cmdstanpy 1.2.1__tar.gz → 1.2.3__tar.gz

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/MANIFEST.in

@@ -1,6 +1,4 @@
 # This file is used to include extra files in source distributions.
-# (Source distributions are generated by running `python setup.py sdist`.)
 
-include requirements*.txt
 include LICENSE.md
 include cmdstanpy/py.typed

{cmdstanpy-1.2.1/cmdstanpy.egg-info → cmdstanpy-1.2.3}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.1
+Version: 1.2.3
 Summary: Python interface to CmdStan
-Home-page: https://github.com/stan-dev/cmdstanpy
 Author: Stan Dev Team
-License: UNKNOWN
-Platform: UNKNOWN
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/stan-dev/cmdstanpy
+Project-URL: Bug Tracker, https://github.com/stan-dev/cmdstanpy/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
@@ -16,10 +16,31 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: pandas
+Requires-Dist: numpy>=1.21
+Requires-Dist: tqdm
+Requires-Dist: stanio<2.0.0,>=0.4.0
 Provides-Extra: all
-Provides-Extra: tests
+Requires-Dist: xarray; extra == "all"
+Provides-Extra: test
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: pylint; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-order; extra == "test"
+Requires-Dist: mypy; extra == "test"
+Requires-Dist: xarray; extra == "test"
 Provides-Extra: docs
-License-File: LICENSE.md
+Requires-Dist: sphinx<6,>5; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.9; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Requires-Dist: ipywidgets; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: xarray; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
 
 # CmdStanPy
 
@@ -79,5 +100,3 @@ fit = model.sample(chains=4, data=data_file)
 # summarize the results (wraps CmdStan `bin/stansummary`):
 fit.summary()
 ```
-
-

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/__init__.py

@@ -22,7 +22,7 @@ atexit.register(_cleanup_tmpdir)
 
 
 from ._version import __version__  # noqa
-from .compilation import compile_stan_file
+from .compilation import compile_stan_file, format_stan_file
 from .install_cmdstan import rebuild_cmdstan
 from .model import CmdStanModel
 from .stanfit import (
@@ -50,6 +50,7 @@ __all__ = [
     'set_make_env',
     'install_cmdstan',
     'compile_stan_file',
+    'format_stan_file',
     'CmdStanMCMC',
     'CmdStanMLE',
     'CmdStanGQ',

cmdstanpy-1.2.3/cmdstanpy/_version.py

@@ -0,0 +1,3 @@
+"""PyPi Version"""
+
+__version__ = '1.2.3'

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/cmdstan_args.py

@@ -930,6 +930,7 @@ class CmdStanArgs:
                 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))

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/compilation.py

@@ -9,11 +9,17 @@ import platform
 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
 
@@ -476,3 +482,98 @@ def compile_stan_file(
                 f"Failed to compile Stan model '{src}'. " f"Console:\n{console}"
             )
         return str(exe_target)
+
+
+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

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/install_cmdstan.py

@@ -523,6 +523,8 @@ def retrieve_version(version: str, progress: bool = True) -> None:
         first = tar.next()
         if first is not None:
             top_dir = first.name
+        else:
+            top_dir = ''
         cmdstan_dir = f'cmdstan-{version}'
         if top_dir != cmdstan_dir:
             raise CmdStanInstallError(

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/install_cxx_toolchain.py

@@ -235,8 +235,10 @@ def get_toolchain_name() -> str:
     return ''
 
 
+# TODO(2.0): drop 3.5 support
 def get_url(version: str) -> str:
     """Return URL for toolchain."""
+    url = ''
     if platform.system() == 'Windows':
         if version == '4.0':
             # pylint: disable=line-too-long
@@ -277,6 +279,8 @@ def run_rtools_install(args: Dict[str, Any]) -> None:
 
     if 'verbose' in args:
         verbose = args['verbose']
+    else:
+        verbose = False
 
     install_dir = args['dir']
     if install_dir is None:

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/model.py

@@ -10,7 +10,6 @@ import tempfile
 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 (
@@ -57,9 +56,7 @@ from cmdstanpy.stanfit import (
     from_csv,
 )
 from cmdstanpy.utils import (
-    EXTENSION,
     cmdstan_path,
-    cmdstan_version,
     cmdstan_version_before,
     do_command,
     get_logger,
@@ -320,6 +317,7 @@ class CmdStanModel:
             return {}
         return compilation.src_info(str(self.stan_file), self._compiler_options)
 
+    # TODO(2.0) remove
     def format(
         self,
         overwrite_file: bool = False,
@@ -329,6 +327,8 @@ class CmdStanModel:
         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
 
@@ -345,72 +345,24 @@ class CmdStanModel:
             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]]:
@@ -1635,6 +1587,7 @@ class CmdStanModel:
         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.
@@ -1737,6 +1690,10 @@ class CmdStanModel:
         :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
@@ -1763,6 +1720,17 @@ class CmdStanModel:
                 "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

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/stanfit/pathfinder.py

@@ -214,8 +214,10 @@ class CmdStanPathfinder:
         """
         return (  # type: ignore
             self._metadata.cmdstan_config.get("num_paths", 4) > 1
-            and self._metadata.cmdstan_config.get('psis_resample', 1) == 1
-            and self._metadata.cmdstan_config.get('calculate_lp', 1) == 1
+            and self._metadata.cmdstan_config.get('psis_resample', 1)
+            in (1, 'true')
+            and self._metadata.cmdstan_config.get('calculate_lp', 1)
+            in (1, 'true')
         )
 
     def save_csvfiles(self, dir: Optional[str] = None) -> None:

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/stanfit/runset.py

@@ -61,18 +61,26 @@ class RunSet:
         self._base_outfile = (
             f'{args.model_name}-{datetime.now().strftime(time_fmt)}'
         )
-        # per-process console messages
+        # per-process outputs
         self._stdout_files = [''] * self._num_procs
+        self._profile_files = [''] * self._num_procs  # optional
         if one_process_per_chain:
             for i in range(chains):
                 self._stdout_files[i] = self.file_path("-stdout.txt", id=i)
+                if args.save_profile:
+                    self._profile_files[i] = self.file_path(
+                        ".csv", extra="-profile", id=chain_ids[i]
+                    )
         else:
             self._stdout_files[0] = self.file_path("-stdout.txt")
+            if args.save_profile:
+                self._profile_files[0] = self.file_path(
+                    ".csv", extra="-profile"
+                )
 
         # per-chain output files
         self._csv_files: List[str] = [''] * chains
         self._diagnostic_files = [''] * chains  # optional
-        self._profile_files = [''] * chains  # optional
 
         if chains == 1:
             self._csv_files[0] = self.file_path(".csv")
@@ -80,10 +88,6 @@ class RunSet:
                 self._diagnostic_files[0] = self.file_path(
                     ".csv", extra="-diagnostic"
                 )
-            if args.save_profile:
-                self._profile_files[0] = self.file_path(
-                    ".csv", extra="-profile"
-                )
         else:
             for i in range(chains):
                 self._csv_files[i] = self.file_path(".csv", id=chain_ids[i])
@@ -91,10 +95,6 @@ class RunSet:
                     self._diagnostic_files[i] = self.file_path(
                         ".csv", extra="-diagnostic", id=chain_ids[i]
                     )
-                if args.save_profile:
-                    self._profile_files[i] = self.file_path(
-                        ".csv", extra="-profile", id=chain_ids[i]
-                    )
 
     def __repr__(self) -> str:
         repr = 'RunSet: chains={}, chain_ids={}, num_processes={}'.format(

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy/utils/stancsv.py

@@ -52,7 +52,7 @@ def check_sampler_csv(
             )
         )
     if save_warmup:
-        if not ('save_warmup' in meta and meta['save_warmup'] == 1):
+        if not ('save_warmup' in meta and meta['save_warmup'] in (1, 'true')):
             raise ValueError(
                 'bad Stan CSV file {}, '
                 'config error, expected save_warmup = 1'.format(path)
@@ -116,6 +116,7 @@ def scan_optimize_csv(path: str, save_iters: bool = False) -> Dict[str, Any]:
                 all_iters[i, :] = [float(x) for x in xs]
             if i == iters - 1:
                 mle: np.ndarray = np.array(xs, dtype=float)
+    # pylint: disable=possibly-used-before-assignment
     dict['mle'] = mle
     if save_iters:
         dict['all_iters'] = all_iters

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3/cmdstanpy.egg-info}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: cmdstanpy
-Version: 1.2.1
+Version: 1.2.3
 Summary: Python interface to CmdStan
-Home-page: https://github.com/stan-dev/cmdstanpy
 Author: Stan Dev Team
-License: UNKNOWN
-Platform: UNKNOWN
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/stan-dev/cmdstanpy
+Project-URL: Bug Tracker, https://github.com/stan-dev/cmdstanpy/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
@@ -16,10 +16,31 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: pandas
+Requires-Dist: numpy>=1.21
+Requires-Dist: tqdm
+Requires-Dist: stanio<2.0.0,>=0.4.0
 Provides-Extra: all
-Provides-Extra: tests
+Requires-Dist: xarray; extra == "all"
+Provides-Extra: test
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: pylint; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-order; extra == "test"
+Requires-Dist: mypy; extra == "test"
+Requires-Dist: xarray; extra == "test"
 Provides-Extra: docs
-License-File: LICENSE.md
+Requires-Dist: sphinx<6,>5; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.9; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Requires-Dist: ipywidgets; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: xarray; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
 
 # CmdStanPy
 
@@ -79,5 +100,3 @@ fit = model.sample(chains=4, data=data_file)
 # summarize the results (wraps CmdStan `bin/stansummary`):
 fit.summary()
 ```
-
-

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy.egg-info/SOURCES.txt

@@ -2,10 +2,6 @@ LICENSE.md
 MANIFEST.in
 README.md
 pyproject.toml
-requirements-optional.txt
-requirements-test.txt
-requirements.txt
-setup.py
 cmdstanpy/__init__.py
 cmdstanpy/_version.py
 cmdstanpy/cmdstan_args.py

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/cmdstanpy.egg-info/entry_points.txt

@@ -1,4 +1,3 @@
 [console_scripts]
 install_cmdstan = cmdstanpy.install_cmdstan:__main__
 install_cxx_toolchain = cmdstanpy.install_cxx_toolchain:__main__
-

cmdstanpy-1.2.3/cmdstanpy.egg-info/requires.txt

@@ -0,0 +1,27 @@
+pandas
+numpy>=1.21
+tqdm
+stanio<2.0.0,>=0.4.0
+
+[all]
+xarray
+
+[docs]
+sphinx<6,>5
+pydata-sphinx-theme<0.9
+nbsphinx
+ipython
+ipykernel
+ipywidgets
+sphinx-copybutton
+xarray
+matplotlib
+
+[test]
+flake8
+pylint
+pytest
+pytest-cov
+pytest-order
+mypy
+xarray

cmdstanpy-1.2.3/pyproject.toml

@@ -0,0 +1,95 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cmdstanpy"
+description = "Python interface to CmdStan"
+readme = "README.md"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Stan Dev Team" }]
+requires-python = ">=3.8"
+dependencies = ["pandas", "numpy>=1.21", "tqdm", "stanio>=0.4.0,<2.0.0"]
+dynamic = ["version"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/stan-dev/cmdstanpy"
+"Bug Tracker" = "https://github.com/stan-dev/cmdstanpy/issues"
+
+[project.scripts]
+install_cmdstan = "cmdstanpy.install_cmdstan:__main__"
+install_cxx_toolchain = "cmdstanpy.install_cxx_toolchain:__main__"
+
+[tool.setuptools.dynamic]
+version = { attr = "cmdstanpy._version.__version__" }
+
+[tool.setuptools]
+packages = ["cmdstanpy", "cmdstanpy.stanfit", "cmdstanpy.utils"]
+
+[tool.setuptools.package-data]
+"cmdstanpy" = ["py.typed"]
+
+[project.optional-dependencies]
+all = ["xarray"]
+test = [
+    "flake8",
+    "pylint",
+    "pytest",
+    "pytest-cov",
+    "pytest-order",
+    "mypy",
+    "xarray",
+]
+docs = [
+    "sphinx>5,<6",
+    "pydata-sphinx-theme<0.9",
+    "nbsphinx",
+    "ipython",
+    "ipykernel",
+    "ipywidgets",
+    "sphinx-copybutton",
+    "xarray",
+    "matplotlib",
+]
+
+
+[tool.black]
+line-length = 80
+skip-string-normalization = true
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+ensure_newline_before_comments = true
+line_length = 80
+
+[tool.mypy]
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+no_implicit_optional = true
+# disallow_any_generics = true # disabled due to issues with numpy
+warn_return_any = true
+# warn_unused_ignores = true # can't be run on CI due to windows having different ctypes
+check_untyped_defs = true
+warn_redundant_casts = true
+strict_equality = true
+disallow_untyped_calls = true
+
+[[tool.mypy.overrides]]
+module = ['tqdm.auto', 'pandas']
+ignore_missing_imports = true
+
+[tool.coverage.run]
+source = ["cmdstanpy"]

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/test/test_optimize.py

@@ -262,12 +262,13 @@ def test_variables_3d() -> None:
     )
     vars_iters = multidim_mle_iters.stan_variables(inc_iterations=True)
     assert len(vars_iters) == len(multidim_mle_iters.metadata.stan_vars)
+    assert 'frac_60' in vars_iters
+    n_iter = vars_iters['frac_60'].shape[0]
+    assert n_iter > 1
     assert 'y_rep' in vars_iters
-    assert vars_iters['y_rep'].shape == (8, 5, 4, 3)
+    assert vars_iters['y_rep'].shape == (n_iter, 5, 4, 3)
     assert 'beta' in vars_iters
-    assert vars_iters['beta'].shape == (8, 2)
-    assert 'frac_60' in vars_iters
-    assert vars_iters['frac_60'].shape == (8,)
+    assert vars_iters['beta'].shape == (n_iter, 2)
 
 
 def test_optimize_good() -> None:

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/test/test_pathfinder.py

@@ -2,6 +2,8 @@
     Tests for the Pathfinder method.
 """
 
+import contextlib
+from io import StringIO
 from pathlib import Path
 
 import numpy as np
@@ -129,6 +131,26 @@ def test_pathfinder_init_sampling():
     assert fit.draws().shape == (1000, 4, 9)
 
 
+def test_inits_for_pathfinder():
+    stan = DATAFILES_PATH / 'bernoulli.stan'
+    bern_model = cmdstanpy.CmdStanModel(stan_file=stan)
+    jdata = str(DATAFILES_PATH / 'bernoulli.data.json')
+    bern_model.pathfinder(
+        jdata, inits=[{"theta": 0.1}, {"theta": 0.9}], num_paths=2
+    )
+
+    # second path is initialized too large!
+    with contextlib.redirect_stdout(StringIO()) as captured:
+        bern_model.pathfinder(
+            jdata,
+            inits=[{"theta": 0.1}, {"theta": 1.1}],
+            num_paths=2,
+            show_console=True,
+        )
+
+    assert "Bounded variable is 1.1" in captured.getvalue()
+
+
 def test_pathfinder_no_psis():
     stan = DATAFILES_PATH / 'bernoulli.stan'
     bern_model = cmdstanpy.CmdStanModel(stan_file=stan)
@@ -152,3 +174,20 @@ def test_pathfinder_no_lp_calc():
     n_lp_nan = np.sum(np.isnan(pathfinder.method_variables()['lp__']))
     assert n_lp_nan < 4000  # some lp still calculated during pathfinder
     assert n_lp_nan > 3000  # but most are not
+
+
+def test_pathfinder_threads():
+    stan = DATAFILES_PATH / 'bernoulli.stan'
+    bern_model = cmdstanpy.CmdStanModel(stan_file=stan)
+    jdata = str(DATAFILES_PATH / 'bernoulli.data.json')
+
+    bern_model.pathfinder(data=jdata, num_threads=1)
+
+    with pytest.raises(ValueError, match="STAN_THREADS"):
+        bern_model.pathfinder(data=jdata, num_threads=4)
+
+    bern_model = cmdstanpy.CmdStanModel(
+        stan_file=stan, cpp_options={'STAN_THREADS': True}, force_compile=True
+    )
+    pathfinder = bern_model.pathfinder(data=jdata, num_threads=4)
+    assert pathfinder.draws().shape == (1000, 3)

{cmdstanpy-1.2.1 → cmdstanpy-1.2.3}/test/test_sample.py

@@ -55,7 +55,7 @@ BERNOULLI_COLS = SAMPLER_STATE + ['theta']
 )
 def test_bernoulli_good(stanfile: str):
     stan = os.path.join(DATAFILES_PATH, stanfile)
-    bern_model = CmdStanModel(stan_file=stan)
+    bern_model = CmdStanModel(stan_file=stan, force_compile=True)
 
     jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
     bern_fit = bern_model.sample(
@@ -74,6 +74,8 @@ def test_bernoulli_good(stanfile: str):
 
     for i in range(bern_fit.runset.chains):
         csv_file = bern_fit.runset.csv_files[i]
+        # NB: This will fail if STAN_THREADS is enabled
+        # due to sampling only producing 1 stdout file in that case
         stdout_file = bern_fit.runset.stdout_files[i]
         assert os.path.exists(csv_file)
         assert os.path.exists(stdout_file)
@@ -1746,33 +1748,36 @@ def test_save_latent_dynamics() -> None:
 
 def test_save_profile() -> None:
     stan = os.path.join(DATAFILES_PATH, 'profile_likelihood.stan')
-    profile_model = CmdStanModel(stan_file=stan)
+    profile_model = CmdStanModel(
+        stan_file=stan, cpp_options={"STAN_THREADS": '1'}, force_compile=True
+    )
+
     profile_fit = profile_model.sample(
         chains=2,
         parallel_chains=2,
+        force_one_process_per_chain=True,
         seed=12345,
         iter_warmup=100,
         iter_sampling=200,
         save_profile=True,
     )
-    for i in range(profile_fit.runset.chains):
-        profile_file = profile_fit.runset.profile_files[i]
+    assert len(profile_fit.runset.profile_files) == 2
+    for profile_file in profile_fit.runset.profile_files:
         assert os.path.exists(profile_file)
 
     profile_fit = profile_model.sample(
         chains=2,
         parallel_chains=2,
+        force_one_process_per_chain=False,
         seed=12345,
+        iter_warmup=100,
         iter_sampling=200,
-        save_latent_dynamics=True,
         save_profile=True,
     )
 
-    for i in range(profile_fit.runset.chains):
-        profile_file = profile_fit.runset.profile_files[i]
+    assert len(profile_fit.runset.profile_files) == 1
+    for profile_file in profile_fit.runset.profile_files:
         assert os.path.exists(profile_file)
-        diagnostics_file = profile_fit.runset.diagnostic_files[i]
-        assert os.path.exists(diagnostics_file)
 
 
 def test_xarray_draws() -> None:

cmdstanpy-1.2.1/cmdstanpy/_version.py

@@ -1,3 +0,0 @@
-"""PyPi Version"""
-
-__version__ = '1.2.1'

cmdstanpy-1.2.1/cmdstanpy.egg-info/requires.txt

@@ -1,24 +0,0 @@
-pandas
-numpy>=1.21
-tqdm
-stanio~=0.3.0
-
-[all]
-xarray
-
-[docs]
-sphinx
-sphinx-gallery
-sphinx_rtd_theme
-numpydoc
-matplotlib
-
-[tests]
-flake8
-pylint
-pytest
-pytest-cov
-pytest-order
-mypy
-tqdm
-xarray

cmdstanpy-1.2.1/pyproject.toml

@@ -1,30 +0,0 @@
-[tool.black]
-line-length = 80
-skip-string-normalization = true
-
-[tool.isort]
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-ensure_newline_before_comments = true
-line_length = 80
-
-[tool.mypy]
-disallow_untyped_defs = true
-disallow_incomplete_defs = true
-no_implicit_optional = true
-# disallow_any_generics = true # disabled due to issues with numpy
-warn_return_any = true
-# warn_unused_ignores = true # can't be run on CI due to windows having different ctypes
-check_untyped_defs = true
-warn_redundant_casts = true
-strict_equality = true
-disallow_untyped_calls = true
-
-[[tool.mypy.overrides]]
-module = [
-    'tqdm.auto',
-    'pandas',
-    ]
-ignore_missing_imports = true

cmdstanpy-1.2.1/requirements-optional.txt

@@ -1 +0,0 @@
-xarray

cmdstanpy-1.2.1/requirements-test.txt

@@ -1,8 +0,0 @@
-flake8
-pylint
-pytest
-pytest-cov
-pytest-order
-mypy
-tqdm
-xarray

cmdstanpy-1.2.1/requirements.txt

@@ -1,4 +0,0 @@
-pandas
-numpy>=1.21
-tqdm
-stanio~=0.3.0

cmdstanpy-1.2.1/setup.py

@@ -1,90 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import re
-from typing import List
-
-import setuptools
-
-HERE = os.path.dirname(__file__)
-
-
-def readme_contents() -> str:
-    with open(os.path.join(HERE, 'README.md'), 'r') as fd:
-        src = fd.read()
-    return src
-
-
-def requirements() -> List[str]:
-    with open(os.path.join(HERE, 'requirements.txt'), 'r') as fd:
-        src = fd.read()
-    return src.splitlines()
-
-
-def requirements_test() -> List[str]:
-    with open(os.path.join(HERE, 'requirements-test.txt'), 'r') as fd:
-        src = fd.read()
-    return src.splitlines()
-
-
-def requirements_optional() -> List[str]:
-    with open(os.path.join(HERE, 'requirements-optional.txt'), 'r') as fd:
-        src = fd.read()
-    return src.splitlines()
-
-
-def get_version() -> str:
-    version_file = open(os.path.join('cmdstanpy', '_version.py'))
-    version_contents = version_file.read()
-    return re.search("__version__ = '(.*?)'", version_contents).group(1)
-
-
-_classifiers = """
-Programming Language :: Python :: 3
-License :: OSI Approved :: BSD License
-Operating System :: OS Independent
-Development Status :: 5 - Production/Stable
-Intended Audience :: Science/Research
-Natural Language :: English
-Programming Language :: Python
-Topic :: Scientific/Engineering :: Information Analysis
-"""
-
-INSTALL_REQUIRES = requirements()
-
-EXTRAS_REQUIRE = {
-    'all': requirements_optional(),
-    'tests': requirements_test(),
-    'docs': [
-        'sphinx',
-        'sphinx-gallery',
-        'sphinx_rtd_theme',
-        'numpydoc',
-        'matplotlib',
-    ],
-}
-
-setuptools.setup(
-    name='cmdstanpy',
-    version=get_version(),
-    description='Python interface to CmdStan',
-    long_description=readme_contents(),
-    long_description_content_type="text/markdown",
-    author='Stan Dev Team',
-    url='https://github.com/stan-dev/cmdstanpy',
-    license_files=['LICENSE.md'],
-    packages=['cmdstanpy', 'cmdstanpy.stanfit', 'cmdstanpy.utils'],
-    package_data={
-        'cmdstanpy': ['py.typed'],
-    },
-    entry_points={
-        'console_scripts': [
-            'install_cmdstan=cmdstanpy.install_cmdstan:__main__',
-            'install_cxx_toolchain=cmdstanpy.install_cxx_toolchain:__main__',
-        ]
-    },
-    install_requires=INSTALL_REQUIRES,
-    python_requires='>=3.8',
-    extras_require=EXTRAS_REQUIRE,
-    classifiers=_classifiers.strip().split('\n'),
-)