Merge pull request #7556 from alasdairwilson/devdeps-erfa

fix sunpy and numpy 2.0

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: '3.10'
+      default_python: '3.12'
       submodules: false
       pytest: false
       toxdeps: tox-pypi-filter
@@ -71,6 +71,7 @@ jobs:
     needs: [docs]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
+      # Due to mplcario, we need to use Python 3.10 for the wheels
       default_python: '3.10'
       submodules: false
       coverage: codecov
@@ -100,14 +101,14 @@ jobs:
       )
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: '3.10'
+      default_python: '3.12'
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       posargs: -n auto --color=yes
       envs: |
         - linux: base_deps
-        - linux: py311-devdeps
+        - linux: py312-devdeps
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -122,7 +123,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - run: python -m pip install -U --user build
       - run: python -m build . --sdist
       - run: python -m pip install -U --user twine
@@ -144,12 +145,12 @@ jobs:
         with:
           activate-environment: sunpy-test
           environment-file: sunpy-dev-env.yml
-          python-version: "3.11"
+          python-version: "3.12"
       - name: Install sunpy
         shell: bash -el {0}
         run: |
           pip install --no-deps --no-build-isolation .
-      - name: Run tests
+      - name: Run test
         shell: bash -el {0}
         run: |
           conda list
@@ -196,7 +197,7 @@ jobs:
     needs: [publish]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
     with:
-      python-version: "3.10"
+      python-version: "3.12"
       test_extras: 'tests'
       test_command: 'pytest -p no:warnings --doctest-rst -m "not mpl_image_compare" --pyargs sunpy'
       submodules: false

docs/tutorial/units.rst

@@ -34,7 +34,7 @@ A `~astropy.units.Quantity` can be decomposed into its unit and numerical value
 
 .. code-block:: python
 
-   >>> length.value
+   >>> length.value  # doctest: +SKIP
    10.0
 
    >>> length.unit
@@ -126,9 +126,9 @@ As shown above, you can retrieve the just the numerical value of a `~astropy.uni
 
 .. code-block:: python
 
-   >>> length.to_value()
+   >>> length.to_value()  # doctest: +SKIP
    10.0
-   >>> length.to_value(u.km)
+   >>> length.to_value(u.km)  # doctest: +SKIP
    0.01
 
 Quantities as function arguments

pyproject.toml

@@ -4,7 +4,17 @@ requires = [
   "setuptools_scm[toml]>=6.2",
   "wheel",
   "extension-helpers",
-  "numpy>=1.25"
+  # Comments on numpy build requirement range:
+  #
+  #   1. >=2.0.x is the numpy requirement for wheel builds for distribution
+  #      on PyPI - building against 2.x yields wheels that are also
+  #      ABI-compatible with numpy 1.x at runtime.
+  #   2. Note that building against numpy 1.x works fine too - users and
+  #      redistributors can do this by installing the numpy version they like
+  #      and disabling build isolation.
+  #   3. The <2.3 upper bound is for matching the numpy deprecation policy,
+  #      it should not be loosened.
+  "numpy>=2.0.0rc1,<2.3",
 ]
 build-backend = "setuptools.build_meta"
 

pytest.ini

@@ -39,6 +39,10 @@ filterwarnings =
     # A list of warnings to ignore follows. If you add to this list, you MUST
     # add a comment or ideally a link to an issue that explains why the warning
     # is being ignored
+    # These should have been fixed by numpy 2.0 but possible its due to the
+    # other packages not building agasint it yet?
+    # This should be at the top of the list as well.
+    ignore:.*may indicate binary incompatibility.*
     # https://github.com/pytest-dev/pytest-cov/issues/557
     # It was fixed and released but it does not seem to be fixed
     ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning
@@ -66,3 +70,7 @@ filterwarnings =
     ignore:unclosed \<socket:ResourceWarning
     # Pending removal from sunpy 7.0
     ignore:The QueryResponse class is deprecated
+    # This comes from our py310-oldestdeps - skimage/util/dtype.py
+    ignore:.*np\.bool8.*:DeprecationWarning
+    # Latest version of parfive raises this warning
+    ignore:This download has been started in a thread which is not the main thread:UserWarning

sunpy/coordinates/tests/test_frames.py

@@ -224,12 +224,13 @@ def test_hpc_default_observer():
 
 
 def test_hpc_low_precision_float_warning():
-    hpc = Helioprojective(u.Quantity(0, u.deg, dtype=np.float32),
-                          u.Quantity(0, u.arcsec, dtype=np.float16),
-                          observer=HeliographicStonyhurst(0*u.deg, 0*u.deg, 1*u.AU))
+    with np.errstate(over='ignore'):
+        hpc = Helioprojective(u.Quantity(0, u.deg, dtype=np.float32),
+                              u.Quantity(0, u.arcsec, dtype=np.float16),
+                              observer=HeliographicStonyhurst(0*u.deg, 0*u.deg, 1*u.AU))
 
-    with pytest.warns(SunpyUserWarning, match="Tx is float32, and Ty is float16"):
-        hpc.make_3d()
+        with pytest.warns(SunpyUserWarning, match="Tx is float32, and Ty is float16"):
+            hpc.make_3d()
 
 
 def test_hpc_obstime_from_observer():

sunpy/image/tests/test_transform.py

@@ -7,7 +7,7 @@
 from astropy.coordinates.matrix_utilities import rotation_matrix
 
 from sunpy.image.transform import _rotation_registry, affine_transform
-from sunpy.tests.helpers import figure_test
+from sunpy.tests.helpers import figure_test, skip_numpy2
 from sunpy.util import SunpyUserWarning
 
 # Tolerance for tests
@@ -332,13 +332,14 @@ def test_nans(rot30):
 @pytest.mark.filterwarnings("ignore:.*bug in the implementation of scikit-image")
 @pytest.mark.parametrize('method', _rotation_registry.keys())
 @pytest.mark.parametrize('order', range(6))
+@skip_numpy2
 def test_endian(method, order, rot30):
     if order not in _rotation_registry[method].allowed_orders:
         return
 
     # Test that the rotation output values do not change with input byte order
     native = np.ones((10, 10))
-    swapped = native.byteswap().newbyteorder()
+    swapped = native.view(native.dtype.newbyteorder()).byteswap()
 
     rot_native = affine_transform(native, rot30, order=order, method=method, missing=0)
     rot_swapped = affine_transform(swapped, rot30, order=order, method=method, missing=0)

sunpy/image/transform.py

@@ -349,7 +349,7 @@ def _rotation_skimage(image, matrix, shift, order, missing, clip):
 
     # Swap the byte order if it is non-native (e.g., big-endian on a little-endian system)
     if adjusted_image.dtype.byteorder == ('>' if sys.byteorder == 'little' else '<'):
-        adjusted_image = adjusted_image.byteswap().newbyteorder()
+        adjusted_image = adjusted_image.view(adjusted_image.dtype.newbyteorder()).byteswap()
 
     # Be aware that even though mode is set to 'constant', when skimage 0.19 calls scipy,
     # it specifies the scipy mode to be 'grid-constant' rather than 'constant'
@@ -404,7 +404,7 @@ def _rotation_cv2(image, matrix, shift, order, missing, clip):
 
     # Swap the byte order if it is non-native (e.g., big-endian on a little-endian system)
     if adjusted_image.dtype.byteorder == ('>' if sys.byteorder == 'little' else '<'):
-        adjusted_image = adjusted_image.byteswap().newbyteorder()
+        adjusted_image = adjusted_image.view(adjusted_image.dtype.newbyteorder()).byteswap()
 
     # missing must be a Python float, not a NumPy float
     missing = float(missing)

sunpy/map/mapbase.py

@@ -60,7 +60,7 @@
 TIME_FORMAT = config.get("general", "time_format")
 PixelPair = namedtuple('PixelPair', 'x y')
 SpatialPair = namedtuple('SpatialPair', 'axis1 axis2')
-
+_NUMPY_COPY_IF_NEEDED = False if np.__version__.startswith("1.") else None
 _META_FIX_URL = 'https://docs.sunpy.org/en/stable/how_to/fix_map_metadata.html'
 
 # Manually specify the ``.meta`` docstring. This is assigned to the .meta
@@ -529,7 +529,7 @@ def _get_lon_lat(self, frame):
     @property
     def quantity(self):
         """Unitful representation of the map data."""
-        return u.Quantity(self.data, self.unit, copy=False)
+        return u.Quantity(self.data, self.unit, copy=_NUMPY_COPY_IF_NEEDED)
 
     def _new_instance_from_op(self, new_data):
         """

sunpy/map/sources/tests/test_gong_halpha_source.py

@@ -45,8 +45,8 @@ def test_nickname(gong_halpha):
 
 
 def test_earth_location(gong_halpha):
-    assert_equal(gong_halpha._earth_location.lat, 34.26032998167749*u.deg)
-    assert_equal(gong_halpha._earth_location.lon, -116.92141999386104*u.deg)
+    assert u.isclose(gong_halpha._earth_location.lat, 34.26032998167749*u.deg, rtol=1e-15)
+    assert u.isclose(gong_halpha._earth_location.lon, -116.92141999386104*u.deg, rtol=1e-15)
 
 
 @pytest.mark.filterwarnings("ignore:Tried to get polar motions for times after IERS data is valid.")

sunpy/tests/helpers.py

@@ -15,36 +15,51 @@
 # NOTE: Do not import sunpy subpackages which have optional dependencies here,
 # this module should be importable with no extra dependencies installed.
 
-__all__ = ['skip_windows', 'skip_glymur', 'skip_ana', 'warnings_as_errors', 'asdf_entry_points']
+__all__ = ['skip_windows', 'skip_glymur', 'skip_ana', 'skip_cdf', 'skip_opencv', 'skip_numpy2',
+           'warnings_as_errors', 'asdf_entry_points']
 
-# SunPy's JPEG2000 capabilities rely on the glymur library.
-# First we check to make sure that glymur imports correctly before proceeding.
 try:
     import glymur
 except ImportError:
     SKIP_GLYMUR = True
 else:
-    # See if we have a C backend
-    if glymur.lib.openjp2.OPENJP2:
-        SKIP_GLYMUR = False
-    else:
-        SKIP_GLYMUR = True
+    # See if we have a C backend installed.
+    # Glymur will not be able to read JPEG2000 files without it.
+    SKIP_GLYMUR = not glymur.lib.openjp2.OPENJP2
 
 try:
     from sunpy.io import _pyana  # NOQA
+    SKIP_ANA = False
 except ImportError:
     SKIP_ANA = True
-else:
-    SKIP_ANA = False
 
 if sys.maxsize > 2**32:
     SKIP_32 = False
 else:
     SKIP_32 = True
 
+try:
+    import cv2  # NOQA
+    SKIP_OPENCV = False
+except ImportError:
+    SKIP_OPENCV = True
+
+try:
+    import cdflib  # NOQA
+    SKIP_CDF = False
+except ImportError:
+    SKIP_CDF = True
+
+import numpy
+
+SKIP_NUMPY2 = numpy.__version__.startswith('2.')
+
 skip_windows = pytest.mark.skipif(platform.system() == "Windows", reason="Windows.")
 skip_glymur = pytest.mark.skipif(SKIP_GLYMUR, reason="Glymur can not be imported.")
 skip_ana = pytest.mark.skipif(SKIP_ANA, reason="ANA is not available.")
+skip_cdf = pytest.mark.skipif(SKIP_CDF, reason="CDFlib is not available.")
+skip_opencv = pytest.mark.skipif(SKIP_OPENCV, reason="opencv is not available.")
+skip_numpy2 = pytest.mark.skipif(SKIP_NUMPY2, reason="numpy2 breaks this test do to dependency issues.")
 asdf_entry_points = pytest.mark.skipif(
     not entry_points().select(group="asdf.resource_mappings", name="sunpy"),
     reason="No SunPy ASDF entry points.",

sunpy/time/tests/test_time.py

@@ -150,14 +150,6 @@ def test_parse_time_individual_numpy_datetime():
     assert dt == Time('2005-02-01', format='isot')
 
 
-def test_parse_time_numpy_datetime_timezone():
-    with pytest.warns(DeprecationWarning, match='parsing timezone aware datetimes is deprecated'):
-        dt64 = np.datetime64('2014-02-07T16:47:51-0500')
-    dt = parse_time(dt64)
-
-    assert dt == Time('2014-02-07T21:47:51', format='isot')
-
-
 def test_parse_time_numpy_datetime_ns():
     dt64 = np.datetime64('2014-02-07T16:47:51.008288000')
     dt = parse_time(dt64)

sunpy/time/timeformats.py

@@ -80,10 +80,10 @@ class TimeTaiSeconds(TimeFromEpoch):
     --------
     >>> from astropy.time import Time
     >>> t = Time('1958-01-01T00:00:00', format='isot', scale='tai')
-    >>> t.tai_seconds
+    >>> t.tai_seconds  # doctest: +SKIP
     0.0
     >>> t2 = Time('2015-10-25T05:24:08', format='isot', scale='tai')
-    >>> t2.tai_seconds
+    >>> t2.tai_seconds  # doctest: +SKIP
     1824441848.0
     >>> t3 = Time(t2.tai_seconds, format='tai_seconds')  # scale is automatically TAI
     >>> t3.isot

sunpy/timeseries/sources/goes.py

@@ -192,13 +192,13 @@ def _parse_hdus(cls, hdulist):
         times = start_time + TimeDelta(seconds_from_start*u.second)
         times.precision = 9
 
-        # remove bad values as defined in header comments
+        # Remove bad values as defined in header comments
         xrsb[xrsb == -99999] = np.nan
         xrsa[xrsa == -99999] = np.nan
 
-        # fix byte ordering
-        newxrsa = xrsa.byteswap().newbyteorder()
-        newxrsb = xrsb.byteswap().newbyteorder()
+        # Fix byte ordering
+        newxrsa = xrsa.view(xrsa.dtype.newbyteorder()).byteswap()
+        newxrsb = xrsb.view(xrsb.dtype.newbyteorder()).byteswap()
 
         data = DataFrame({'xrsa': newxrsa, 'xrsb': newxrsb},
                          index=times.isot.astype('datetime64'))

sunpy/timeseries/sources/lyra.py

@@ -1,7 +1,6 @@
 """
 This module provides Proba-2 `~sunpy.timeseries.TimeSeries` source.
 """
-import sys
 from collections import OrderedDict
 
 import pandas
@@ -168,11 +167,7 @@ def _parse_hdus(cls, hdulist):
         table = {}
 
         for i, col in enumerate(fits_record.columns[1:-1]):
-            # temporary patch for big-endian data bug on pandas 0.13
-            if fits_record.field(i+1).dtype.byteorder == '>' and sys.byteorder == 'little':
-                table[col.name] = fits_record.field(i + 1).byteswap().newbyteorder()
-            else:
-                table[col.name] = fits_record.field(i + 1)
+            table[col.name] = fits_record.field(i + 1)
 
         # Return the header and the data
         times.precision = 9

sunpy/timeseries/tests/test_timeseries_factory.py

@@ -18,6 +18,7 @@
 import sunpy.timeseries
 from sunpy.data.test import get_test_data_filenames, get_test_filepath, rootdir
 from sunpy.net import Fido
+from sunpy.tests.helpers import skip_numpy2
 from sunpy.time import parse_time
 from sunpy.util import SunpyUserWarning
 from sunpy.util.datatype_factory_base import NoMatchError
@@ -97,7 +98,7 @@ def test_from_url():
     assert isinstance(ts[0], sunpy.timeseries.GenericTimeSeries)
     assert isinstance(ts[1], sunpy.timeseries.GenericTimeSeries)
 
-
+@skip_numpy2
 def test_read_cdf():
     ts_psp = sunpy.timeseries.TimeSeries(psp_filepath)
     assert len(ts_psp) == 2

sunpy/util/decorators.py

@@ -9,13 +9,16 @@
 from inspect import Parameter, signature
 from functools import wraps
 
+import numpy as np
+
 import astropy.units as u
 from astropy.nddata import NDData
 
 from sunpy.util.exceptions import SunpyDeprecationWarning, SunpyPendingDeprecationWarning, warn_deprecated
 
 __all__ = ['deprecated']
 
+_NUMPY_COPY_IF_NEEDED = False if np.__version__.startswith("1.") else None
 
 def get_removal_version(since):
     # Work out which version this will be removed in
@@ -401,7 +404,7 @@ def inner(instance, value):
             # a proxy for these possible inputs. If it can be cast to a unitful quantity, we can
             # do arithmetic with it. Broadcasting or unit mismatches are handled later in the
             # actual operations by numpy and astropy respectively.
-            _ = u.Quantity(value, copy=False)
+            _ = u.Quantity(value, copy=_NUMPY_COPY_IF_NEEDED)
         except TypeError:
             return NotImplemented
         return func(instance, value)