MNT: Python3.13 and minor updates

Author: greglucas

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.13'
 
     - name: Download source files
       run: |
@@ -38,7 +38,7 @@ jobs:
         cd docs
         make html
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       with:
         name: DocumentationHTML
         path: docs/build/html/

.github/workflows/tests.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest, macos-14]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
     defaults:
       run:
         shell: bash

.github/workflows/wheels.yml

@@ -41,9 +41,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      # Used to host cibuildwheel
-      - uses: actions/setup-python@v3
-
       - name: Download source files
         run: |
           python .github/workflows/download_mirror.py
@@ -78,12 +75,13 @@ jobs:
           echo "PYTHONUTF8=1" >> $GITHUB_ENV
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17.0
+        uses: pypa/cibuildwheel@v2.21.3
         env:
-          CIBW_BUILD: "cp310-* cp311-* cp312-*"
-          # skip 32 bit windows and linux builds because numpy
-          # does not provide wheels for these platforms
-          CIBW_SKIP: "*-win32 *_i686"
+          # The brew built gfortran linked libraries have minimum macOS versions
+          # of the macOS version they were built on. We would need to compile
+          # from source rather than use setup-fortran if we want to support
+          # lower macOS versions.
+          MACOSX_DEPLOYMENT_TARGET: "${{ matrix.os == 'macos-13' && '13.0' || '14.0' }}"
 
       - uses: actions/upload-artifact@v4
         with:

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
   autoupdate_schedule: 'quarterly'
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.5.0'
+    rev: 'v0.7.3'
     hooks:
     - id: ruff
       args: [--fix]

CITATION.cff

@@ -9,7 +9,7 @@ authors:
       Atmospheric and Space Physics (LASP)
     orcid: "https://orcid.org/0000-0003-1331-1863"
 title: "pymsis"
-version: v0.9.0
+version: v0.10.0
 doi: 10.5281/zenodo.5348502
 date-released: 2024-04-04
 url: "https://github.com/SWxTREC/pymsis"

README.md

@@ -13,10 +13,10 @@ models (MSISE-00, MSIS2.0, MSIS2.1).
 
 ## Quickstart
 
-[Web viewer](https://swx-trec.com/msis): An interactive website using pymsis through cloud-based serverless functions.
-[Project homepage](https://swxtrec.github.io/pymsis/): Location for all documentation.
-[API Reference](https://swxtrec.github.io/pymsis/reference/index.html): Details about the various options and configurations available in the functions.
-[Examples](https://swxtrec.github.io/pymsis/examples/index.html): Demo for how to access and plot the data.
+- [Documentation](https://swxtrec.github.io/pymsis/)
+- [API Reference](https://swxtrec.github.io/pymsis/reference/index.html): Details about the various options and configurations available in the functions.
+- [Examples](https://swxtrec.github.io/pymsis/examples/index.html): Demo for how to access and plot the data.
+- [Web viewer](https://swx-trec.com/msis): An interactive website using pymsis through cloud-based serverless functions.
 
 **A few short lines of code to get started quickly with pymsis.**
 

docs/source/conf.py

@@ -76,6 +76,7 @@
 
 # Autosummary
 autosummary_generate = True
+autodoc_typehints = "none"
 
 # Sphinx gallery
 sphinx_gallery_conf = {

meson.build

@@ -2,7 +2,7 @@ project(
   'pymsis',
   'c',
   # Note that the git commit hash cannot be added dynamically here
-  version: '0.9.0',
+  version: '0.10.0',
   license: 'MIT',
   meson_version: '>=1.2.99',
   default_options: [

pymsis/__init__.py

@@ -1,3 +1,3 @@
 """Python interface to the MSIS codes."""
 
-__version__ = "0.9.0"
+__version__ = "0.10.0"

pymsis/msis.py

@@ -1,7 +1,6 @@
 """Interface for running and creating input for the MSIS models."""
 
 from pathlib import Path
-from typing import Optional, Union
 
 import numpy as np
 import numpy.typing as npt
@@ -15,12 +14,12 @@ def run(
     lons: npt.ArrayLike,
     lats: npt.ArrayLike,
     alts: npt.ArrayLike,
-    f107s: Optional[npt.ArrayLike] = None,
-    f107as: Optional[npt.ArrayLike] = None,
-    aps: Optional[npt.ArrayLike] = None,
+    f107s: npt.ArrayLike | None = None,
+    f107as: npt.ArrayLike | None = None,
+    aps: npt.ArrayLike | None = None,
     *,
-    options: Optional[list[float]] = None,
-    version: Union[float, str] = 2.1,
+    options: list[float] | None = None,
+    version: float | str = 2.1,
     **kwargs: dict,
 ) -> npt.NDArray:
     """
@@ -69,7 +68,7 @@ def run(
     -------
     ndarray (ndates, nlons, nlats, nalts, 11) or (ndates, 11)
         | The data calculated at each grid point:
-        | [Total mass density (kg/m3)
+        | [Total mass density (kg/m3),
         | N2 # density (m-3),
         | O2 # density (m-3),
         | O # density (m-3),
@@ -266,9 +265,9 @@ def create_input(
     lons: npt.ArrayLike,
     lats: npt.ArrayLike,
     alts: npt.ArrayLike,
-    f107s: Optional[npt.ArrayLike] = None,
-    f107as: Optional[npt.ArrayLike] = None,
-    aps: Optional[npt.ArrayLike] = None,
+    f107s: npt.ArrayLike | None = None,
+    f107as: npt.ArrayLike | None = None,
+    aps: npt.ArrayLike | None = None,
 ) -> tuple[tuple, npt.NDArray]:
     """
     Combine all input values into a single flattened array.

pymsis/utils.py

@@ -4,7 +4,6 @@
 import warnings
 from io import BytesIO
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 import numpy.typing as npt
@@ -15,7 +14,7 @@
 _DATA_FNAME: str = "SW-All.csv"
 _F107_AP_URL: str = f"https://celestrak.org/SpaceData/{_DATA_FNAME}"
 _F107_AP_PATH: Path = Path(pymsis.__file__).parent / _DATA_FNAME
-_DATA: Optional[dict[str, npt.NDArray]] = None
+_DATA: dict[str, npt.NDArray] | None = None
 
 
 def download_f107_ap() -> None:

pyproject.toml

@@ -2,12 +2,12 @@
 build-backend = "mesonpy"
 requires = [
     "meson-python>=0.10.0",
-    "numpy>=2.0.0rc1",
+    "numpy>=2",
 ]
 
 [project]
 name = "pymsis"
-version = "0.9.0"
+version = "0.10.0"
 description = "A Python wrapper around the NRLMSIS model."
 readme = "README.md"
 license = {file = "LICENSE"}
@@ -22,6 +22,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Software Development",
     "Topic :: Scientific/Engineering",
     "Operating System :: Microsoft :: Windows",
@@ -39,7 +40,7 @@ tests = [
 ]
 docs = [
     "matplotlib",
-    "sphinx<6",
+    "sphinx",
     "sphinx_gallery",
     "pydata-sphinx-theme",
 ]
@@ -64,11 +65,14 @@ addopts = [
 ]
 
 [tool.cibuildwheel]
+build = "cp310-* cp311-* cp312-* cp313-*"
+# skip 32 bit windows and linux builds for lack of numpy wheels
+skip = "*-win32 *_i686"
 test-requires = "pytest"
 test-command = "pytest --pyargs pymsis"
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 lint.select = ["B", "D", "E", "F", "I", "N", "S", "W", "PL", "PT", "UP", "RUF", "ANN"]
 lint.ignore = ["B028", "D203", "D212", "PLR0913", "S310"]
 

tests/test_msis.py

@@ -5,7 +5,7 @@
 from pymsis import msis, msis00f, msis20f, msis21f
 
 
-@pytest.fixture()
+@pytest.fixture
 def input_data():
     date = np.datetime64("2010-01-01T12:00")
     lon = 0
@@ -17,12 +17,12 @@ def input_data():
     return (date, lon, lat, alt, f107, f107a, ap)
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_input():
     return [1.0, 86400 / 2, 0, 0, 200, 150, 150] + [3] * 7
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_output():
     return np.array(
         [
@@ -42,7 +42,7 @@ def expected_output():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def expected_output00():
     return np.array(
         [
@@ -62,7 +62,7 @@ def expected_output00():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def input_auto_f107_ap():
     return (
         np.datetime64("2000-07-01T12:00"),