Merge pull request #825 from stan-dev/2.0-more-deprecation-removals

2.0 more deprecation removals

Author: WardBrian

cmdstanpy/model.py

@@ -13,7 +13,7 @@
 from concurrent.futures import ThreadPoolExecutor
 from io import StringIO
 from multiprocessing import cpu_count
-from typing import Any, Callable, Iterable, Mapping, Optional, TypeVar, Union
+from typing import Any, Callable, Mapping, Optional, TypeVar, Union
 
 import numpy as np
 import pandas as pd
@@ -242,53 +242,6 @@ def src_info(self) -> dict[str, Any]:
             return {}
         return compilation.src_info(str(self.stan_file), self._stanc_options)
 
-    # TODO(2.0) remove
-    def format(
-        self,
-        overwrite_file: bool = False,
-        canonicalize: Union[bool, str, Iterable[str]] = False,
-        max_line_length: int = 78,
-        *,
-        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
-
-
-        :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.
-        """
-
-        get_logger().warning(
-            "CmdStanModel.format() is deprecated and will be "
-            "removed in the next major version.\n"
-            "Use cmdstanpy.format_stan_file() instead."
-        )
-
-        if self.stan_file is None:
-            raise ValueError("No Stan file found for this module")
-
-        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,
-        )
-
     def code(self) -> Optional[str]:
         """Return Stan program as a string."""
         if not self._stan_file:
@@ -517,9 +470,7 @@ def sample(
         save_warmup: bool = False,
         thin: Optional[int] = None,
         max_treedepth: Optional[int] = None,
-        metric: Union[
-            str, dict[str, Any], list[str], list[dict[str, Any]], None
-        ] = None,
+        metric: Optional[str] = None,
         step_size: Union[float, list[float], None] = None,
         adapt_engaged: bool = True,
         adapt_delta: Optional[float] = None,
@@ -845,27 +796,6 @@ def sample(
                             'Chain_id must be a non-negative integer value,'
                             ' found {}.'.format(chain_id)
                         )
-        if metric is not None and metric not in (
-            'diag',
-            'dense',
-            'unit_e',
-            'diag_e',
-            'dense_e',
-        ):
-            get_logger().warning(
-                "Providing anything other than metric type for"
-                " 'metric' is deprecated and will be removed"
-                " in the next major release."
-                " Please provide such information via"
-                " 'inv_metric' argument."
-            )
-            if inv_metric is not None:
-                raise ValueError(
-                    "Cannot provide both (deprecated) non-metric-type 'metric'"
-                    " argument and 'inv_metric' argument."
-                )
-            inv_metric = metric  # type: ignore # for backwards compatibility
-            metric = None
 
         if metric is None and inv_metric is not None:
             metric = try_deduce_metric_type(inv_metric)
@@ -908,7 +838,7 @@ def sample(
                 save_warmup=save_warmup,
                 thin=thin,
                 max_treedepth=max_treedepth,
-                metric_type=metric,  # type: ignore
+                metric_type=metric,
                 metric_file=cmdstan_metrics,
                 step_size=step_size,
                 adapt_engaged=adapt_engaged,
@@ -1037,8 +967,6 @@ def generate_quantities(
         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]:
         """
         Run CmdStan's generate_quantities method which runs the generated
@@ -1104,19 +1032,6 @@ def generate_quantities(
 
         :return: CmdStanGQ object
         """
-        # TODO(2.0): remove
-        if mcmc_sample is not None:
-            if previous_fit:
-                raise ValueError(
-                    "Cannot supply both 'previous_fit' and "
-                    "deprecated argument 'mcmc_sample'"
-                )
-            get_logger().warning(
-                "Argument name `mcmc_sample` is deprecated, please "
-                "rename to `previous_fit`."
-            )
-
-            previous_fit = mcmc_sample  # type: ignore
 
         if isinstance(previous_fit, (CmdStanMCMC, CmdStanMLE, CmdStanVB)):
             fit_object = previous_fit
@@ -1243,8 +1158,6 @@ def variational(
         refresh: Optional[int] = None,
         time_fmt: str = "%Y%m%d%H%M%S",
         timeout: Optional[float] = None,
-        *,
-        output_samples: Optional[int] = None,
     ) -> CmdStanVB:
         """
         Run CmdStan's variational inference algorithm to approximate
@@ -1342,19 +1255,6 @@ def variational(
 
         :return: CmdStanVB object
         """
-        # TODO(2.0): remove
-        if output_samples is not None:
-            if draws is not None:
-                raise ValueError(
-                    "Cannot supply both 'draws' and deprecated argument "
-                    "'output_samples'"
-                )
-            get_logger().warning(
-                "Argument name `output_samples` is deprecated, please "
-                "rename to `draws`."
-            )
-
-            draws = output_samples
 
         variational_args = VariationalArgs(
             algorithm=algorithm,

cmdstanpy/stanfit/mle.py

@@ -1,7 +1,7 @@
 """Container for the result of running optimization"""
 
 from collections import OrderedDict
-from typing import Optional, Union
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -77,9 +77,7 @@ def create_inits(
         """
         # pylint: disable=unused-argument
 
-        return {
-            name: np.array(val) for name, val in self.stan_variables().items()
-        }
+        return self.stan_variables()
 
     def __repr__(self) -> str:
         repr = 'CmdStanMLE: model={}{}'.format(
@@ -95,7 +93,7 @@ def __repr__(self) -> str:
             repr = '{} optimization failed to converge.'.format(repr)
         return repr
 
-    def __getattr__(self, attr: str) -> Union[np.ndarray, float]:
+    def __getattr__(self, attr: str) -> np.ndarray:
         """Synonymous with ``fit.stan_variable(attr)"""
         if attr.startswith("_"):
             raise AttributeError(f"Unknown variable name {attr}")
@@ -206,7 +204,7 @@ def stan_variable(
         *,
         inc_iterations: bool = False,
         warn: bool = True,
-    ) -> Union[np.ndarray, float]:
+    ) -> np.ndarray:
         """
         Return a numpy.ndarray which contains the estimates for the
         for the named Stan program variable where the dimensions of the
@@ -254,14 +252,6 @@ def stan_variable(
             out: np.ndarray = self._metadata.stan_vars[var].extract_reshape(
                 data
             )
-            # TODO(2.0) remove
-            if out.shape == () or out.shape == (1,):
-                get_logger().warning(
-                    "The default behavior of CmdStanMLE.stan_variable() "
-                    "will change in a future release to always return a "
-                    "numpy.ndarray, even for scalar variables."
-                )
-                return out.item()  # type: ignore
             return out
         except KeyError:
             # pylint: disable=raise-missing-from
@@ -273,7 +263,7 @@ def stan_variable(
 
     def stan_variables(
         self, inc_iterations: bool = False
-    ) -> dict[str, Union[np.ndarray, float]]:
+    ) -> dict[str, np.ndarray]:
         """
         Return a dictionary mapping Stan program variables names
         to the corresponding numpy.ndarray containing the inferred values.

cmdstanpy/stanfit/vb.py

@@ -8,7 +8,6 @@
 
 from cmdstanpy.cmdstan_args import Method
 from cmdstanpy.utils import stancsv
-from cmdstanpy.utils.logging import get_logger
 
 from .metadata import InferenceMetadata
 from .runset import RunSet
@@ -100,7 +99,7 @@ def __repr__(self) -> str:
         # TODO - diagnostic, profiling files
         return repr
 
-    def __getattr__(self, attr: str) -> Union[np.ndarray, float]:
+    def __getattr__(self, attr: str) -> np.ndarray:
         """Synonymous with ``fit.stan_variable(attr)"""
         if attr.startswith("_"):
             raise AttributeError(f"Unknown variable name {attr}")
@@ -163,9 +162,7 @@ def metadata(self) -> InferenceMetadata:
         """
         return self._metadata
 
-    def stan_variable(
-        self, var: str, *, mean: Optional[bool] = None
-    ) -> Union[np.ndarray, float]:
+    def stan_variable(self, var: str, *, mean: bool = False) -> np.ndarray:
         """
         Return a numpy.ndarray which contains the estimates for the
         for the named Stan program variable where the dimensions of the
@@ -188,8 +185,7 @@ def stan_variable(
         :param var: variable name
 
         :param mean: if True, return the variational mean. Otherwise,
-            return the variational sample.  The default behavior will
-            change in a future release to return the variational sample.
+            return the variational sample. Defaults to False.
 
         See Also
         --------
@@ -200,16 +196,7 @@ def stan_variable(
         CmdStanGQ.stan_variable
         CmdStanLaplace.stan_variable
         """
-        # TODO(2.0): remove None case, make default `False`
-        if mean is None:
-            get_logger().warning(
-                "The default behavior of CmdStanVB.stan_variable() "
-                "will change in a future release to return the "
-                "variational sample, rather than the mean.\n"
-                "To maintain the current behavior, pass the argument "
-                "mean=True"
-            )
-            mean = True
+
         if mean:
             draws = self._variational_mean
         else:
@@ -219,16 +206,7 @@ def stan_variable(
             out: np.ndarray = self._metadata.stan_vars[var].extract_reshape(
                 draws
             )
-            # TODO(2.0): remove
-            if out.shape == () or out.shape == (1,):
-                if mean:
-                    get_logger().warning(
-                        "The default behavior of "
-                        "CmdStanVB.stan_variable(mean=True) will change in a "
-                        "future release to always return a numpy.ndarray, even "
-                        "for scalar variables."
-                    )
-                return out.item()  # type: ignore
+
             return out
         except KeyError:
             # pylint: disable=raise-missing-from
@@ -238,9 +216,7 @@ def stan_variable(
                 + ", ".join(self._metadata.stan_vars.keys())
             )
 
-    def stan_variables(
-        self, *, mean: Optional[bool] = None
-    ) -> dict[str, Union[np.ndarray, float]]:
+    def stan_variables(self, *, mean: bool = False) -> dict[str, np.ndarray]:
         """
         Return a dictionary mapping Stan program variables names
         to the corresponding numpy.ndarray containing the inferred values.

test/test_compiler_opts.py test/test_compilation.pytest/test_compiler_opts.py renamed to test/test_compilation.py

@@ -1,12 +1,16 @@
 """Compiler options tests"""
 
+import contextlib
+import io
 import logging
 import os
-from test import check_present
+from test import check_present, raises_nested
+from unittest.mock import MagicMock, patch
 
 import pytest
 
-from cmdstanpy.compilation import CompilerOptions
+from cmdstanpy.compilation import CompilerOptions, format_stan_file
+from cmdstanpy.utils import cmdstan_version_before
 
 HERE = os.path.dirname(os.path.abspath(__file__))
 DATAFILES_PATH = os.path.join(HERE, 'data')
@@ -191,3 +195,50 @@ def test_user_header() -> None:
     )
     with pytest.raises(ValueError, match="Disagreement"):
         opts.validate()
+
+
+def test_model_format_options() -> None:
+    stan = os.path.join(DATAFILES_PATH, 'format_me.stan')
+
+    sys_stdout = io.StringIO()
+    with contextlib.redirect_stdout(sys_stdout):
+        format_stan_file(stan, max_line_length=10)
+    formatted = sys_stdout.getvalue()
+    assert len(formatted.splitlines()) > 11
+
+    sys_stdout = io.StringIO()
+    with contextlib.redirect_stdout(sys_stdout):
+        format_stan_file(stan, canonicalize='braces')
+    formatted = sys_stdout.getvalue()
+    assert formatted.count('{') == 3
+    assert formatted.count('(') == 4
+
+    sys_stdout = io.StringIO()
+    with contextlib.redirect_stdout(sys_stdout):
+        format_stan_file(stan, canonicalize=['parentheses'])
+    formatted = sys_stdout.getvalue()
+    assert formatted.count('{') == 1
+    assert formatted.count('(') == 1
+
+    sys_stdout = io.StringIO()
+    with contextlib.redirect_stdout(sys_stdout):
+        format_stan_file(stan, canonicalize=True)
+    formatted = sys_stdout.getvalue()
+    assert formatted.count('{') == 3
+    assert formatted.count('(') == 1
+
+
+@patch(
+    'cmdstanpy.utils.cmdstan.cmdstan_version',
+    MagicMock(return_value=(2, 27)),
+)
+def test_format_old_version() -> None:
+    assert cmdstan_version_before(2, 28)
+
+    stan = os.path.join(DATAFILES_PATH, 'format_me.stan')
+    with raises_nested(RuntimeError, r"--canonicalize"):
+        format_stan_file(stan, canonicalize='braces')
+    with raises_nested(RuntimeError, r"--max-line"):
+        format_stan_file(stan, max_line_length=88)
+
+    format_stan_file(stan, canonicalize=True)