Bump version for release (#683)

* Remove git install from testing env and deps

* Fix statespace fixture scope

* Python 3.12 linting

* Add arviz dependency

* Bump preliz pin

* move pymc out of pip

* Bump action versions

* Remove scikit-learn dependency

* Remove pytensor pin

* use windows-2022 instance for test job

* pin micromamba version

Author: jessegrabowski

.github/workflows/pypi.yml

@@ -12,10 +12,10 @@ jobs:
     name: build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405  # v6.2.0
         with:
           python-version: "3.12"
       - name: Build the sdist and the wheel
@@ -41,7 +41,7 @@ jobs:
               echo "Checking import and version number (on release)"
               venv-bdist/bin/python -c "import pymc_extras as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else pmx.__version__; print(pmx.__version__)"
               cd ..
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
         with:
           name: artifact
           path: dist/*
@@ -58,8 +58,8 @@ jobs:
       # write id-token is necessary for trusted publishing (OIDC)
       id-token: write
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c  # v8.0.1
         with:
           name: artifact
           path: dist
-      - uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b  # v1.14.0

.github/workflows/test.yml

@@ -43,8 +43,8 @@ jobs:
       run:
         shell: bash -leo pipefail {0}
     steps:
-      - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476  # v3.0.0
         with:
           environment-file: conda-envs/environment-test.yml
           create-args: >-
@@ -62,7 +62,7 @@ jobs:
         run: |
           python -m pytest --color=yes -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2  # v6.0.0
         with:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }}
@@ -89,11 +89,13 @@ jobs:
       run:
         shell: cmd /C call {0}
     steps:
-      - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
+      - uses: mamba-org/setup-micromamba@d7c9bd84e824b79d2af72a2d4196c7f4300d3476  # v3.0.0
         with:
           environment-file: conda-envs/environment-test.yml
-          micromamba-version: "latest"
+          # Pinned: micromamba 2.6.1-0 ships a Windows binary with a missing DLL
+          # dependency that breaks GitHub-hosted runners (STATUS_DLL_NOT_FOUND).
+          micromamba-version: "2.6.0-0"
           create-args: >-
             python=${{matrix.python-version}}
           environment-name: pymc-extras-test
@@ -110,7 +112,7 @@ jobs:
         run: >-
           python -m pytest --color=yes -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2  # v6.0.0
         with:
           env_vars: TEST_SUBSET
           name: ${{ matrix.os }}

conda-envs/environment-test.yml

@@ -4,7 +4,7 @@ channels:
 - nodefaults
 dependencies:
   - scikit-learn
-  - better-optimize>=0.3.2
+  - better-optimize>=0.4.1
   - dask<2025.1.1
   - xhistogram
   - statsmodels
@@ -13,9 +13,9 @@ dependencies:
   - pytest-cov
   - pydantic>=2.0.0
   - h5netcdf
+  - pymc>=6.0,<7.0
   - pip
   - pip:
       - jax
       - blackjax
-      - pymc @ git+https://github.com/pymc-devs/pymc.git
-      - preliz @ git+https://github.com/arviz-devs/preliz.git
+      - preliz>=0.25

pymc_extras/inference/pathfinder/pathfinder.py

@@ -24,7 +24,7 @@
 from collections.abc import Callable, Iterator
 from dataclasses import asdict, dataclass, field, replace
 from enum import Enum, auto
-from typing import Any, Literal, Self, TypeAlias
+from typing import Any, Literal, Self
 
 import numpy as np
 import pymc as pm
@@ -79,7 +79,7 @@
 REGULARISATION_TERM = 1e-8
 DEFAULT_LINKER = "cvm_nogc"
 
-SinglePathfinderFn: TypeAlias = Callable[[int], "PathfinderResult"]
+type SinglePathfinderFn = Callable[[int], "PathfinderResult"]
 
 
 def get_jaxified_logp_of_ravel_inputs(model: Model, jacobian: bool = True) -> Callable:

pymc_extras/linearmodel.py

@@ -2,7 +2,16 @@
 import pandas as pd
 import pymc as pm
 
-from sklearn.base import BaseEstimator
+# If scikit-learn is available, inherit from BaseEstimator for sklearn-pipeline interop
+# (Pipeline, TransformedTargetRegressor, get_params). Without it, fall back to a stub
+# so LinearModel still works as a standalone Bayesian model.
+try:
+    from sklearn.base import BaseEstimator
+except ImportError:
+
+    class BaseEstimator:
+        pass
+
 
 from pymc_extras.model_builder import ModelBuilder
 

pymc_extras/prior.py

@@ -90,7 +90,7 @@ def custom_transform(x):
 from functools import partial
 from inspect import signature
 from numbers import Number
-from typing import TYPE_CHECKING, Any, Protocol, TypeAlias, runtime_checkable
+from typing import TYPE_CHECKING, Any, Protocol, runtime_checkable
 
 import numpy as np
 import pymc as pm
@@ -111,7 +111,7 @@ def custom_transform(x):
     from pytensor.tensor import TensorLike
     from pytensor.xtensor.type import XTensorVariable
 
-    XTensorLike: TypeAlias = TensorLike | DataArray
+    type XTensorLike = TensorLike | DataArray
 
 
 class UnsupportedShapeError(Exception):

pyproject.toml

@@ -12,9 +12,9 @@ classifiers = [
   "Development Status :: 5 - Production/Stable",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "License :: OSI Approved :: Apache Software License",
   "Intended Audience :: Science/Research",
   "Topic :: Scientific/Engineering",
@@ -34,11 +34,11 @@ keywords = [
 license = {file = "LICENSE"}
 dynamic = ["version"]  # specify the version in the __init__.py file
 dependencies = [
-  "pymc@git+https://github.com/pymc-devs/pymc.git",
-  "scikit-learn",
-  "better-optimize>=0.3.1",
+  "pymc>=6.0,<7.0",
+  "arviz>=1.1",
+  "better-optimize>=0.4.1,<1.0",
   "pydantic>=2.0.0",
-  "preliz>=0.20.0",
+  "preliz>=0.25.0",
 ]
 
 [project.optional-dependencies]
@@ -131,7 +131,7 @@ exclude_lines = [
 
 [tool.ruff]
 line-length = 100
-target-version = "py311"
+target-version = "py312"
 
 [tool.ruff.format]
 docstring-code-format = true

tests/statespace/core/test_statespace.py

@@ -36,7 +36,7 @@
 floatX = pytensor.config.floatX
 nile = load_nile_test_data()
 ALL_SAMPLE_OUTPUTS = MATRIX_NAMES + FILTER_OUTPUT_NAMES + SMOOTHER_OUTPUT_NAMES
-mock_pymc_sample = pytest.fixture(scope="session")(mock_sample_setup_and_teardown)
+mock_pymc_sample = pytest.fixture(scope="module")(mock_sample_setup_and_teardown)
 
 
 def make_statespace_mod(k_endog, k_states, k_posdef, filter_type, verbose=False, data_info=None):
@@ -393,7 +393,7 @@ def pymc_mod_time_varying(ss_mod_time_varying, rng):
     return m
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata(pymc_mod, rng, mock_pymc_sample):
     with pymc_mod:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -403,7 +403,7 @@ def idata(pymc_mod, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_exog(exog_pymc_mod, rng, mock_pymc_sample):
     with exog_pymc_mod:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -412,7 +412,7 @@ def idata_exog(exog_pymc_mod, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_exog_mv(exog_pymc_mod_mv, rng, mock_pymc_sample):
     with exog_pymc_mod_mv:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -421,7 +421,7 @@ def idata_exog_mv(exog_pymc_mod_mv, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_no_exog(pymc_mod_no_exog, rng, mock_pymc_sample):
     with pymc_mod_no_exog:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -430,7 +430,7 @@ def idata_no_exog(pymc_mod_no_exog, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_no_exog_mv(pymc_mod_no_exog_mv, rng, mock_pymc_sample):
     with pymc_mod_no_exog_mv:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -439,7 +439,7 @@ def idata_no_exog_mv(pymc_mod_no_exog_mv, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_no_exog_mv_dt(pymc_mod_no_exog_mv_dt, rng, mock_pymc_sample):
     with pymc_mod_no_exog_mv_dt:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -448,7 +448,7 @@ def idata_no_exog_mv_dt(pymc_mod_no_exog_mv_dt, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_no_exog_dt(pymc_mod_no_exog_dt, rng, mock_pymc_sample):
     with pymc_mod_no_exog_dt:
         idata = pm.sample(draws=10, tune=0, chains=1, random_seed=rng)
@@ -457,7 +457,7 @@ def idata_no_exog_dt(pymc_mod_no_exog_dt, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_time_varying(pymc_mod_time_varying, rng, mock_pymc_sample):
     """Inference data for time-varying model."""
     with pymc_mod_time_varying:

tests/statespace/core/test_statespace_JAX.py

@@ -31,7 +31,7 @@
 nile = load_nile_test_data()
 ALL_SAMPLE_OUTPUTS = MATRIX_NAMES + FILTER_OUTPUT_NAMES + SMOOTHER_OUTPUT_NAMES
 
-mock_pymc_sample = pytest.fixture(scope="session")(mock_sample_setup_and_teardown)
+mock_pymc_sample = pytest.fixture(scope="module")(mock_sample_setup_and_teardown)
 
 
 @pytest.fixture(scope="session")
@@ -68,7 +68,7 @@ def exog_pymc_mod(exog_ss_mod, rng):
     return m
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata(pymc_mod, rng, mock_pymc_sample):
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")
@@ -91,7 +91,7 @@ def idata(pymc_mod, rng, mock_pymc_sample):
     return idata
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="module")
 def idata_exog(exog_pymc_mod, rng, mock_pymc_sample):
     with warnings.catch_warnings():
         warnings.simplefilter("ignore")