Drop Python<3.9 according to NEP29 (#704)

* Support Python>=3.9 according to NEP 29

* pyupgrade

* Lint

* Fix flake8 hook

* changelog

* Remove 3.8 from classifiers

.github/workflows/build_wheels.yml

@@ -32,7 +32,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.11'
       - name: Install build dependencies
         run: python -m pip install setuptools setuptools-scm wheel Cython numpy scikit-learn
       - name: Build sdist

.github/workflows/ci.yml

@@ -3,7 +3,7 @@ on: [push]
 
 jobs:
   pre-commit-checks:
-    name: Linux - pre-commit checks - Python 3.10
+    name: Linux - pre-commit checks - Python 3.11
     timeout-minutes: 30
     runs-on: ubuntu-latest
     env:
@@ -15,10 +15,10 @@ jobs:
         uses: mamba-org/setup-micromamba@2b72821d5ad7f6da3c003a3684ce341bf187b46f
       - name: Add micromamba to GITHUB_PATH
         run: echo "${HOME}/micromamba-bin" >> "$GITHUB_PATH"
-      - name: Install Python 3.10
+      - name: Install Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - name: Run pre-commit checks
         uses: pre-commit/action@v3.0.0
 
@@ -31,7 +31,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - { os: ubuntu-latest, python-version: '3.8' }
           - { os: ubuntu-latest, python-version: '3.9' }
           - { os: ubuntu-latest, python-version: '3.10' }
           - { os: ubuntu-latest, python-version: '3.11' }

.github/workflows/conda-build.yml

@@ -20,14 +20,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { conda_build_yml: linux_64_numpy1.20python3.8.____cpython,   os: ubuntu-latest,  conda-build-args: '' }
           - { conda_build_yml: linux_64_numpy1.20python3.9.____cpython,   os: ubuntu-latest,  conda-build-args: '' }
           - { conda_build_yml: linux_64_numpy1.23python3.11.____cpython,  os: ubuntu-latest,  conda-build-args: '' }
           - { conda_build_yml: osx_64_numpy1.20python3.9.____cpython,     os: macos-latest,   conda-build-args: '' }
           - { conda_build_yml: osx_64_numpy1.23python3.11.____cpython,    os: macos-latest,   conda-build-args: '' }
-          - { conda_build_yml: osx_arm64_numpy1.20python3.8.____cpython,  os: macos-latest,   conda-build-args: ' --no-test' }
           - { conda_build_yml: osx_arm64_numpy1.21python3.10.____cpython, os: macos-latest,   conda-build-args: ' --no-test' }
-          - { conda_build_yml: win_64_numpy1.20python3.8.____cpython,     os: windows-latest, conda-build-args: '' }
+          - { conda_build_yml: win_64_numpy1.20python3.9.____cpython,     os: windows-latest, conda-build-args: '' }
           - { conda_build_yml: win_64_numpy1.23python3.11.____cpython,    os: windows-latest, conda-build-args: '' }
     steps:
       - name: Checkout branch

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
      - id: black-conda
        args:
          - --safe
-         - --target-version=py37
+         - --target-version=py39
  - repo: https://github.com/Quantco/pre-commit-mirrors-flake8
    rev: 6.1.0
    hooks:
@@ -19,6 +19,7 @@ repos:
           flake8-docstrings=1.6.0,
           flake8-print=5.0.0,
           pep8-naming=0.13.3,
+          python<3.12,
         ]
       exclude: (^src/glum_benchmarks/orig_sklearn_fork/|^docs)
  - repo: https://github.com/Quantco/pre-commit-mirrors-isort
@@ -41,9 +42,10 @@ repos:
    hooks:
     - id: pyupgrade-conda
       exclude: ^src/glum_benchmarks/orig_sklearn_fork/
+      args: [--py39-plus]
  - repo: https://github.com/Quantco/pre-commit-mirrors-cython-lint
    rev: 0.15.0
    hooks:
     - id: cython-lint-conda
       args: [--no-pycodestyle]
-    - id: double-quote-cython-strings-conda
+    - id: double-quote-cython-strings-conda

CHANGELOG.rst

@@ -7,6 +7,13 @@
 Changelog
 =========
 
+2.7.0 - 2023-10-xx
+------------------
+
+**Other changes:**
+
+- Require Python>=3.9 in line with `NEP 29 <https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table>`_
+
 2.6.0 - 2023-09-05
 ------------------
 

setup.py

@@ -66,7 +66,6 @@
     license="BSD",
     classifiers=[  # Optional
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
@@ -78,6 +77,7 @@
         if os.environ.get("CONDA_BUILD")
         else ["glum", "glum_benchmarks"],
     ),
+    python_requires=">=3.9",
     install_requires=[
         "joblib",
         "numexpr",

src/glum/_distribution.py

@@ -1,6 +1,6 @@
 from abc import ABCMeta, abstractmethod
 from functools import partial
-from typing import Tuple, Union
+from typing import Union
 
 import numexpr
 import numpy as np
@@ -318,7 +318,7 @@ def _mu_deviance_derivative(
         sample_weight: np.ndarray,
         link: Link,
         offset: np.ndarray = None,
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """Compute ``mu`` and the derivative of the deviance \
             with respect to coefficients."""
         lin_pred = _safe_lin_pred(X, coef, offset)
@@ -1157,7 +1157,7 @@ def theta(self, theta):
             raise TypeError(f"theta must be an int or float, input was {theta}")
         if not theta > 0:
             raise ValueError(
-                "theta must be strictly positive number, input was {}".format(theta)
+                f"theta must be strictly positive number, input was {theta}"
             )
 
         # Prevents upcasting when working with 32-bit data

src/glum/_glm.py

@@ -19,9 +19,9 @@
 import re
 import sys
 import warnings
-from collections.abc import Iterable
+from collections.abc import Iterable, Sequence
 from itertools import chain
-from typing import Any, List, NamedTuple, Optional, Sequence, Tuple, Union, cast
+from typing import Any, NamedTuple, Optional, Union, cast
 
 import numpy as np
 import pandas as pd
@@ -126,7 +126,7 @@ def check_array_tabmat_compliant(mat: ArrayLike, drop_first: int = False, **kwar
 
 def check_X_y_tabmat_compliant(
     X: ArrayLike, y: Union[VectorLike, sparse.spmatrix], **kwargs
-) -> Tuple[Union[tm.MatrixBase, sparse.spmatrix, np.ndarray], np.ndarray]:
+) -> tuple[Union[tm.MatrixBase, sparse.spmatrix, np.ndarray], np.ndarray]:
     """
     See the documentation for :func:`sklearn.utils.check_X_y`. This function
     behaves identically for inputs that are not from the Matrix package and
@@ -219,7 +219,7 @@ def _check_offset(
 
 
 def _name_categorical_variables(
-    categories: Tuple[str], column_name: str, drop_first: bool
+    categories: tuple[str], column_name: str, drop_first: bool
 ):
     new_names = [
         f"{column_name}__{category}" for category in categories[int(drop_first) :]
@@ -264,7 +264,7 @@ def check_inequality_constraints(
     b_ineq: Optional[np.ndarray],
     n_features: int,
     dtype,
-) -> Tuple[Union[None, np.ndarray], Union[None, np.ndarray]]:
+) -> tuple[Union[None, np.ndarray], Union[None, np.ndarray]]:
     """Check that the inequality constraints are well-defined."""
     if A_ineq is None or b_ineq is None:
         return None, None
@@ -304,7 +304,7 @@ def _standardize(
     A_ineq: Optional[np.ndarray],
     P1: Union[np.ndarray, sparse.spmatrix],
     P2: Union[np.ndarray, sparse.spmatrix],
-) -> Tuple[
+) -> tuple[
     tm.StandardizedMatrix,
     np.ndarray,
     Optional[np.ndarray],
@@ -378,7 +378,7 @@ def _unstandardize(
     col_stds: Optional[np.ndarray],
     intercept: Union[float, np.ndarray],
     coef: np.ndarray,
-) -> Tuple[Union[float, np.ndarray], np.ndarray]:
+) -> tuple[Union[float, np.ndarray], np.ndarray]:
     if col_stds is None:
         intercept -= np.squeeze(np.squeeze(col_means).dot(np.atleast_1d(coef).T))
     else:
@@ -1429,7 +1429,7 @@ def coef_table(
     def wald_test(
         self,
         R: Optional[np.ndarray] = None,
-        features: Optional[Union[str, List[str]]] = None,
+        features: Optional[Union[str, list[str]]] = None,
         r: Optional[Sequence] = None,
         X=None,
         y=None,
@@ -1638,7 +1638,7 @@ def _wald_test_matrix(
 
     def _wald_test_feature_names(
         self,
-        features: Union[str, List[str]],
+        features: Union[str, list[str]],
         values: Optional[Sequence] = None,
         X=None,
         y=None,
@@ -2226,7 +2226,7 @@ def _set_up_and_check_fit_args(
         offset: Optional[VectorLike],
         solver: str,
         force_all_finite,
-    ) -> Tuple[
+    ) -> tuple[
         tm.MatrixBase,
         np.ndarray,
         np.ndarray,