Merge upstream/develop

Author: amas0

.github/workflows/main.yml

@@ -68,11 +68,11 @@ jobs:
         run: python -m pip freeze
 
       - name: Run flake8, pylint, mypy
-        if: matrix.python-version == '3.11'
+        if: matrix.python-version == '3.14'
         run: |
           flake8 cmdstanpy test
           pylint -v cmdstanpy test
-          mypy cmdstanpy
+          mypy cmdstanpy test
 
       - name: CmdStan installation cacheing
         id: cache-cmdstan

.pre-commit-config.yaml

@@ -23,7 +23,6 @@ repos:
     rev: v1.5.0
     hooks:
       - id: mypy
-        exclude: ^test/
         additional_dependencies: [ numpy >= 1.22]
   # local uses the user-installed pylint, this allows dependency checking
   - repo: local

CONTRIBUTING.md

@@ -19,7 +19,7 @@ We welcome contributions!  Contributions should follow the general outlines of t
 
 * The GitHub repo organization follows the gitflow model described by Vincent Driessen in the blog post ["A successful Git branching model."](https://nvie.com/posts/a-successful-git-branching-model/).  The main developer branch is `develop`; it should always be runnable.
 
-* Unit tests must be runnable under both the [unittest](https://docs.python.org/3/library/unittest.html#module-unittest) and [PyTest](https://docs.pytest.org/en/stable/) frameworks.
+* Unit tests must be runnable under the [PyTest](https://docs.pytest.org/en/stable/) framework, and must pass against the latest release of [CmdStan](https://github.com/stan-dev/cmdstan).
 
 * Both [PyLint](https://www.pylint.org) and [Flake8](https://flake8.pycqa.org/en/latest/) are used to check code style and formatting according to rules in https://github.com/stan-dev/cmdstanpy/blob/develop/.pylintrc  and https://github.com/stan-dev/cmdstanpy/blob/a6e09190af555aa6d05993d630ebf39a3d4bb867/.travis.yml#L30. Code is formatted with [isort](https://pycqa.github.io/isort/) and [black](https://black.readthedocs.io/en/stable/).
 

cmdstanpy/cmdstan_args.py

@@ -643,7 +643,7 @@ def __init__(
             | PathfinderArgs
         ),
         data: Mapping[str, Any] | str | None = None,
-        seed: int | list[int] | None = None,
+        seed: int | np.integer | list[int] | list[np.integer] | None = None,
         inits: int | float | str | list[str] | None = None,
         output_dir: OptionalPath = None,
         sig_figs: int | None = None,

cmdstanpy/install_cmdstan.py

@@ -29,9 +29,10 @@
 import urllib.error
 import urllib.request
 from collections import OrderedDict
+from functools import cached_property
 from pathlib import Path
 from time import sleep
-from typing import TYPE_CHECKING, Any, Callable
+from typing import Any, Callable
 
 from tqdm.auto import tqdm
 
@@ -47,18 +48,6 @@
 
 from . import progress as progbar
 
-if sys.version_info >= (3, 8) or TYPE_CHECKING:
-    # mypy only knows about the new built-in cached_property
-    from functools import cached_property
-else:
-    # on older Python versions, this is the recommended
-    # way to get the same effect
-    from functools import lru_cache
-
-    def cached_property(fun):
-        return property(lru_cache(maxsize=None)(fun))
-
-
 try:
     # on MacOS and Linux, importing this
     # improves the UX of the input() function

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, Mapping, TypeVar
+from typing import Any, Callable, Mapping, Sequence, TypeVar
 
 import numpy as np
 import pandas as pd
@@ -461,8 +461,7 @@ def sample(
             Mapping[str, Any]
             | float
             | str
-            | list[str]
-            | list[Mapping[str, Any]]
+            | Sequence[str | Mapping[str, Any]]
             | None
         ) = None,
         iter_warmup: int | None = None,
@@ -493,7 +492,7 @@ def sample(
             str
             | np.ndarray
             | Mapping[str, Any]
-            | list[str | np.ndarray | Mapping[str, Any]]
+            | Sequence[str | np.ndarray | Mapping[str, Any]]
             | None
         ) = None,
     ) -> CmdStanMCMC:
@@ -1360,7 +1359,13 @@ def pathfinder(
         calculate_lp: bool = True,
         # arguments standard to all methods
         seed: int | None = None,
-        inits: dict[str, float] | float | str | os.PathLike | None = None,
+        inits: (
+            Mapping[str, Any]
+            | float
+            | str
+            | Sequence[str | Mapping[str, Any]]
+            | None
+        ) = None,
         output_dir: OptionalPath = None,
         sig_figs: int | None = None,
         save_profile: bool = False,

cmdstanpy/stanfit/__init__.py

@@ -252,7 +252,7 @@ def from_csv(
             mode: CmdStanMLE = from_csv(
                 config_dict['mode'],  # type: ignore
                 method='optimize',
-            )  # type: ignore
+            )
             return CmdStanLaplace(runset, mode=mode)
         elif config_dict['method'] == 'pathfinder':
             pathfinder_args = PathfinderArgs(

cmdstanpy/stanfit/mcmc.py

@@ -348,7 +348,7 @@ def _validate_csv_files(self) -> dict[str, Any]:
                     save_warmup=self._save_warmup,
                     thin=self._thin,
                 )
-                self._chain_time.append(dzero['time'])  # type: ignore
+                self._chain_time.append(dzero['time'])
                 if not self._is_fixed_param:
                     self._divergences[i] = dzero['ct_divergences']
                     self._max_treedepths[i] = dzero['ct_max_treedepth']
@@ -360,7 +360,7 @@ def _validate_csv_files(self) -> dict[str, Any]:
                     save_warmup=self._save_warmup,
                     thin=self._thin,
                 )
-                self._chain_time.append(drest['time'])  # type: ignore
+                self._chain_time.append(drest['time'])
                 for key in dzero:
                     # check args that matter for parsing, plus name, version
                     if (

cmdstanpy/stanfit/pathfinder.py

@@ -206,7 +206,7 @@ def is_resampled(self) -> bool:
         Returns True if the draws were resampled from several Pathfinder
         approximations, False otherwise.
         """
-        return (  # type: ignore
+        return (
             self._metadata.cmdstan_config.get("num_paths", 4) > 1
             and self._metadata.cmdstan_config.get('psis_resample', 1)
             in (1, 'true')

cmdstanpy/utils/__init__.py

@@ -80,7 +80,7 @@ def show_versions(output: bool = True) -> str:
             deps_info.append((module, None))
         else:
             try:
-                ver = mod.__version__  # type: ignore
+                ver = mod.__version__
                 deps_info.append((module, ver))
             # pylint: disable=broad-except
             except Exception: