cmdstanpy 1.3.0__tar.gz → 1.3.2__tar.gz

{cmdstanpy-1.3.0/cmdstanpy.egg-info → cmdstanpy-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cmdstanpy
-Version: 1.3.0
+Version: 1.3.2
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause
@@ -34,8 +34,8 @@ Requires-Dist: mypy; extra == "test"
 Requires-Dist: xarray; extra == "test"
 Requires-Dist: polars>=1.8.2; extra == "test"
 Provides-Extra: docs
-Requires-Dist: sphinx<6,>5; extra == "docs"
-Requires-Dist: pydata-sphinx-theme<0.9; extra == "docs"
+Requires-Dist: sphinx<9; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.17; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: ipykernel<7; extra == "docs"

cmdstanpy-1.3.2/cmdstanpy/_version.py

@@ -0,0 +1,3 @@
+"""PyPi Version"""
+
+__version__ = '1.3.2'

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/install_cxx_toolchain.py

@@ -33,16 +33,14 @@ IS_64BITS = sys.maxsize > 2**32
 
 def usage() -> None:
     """Print usage."""
-    print(
-        """Arguments:
+    print("""Arguments:
         -v (--version) :CmdStan version
         -d (--dir) : install directory
         -s (--silent) : install with /VERYSILENT instead of /SILENT for RTools
         -m (--no-make) : don't install mingw32-make (Windows RTools 4.0 only)
         --progress : flag, when specified show progress bar for RTools download
         -h (--help) : this message
-        """
-    )
+        """)
 
 
 def get_config(dir: str, silent: bool) -> list[str]:
@@ -244,11 +242,11 @@ def get_url(version: str) -> str:
         if version == '4.0':
             # pylint: disable=line-too-long
             if IS_64BITS:
-                url = 'https://cran.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe'  # noqa: disable=E501
+                url = 'https://cran-archive.r-project.org/bin/windows/Rtools/rtools40-x86_64.exe'  # noqa: disable=E501
             else:
-                url = 'https://cran.r-project.org/bin/windows/Rtools/rtools40-i686.exe'  # noqa: disable=E501
+                url = 'https://cran-archive.r-project.org/bin/windows/Rtools/rtools40-i686.exe'  # noqa: disable=E501
         elif version == '3.5':
-            url = 'https://cran.r-project.org/bin/windows/Rtools/Rtools35.exe'
+            url = 'https://cran-archive.r-project.org/bin/windows/Rtools/Rtools35.exe'  # noqa: disable=E501
     return url
 
 

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/model.py

@@ -55,6 +55,7 @@ from cmdstanpy.utils import (
     do_command,
     get_logger,
 )
+from cmdstanpy.utils.deprecation import deprecate_positional_args
 from cmdstanpy.utils.filesystem import (
     temp_inits,
     temp_metrics,
@@ -468,9 +469,11 @@ class CmdStanModel:
             user_header=self._compiler_options.user_header,
         )
 
+    @deprecate_positional_args(last_deprecated="jacobian")
     def optimize(
         self,
         data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
+        *,
         seed: Optional[int] = None,
         inits: Union[Mapping[str, Any], float, str, os.PathLike, None] = None,
         output_dir: OptionalPath = None,
@@ -492,7 +495,6 @@ class CmdStanModel:
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
         jacobian: bool = False,
-        # would be nice to move this further up, but that's a breaking change
     ) -> CmdStanMLE:
         """
         Run the specified CmdStan optimize algorithm to produce a
@@ -660,9 +662,11 @@ class CmdStanModel:
         return mle
 
     # pylint: disable=too-many-arguments
+    @deprecate_positional_args(last_deprecated="timeout")
     def sample(
         self,
         data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
+        *,
         chains: Optional[int] = None,
         parallel_chains: Optional[int] = None,
         threads_per_chain: Optional[int] = None,
@@ -693,14 +697,13 @@ class CmdStanModel:
         fixed_param: bool = False,
         output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
-        save_latent_dynamics: bool = False,
+        save_diagnostics: bool = False,
         save_profile: bool = False,
         show_progress: bool = True,
         show_console: bool = False,
         refresh: Optional[int] = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
-        *,
         force_one_process_per_chain: Optional[bool] = None,
         inv_metric: Union[
             str,
@@ -709,6 +712,7 @@ class CmdStanModel:
             list[Union[str, np.ndarray, Mapping[str, Any]]],
             None,
         ] = None,
+        save_latent_dynamics: Optional[bool] = None,
     ) -> CmdStanMCMC:
         """
         Run or more chains of the NUTS-HMC sampler to produce a set of draws
@@ -907,6 +911,13 @@ class CmdStanModel:
         if fixed_param is None:
             fixed_param = self._fixed_param
 
+        if save_latent_dynamics is not None:
+            get_logger().warning(
+                "Argument name `save_latent_dynamics` is deprecated, please "
+                "rename to `save_diagnostics`."
+            )
+            save_diagnostics = save_latent_dynamics  # type: ignore
+
         if chains is None:
             chains = 4
         if chains < 1:
@@ -1092,7 +1103,7 @@ class CmdStanModel:
                 inits=cmdstan_inits,
                 output_dir=output_dir,
                 sig_figs=sig_figs,
-                save_latent_dynamics=save_latent_dynamics,
+                save_latent_dynamics=save_diagnostics,
                 save_profile=save_profile,
                 method_args=sampler_args,
                 refresh=refresh,
@@ -1190,10 +1201,12 @@ class CmdStanModel:
             mcmc = CmdStanMCMC(runset)
         return mcmc
 
+    @deprecate_positional_args(last_deprecated="timeout")
     def generate_quantities(
         self,
         data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
         previous_fit: Union[Fit, list[str], None] = None,
+        *,
         seed: Optional[int] = None,
         gq_output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
@@ -1201,7 +1214,6 @@ class CmdStanModel:
         refresh: Optional[int] = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
-        *,
         mcmc_sample: Union[CmdStanMCMC, list[str], None] = None,
     ) -> CmdStanGQ[Fit]:
         """
@@ -1383,14 +1395,16 @@ class CmdStanModel:
             quantities = CmdStanGQ(runset=runset, previous_fit=fit_object)
         return quantities
 
+    @deprecate_positional_args(last_deprecated="timeout")
     def variational(
         self,
         data: Union[Mapping[str, Any], str, os.PathLike, None] = None,
+        *,
         seed: Optional[int] = None,
         inits: Optional[float] = None,
         output_dir: OptionalPath = None,
         sig_figs: Optional[int] = None,
-        save_latent_dynamics: bool = False,
+        save_diagnostics: bool = False,
         save_profile: bool = False,
         algorithm: Optional[str] = None,
         iter: Optional[int] = None,
@@ -1407,8 +1421,8 @@ class CmdStanModel:
         refresh: Optional[int] = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
-        *,
         output_samples: Optional[int] = None,
+        save_latent_dynamics: Optional[bool] = None,
     ) -> CmdStanVB:
         """
         Run CmdStan's variational inference algorithm to approximate
@@ -1520,6 +1534,13 @@ class CmdStanModel:
 
             draws = output_samples
 
+        if save_latent_dynamics is not None:
+            get_logger().warning(
+                "Argument name `save_latent_dynamics` is deprecated, please "
+                "rename to `save_diagnostics`."
+            )
+            save_diagnostics = save_latent_dynamics  # type: ignore
+
         variational_args = VariationalArgs(
             algorithm=algorithm,
             iter=iter,
@@ -1546,7 +1567,7 @@ class CmdStanModel:
                 inits=_inits,
                 output_dir=output_dir,
                 sig_figs=sig_figs,
-                save_latent_dynamics=save_latent_dynamics,
+                save_latent_dynamics=save_diagnostics,
                 save_profile=save_profile,
                 method_args=variational_args,
                 refresh=refresh,

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/progress.py

@@ -43,8 +43,7 @@ def wrap_callback(func):  # type: ignore
 
         try:
             return func(*args, **kwargs)
-        # pylint: disable=broad-except
-        except Exception as e:
+        except Exception as e:  # pylint: disable=broad-exception-caught
             _disable_progress(e)
             return callback
 

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/stanfit/gq.py

@@ -4,10 +4,10 @@ generate quantities (GQ) method
 """
 
 from collections import Counter
+from collections.abc import Hashable
 from typing import (
     Any,
     Generic,
-    Hashable,
     MutableMapping,
     NoReturn,
     Optional,

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/stanfit/laplace.py

@@ -2,7 +2,8 @@
 Container for the result of running a laplace approximation.
 """
 
-from typing import Any, Hashable, MutableMapping, Optional, Union
+from collections.abc import Hashable
+from typing import Any, MutableMapping, Optional, Union
 
 import numpy as np
 import pandas as pd

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/stanfit/mcmc.py

@@ -4,8 +4,9 @@ Container for the result of running the sample (MCMC) method
 
 import math
 import os
+from collections.abc import Hashable
 from io import StringIO
-from typing import Any, Hashable, MutableMapping, Optional, Sequence, Union
+from typing import Any, MutableMapping, Optional, Sequence, Union
 
 import numpy as np
 import pandas as pd

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/stanfit/runset.py

@@ -162,23 +162,29 @@ class RunSet:
             return self._args.compose_command(
                 idx,
                 csv_file=self.csv_files[idx],
-                diagnostic_file=self.diagnostic_files[idx]
-                if self._args.save_latent_dynamics
-                else None,
-                profile_file=self.profile_files[idx]
-                if self._args.save_profile
-                else None,
+                diagnostic_file=(
+                    self.diagnostic_files[idx]
+                    if self._args.save_latent_dynamics
+                    else None
+                ),
+                profile_file=(
+                    self.profile_files[idx] if self._args.save_profile else None
+                ),
             )
         else:
             return self._args.compose_command(
                 idx,
                 csv_file=self.file_path('.csv'),
-                diagnostic_file=self.file_path(".csv", extra="-diagnostic")
-                if self._args.save_latent_dynamics
-                else None,
-                profile_file=self.file_path(".csv", extra="-profile")
-                if self._args.save_profile
-                else None,
+                diagnostic_file=(
+                    self.file_path(".csv", extra="-diagnostic")
+                    if self._args.save_latent_dynamics
+                    else None
+                ),
+                profile_file=(
+                    self.file_path(".csv", extra="-profile")
+                    if self._args.save_profile
+                    else None
+                ),
             )
 
     @property

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/utils/__init__.py

@@ -42,7 +42,7 @@ def show_versions(output: bool = True) -> str:
 
     deps_info = []
     try:
-        (sysname, _, release, _, machine, processor) = platform.uname()
+        sysname, _, release, _, machine, processor = platform.uname()
         deps_info.extend(
             [
                 ("python", sys.version),
@@ -57,15 +57,13 @@ def show_versions(output: bool = True) -> str:
                 ("LOCALE", f"{locale.getlocale()}"),
             ]
         )
-    # pylint: disable=broad-except
-    except Exception:
+    except Exception:  # pylint: disable=broad-exception-caught
         pass
 
     try:
         deps_info.append(('cmdstan_folder', cmdstan_path()))
         deps_info.append(('cmdstan', str(cmdstan_version())))
-    # pylint: disable=broad-except
-    except Exception:
+    except Exception:  # pylint: disable=broad-exception-caught
         deps_info.append(('cmdstan', 'NOT FOUND'))
 
     deps = ['cmdstanpy', 'pandas', 'xarray', 'tqdm', 'numpy']

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/utils/cmdstan.py

@@ -14,6 +14,7 @@ from tqdm.auto import tqdm
 from cmdstanpy import _DOT_CMDSTAN
 
 from .. import progress as progbar
+from .deprecation import deprecate_positional_args
 from .logging import get_logger
 
 EXTENSION = '.exe' if platform.system() == 'Windows' else ''
@@ -433,15 +434,16 @@ def cxx_toolchain_path(
     return compiler_path, tool_path
 
 
+@deprecate_positional_args(last_deprecated="cores")
 def install_cmdstan(
     version: Optional[str] = None,
+    *,
     dir: Optional[str] = None,
     overwrite: bool = False,
     compiler: bool = False,
     progress: bool = False,
     verbose: bool = False,
     cores: int = 1,
-    *,
     interactive: bool = False,
 ) -> bool:
     """
@@ -523,8 +525,7 @@ def install_cmdstan(
                 cores=cores,
             )
         run_install(args)
-    # pylint: disable=broad-except
-    except Exception as e:
+    except Exception as e:  # pylint: disable=broad-exception-caught
         logger.warning('CmdStan installation failed.\n%s', str(e))
         return False
 

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy/utils/data_munging.py

@@ -2,7 +2,8 @@
 Common functions for reshaping numpy arrays
 """
 
-from typing import Hashable, MutableMapping
+from collections.abc import Hashable
+from typing import MutableMapping
 
 import numpy as np
 import stanio

cmdstanpy-1.3.2/cmdstanpy/utils/deprecation.py

@@ -0,0 +1,58 @@
+"""
+Temporary helpers for deprecations in the 1.x series.
+"""
+
+import functools
+import inspect
+from typing import Any, Callable, TypeVar
+
+from .logging import get_logger
+
+F = TypeVar('F', bound=Callable[..., Any])
+
+
+def deprecate_positional_args(last_deprecated: str) -> Callable[[F], F]:
+    """
+    Allow keyword-only arguments up to and including ``last_deprecated``
+    to still be passed by position, logging a deprecation warning.
+
+    Positional use of these arguments becomes an error in CmdStanPy 2.0.
+    """
+
+    def decorator(func: F) -> F:
+        params = inspect.signature(func).parameters.values()
+        n_positional = sum(
+            p.kind == inspect.Parameter.POSITIONAL_OR_KEYWORD for p in params
+        )
+        kw_only = [
+            p.name for p in params if p.kind == inspect.Parameter.KEYWORD_ONLY
+        ]
+        deprecated = kw_only[: kw_only.index(last_deprecated) + 1]
+
+        @functools.wraps(func)
+        def wrapper(*args: Any, **kwargs: Any) -> Any:
+            extra = args[n_positional:]
+            if not extra or len(extra) > len(deprecated):
+                # either nothing to do, or let Python raise its usual error
+                return func(*args, **kwargs)
+            names = deprecated[: len(extra)]
+            for name in names:
+                if name in kwargs:
+                    raise TypeError(
+                        f"{func.__qualname__}() got multiple values for "
+                        f"argument '{name}'"
+                    )
+            quoted = ", ".join("`" + name + "`" for name in names)
+            get_logger().warning(
+                "Passing %s to %s() by position is deprecated and will raise "
+                "an error in CmdStanPy 2.0. Please pass them as keyword "
+                "arguments instead.",
+                quoted,
+                func.__qualname__,
+            )
+            kwargs.update(zip(names, extra))
+            return func(*args[:n_positional], **kwargs)
+
+        return wrapper  # type: ignore[return-value]
+
+    return decorator

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2/cmdstanpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cmdstanpy
-Version: 1.3.0
+Version: 1.3.2
 Summary: Python interface to CmdStan
 Author: Stan Dev Team
 License: BSD-3-Clause
@@ -34,8 +34,8 @@ Requires-Dist: mypy; extra == "test"
 Requires-Dist: xarray; extra == "test"
 Requires-Dist: polars>=1.8.2; extra == "test"
 Provides-Extra: docs
-Requires-Dist: sphinx<6,>5; extra == "docs"
-Requires-Dist: pydata-sphinx-theme<0.9; extra == "docs"
+Requires-Dist: sphinx<9; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.17; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: ipython; extra == "docs"
 Requires-Dist: ipykernel<7; extra == "docs"

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy.egg-info/SOURCES.txt

@@ -30,6 +30,7 @@ cmdstanpy/utils/__init__.py
 cmdstanpy/utils/cmdstan.py
 cmdstanpy/utils/command.py
 cmdstanpy/utils/data_munging.py
+cmdstanpy/utils/deprecation.py
 cmdstanpy/utils/filesystem.py
 cmdstanpy/utils/json.py
 cmdstanpy/utils/logging.py
@@ -38,6 +39,7 @@ test/test_cmdstan_args.py
 test/test_compiler_opts.py
 test/test_compliance.py
 test/test_cxx_installation.py
+test/test_deprecations.py
 test/test_generate_quantities.py
 test/test_install_cmdstan.py
 test/test_laplace.py

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/cmdstanpy.egg-info/requires.txt

@@ -8,8 +8,8 @@ xarray
 polars>=1.8.2
 
 [docs]
-sphinx<6,>5
-pydata-sphinx-theme<0.9
+sphinx<9
+pydata-sphinx-theme<0.17
 nbsphinx
 ipython
 ipykernel<7

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/pyproject.toml

@@ -52,8 +52,8 @@ test = [
     "polars>=1.8.2"
 ]
 docs = [
-    "sphinx>5,<6",
-    "pydata-sphinx-theme<0.9",
+    "sphinx<9",
+    "pydata-sphinx-theme<0.17",
     "nbsphinx",
     "ipython",
     "ipykernel<7",

cmdstanpy-1.3.2/test/test_deprecations.py

@@ -0,0 +1,140 @@
+"""Tests for deprecated positional arguments to public functions"""
+
+# positional calls below are deliberate
+# pylint: disable=too-many-function-args
+
+import inspect
+import logging
+import os
+import re
+import sys
+from test import check_present
+from typing import Any, Callable
+from unittest import mock
+
+import pytest
+
+from cmdstanpy.model import CmdStanModel
+from cmdstanpy.utils import install_cmdstan
+from cmdstanpy.utils.deprecation import deprecate_positional_args
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+DATAFILES_PATH = os.path.join(HERE, 'data')
+
+
+class Dummy:
+    @deprecate_positional_args(last_deprecated="c")
+    def method(
+        self, a: Any = None, *, b: Any = None, c: Any = None, d: Any = None
+    ) -> tuple[Any, Any, Any, Any]:
+        return a, b, c, d
+
+
+def test_keywords_do_not_warn(caplog: pytest.LogCaptureFixture) -> None:
+    with caplog.at_level(logging.WARNING):
+        assert Dummy().method(1, b=2, c=3, d=4) == (1, 2, 3, 4)
+        assert Dummy().method() == (None, None, None, None)
+    assert not caplog.records
+
+
+def test_positional_maps_to_keywords(caplog: pytest.LogCaptureFixture) -> None:
+    with caplog.at_level(logging.WARNING):
+        assert Dummy().method(1, 2, 3, d=4) == (1, 2, 3, 4)
+    check_present(
+        caplog,
+        (
+            'cmdstanpy',
+            'WARNING',
+            re.compile(r"Passing `b`, `c` to Dummy\.method\(\) by position"),
+        ),
+    )
+
+
+def test_positional_and_keyword_collision() -> None:
+    with pytest.raises(TypeError, match="multiple values for argument 'b'"):
+        Dummy().method(1, 2, b=3)
+
+
+def test_too_many_positional() -> None:
+    # `d` was never positional, so it must not be filled by position
+    with pytest.raises(TypeError):
+        Dummy().method(1, 2, 3, 4)
+
+
+def test_signature_is_keyword_only() -> None:
+    params = inspect.signature(Dummy.method).parameters
+    assert params['a'].kind == inspect.Parameter.POSITIONAL_OR_KEYWORD
+    assert params['b'].kind == inspect.Parameter.KEYWORD_ONLY
+
+
+@pytest.mark.parametrize(
+    'func, positional, last_deprecated',
+    [
+        (CmdStanModel.sample, ['self', 'data'], 'timeout'),
+        (CmdStanModel.optimize, ['self', 'data'], 'jacobian'),
+        (CmdStanModel.variational, ['self', 'data'], 'timeout'),
+        (
+            CmdStanModel.generate_quantities,
+            ['self', 'data', 'previous_fit'],
+            'timeout',
+        ),
+        (install_cmdstan, ['version'], 'cores'),
+    ],
+)
+def test_public_signatures(
+    func: Callable[..., Any], positional: list[str], last_deprecated: str
+) -> None:
+    params = inspect.signature(func).parameters
+    kinds = {name: p.kind for name, p in params.items()}
+    assert [
+        n
+        for n, k in kinds.items()
+        if k == inspect.Parameter.POSITIONAL_OR_KEYWORD
+    ] == positional
+    # guards against a rename silently shifting the positional mapping
+    assert kinds[last_deprecated] == inspect.Parameter.KEYWORD_ONLY
+
+
+def test_optimize_positional_seed(caplog: pytest.LogCaptureFixture) -> None:
+    stan = os.path.join(DATAFILES_PATH, 'bernoulli.stan')
+    jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
+    model = CmdStanModel(stan_file=stan)
+    with caplog.at_level(logging.WARNING):
+        mle_pos = model.optimize(jdata, 1234)
+    check_present(
+        caplog,
+        (
+            'cmdstanpy',
+            'WARNING',
+            re.compile(r"Passing `seed` to CmdStanModel\.optimize\(\)"),
+        ),
+    )
+    mle_kw = model.optimize(jdata, seed=1234)
+    assert mle_pos.metadata.cmdstan_config['seed'] == 1234
+    assert mle_pos.optimized_params_dict == mle_kw.optimized_params_dict
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 11),
+    reason="mock.patch resolves `cmdstanpy.install_cmdstan` to the "
+    "re-exported function, not the module, before Python 3.11",
+)
+def test_install_cmdstan_positional(caplog: pytest.LogCaptureFixture) -> None:
+    # stop right after argument handling; nothing is downloaded
+    with mock.patch(
+        'cmdstanpy.install_cmdstan.run_install', side_effect=RuntimeError
+    ) as run_install:
+        with caplog.at_level(logging.WARNING):
+            install_cmdstan("2.36.0", "some_dir", True)
+    check_present(
+        caplog,
+        (
+            'cmdstanpy',
+            'WARNING',
+            re.compile(r"Passing `dir`, `overwrite` to install_cmdstan\(\)"),
+        ),
+    )
+    settings = run_install.call_args.args[0]
+    assert settings.version == "2.36.0"
+    assert settings.dir == "some_dir"
+    assert settings.overwrite

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/test/test_generate_quantities.py

@@ -565,7 +565,7 @@ def test_from_optimization() -> None:
     assert os.path.exists(csv_file)
 
     assert bern_gqs.draws().shape == (1, 1, 10)
-    assert bern_gqs.draws(inc_sample=True).shape == (1, 1, 12)
+    assert bern_gqs.draws(inc_sample=True).shape == (1, 1, 13)
 
     # draws_pd()
     assert bern_gqs.draws_pd().shape == (1, 13)
@@ -610,18 +610,18 @@ def test_opt_save_iterations(caplog: pytest.LogCaptureFixture):
     assert bern_gqs.draws(inc_warmup=True, inc_sample=True).shape == (
         iters,
         1,
-        12,
+        13,
     )
 
     assert bern_gqs.draws(concat_chains=True).shape == (1, 10)
-    assert bern_gqs.draws(concat_chains=True, inc_sample=True).shape == (1, 12)
+    assert bern_gqs.draws(concat_chains=True, inc_sample=True).shape == (1, 13)
     assert bern_gqs.draws(concat_chains=True, inc_warmup=True).shape == (
         iters,
         10,
     )
     assert bern_gqs.draws(
         concat_chains=True, inc_warmup=True, inc_sample=True
-    ).shape == (iters, 12)
+    ).shape == (iters, 13)
 
     # stan_variable
     theta = bern_gqs.stan_variable(var='theta')

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/test/test_logging.py

@@ -1,6 +1,7 @@
 """Logging control tests"""
 
 import logging
+
 import cmdstanpy
 
 

{cmdstanpy-1.3.0 → cmdstanpy-1.3.2}/test/test_optimize.py

@@ -92,13 +92,13 @@ def test_rosenbrock(caplog: pytest.LogCaptureFixture) -> None:
     assert 'CmdStanMLE: model=rosenbrock' in repr(mle)
     assert 'method=optimize' in repr(mle)
     assert mle.converged
-    assert mle.column_names == ('lp__', 'x', 'y')
+    assert mle.column_names == ('lp__', 'converged__', 'x', 'y')
     np.testing.assert_almost_equal(mle.stan_variable('x'), 1, decimal=3)
     np.testing.assert_almost_equal(mle.stan_variable('y'), 1, decimal=3)
     np.testing.assert_almost_equal(
         mle.optimized_params_pd['x'][0], 1, decimal=3
     )
-    np.testing.assert_almost_equal(mle.optimized_params_np[1], 1, decimal=3)
+    np.testing.assert_almost_equal(mle.optimized_params_np[2], 1, decimal=3)
     np.testing.assert_almost_equal(mle.optimized_params_dict['x'], 1, decimal=3)
     with caplog.at_level(logging.WARNING):
         assert mle.optimized_iterations_np is None
@@ -128,8 +128,8 @@ def test_rosenbrock(caplog: pytest.LogCaptureFixture) -> None:
     np.testing.assert_almost_equal(mle.stan_variable('x'), 1, decimal=3)
     np.testing.assert_almost_equal(mle.stan_variable('y'), 1, decimal=3)
 
-    assert mle.optimized_params_np.shape == (3,)
-    np.testing.assert_almost_equal(mle.optimized_params_np[1], 1, decimal=3)
+    assert mle.optimized_params_np.shape == (4,)
+    np.testing.assert_almost_equal(mle.optimized_params_np[2], 1, decimal=3)
     np.testing.assert_almost_equal(
         mle.optimized_params_pd['x'][0], 1, decimal=3
     )
@@ -140,7 +140,7 @@ def test_rosenbrock(caplog: pytest.LogCaptureFixture) -> None:
         mle.optimized_iterations_np[0, 1]
         != mle.optimized_iterations_np[last_iter, 1]
     )
-    for i in range(3):
+    for i in range(4):
         assert (
             mle.optimized_params_np[i]
             == mle.optimized_iterations_np[last_iter, i]
@@ -159,7 +159,7 @@ def test_eight_schools(caplog: pytest.LogCaptureFixture) -> None:
     assert 'method=optimize' in repr(mle)
     assert not mle.converged
     with caplog.at_level(logging.WARNING):
-        assert mle.optimized_params_pd.shape == (1, 11)
+        assert mle.optimized_params_pd.shape == (1, 12)
     check_present(
         caplog,
         (
@@ -294,15 +294,15 @@ def test_optimize_good() -> None:
     # test numpy output
     assert isinstance(mle.optimized_params_np, np.ndarray)
     np.testing.assert_almost_equal(mle.optimized_params_np[0], -5, decimal=2)
-    np.testing.assert_almost_equal(mle.optimized_params_np[1], 0.2, decimal=3)
+    np.testing.assert_almost_equal(mle.optimized_params_np[2], 0.2, decimal=3)
 
     # test pandas output
     assert mle.optimized_params_np[0] == mle.optimized_params_pd['lp__'][0]
-    assert mle.optimized_params_np[1] == mle.optimized_params_pd['theta'][0]
+    assert mle.optimized_params_np[2] == mle.optimized_params_pd['theta'][0]
 
     # test dict output
     assert mle.optimized_params_np[0] == mle.optimized_params_dict['lp__']
-    assert mle.optimized_params_np[1] == mle.optimized_params_dict['theta']
+    assert mle.optimized_params_np[2] == mle.optimized_params_dict['theta']
 
 
 def test_negative_parameter_values() -> None:
@@ -530,14 +530,14 @@ def test_optimize_good_dict() -> None:
     )
     # test numpy output
     np.testing.assert_almost_equal(mle.optimized_params_np[0], -5, decimal=2)
-    np.testing.assert_almost_equal(mle.optimized_params_np[1], 0.2, decimal=3)
+    np.testing.assert_almost_equal(mle.optimized_params_np[2], 0.2, decimal=3)
 
 
 def test_optimize_rosenbrock() -> None:
     stan = os.path.join(DATAFILES_PATH, 'optimize', 'rosenbrock.stan')
     rose_model = CmdStanModel(stan_file=stan)
     mle = rose_model.optimize(seed=1239812093, inits=None, algorithm='BFGS')
-    assert mle.column_names == ('lp__', 'x', 'y')
+    assert mle.column_names == ('lp__', 'converged__', 'x', 'y')
     np.testing.assert_almost_equal(mle.optimized_params_dict['x'], 1, decimal=3)
     np.testing.assert_almost_equal(mle.optimized_params_dict['y'], 1, decimal=3)
 
@@ -546,7 +546,7 @@ def test_optimize_no_data() -> None:
     stan = os.path.join(DATAFILES_PATH, 'optimize', 'no_data.stan')
     rose_model = CmdStanModel(stan_file=stan)
     mle = rose_model.optimize(seed=1239812093)
-    assert mle.column_names == ('lp__', 'a')
+    assert mle.column_names == ('lp__', 'converged__', 'a')
     np.testing.assert_almost_equal(mle.optimized_params_dict['a'], 0, decimal=3)
 
 
@@ -600,7 +600,7 @@ def test_exe_only() -> None:
     jdata = os.path.join(DATAFILES_PATH, 'bernoulli.data.json')
     mle = bern2_model.optimize(data=jdata)
     assert mle.optimized_params_np[0] == mle.optimized_params_dict['lp__']
-    assert mle.optimized_params_np[1] == mle.optimized_params_dict['theta']
+    assert mle.optimized_params_np[2] == mle.optimized_params_dict['theta']
 
 
 def test_complex_output() -> None:

cmdstanpy-1.3.0/cmdstanpy/_version.py

@@ -1,3 +0,0 @@
-"""PyPi Version"""
-
-__version__ = '1.3.0'