chore: drop python 3.8, support 3.13 (#168)

Drop Python 3.8 support and add 3.13 to the test matrix. Other changes:

- Ruff's UP check automatically fixes some of the Python code for 3.9+
- Clean-up the `setup.py` wrapper file
- Some of the CI jobs have used `python-version: 3.x` to specify the latest stable version of Python
- Several steps of the CI workflow use conditionals `if: matrix.python != 3.8`, which are removed
- Upgrade ReadTheDocs configuration to use ubuntu-24.04 with python 3.13

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.x
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
@@ -52,7 +52,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.x
 
       - name: Install Python packages
         run: |
@@ -79,7 +79,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-22.04, macos-13, windows-2022 ]
-        python: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
+        python: [ 3.9, "3.10", "3.11", "3.12", "3.13" ]
     env:
       GCC_V: 11
     steps:
@@ -137,26 +137,23 @@ jobs:
         run: pip install ".[test]"
 
       - name: Cache modflow6 examples
-        if: matrix.python != 3.8
         id: cache-examples
         uses: actions/cache@v3
         with:
           path: modflow6-examples/examples
           key: modflow6-examples-${{ hashFiles('modflow6-examples/data/**') }}
 
       - name: Install extra Python packages
-        if: matrix.python != 3.8
         working-directory: modflow6-examples/etc
         run: |
           pip install -r requirements.pip.txt
           pip install -r requirements.usgs.txt
 
       - name: Update FloPy packages
-        if: matrix.python != 3.8
         run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Build modflow6 example models
-        if: matrix.python != 3.8 && steps.cache-examples.outputs.cache-hit != 'true'
+        if: steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6-examples/autotest
         run: pytest -v -n auto test_scripts.py --init
 
@@ -171,7 +168,7 @@ jobs:
         # only invoke the GH API on one OS and Python version
         # to avoid rate limits (1000 rqs / hour / repository)
         # https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits
-        if: runner.os == 'Linux' && matrix.python == '3.8'
+        if: runner.os == 'Linux' && matrix.python == '3.9'
         working-directory: modflow-devtools/autotest
         env:
           REPOS_PATH: ${{ github.workspace }}

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.x
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
@@ -177,7 +177,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.x
 
       - name: Install Python dependencies
         run: |

.readthedocs.yml

@@ -1,8 +1,8 @@
 version: 2
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.8"
+    python: "3.13"
 sphinx:
   configuration: docs/conf.py
 formats:

DEVELOPER.md

@@ -19,7 +19,7 @@ This document provides guidance to set up a development environment and discusse
 
 ## Requirements
 
-Python3.8+ is currently required. This project supports several recent versions of Python, loosely following [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html#implementation) and aiming to stay synchronized with [FloPy](https://github.com/modflowpy/flopy).
+Python3.9+ is currently required. This project supports several recent versions of Python, loosely following [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html#implementation) and aiming to stay synchronized with [FloPy](https://github.com/modflowpy/flopy).
 
 ## Installation
 

README.md

@@ -52,7 +52,7 @@ Pytest features include:
 
 ## Requirements
 
-Python3.8+, dependency-free, but pairs well with `pytest` and select plugins, e.g.
+Python3.9+, dependency-free, but pairs well with `pytest` and select plugins, e.g.
 
 - [`pytest-dotenv`](https://github.com/quiqua/pytest-dotenv)
 - [`pytest-xdist`](https://github.com/pytest-dev/pytest-xdist)

autotest/test_misc.py

@@ -4,7 +4,6 @@
 from os import environ
 from pathlib import Path
 from time import sleep
-from typing import List
 
 import pytest
 
@@ -122,7 +121,7 @@ def test_has_package():
     assert not has_package(namefile_path, "wel")
 
 
-def get_expected_model_dirs(path, pattern="mfsim.nam") -> List[Path]:
+def get_expected_model_dirs(path, pattern="mfsim.nam") -> list[Path]:
     folders = []
     for root, dirs, _ in os.walk(path):
         for d in dirs:
@@ -132,7 +131,7 @@ def get_expected_model_dirs(path, pattern="mfsim.nam") -> List[Path]:
     return sorted(set(folders))
 
 
-def get_expected_namefiles(path, pattern="mfsim.nam") -> List[Path]:
+def get_expected_namefiles(path, pattern="mfsim.nam") -> list[Path]:
     folders = []
     for root, dirs, _ in os.walk(path):
         for d in dirs:

modflow_devtools/download.py

@@ -6,7 +6,7 @@
 import urllib.request
 from os import PathLike
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import Optional, Union
 from uuid import uuid4
 from warnings import warn
 
@@ -39,7 +39,7 @@ def get_request(url, params={}):
 
 def get_releases(
     repo, per_page=30, max_pages=10, retries=3, verbose=False
-) -> List[dict]:
+) -> list[dict]:
     """
     Get available releases for the given repository.
 
@@ -221,7 +221,7 @@ def get_latest_version(repo, retries=3, verbose=False) -> str:
 
 def get_release_assets(
     repo, tag="latest", simple=False, retries=3, verbose=False
-) -> Union[dict, List[dict]]:
+) -> Union[dict, list[dict]]:
     """
     Get assets corresponding to the given release.
 
@@ -264,7 +264,7 @@ def get_release_assets(
 
 def list_artifacts(
     repo, name=None, per_page=30, max_pages=10, retries=3, verbose=False
-) -> List[dict]:
+) -> list[dict]:
     """
     List artifacts for the given repository, optionally filtering by name (exact match).
     If more artifacts are available than will fit within the given page size, by default
@@ -401,9 +401,10 @@ def download_artifact(
     while True:
         tries += 1
         try:
-            with urllib.request.urlopen(request) as url_file, zip_path.open(
-                "wb"
-            ) as out_file:
+            with (
+                urllib.request.urlopen(request) as url_file,
+                zip_path.open("wb") as out_file,
+            ):
                 content = url_file.read()
                 out_file.write(content)
                 break
@@ -479,9 +480,10 @@ def download_and_unzip(
     while True:
         tries += 1
         try:
-            with urllib.request.urlopen(request) as url_file, file_path.open(
-                "wb"
-            ) as out_file:
+            with (
+                urllib.request.urlopen(request) as url_file,
+                file_path.open("wb") as out_file,
+            ):
                 content = url_file.read()
                 out_file.write(content)
 

modflow_devtools/fixtures.py

@@ -1,9 +1,10 @@
 from collections import OrderedDict
+from collections.abc import Generator
 from itertools import groupby
 from os import PathLike, environ
 from pathlib import Path
 from shutil import copytree, rmtree
-from typing import Dict, Generator, List, Optional
+from typing import Optional
 
 from modflow_devtools.imports import import_optional_dependency
 from modflow_devtools.misc import get_namefile_paths, get_packages
@@ -313,7 +314,7 @@ def example_path_from_namfile_path(path: PathLike) -> Path:
         def example_name_from_namfile_path(path: PathLike) -> str:
             return example_path_from_namfile_path(path).name
 
-        def group_examples(namefile_paths) -> Dict[str, List[Path]]:
+        def group_examples(namefile_paths) -> dict[str, list[Path]]:
             d = OrderedDict()
             for name, paths in groupby(
                 namefile_paths, key=example_name_from_namfile_path

modflow_devtools/latex.py

@@ -1,6 +1,7 @@
+from collections.abc import Iterable
 from os import PathLike
 from pathlib import Path
-from typing import Iterable, Optional, Union
+from typing import Optional, Union
 
 
 def build_table(

modflow_devtools/markers.py

@@ -5,7 +5,7 @@
 
 from os import environ
 from platform import python_version, system
-from typing import Dict, Optional
+from typing import Optional
 
 from packaging.version import Version
 
@@ -48,7 +48,7 @@ def requires_python(version, bound="lower"):
         )
 
 
-def requires_pkg(*pkgs, name_map: Optional[Dict[str, str]] = None):
+def requires_pkg(*pkgs, name_map: Optional[dict[str, str]] = None):
     missing = {pkg for pkg in pkgs if not has_pkg(pkg, strict=True, name_map=name_map)}
     return pytest.mark.skipif(
         missing,

modflow_devtools/misc.py

@@ -12,7 +12,7 @@
 from shutil import which
 from subprocess import run
 from timeit import timeit
-from typing import Dict, List, Optional, Tuple
+from typing import Optional
 from urllib import request
 from urllib.error import URLError
 
@@ -67,7 +67,7 @@ def get_ostag() -> str:
     raise ValueError(f"platform {sys.platform!r} not supported")
 
 
-def get_suffixes(ostag) -> Tuple[str, str]:
+def get_suffixes(ostag) -> tuple[str, str]:
     """
     Returns executable and library suffixes for the
     given OS (as returned by sys.platform)
@@ -144,7 +144,7 @@ def get_current_branch() -> str:
     raise ValueError(f"Could not determine current branch: {stderr}")
 
 
-def get_packages(namefile_path: PathLike) -> List[str]:
+def get_packages(namefile_path: PathLike) -> list[str]:
     """
     Return a list of packages used by the simulation
     or model defined in the given namefile. The namefile
@@ -273,7 +273,7 @@ def get_model_paths(
     excluded=None,
     selected=None,
     packages=None,
-) -> List[Path]:
+) -> list[Path]:
     """
     Find model directories recursively in the given location.
     A model directory is any directory containing one or more
@@ -378,7 +378,7 @@ def has_exe(exe):
 
 
 def has_pkg(
-    pkg: str, strict: bool = False, name_map: Optional[Dict[str, str]] = None
+    pkg: str, strict: bool = False, name_map: Optional[dict[str, str]] = None
 ) -> bool:
     """
     Determines if the given Python package is installed.

modflow_devtools/ostags.py

@@ -5,7 +5,7 @@
 
 import sys
 from platform import processor, system
-from typing import Optional, Tuple
+from typing import Optional
 
 _system = system()
 _processor = processor()
@@ -42,7 +42,7 @@ def get_ostag(kind: str = "modflow") -> str:
         raise ValueError(f"Invalid kind: {kind}")
 
 
-def get_binary_suffixes(ostag: Optional[str] = None) -> Tuple[str, str]:
+def get_binary_suffixes(ostag: Optional[str] = None) -> tuple[str, str]:
     """
     Returns executable and library suffixes for the given OS tag, if provided,
     otherwise for the current operating system.

pyproject.toml

@@ -32,14 +32,14 @@ classifiers = [
     "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
     "Programming Language :: Python :: 3 :: Only",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Hydrology"
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dynamic = ["version"]
 
 [project.optional-dependencies]