Update CI workflows and package requirements (#419)

* Update testing and requirements for Python, numpy, and scipy.

* Update matplotlib to >=3.8

* Update versions in gh workflows

* Also limit python version for linkcheck

* Update type annotations following deprecations in python 3.9

* Update change log.

* py313 test should use numpy 2.1; Fix tests for numpy 2

* Remove E203 from pycodestyle

It conflicts with https://peps.python.org/pep-0008/#whitespace-in-expressions-and-statements

* Just use one pep8speaks config

* More explicit code branching based on python version.

.github/workflows/ci_cron_weekly.yml

@@ -39,8 +39,8 @@ jobs:
         - name: Link check
           linux: linkcheck
 
-        - name: Python 3.11 with dev versions of key dependencies
-          linux: py311-test-devdeps-cov
+        - name: Python 3.13 with dev versions of key dependencies
+          linux: py313-test-devdeps-cov
           posargs: --verbose
 
   allowed_failures:

.github/workflows/ci_tests.yml

@@ -3,6 +3,7 @@
 # This file performs testing using tox and tox.ini to define and configure the test environments.
 
 # Remove -numpy126 when we support testing with numpy 2.0
+# Allow testing of optional dependencies on Python 3.12+ when pyoorb is updated.
 
 name: CI Tests
 
@@ -45,12 +46,12 @@ jobs:
         - name: Code style checks
           linux: codestyle
 
-        - name: Python 3.11 with minimal dependencies, measuring coverage
-          linux: py311-test-numpy126-cov
+        - name: Python 3.13 with minimal dependencies, measuring coverage
+          linux: py313-test-cov
           coverage: codecov
 
-        - name: Python 3.10 with all optional dependencies, measuring coverage
-          linux: py310-test-numpy126-alldeps-cov
+        - name: Python 3.11 with all optional dependencies, measuring coverage
+          linux: py311-test-numpy126-alldeps-cov
           coverage: codecov
 
         - name: Python 3.9 with oldest supported versions

.pep8speaks.yml

@@ -1,2 +1,13 @@
 pycodestyle:
   max-line-length: 88
+
+  ignore:
+    - E741 # single-letter small-caps
+    - E226 # Don't force "missing whitespace around arithmetic operator"
+    - E402 # .conf has to be set in the __init__.py modules imports
+    - E501 # line too long
+    - E203 # whitespace before colon
+
+  exclude:
+    - _astropy_init.py
+    - version.py

CHANGES.rst

@@ -1,6 +1,12 @@
 0.6.0 (unreleased)
 ==================
 
+Update supported versions [#419]:
+- Python >= 3.9
+- numpy >= 1.26
+- scipy >= 1.10
+
+
 New Features
 ------------
 

docs/sbpy/time.rst

@@ -22,7 +22,7 @@ Or, use the ``et`` property to transform dates to ephemeris time:
 
 .. doctest::
 
-    >>> Time("2010-11-04 13:59:47.31", scale="utc").et
+    >>> print(Time("2010-11-04 13:59:47.31", scale="utc").et)  # doctest: +FLOAT_CMP
     342151253.4925505
 
 The conversion from UTC is thought to be good to the 0.1 ms level.  See the `sbpy` tests for more information.

sbpy/activity/gas/core.py

@@ -13,10 +13,8 @@
 
 from abc import ABC, abstractmethod
 
-# distutils is deprecated in python 3.10 and will be removed in 3.12 (PEP 632).
-# Migration from distutils.log -> logging
 from dataclasses import dataclass
-from typing import Callable, Tuple
+from typing import Callable
 
 import numpy as np
 import astropy.units as u
@@ -1354,7 +1352,7 @@ def _make_radial_logspace_grid(self) -> np.ndarray:
 
     def _outflow_axis_sampling(
         self, x: np.float64, y: np.float64, theta: np.float64
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """Construct a list of points along the outflow axis, sampled to be
         more dense around the minimum distance to (x, y).
 

sbpy/dynamics/state.py

@@ -16,14 +16,14 @@
 ]
 
 import abc
-from typing import Iterable, List, Optional, Tuple, TypeVar, Union
+import sys
+from typing import Iterable, Optional, TypeVar, Union
 from packaging.version import Version
 
-try:
-    # python 3.11 feature
-    from typing import Self
-except ImportError:
+if sys.version_info[:2] < (3, 11):
     Self = TypeVar("Self", bound="StateBase")
+else:
+    from typing import Self
 
 import numpy as np
 import astropy
@@ -204,7 +204,7 @@ def __neg__(self) -> Self:
             frame=self.frame,
         )
 
-    def __abs__(self) -> Tuple[u.Quantity, u.Quantity]:
+    def __abs__(self) -> tuple[u.Quantity, u.Quantity]:
         """Return the magnitude of the position and velocity."""
         r = np.sqrt(np.sum(self.r**2, axis=-1))
         v = np.sqrt(np.sum(self.v**2, axis=-1))
@@ -347,11 +347,11 @@ def from_states(cls, states: Iterable[Self]) -> Self:
         """
 
         frame: BaseCoordinateFrame = states[0].frame
-        states_: List[State] = [state.transform_to(frame) for state in states]
+        states_: list[State] = [state.transform_to(frame) for state in states]
 
-        r: List[u.Quantity] = [state.r for state in states_]
-        v: List[u.Quantity] = [state.v for state in states_]
-        t: List[Union[u.Quantity, Time]] = [state.t for state in states_]
+        r: list[u.Quantity] = [state.r for state in states_]
+        v: list[u.Quantity] = [state.v for state in states_]
+        t: list[Union[u.Quantity, Time]] = [state.t for state in states_]
 
         return State(r, v, t, frame=frame)
 
@@ -399,8 +399,8 @@ def from_ephem(
 
         """
 
-        rectangular: Tuple[str] = ("x", "y", "z", "vx", "vy", "vz", "date")
-        spherical: Tuple[str] = (
+        rectangular: tuple[str] = ("x", "y", "z", "vx", "vy", "vz", "date")
+        spherical: tuple[str] = (
             "ra",
             "dec",
             "Delta",

sbpy/dynamics/syndynes.py

@@ -18,15 +18,15 @@
 ]
 
 import abc
+import sys
 import time
 import logging
-from typing import Iterable, List, Tuple, Union, Optional, TypeVar
+from typing import Iterable, Union, Optional, TypeVar
 
-try:
-    # python 3.11 feature
+if sys.version_info[:2] < (3, 11):
+    Self = TypeVar("Self", bound="StateBase")
+else:
     from typing import Self
-except ImportError:
-    Self = TypeVar("Self", bound="SynGenerator")
 
 import numpy as np
 import astropy.units as u
@@ -327,7 +327,7 @@ def to_ephem(self) -> Ephem:
         if len(self) == 0:
             return Ephem()
 
-        tables: List[Ephem] = [s.to_ephem().table for s in self]
+        tables: list[Ephem] = [s.to_ephem().table for s in self]
 
         return Ephem.from_table(
             vstack(tables, metadata_conflicts="error"),
@@ -477,7 +477,7 @@ def initialize_states(self) -> None:
 
         """
 
-        states: List[State] = []
+        states: list[State] = []
         for age in self.ages:
             t_i: Time = self.source.t - age
             state = self.solver.solve(self.source, t_i, 0)
@@ -497,7 +497,7 @@ def solve(self) -> None:
 
         logger: logging.Logger = logging.getLogger()
 
-        particles: List[State] = []
+        particles: list[State] = []
         t0: float = time.monotonic()
         for i in range(self.betas.size):
             for j in range(self.ages.size):
@@ -603,7 +603,7 @@ def synchrones(self) -> Synchrones:
 
         return Synchrones([self.synchrone(i) for i in range(len(self.ages))])
 
-    def source_orbit(self, dt: u.Quantity) -> Union[State, Tuple[State, SkyCoord]]:
+    def source_orbit(self, dt: u.Quantity) -> Union[State, tuple[State, SkyCoord]]:
         """Calculate and observe the orbit of the dust source.
 
 
@@ -627,7 +627,7 @@ def source_orbit(self, dt: u.Quantity) -> Union[State, Tuple[State, SkyCoord]]:
 
         """
 
-        states: List[State] = []
+        states: list[State] = []
         for i in range(len(dt)):
             t: Time = self.source.t + dt[i]
             states.append(self.solver.solve(self.source, t, 0))

sbpy/dynamics/tests/test_models.py

@@ -159,9 +159,6 @@ def test_GM(self):
         solver = SolarGravity()
         assert u.isclose(solver.GM, const.G * const.M_sun, rtol=1e-12)
 
-    @pytest.mark.skipif(
-        "scipy_version[0] < 2 and scipy_version[1] < 8", reason="requires scipy>=1.10"
-    )
     def test_solverfailed(self):
         r = [0, 1, 0] * u.au
         v = [0, -1, 1] * u.km / u.s

sbpy/imageanalysis/utils.py

@@ -32,10 +32,10 @@ def rarray(shape, yx=None, subsample=0):
     -------
     >>> from sbpy.imageanalysis.utils import rarray
     >>> r = rarray((5, 5))
-    >>> r[2, 2]  # docest: +FLOAT_CMP
+    >>> print(r[2, 2])  # docest: +FLOAT_CMP
     0.0
     >>> r = rarray((5, 5), yx=(0, 0))
-    >>> r[2, 2]  # docest: +FLOAT_CMP
+    >>> print(r[2, 2])  # docest: +FLOAT_CMP
     2.8284271247461903
 
     """
@@ -89,10 +89,10 @@ def rebin(a, factor, flux=False, trim=False):
     -------
     >>> from sbpy.imageanalysis.utils import xarray, rebin
     >>> x = xarray((10, 10))
-    >>> x[0, :2].mean()  # docest: +FLOAT_CMP
+    >>> print(x[0, :2].mean())  # docest: +FLOAT_CMP
     0.5
     >>> x2 = rebin(x, -2)
-    >>> x2[0, 0]  # docest: +FLOAT_CMP
+    >>> print(x2[0, 0])  # docest: +FLOAT_CMP
     0.5
 
     """
@@ -102,7 +102,7 @@ def rebin(a, factor, flux=False, trim=False):
     def mini(a, factor):
         b = a[::-factor]
         for i in range(-factor - 1):
-            b += a[(i + 1)::-factor]
+            b += a[(i + 1) :: -factor]
         if not flux:
             b = b / -factor
         return b
@@ -176,10 +176,10 @@ def refine_pixel(func, subsample, yx_pixel, yx, **kwargs):
     >>> from sbpy.imageanalysis.utils import rarray, refine_pixel
     >>> yx = (2, 2)  # the center of the radial array
     >>> r = rarray((5, 5), yx=yx)
-    >>> r[2, 2]  # docest: +FLOAT_CMP
+    >>> print(r[2, 2])  # docest: +FLOAT_CMP
     0.0
     >>> f = refine_pixel(rarray, 10, (2, 2), yx)
-    >>> np.isclose(f, 0.03826, rtol=0.01, atol=0.01)
+    >>> print(np.isclose(f, 0.03826, rtol=0.01, atol=0.01))
     True
     """
 
@@ -212,7 +212,7 @@ def xarray(shape, yx=[0, 0], th=None):
     --------
     >>> from sbpy.imageanalysis.utils import xarray
     >>> x = xarray((10, 10))
-    >>> x[0, 3]
+    >>> print(x[0, 3])
     3
 
     """
@@ -250,7 +250,7 @@ def yarray(shape, yx=[0, 0], th=None):
 
     >>> from sbpy.imageanalysis.utils import yarray
     >>> y = yarray((10, 10))
-    >>> y[3, 0]
+    >>> print(y[3, 0])
     3
 
     """

sbpy/time.py

@@ -26,7 +26,7 @@ class SpiceEphemerisTime(TimeFromEpoch):
     >>> import sbpy.time
     >>>
     >>> t = Time("2023-11-21")
-    >>> print(t.et)
+    >>> print(float(t.et))  # doctest: +FLOAT_CMP
     753796869.1828325
 
     >>> t = Time(0, format="et")

setup.cfg

@@ -25,20 +25,20 @@ classifiers =
 [options]
 packages = find:
 zip_save = False
-python_requires = >=3.8
+python_requires = >=3.9
 setup_requires = setuptools_scm
 
 # keep requirements in synchronization with docs/install.rst
 install_requires =
-    numpy>=1.21.0
+    numpy>=1.24.0
     astropy>=5.3.3
 include_package_data = True
 
 [options.extras_require]
 recommended =
     ads>=0.12
     astroquery>=0.4.5
-    scipy>=1.6
+    scipy>=1.10
     synphot>=1.1.1
 all =
     ads>=0.12
@@ -47,7 +47,7 @@ all =
     photutils
     pyoorb
     pyyaml
-    scipy>=1.6
+    scipy>=1.10
     synphot>=1.1.1
 test =
     pytest>=7.0
@@ -59,10 +59,10 @@ test =
     coverage
 docs =
     sbpy[all,test]
-    matplotlib>=3.3
+    matplotlib>=3.8
     sphinx-astropy>=1.3
     astropy!=6.1.*
-    scipy>=1.6
+    scipy>=1.10
     numpy<2
 
 [options.package_data]