   \n",
-       "2   7.44403  0.411715      1.0     3.0  ...       1.0       1.0       0.0   \n",
+       "0   7.55922  0.320028      1.0     1.0  ...       0.0       0.0       0.0   \n",
+       "1   6.96935  0.327844      1.0     2.0  ...       0.0       0.0       0.0   \n",
+       "2   6.94984  0.220845      1.0     3.0  ...       0.0       0.0       0.0   \n",
        "\n",
        "   y_rep[4]  y_rep[5]  y_rep[6]  y_rep[7]  y_rep[8]  y_rep[9]  y_rep[10]  \n",
-       "0       1.0       1.0       0.0       0.0       0.0       0.0        0.0  \n",
-       "1       1.0       0.0       0.0       1.0       1.0       0.0        1.0  \n",
-       "2       0.0       0.0       0.0       0.0       1.0       0.0        0.0  \n",
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diff --git a/docs/users-guide/examples/Using External C++.html b/docs/users-guide/examples/Using External C++.html
index fcbf2c41..6b17cd33 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 1.2.1 documentation
+    Advanced Topic: Using External C++ Functions — CmdStanPy 1.2.2 documentation
     
     
 
@@ -39,6 +39,7 @@
     
     
     
+    
     
     
     
@@ -64,7 +65,7 @@
   
 
diff --git a/docs/users-guide/examples/VI as Sampler Inits.html b/docs/users-guide/examples/VI as Sampler Inits.html
index 22ef9a13..72a53041 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 1.2.1 documentation
+    Using Variational Estimates to Initialize the NUTS-HMC Sampler — CmdStanPy 1.2.2 documentation
     
     
 
@@ -39,6 +39,7 @@
     
     
     
+    
     
     
     
@@ -64,7 +65,7 @@
   
 
diff --git a/docs/users-guide/examples/Variational Inference.html b/docs/users-guide/examples/Variational Inference.html
index b5afc877..de350720 100644
--- a/docs/users-guide/examples/Variational Inference.html	
+++ b/docs/users-guide/examples/Variational Inference.html	
@@ -6,7 +6,7 @@
     
     
 
-    Variational Inference using ADVI — CmdStanPy 1.2.1 documentation
+    Variational Inference using ADVI — CmdStanPy 1.2.2 documentation
     
     
 
@@ -39,6 +39,7 @@
     
     
     
+    
     
     
     
@@ -64,7 +65,7 @@
   
 
@@ -310,16 +311,7 @@ 
    Example: variational inference for model 
 
    -/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/tqdm/auto.py:21: 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
-
    
-
    
-
    
-
    
-
    
-
    
-
    -20:41:57 - cmdstanpy - INFO - Chain [1] start processing
+16:30:04 - cmdstanpy - INFO - Chain [1] start processing
 
    
 
    
 
    
@@ -327,7 +319,7 @@ 
    Example: variational inference for model 
 
    -20:41:57 - cmdstanpy - INFO - Chain [1] done processing
+16:30:04 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
 
    The class `CmdStanVB <https://mc-stan.org/cmdstanpy/api.html#cmdstanvb>`__ provides the following properties to access information about the parameter names, estimated means, and the sample:
    
@@ -370,7 +362,7 @@ 
    Example: variational inference for model 
 
    -0.234156
+0.228927
 
    
 
 
    
@@ -404,7 +396,7 @@ 
    Example: variational inference for model 
 
    -20:41:57 - 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
+16:30:04 - 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
 
    
 
 
    
@@ -412,7 +404,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
+16:30:21 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail
 
    
 
 
    
@@ -420,7 +412,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - INFO - Chain [1] start processing
+16:30:21 - cmdstanpy - INFO - Chain [1] start processing
 
    
 
 
    
@@ -428,7 +420,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - INFO - Chain [1] done processing
+16:30:21 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
 
    
@@ -442,20 +434,20 @@ 
    Example: variational inference for model       1 model_fail = CmdStanModel(stan_file='eta_should_fail.stan')
 ----> 2 vi_fail = model_fail.variational()
 
-File ~/work/cmdstanpy/cmdstanpy/cmdstanpy/model.py:1575, in CmdStanModel.variational(self, data, seed, inits, output_dir, sig_figs, save_latent_dynamics, save_profile, algorithm, iter, grad_samples, elbo_samples, eta, adapt_engaged, adapt_iter, tol_rel_obj, eval_elbo, draws, require_converged, show_console, refresh, time_fmt, timeout, output_samples)
-   1573 if len(re.findall(pat, contents)) > 0:
-   1574     if require_converged:
--> 1575         raise RuntimeError(
-   1576             'The algorithm may not have converged.\n'
-   1577             'If you would like to inspect the output, '
-   1578             're-call with require_converged=False'
-   1579         )
-   1580     # else:
-   1581     get_logger().warning(
-   1582         '%s\n%s',
-   1583         'The algorithm may not have converged.',
-   1584         'Proceeding because require_converged is set to False',
-   1585     )
+File ~/work/cmdstanpy/cmdstanpy/cmdstanpy/model.py:1527, in CmdStanModel.variational(self, data, seed, inits, output_dir, sig_figs, save_latent_dynamics, save_profile, algorithm, iter, grad_samples, elbo_samples, eta, adapt_engaged, adapt_iter, tol_rel_obj, eval_elbo, draws, require_converged, show_console, refresh, time_fmt, timeout, output_samples)
+   1525 if len(re.findall(pat, contents)) > 0:
+   1526     if require_converged:
+-> 1527         raise RuntimeError(
+   1528             'The algorithm may not have converged.\n'
+   1529             'If you would like to inspect the output, '
+   1530             're-call with require_converged=False'
+   1531         )
+   1532     # else:
+   1533     get_logger().warning(
+   1534         '%s\n%s',
+   1535         'The algorithm may not have converged.',
+   1536         'Proceeding because require_converged is set to False',
+   1537     )
 
 RuntimeError: The algorithm may not have converged.
 If you would like to inspect the output, re-call with require_converged=False
@@ -475,7 +467,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - INFO - Chain [1] start processing
+16:30:21 - cmdstanpy - INFO - Chain [1] start processing
 
    
 
 
    
@@ -483,7 +475,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - INFO - Chain [1] done processing
+16:30:21 - cmdstanpy - INFO - Chain [1] done processing
 
    
 
 
    
@@ -491,7 +483,7 @@ 
    Example: variational inference for model 
 
    -20:42:13 - cmdstanpy - WARNING - The algorithm may not have converged.
+16:30:21 - cmdstanpy - WARNING - The algorithm may not have converged.
 Proceeding because require_converged is set to False
 
    
 
@@ -513,8 +505,8 @@ 
    Example: variational inference for model API documentation 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 ba94c842..809a35ff 100644
--- a/docs/users-guide/examples/Variational Inference.ipynb	
+++ b/docs/users-guide/examples/Variational Inference.ipynb	
@@ -38,10 +38,10 @@
    "execution_count": 1,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:57.025293Z",
-     "iopub.status.busy": "2024-02-05T20:41:57.024750Z",
-     "iopub.status.idle": "2024-02-05T20:41:57.412180Z",
-     "shell.execute_reply": "2024-02-05T20:41:57.411608Z"
+     "iopub.execute_input": "2024-03-26T16:30:04.461512Z",
+     "iopub.status.busy": "2024-03-26T16:30:04.461313Z",
+     "iopub.status.idle": "2024-03-26T16:30:04.909486Z",
+     "shell.execute_reply": "2024-03-26T16:30:04.908727Z"
     }
    },
    "outputs": [
@@ -49,22 +49,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
+      "16:30:04 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:57 - cmdstanpy - INFO - Chain [1] start processing\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "20:41:57 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "16:30:04 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     }
    ],
@@ -103,10 +95,10 @@
    "execution_count": 2,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:57.415226Z",
-     "iopub.status.busy": "2024-02-05T20:41:57.414803Z",
-     "iopub.status.idle": "2024-02-05T20:41:57.418492Z",
-     "shell.execute_reply": "2024-02-05T20:41:57.417892Z"
+     "iopub.execute_input": "2024-03-26T16:30:04.912629Z",
+     "iopub.status.busy": "2024-03-26T16:30:04.912204Z",
+     "iopub.status.idle": "2024-03-26T16:30:04.916012Z",
+     "shell.execute_reply": "2024-03-26T16:30:04.915339Z"
     },
     "scrolled": true
    },
@@ -128,10 +120,10 @@
    "execution_count": 3,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:57.420923Z",
-     "iopub.status.busy": "2024-02-05T20:41:57.420528Z",
-     "iopub.status.idle": "2024-02-05T20:41:57.424135Z",
-     "shell.execute_reply": "2024-02-05T20:41:57.423500Z"
+     "iopub.execute_input": "2024-03-26T16:30:04.918680Z",
+     "iopub.status.busy": "2024-03-26T16:30:04.918296Z",
+     "iopub.status.idle": "2024-03-26T16:30:04.921670Z",
+     "shell.execute_reply": "2024-03-26T16:30:04.920959Z"
     }
    },
    "outputs": [
@@ -139,7 +131,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "0.234156\n"
+      "0.228927\n"
      ]
     }
    ],
@@ -152,10 +144,10 @@
    "execution_count": 4,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:41:57.426522Z",
-     "iopub.status.busy": "2024-02-05T20:41:57.426142Z",
-     "iopub.status.idle": "2024-02-05T20:41:57.429634Z",
-     "shell.execute_reply": "2024-02-05T20:41:57.428999Z"
+     "iopub.execute_input": "2024-03-26T16:30:04.923992Z",
+     "iopub.status.busy": "2024-03-26T16:30:04.923642Z",
+     "iopub.status.idle": "2024-03-26T16:30:04.926981Z",
+     "shell.execute_reply": "2024-03-26T16:30:04.926356Z"
     }
    },
    "outputs": [
@@ -185,10 +177,10 @@
    "execution_count": 5,
    "metadata": {
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-     "iopub.execute_input": "2024-02-05T20:41:57.432000Z",
-     "iopub.status.busy": "2024-02-05T20:41:57.431700Z",
-     "iopub.status.idle": "2024-02-05T20:42:13.701188Z",
-     "shell.execute_reply": "2024-02-05T20:42:13.700551Z"
+     "iopub.execute_input": "2024-03-26T16:30:04.929323Z",
+     "iopub.status.busy": "2024-03-26T16:30:04.928957Z",
+     "iopub.status.idle": "2024-03-26T16:30:21.609075Z",
+     "shell.execute_reply": "2024-03-26T16:30:21.608322Z"
     },
     "tags": [
      "raises-exception"
@@ -199,28 +191,28 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:41:57 - 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"
+      "16:30:04 - 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": [
-      "20:42:13 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n"
+      "16:30:21 - cmdstanpy - INFO - compiled model executable: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/eta_should_fail\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:42:13 - cmdstanpy - INFO - Chain [1] start processing\n"
+      "16:30:21 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:42:13 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "16:30:21 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     },
     {
@@ -231,7 +223,7 @@
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
       "Cell \u001b[0;32mIn[5], line 2\u001b[0m\n\u001b[1;32m      1\u001b[0m model_fail \u001b[38;5;241m=\u001b[39m CmdStanModel(stan_file\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124meta_should_fail.stan\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m----> 2\u001b[0m vi_fail \u001b[38;5;241m=\u001b[39m \u001b[43mmodel_fail\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mvariational\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
-      "File \u001b[0;32m~/work/cmdstanpy/cmdstanpy/cmdstanpy/model.py:1575\u001b[0m, in \u001b[0;36mCmdStanModel.variational\u001b[0;34m(self, data, seed, inits, output_dir, sig_figs, save_latent_dynamics, save_profile, algorithm, iter, grad_samples, elbo_samples, eta, adapt_engaged, adapt_iter, tol_rel_obj, eval_elbo, draws, require_converged, show_console, refresh, time_fmt, timeout, output_samples)\u001b[0m\n\u001b[1;32m   1573\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(re\u001b[38;5;241m.\u001b[39mfindall(pat, contents)) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m   1574\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m require_converged:\n\u001b[0;32m-> 1575\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m   1576\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThe algorithm may not have converged.\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1577\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mIf you would like to inspect the output, \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1578\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mre-call with require_converged=False\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1579\u001b[0m         )\n\u001b[1;32m   1580\u001b[0m     \u001b[38;5;66;03m# else:\u001b[39;00m\n\u001b[1;32m   1581\u001b[0m     get_logger()\u001b[38;5;241m.\u001b[39mwarning(\n\u001b[1;32m   1582\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1583\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThe algorithm may not have converged.\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1584\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mProceeding because require_converged is set to False\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1585\u001b[0m     )\n",
+      "File \u001b[0;32m~/work/cmdstanpy/cmdstanpy/cmdstanpy/model.py:1527\u001b[0m, in \u001b[0;36mCmdStanModel.variational\u001b[0;34m(self, data, seed, inits, output_dir, sig_figs, save_latent_dynamics, save_profile, algorithm, iter, grad_samples, elbo_samples, eta, adapt_engaged, adapt_iter, tol_rel_obj, eval_elbo, draws, require_converged, show_console, refresh, time_fmt, timeout, output_samples)\u001b[0m\n\u001b[1;32m   1525\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(re\u001b[38;5;241m.\u001b[39mfindall(pat, contents)) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m   1526\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m require_converged:\n\u001b[0;32m-> 1527\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m   1528\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThe algorithm may not have converged.\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1529\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mIf you would like to inspect the output, \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1530\u001b[0m             \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mre-call with require_converged=False\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m   1531\u001b[0m         )\n\u001b[1;32m   1532\u001b[0m     \u001b[38;5;66;03m# else:\u001b[39;00m\n\u001b[1;32m   1533\u001b[0m     get_logger()\u001b[38;5;241m.\u001b[39mwarning(\n\u001b[1;32m   1534\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1535\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mThe algorithm may not have converged.\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1536\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mProceeding because require_converged is set to False\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m   1537\u001b[0m     )\n",
       "\u001b[0;31mRuntimeError\u001b[0m: The algorithm may not have converged.\nIf you would like to inspect the output, re-call with require_converged=False"
      ]
     }
@@ -253,10 +245,10 @@
    "execution_count": 6,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:42:13.703755Z",
-     "iopub.status.busy": "2024-02-05T20:42:13.703551Z",
-     "iopub.status.idle": "2024-02-05T20:42:13.746622Z",
-     "shell.execute_reply": "2024-02-05T20:42:13.746094Z"
+     "iopub.execute_input": "2024-03-26T16:30:21.611786Z",
+     "iopub.status.busy": "2024-03-26T16:30:21.611575Z",
+     "iopub.status.idle": "2024-03-26T16:30:21.656310Z",
+     "shell.execute_reply": "2024-03-26T16:30:21.655745Z"
     }
    },
    "outputs": [
@@ -264,21 +256,21 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:42:13 - cmdstanpy - INFO - Chain [1] start processing\n"
+      "16:30:21 - cmdstanpy - INFO - Chain [1] start processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:42:13 - cmdstanpy - INFO - Chain [1] done processing\n"
+      "16:30:21 - cmdstanpy - INFO - Chain [1] done processing\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "20:42:13 - cmdstanpy - WARNING - The algorithm may not have converged.\n",
+      "16:30:21 - cmdstanpy - WARNING - The algorithm may not have converged.\n",
       "Proceeding because require_converged is set to False\n"
      ]
     }
@@ -299,10 +291,10 @@
    "execution_count": 7,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2024-02-05T20:42:13.749332Z",
-     "iopub.status.busy": "2024-02-05T20:42:13.748927Z",
-     "iopub.status.idle": "2024-02-05T20:42:13.756070Z",
-     "shell.execute_reply": "2024-02-05T20:42:13.755478Z"
+     "iopub.execute_input": "2024-03-26T16:30:21.659303Z",
+     "iopub.status.busy": "2024-03-26T16:30:21.658885Z",
+     "iopub.status.idle": "2024-03-26T16:30:21.665849Z",
+     "shell.execute_reply": "2024-03-26T16:30:21.665162Z"
     }
    },
    "outputs": [
@@ -312,8 +304,8 @@
        "OrderedDict([('lp__', 0.0),\n",
        "             ('log_p__', 0.0),\n",
        "             ('log_g__', 0.0),\n",
-       "             ('mu[1]', 0.00316325),\n",
-       "             ('mu[2]', 0.0245446)])"
+       "             ('mu[1]', -0.0227764),\n",
+       "             ('mu[2]', -0.057944)])"
       ]
      },
      "execution_count": 7,
diff --git a/docs/users-guide/hello_world.html b/docs/users-guide/hello_world.html
index e2ae5801..db22686e 100644
--- a/docs/users-guide/hello_world.html
+++ b/docs/users-guide/hello_world.html
@@ -6,7 +6,7 @@
     
     
 
-    “Hello, World!” — CmdStanPy 1.2.1 documentation
+    “Hello, World!” — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
@@ -443,22 +444,22 @@ 
    Accessing the results
 
    # access model variable by name
 In [9]: print(fit.stan_variable('theta'))
-[0.448643 0.176426 0.208806 ... 0.102241 0.145615 0.441178]
+[0.174379 0.142577 0.104175 ... 0.296568 0.275516 0.289409]
 
 In [10]: print(fit.draws_pd('theta')[:3])
       theta
-0  0.448643
-1  0.176426
-2  0.208806
+0  0.174379
+1  0.142577
+2  0.104175
 
 In [11]: print(fit.draws_xr('theta'))
-<xarray.Dataset>
+<xarray.Dataset> Size: 40kB
 Dimensions:  (draw: 1000, chain: 4)
 Coordinates:
-  * 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
+  * chain    (chain) int64 32B 1 2 3 4
+  * draw     (draw) int64 8kB 0 1 2 3 4 5 6 7 ... 993 994 995 996 997 998 999
 Data variables:
-    theta    (chain, draw) float64 0.4486 0.1764 0.2088 ... 0.1022 0.1456 0.4412
+    theta    (chain, draw) float64 32kB 0.1744 0.1426 0.1042 ... 0.2755 0.2894
 Attributes:
     stan_version:        2.34.1
     model:               bernoulli_model
@@ -489,17 +490,17 @@ 
    Accessing the resultsIn [15]: fit.draws_pd()
 Out[15]: 
       chain__  iter__  draw__  ...  divergent__  energy__     theta
-0         1.0     1.0     1.0  ...          0.0   7.87104  0.448643
-1         1.0     2.0     2.0  ...          0.0   8.25851  0.176426
-2         1.0     3.0     3.0  ...          0.0   6.91842  0.208806
-3         1.0     4.0     4.0  ...          0.0   6.79549  0.230222
-4         1.0     5.0     5.0  ...          0.0   6.89761  0.307075
+0         1.0     1.0     1.0  ...          0.0   6.96995  0.174379
+1         1.0     2.0     2.0  ...          0.0   7.23168  0.142577
+2         1.0     3.0     3.0  ...          0.0   8.29890  0.104175
+3         1.0     4.0     4.0  ...          0.0   8.29236  0.083123
+4         1.0     5.0     5.0  ...          0.0   8.59298  0.076468
 ...       ...     ...     ...  ...          ...       ...       ...
-3995      4.0   996.0  3996.0  ...          0.0   8.17578  0.151596
-3996      4.0   997.0  3997.0  ...          0.0   7.24072  0.149352
-3997      4.0   998.0  3998.0  ...          0.0   7.81204  0.102241
-3998      4.0   999.0  3999.0  ...          0.0   7.71005  0.145615
-3999      4.0  1000.0  4000.0  ...          0.0   8.61979  0.441178
+3995      4.0   996.0  3996.0  ...          0.0   7.11186  0.362054
+3996      4.0   997.0  3997.0  ...          0.0   7.09438  0.333609
+3997      4.0   998.0  3998.0  ...          0.0   6.90865  0.296568
+3998      4.0   999.0  3999.0  ...          0.0   6.79980  0.275516
+3999      4.0  1000.0  4000.0  ...          0.0   6.79844  0.289409
 
 [4000 rows x 11 columns]
 
    
@@ -511,13 +512,13 @@ 
    Accessing the resultsdiag_e
 
 In [17]: print(fit.metric)
-[[0.484622]
- [0.449072]
- [0.422025]
- [0.530255]]
+[[0.548827]
+ [0.618353]
+ [0.488154]
+ [0.506284]]
 
 In [18]: print(fit.step_size)
-[0.996862 0.790725 1.14549  0.969396]
+[0.916475 0.945805 0.890823 1.05791 ]
 
    
 
 
    The CmdStanMCMC object also provides access to metadata about the model and the sampler run.
    
@@ -525,7 +526,7 @@ 
    Accessing the resultsbernoulli_model
 
 In [20]: print(fit.metadata.cmdstan_config['seed'])
-38175
+5650
 
 
 
@@ -540,9 +541,9 @@ 
    CmdStan utilities:  
    In [21]: fit.summary()
 Out[21]: 
-           Mean      MCSE    StdDev  ...    N_Eff  N_Eff/s     R_hat
-lp__  -7.282030  0.019091  0.747046  ...  1531.26  31250.2  1.002320
-theta  0.249207  0.003292  0.120195  ...  1333.06  27205.2  0.999556
+           Mean      MCSE    StdDev  ...    N_Eff  N_Eff/s    R_hat
+lp__  -7.244140  0.016066  0.686744  ...  1827.16  45679.0  1.00054
+theta  0.249347  0.003168  0.116642  ...  1356.00  33900.0  1.00428
 
 [2 rows x 9 columns]
 
    
@@ -554,7 +555,7 @@ 
    CmdStan utilities:  diagnose() method runs this utility and prints the output to the console.
    
 
    In [22]: print(fit.diagnose())
-Processing csv files: /tmp/tmpld8wslo1/bernoulliozge2dfm/bernoulli-20240205204228_1.csv, /tmp/tmpld8wslo1/bernoulliozge2dfm/bernoulli-20240205204228_2.csv, /tmp/tmpld8wslo1/bernoulliozge2dfm/bernoulli-20240205204228_3.csv, /tmp/tmpld8wslo1/bernoulliozge2dfm/bernoulli-20240205204228_4.csv
+Processing csv files: /tmp/tmpgvv426mx/bernoullig33uprfe/bernoulli-20240326163037_1.csv, /tmp/tmpgvv426mx/bernoullig33uprfe/bernoulli-20240326163037_2.csv, /tmp/tmpgvv426mx/bernoullig33uprfe/bernoulli-20240326163037_3.csv, /tmp/tmpgvv426mx/bernoullig33uprfe/bernoulli-20240326163037_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 62709097..7f925524 100644
--- a/docs/users-guide/outputs.html
+++ b/docs/users-guide/outputs.html
@@ -6,7 +6,7 @@
     
     
 
-    Controlling Outputs — CmdStanPy 1.2.1 documentation
+    Controlling Outputs — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
@@ -306,15 +307,15 @@ 
    CSV File OutputsIn [7]: print(fit)
 CmdStanMCMC: model=bernoulli chains=4['method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
  csv_files:
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_1.csv
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_2.csv
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_3.csv
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_4.csv
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_1.csv
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_2.csv
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_3.csv
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_4.csv
  output_files:
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_0-stdout.txt
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_1-stdout.txt
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_2-stdout.txt
-	/tmp/tmpld8wslo1/bernoulli_zi120vj/bernoulli-20240205204228_3-stdout.txt
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_0-stdout.txt
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_1-stdout.txt
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_2-stdout.txt
+	/tmp/tmpgvv426mx/bernoulliigzvjuln/bernoulli-20240326163037_3-stdout.txt
 
    
 
    
 
    The output_dir argument is an optional argument which specifies
@@ -328,10 +329,10 @@ 
    CSV File OutputsINFO:cmdstanpy:CmdStan done processing.
 
 In [9]: !ls outputs/
-bernoulli-20240205204229_0-stdout.txt  bernoulli-20240205204229_2.csv
-bernoulli-20240205204229_1-stdout.txt  bernoulli-20240205204229_3-stdout.txt
-bernoulli-20240205204229_1.csv	       bernoulli-20240205204229_3.csv
-bernoulli-20240205204229_2-stdout.txt  bernoulli-20240205204229_4.csv
+bernoulli-20240326163037_0-stdout.txt  bernoulli-20240326163037_2.csv
+bernoulli-20240326163037_1-stdout.txt  bernoulli-20240326163037_3-stdout.txt
+bernoulli-20240326163037_1.csv	       bernoulli-20240326163037_3.csv
+bernoulli-20240326163037_2-stdout.txt  bernoulli-20240326163037_4.csv
 
 
 
    Alternatively, the save_csvfiles() function moves the CSV files
@@ -344,8 +345,8 @@ 
    CSV File OutputsIn [11]: fit.save_csvfiles(dir='some/path')
 
 In [12]: !ls some/path
-bernoulli-20240205204229_1.csv	bernoulli-20240205204229_3.csv
-bernoulli-20240205204229_2.csv	bernoulli-20240205204229_4.csv
+bernoulli-20240326163037_1.csv	bernoulli-20240326163037_3.csv
+bernoulli-20240326163037_2.csv	bernoulli-20240326163037_4.csv
 
 
 
@@ -359,9 +360,9 @@ 
    LoggingINFO:cmdstanpy:Chain [3] start processing
 INFO:cmdstanpy:Chain [4] start processing
 INFO:cmdstanpy:Chain [1] done processing
-INFO:cmdstanpy:Chain [2] done processing
-INFO:cmdstanpy:Chain [3] done processing
 INFO:cmdstanpy:Chain [4] done processing
+INFO:cmdstanpy:Chain [3] done processing
+INFO:cmdstanpy:Chain [2] done processing
 
 
 
    This output is managed through the built-in logging module. For example, it can be disabled entirely:
    
@@ -408,40 +409,40 @@ 
    Logging   ....:     for line in logs.readlines():
    ....:         print(line.strip())
    ....: 
-20:42:29 - cmdstanpy - DEBUG - cmd: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli info
+16:30:38 - cmdstanpy - DEBUG - cmd: /home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli info
 cwd: None
-20:42:29 - cmdstanpy - INFO - CmdStan start processing
-20:42:29 - cmdstanpy - DEBUG - idx 0
-20:42:29 - cmdstanpy - DEBUG - idx 1
-20:42:29 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
-20:42:29 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
-20:42:29 - cmdstanpy - DEBUG - idx 2
-20:42:29 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=2', 'random', 'seed=13203', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_2.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
-20:42:29 - cmdstanpy - DEBUG - idx 3
-20:42:29 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=13203', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
-20:42:29 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
-20:42:29 - cmdstanpy - INFO - Chain [2] start processing
-20:42:29 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
-20:42:29 - cmdstanpy - INFO - Chain [1] start processing
-20:42:29 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=3', 'random', 'seed=13203', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_3.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
-20:42:29 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=4', 'random', 'seed=13203', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_4.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
-20:42:29 - cmdstanpy - INFO - Chain [3] start processing
-20:42:29 - cmdstanpy - INFO - Chain [4] start processing
-20:42:29 - cmdstanpy - INFO - Chain [2] done processing
-20:42:29 - cmdstanpy - INFO - Chain [3] done processing
-20:42:29 - cmdstanpy - INFO - Chain [1] done processing
-20:42:29 - cmdstanpy - INFO - Chain [4] done processing
-20:42:29 - cmdstanpy - DEBUG - runset
+16:30:38 - cmdstanpy - INFO - CmdStan start processing
+16:30:38 - cmdstanpy - DEBUG - idx 0
+16:30:38 - cmdstanpy - DEBUG - idx 1
+16:30:38 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
+16:30:38 - cmdstanpy - DEBUG - idx 2
+16:30:38 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
+16:30:38 - cmdstanpy - DEBUG - idx 3
+16:30:38 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=23084', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
+16:30:38 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
+16:30:38 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=2', 'random', 'seed=23084', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_2.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
+16:30:38 - cmdstanpy - DEBUG - running CmdStan, num_threads: 1
+16:30:38 - cmdstanpy - INFO - Chain [1] start processing
+16:30:38 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=3', 'random', 'seed=23084', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_3.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
+16:30:38 - cmdstanpy - INFO - Chain [2] start processing
+16:30:38 - cmdstanpy - DEBUG - CmdStan args: ['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=4', 'random', 'seed=23084', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_4.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
+16:30:38 - cmdstanpy - INFO - Chain [3] start processing
+16:30:38 - cmdstanpy - INFO - Chain [4] start processing
+16:30:38 - cmdstanpy - INFO - Chain [1] done processing
+16:30:38 - cmdstanpy - INFO - Chain [2] done processing
+16:30:38 - cmdstanpy - INFO - Chain [3] done processing
+16:30:38 - cmdstanpy - INFO - Chain [4] done processing
+16:30:38 - 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=13203', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_1.csv', 'method=sample', 'algorithm=hmc', 'adapt', 'engaged=1']
+['/home/runner/work/cmdstanpy/cmdstanpy/docsrc/users-guide/examples/bernoulli', 'id=1', 'random', 'seed=23084', 'data', 'file=users-guide/examples/bernoulli.data.json', 'output', 'file=/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_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/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_1.csv
+/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_1.csv
 console_msgs (if any):
-/tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_0-stdout.txt
-20:42:29 - cmdstanpy - DEBUG - Chain 1 console:
+/tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_0-stdout.txt
+16:30:38 - cmdstanpy - DEBUG - Chain 1 console:
 method = sample (Default)
 sample
 num_samples = 1000 (Default)
@@ -473,9 +474,9 @@ 
    Loggingfile = users-guide/examples/bernoulli.data.json
 init = 2 (Default)
 random
-seed = 13203
+seed = 23084
 output
-file = /tmp/tmpld8wslo1/bernoulli8r5niwzl/bernoulli-20240205204229_1.csv
+file = /tmp/tmpgvv426mx/bernoulli1wek20la/bernoulli-20240326163038_1.csv
 diagnostic_file =  (Default)
 refresh = 100 (Default)
 sig_figs = -1 (Default)
@@ -484,8 +485,8 @@ 
    Loggingnum_threads = 1 (Default)
 
 
-Gradient evaluation took 1e-06 seconds
-1000 transitions using 10 leapfrog steps per transition would take 0.01 seconds.
+Gradient evaluation took 3e-06 seconds
+1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
 Adjust your expectations accordingly!
 
 
@@ -512,9 +513,9 @@ 
    LoggingIteration: 1900 / 2000 [ 95%]  (Sampling)
 Iteration: 2000 / 2000 [100%]  (Sampling)
 
-Elapsed Time: 0.005 seconds (Warm-up)
-0.014 seconds (Sampling)
-0.019 seconds (Total)
+Elapsed Time: 0.004 seconds (Warm-up)
+0.013 seconds (Sampling)
+0.017 seconds (Total)
 
 
 
diff --git a/docs/users-guide/overview.html b/docs/users-guide/overview.html
index e122aad9..ccbf4db6 100644
--- a/docs/users-guide/overview.html
+++ b/docs/users-guide/overview.html
@@ -6,7 +6,7 @@
     
     
 
-    Overview — CmdStanPy 1.2.1 documentation
+    Overview — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
diff --git a/docs/users-guide/workflow.html b/docs/users-guide/workflow.html
index 692e6d89..332cac28 100644
--- a/docs/users-guide/workflow.html
+++ b/docs/users-guide/workflow.html
@@ -6,7 +6,7 @@
     
     
 
-    CmdStanPy Workflow — CmdStanPy 1.2.1 documentation
+    CmdStanPy Workflow — CmdStanPy 1.2.2 documentation
     
     
 
@@ -38,6 +38,7 @@
     
     
     
+    
     
     
     
@@ -63,7 +64,7 @@
   
 
@@ -465,7 +466,7 @@ 
    Output dataCmdStanMCMC and CmdStanGQ return the sample contents
 in tabular form, see draws() and draws_pd().
 Similarly, the draws_xr() method returns the sample
-contents as an xarray.Dataset which is a mapping from variable names to their respective values.
    
+contents as an xarray.Dataset which is a mapping from variable names to their respective values.