Changes

Author: nabobalis

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.7.1"
+    rev: "v0.7.2"
     hooks:
       - id: ruff
         args: ["--fix"]

.ruff.toml

@@ -44,14 +44,14 @@ extend-ignore = [
   "NPY002", # TODO: migrate from np.random.rand to np.random.Generator
   # upgrades
   "UP038", # Use | in isinstance - not compatible with models and is slower
-  # pytest (PT)
+  # pytest
   "PT001",  # Always use pytest.fixture()
   "PT004",  # Fixtures which don't return anything should have leading _
   "PT011",  # except(ValueRaises) is too broad
   "PT012",  # except statement is too lengthy
   "PT023",  # Always use () on pytest decorators
   "PT023",  # Always use () on pytest decorators
-  # flake8-pie
+  # flake8-use-pathlib
   "PIE808", # Disallow passing 0 as the first argument to range
   # flake8-use-pathlib
   "PTH123", # open() should be replaced by Path.open()
@@ -67,22 +67,22 @@ extend-ignore = [
 "setup.py" = ["INP001"]
 "conftest.py" = ["INP001"]
 "docs/conf.py" = [
+  "INP001",  # Implicit namespace package
   "E402"  # Module imports not at top of file
 ]
-"docs/*.py" = [
-  "INP001",  # Implicit-namespace-package. The examples are not a package.
-]
 "examples/*.py" = [
   "T201",  # We need print in our examples
-  "E501",  # Line too long
-  "INP001",  # implicit namespace package
+  "INP001",  # Implicit namespace package
+]
+"__init__.py" = [
+  "E402", # Module level import not at top of cell
+  "F401", # Unused import
+  "F403", # from {name} import * used; unable to detect undefined names
+  "F405", # {name} may be undefined, or defined from star imports
 ]
-"ndcube/*.py" = [
-  "T201", # allow use of print in examples
-  "INP001", # File is part of an implicit namespace package.
+"test_*.py" = [
+  "E402", # Module level import not at top of cell
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"

ndcube/__init__.py

@@ -1,8 +1,9 @@
 """
+======
 ndcube
 ======
 
-A base package for multi-dimensional contiguous and non-contiguous coordinate-aware arrays.
+A package for multi-dimensional contiguous and non-contiguous coordinate-aware arrays.
 
 * Homepage: https://github.com/sunpy/ndcube
 * Documentation: https://docs.sunpy.org/projects/ndcube/
@@ -14,13 +15,16 @@
 from .ndcube_sequence import NDCubeSequence, NDCubeSequenceBase
 from .version import version as __version__
 
-__all__ = ['NDCube',
-           'NDCubeSequence',
-           "NDCollection",
-           "ExtraCoords",
-           "GlobalCoords",
-           "ExtraCoordsABC",
-           "GlobalCoordsABC",
-           "NDCubeBase",
-           "NDCubeSequenceBase",
-           "__version__"]
+
+__all__ = [
+    'NDCube',
+    'NDCubeSequence',
+    "NDCollection",
+    "ExtraCoords",
+    "GlobalCoords",
+    "ExtraCoordsABC",
+    "GlobalCoordsABC",
+    "NDCubeBase",
+    "NDCubeSequenceBase",
+    "__version__",
+]

ndcube/_dev/scm_version.py

@@ -1,6 +1,5 @@
 # Try to use setuptools_scm to get the current version; this is only used
 # in development installations from the git repository.
-
 from pathlib import Path
 
 try:

ndcube/extra_coords/table_coord.py

@@ -6,6 +6,7 @@
 import gwcs
 import gwcs.coordinate_frames as cf
 import numpy as np
+import scipy.interpolate
 
 import astropy.units as u
 from astropy.coordinates import SkyCoord
@@ -15,16 +16,13 @@
 from astropy.time import Time
 from astropy.wcs.wcsapi.wrappers.sliced_wcs import combine_slices, sanitize_slices
 
-try:
-    import scipy.interpolate
-except ImportError:
-    pass
-
-__all__ = ['TimeTableCoordinate',
-           'SkyCoordTableCoordinate',
-           'QuantityTableCoordinate',
-           'BaseTableCoordinate',
-           'MultipleTableCoordinate']
+__all__ = [
+    'TimeTableCoordinate',
+    'SkyCoordTableCoordinate',
+    'QuantityTableCoordinate',
+    'BaseTableCoordinate',
+    'MultipleTableCoordinate',
+]
 
 
 class Length1Tabular(_Tabular):
@@ -140,7 +138,7 @@ def _generate_tabular(lookup_table, interpolation='linear', points_unit=u.pix, *
         raise TypeError("lookup_table must be a Quantity.")  # pragma: no cover
 
     ndim = lookup_table.ndim
-    tabular_nd = tabular_model(ndim, name=f"Tabular{ndim}D")
+    TabularND = tabular_model(ndim, name=f"Tabular{ndim}D")
 
     # The integer location is at the centre of the pixel.
     points = [(np.arange(size) - 0) * points_unit for size in lookup_table.shape]
@@ -155,7 +153,7 @@ def _generate_tabular(lookup_table, interpolation='linear', points_unit=u.pix, *
     if len(lookup_table) == 1:
         t = Length1Tabular(points, lookup_table, **kwargs)
     else:
-        t = tabular_nd(points, lookup_table, **kwargs)
+        t = TabularND(points, lookup_table, **kwargs)
 
         # TODO: Remove this when there is a new gWCS release
         # Work around https://github.com/spacetelescope/gwcs/pull/331
@@ -352,10 +350,7 @@ def _slice_table(self, i, table, item, new_components, whole_slice):
             dwd["world_axis_physical_types"].append(self.frame.axis_physical_types[i])
             dwd["world_axis_units"].append(table.unit.to_string())
             dwd["world_axis_object_components"].append((f"quantity{i}", 0, "value"))
-            dwd["world_axis_object_classes"].update({f"quantity{i}": (u.Quantity,
-                                                                      (),
-                                                                      {"unit", table.unit.to_string()})})
-            return
+            dwd["world_axis_object_classes"].update({f"quantity{i}": (u.Quantity, (), {"unit", table.unit.to_string()})})
 
         new_components["tables"].append(table[item])
         if self.names:
@@ -923,16 +918,11 @@ def dropped_world_dimensions(self):
 
         dropped_multi_table = MultipleTableCoordinate(*self._dropped_coords)
 
-        dropped_world_dimensions["world_axis_names"] += [name or None for name in
-                                                         dropped_multi_table.frame.axes_names]
-        dropped_world_dimensions["world_axis_physical_types"] += (
-            list(dropped_multi_table.frame.axis_physical_types))
-        dropped_world_dimensions["world_axis_units"] += [u.to_string() for u in
-                                                         dropped_multi_table.frame.unit]
-        dropped_world_dimensions["world_axis_object_components"] += \
-            dropped_multi_table.frame._world_axis_object_components
-        dropped_world_dimensions["world_axis_object_classes"].update(
-            dropped_multi_table.frame._world_axis_object_classes)
+        dropped_world_dimensions["world_axis_names"] += [name or None for name in dropped_multi_table.frame.axes_names]
+        dropped_world_dimensions["world_axis_physical_types"] += list(dropped_multi_table.frame.axis_physical_types)
+        dropped_world_dimensions["world_axis_units"] += [u.to_string() for u in dropped_multi_table.frame.unit]
+        dropped_world_dimensions["world_axis_object_components"] += dropped_multi_table.frame._world_axis_object_components
+        dropped_world_dimensions["world_axis_object_classes"].update(dropped_multi_table.frame._world_axis_object_classes)
 
         for dropped in self._dropped_coords:
             # If the table is a tuple (QuantityTableCoordinate) then we need to

ndcube/tests/helpers.py

@@ -20,31 +20,26 @@
 
 from ndcube import NDCube, NDCubeSequence
 
-__all__ = ['figure_test',
-           'get_hash_library_name',
-           'assert_extra_coords_equal',
-           'assert_metas_equal',
-           'assert_cubes_equal',
-           'assert_cubesequences_equal',
-           'assert_wcs_are_equal']
+__all__ = [
+    'figure_test',
+    'get_hash_library_name',
+    'assert_extra_coords_equal',
+    'assert_metas_equal',
+    'assert_cubes_equal',
+    'assert_cubesequences_equal',
+    'assert_wcs_are_equal',
+]
 
 
 def get_hash_library_name():
     """
     Generate the hash library name for this env.
     """
     ft2_version = f"{mpl.ft2font.__freetype_version__.replace('.', '')}"
-    animators_version = "dev" if (("dev" in mpl_animators.__version__)
-                                  or ("rc" in mpl_animators.__version__))\
-                                  else mpl_animators.__version__.replace('.', '')
-    mpl_version = "dev" if (("dev" in mpl.__version__)
-                            or ("rc" in mpl.__version__)) \
-                            else mpl.__version__.replace('.', '')
-    astropy_version = "dev" if (("dev" in astropy.__version__)
-                                or ("rc" in astropy.__version__)) \
-                                else astropy.__version__.replace('.', '')
-    return (f"figure_hashes_mpl_{mpl_version}_ft_{ft2_version}"
-            f"_astropy_{astropy_version}_animators_{animators_version}.json")
+    animators_version = "dev" if (("dev" in mpl_animators.__version__) or ("rc" in mpl_animators.__version__)) else mpl_animators.__version__.replace('.', '')
+    mpl_version = "dev" if (("dev" in mpl.__version__) or ("rc" in mpl.__version__)) else mpl.__version__.replace('.', '')
+    astropy_version = "dev" if (("dev" in astropy.__version__) or ("rc" in astropy.__version__)) else astropy.__version__.replace('.', '')
+    return f"figure_hashes_mpl_{mpl_version}_ft_{ft2_version}_astropy_{astropy_version}_animators_{animators_version}.json"
 
 
 def figure_test(test_function):
@@ -155,8 +150,7 @@ def assert_wcs_are_equal(wcs1, wcs2):
         # SlicedLowLevelWCS vs BaseHighLevelWCS don't have the same pixel_to_world method
         low_level_wcs1 = wcs1.low_level_wcs if isinstance(wcs1, BaseHighLevelWCS) else wcs1
         low_level_wcs2 = wcs2.low_level_wcs if isinstance(wcs2, BaseHighLevelWCS) else wcs2
-        np.testing.assert_array_equal(low_level_wcs1.pixel_to_world_values(*random_idx.T),
-                                      low_level_wcs2.pixel_to_world_values(*random_idx.T))
+        np.testing.assert_array_equal(low_level_wcs1.pixel_to_world_values(*random_idx.T), low_level_wcs2.pixel_to_world_values(*random_idx.T))
 
 def create_sliced_wcs(wcs, item, dim):
     """

ndcube/tests/test_ndcube.py

@@ -203,7 +203,6 @@ def test_axis_world_coords_empty_ec(ndcube_3d_l_ln_lt_ectime):
     assert awc == ()
 
 
-
 @pytest.mark.xfail(reason=">1D Tables not supported")
 def test_axis_world_coords_complex_ec(ndcube_4d_ln_lt_l_t):
     cube = ndcube_4d_ln_lt_l_t
@@ -818,11 +817,11 @@ def test_rebin(ndcube_3d_l_ln_lt_ectime, bin_shape):
     expected_uncertainty = None
     expected_unit = cube.unit
     expected_meta = cube.meta
-    expected_tx = np.array([[9.99999999, 19.99999994, 29.99999979, 39.9999995,
+    expected_Tx = np.array([[9.99999999, 19.99999994, 29.99999979, 39.9999995,
                              49.99999902, 59.99999831, 69.99999731, 79.99999599],
                             [9.99999999, 19.99999994, 29.99999979, 39.9999995,
                              49.99999902, 59.99999831, 69.99999731, 79.99999599]]) * u.arcsec
-    expected_ty = np.array([[-14.99999996, -14.9999999, -14.99999981, -14.99999969,
+    expected_Ty = np.array([[-14.99999996, -14.9999999, -14.99999981, -14.99999969,
                              -14.99999953, -14.99999934, -14.99999911, -14.99999885],
                             [-4.99999999, -4.99999998, -4.99999995, -4.9999999,
                              -4.99999985, -4.99999979, -4.99999971, -4.99999962]]) * u.arcsec
@@ -837,8 +836,8 @@ def test_rebin(ndcube_3d_l_ln_lt_ectime, bin_shape):
     assert output.uncertainty == expected_uncertainty
     assert output.unit == expected_unit
     assert output.meta == expected_meta
-    assert u.allclose(output_sc.Tx, expected_tx)
-    assert u.allclose(output_sc.Ty, expected_ty)
+    assert u.allclose(output_sc.Tx, expected_Tx)
+    assert u.allclose(output_sc.Ty, expected_Ty)
     assert u.allclose(output_spec, expected_spec)
     assert output_time.scale == expected_time.scale
     assert output_time.format == expected_time.format
@@ -956,15 +955,13 @@ def test_rebin_no_propagate(ndcube_2d_ln_lt_mask_uncert):
     bin_shape = (2, 4)
 
     cube._mask[:] = True
-    with pytest.warns(NDCubeUserWarning, match="Uncertainties cannot be propagated as all values "
-                                               "are masked and operation_ignores_mask is False."):
+    with pytest.warns(NDCubeUserWarning, match="Uncertainties cannot be propagated as all values are masked and operation_ignores_mask is False."):
         output = cube.rebin(bin_shape, operation=np.sum, propagate_uncertainties=True,
                             operation_ignores_mask=False)
     assert output.uncertainty is None
 
     cube._mask = True
-    with pytest.warns(NDCubeUserWarning, match="Uncertainties cannot be propagated as all values "
-                                               "are masked and operation_ignores_mask is False."):
+    with pytest.warns(NDCubeUserWarning, match="Uncertainties cannot be propagated as all values are masked and operation_ignores_mask is False."):
         output = cube.rebin(bin_shape, operation=np.sum, propagate_uncertainties=True,
                             operation_ignores_mask=False)
     assert output.uncertainty is None
@@ -1149,8 +1146,7 @@ def test_cube_arithmetic_rdivide(ndcube_2d_ln_lt_units, value):
 @pytest.mark.parametrize('value', [1, 2, -1])
 def test_cube_arithmetic_rdivide_uncertainty(ndcube_4d_unit_uncertainty, value):
     cube_quantity = u.Quantity(ndcube_4d_unit_uncertainty.data, ndcube_4d_unit_uncertainty.unit)
-    with pytest.warns(NDCubeUserWarning, match="UnknownUncertainty does not support uncertainty "
-                                               "propagation with correlation. Setting uncertainties to None."):
+    with pytest.warns(NDCubeUserWarning, match="UnknownUncertainty does not support uncertainty propagation with correlation. Setting uncertainties to None."):
         with np.errstate(divide='ignore'):
             new_cube =  value / ndcube_4d_unit_uncertainty
             check_arithmetic_value_and_units(new_cube,  value / cube_quantity)
@@ -1189,8 +1185,7 @@ def test_cube_arithmetic_power(ndcube_2d_ln_lt, power):
 @pytest.mark.parametrize('power', [2, -2, 10, 0.5])
 def test_cube_arithmetic_power_unknown_uncertainty(ndcube_4d_unit_uncertainty, power):
     cube_quantity = u.Quantity(ndcube_4d_unit_uncertainty.data, ndcube_4d_unit_uncertainty.unit)
-    with pytest.warns(NDCubeUserWarning, match="UnknownUncertainty does not support uncertainty propagation "
-                                               "with correlation. Setting uncertainties to None."):
+    with pytest.warns(NDCubeUserWarning, match="UnknownUncertainty does not support uncertainty propagation with correlation. Setting uncertainties to None."):
         with np.errstate(divide='ignore'):
             new_cube = ndcube_4d_unit_uncertainty ** power
             check_arithmetic_value_and_units(new_cube, cube_quantity**power)
@@ -1199,9 +1194,7 @@ def test_cube_arithmetic_power_unknown_uncertainty(ndcube_4d_unit_uncertainty, p
 @pytest.mark.parametrize('power', [2, -2, 10, 0.5])
 def test_cube_arithmetic_power_std_uncertainty(ndcube_2d_ln_lt_uncert, power):
     cube_quantity = u.Quantity(ndcube_2d_ln_lt_uncert.data, ndcube_2d_ln_lt_uncert.unit)
-    with pytest.warns(NDCubeUserWarning, match=r"<class 'astropy.nddata.nduncertainty.StdDevUncertainty'> "
-                                               r"does not support propagation of uncertainties for power. "
-                                               r"Setting uncertainties to None."):
+    with pytest.warns(NDCubeUserWarning, match=r"<class 'astropy.nddata.nduncertainty.StdDevUncertainty'> does not support propagation of uncertainties for power. Setting uncertainties to None."):
         with np.errstate(divide='ignore'):
             new_cube = ndcube_2d_ln_lt_uncert ** power
             check_arithmetic_value_and_units(new_cube, cube_quantity**power)
@@ -1235,11 +1228,9 @@ def test_squeeze(ndcube_4d_ln_l_t_lt):
 
 def test_squeeze_error(ndcube_4d_ln_l_t_lt):
     same = ndcube_4d_ln_l_t_lt.squeeze()[0:1,:,:,:]
-    with pytest.raises(ValueError, match="Cannot select any axis to squeeze out, "
-                                         "as none of them has size equal to one."):
+    with pytest.raises(ValueError, match="Cannot select any axis to squeeze out, as none of them has size equal to one."):
         same.squeeze([0,1])
-    with pytest.raises(ValueError, match="All axes are of length 1, therefore we will not squeeze NDCube to become "
-                                         "a scalar. Use `axis=` keyword to specify a subset of axes to squeeze."):
+    with pytest.raises(ValueError, match="All axes are of length 1, therefore we will not squeeze NDCube to become a scalar. Use `axis=` keyword to specify a subset of axes to squeeze."):
         same[0:1,0:1,0:1,0:1].squeeze()
 
 

ndcube/utils/collection.py

@@ -159,6 +159,5 @@ def assert_aligned_axes_compatible(data_dimensions1, data_dimensions2, data_axes
         if len(data_axes1) != len(data_axes2):
             raise ValueError(f"Number of aligned axes must be equal: {len(data_axes1)} != {len(data_axes2)}")
         # Confirm dimension lengths of each aligned axis is the same.
-        if not all(np.array(data_dimensions1)[np.array(data_axes1)] ==
-                   np.array(data_dimensions2)[np.array(data_axes2)]):
+        if not all(np.array(data_dimensions1)[np.array(data_axes1)] == np.array(data_dimensions2)[np.array(data_axes2)]):
             raise ValueError("All corresponding aligned axes between cubes must be of same length.")

ndcube/visualization/mpl_plotter.py

@@ -79,11 +79,11 @@ def plot(self, axes=None, plot_axes=None, axes_coordinates=None,
         with warnings.catch_warnings():
             warnings.simplefilter('ignore', AstropyUserWarning)
             if naxis == 1:
-                ax = self._plot_1d_cube(plot_wcs, axes, axes_coordinates,
+                ax = self._plot_1D_cube(plot_wcs, axes, axes_coordinates,
                                         axes_units, data_unit, **kwargs)
 
             elif naxis == 2 and 'y' in plot_axes:
-                ax = self._plot_2d_cube(plot_wcs, axes, plot_axes, axes_coordinates,
+                ax = self._plot_2D_cube(plot_wcs, axes, plot_axes, axes_coordinates,
                                         axes_units, data_unit, **kwargs)
             else:
                 ax = self._animate_cube(plot_wcs, plot_axes=plot_axes,
@@ -107,7 +107,7 @@ def _apply_axes_coordinates(self, axes, axes_coordinates):
             axes.coords[coord_index].set_ticks_visible(False)
             axes.coords[coord_index].set_ticklabel_visible(False)
 
-    def _plot_1d_cube(self, wcs, axes=None, axes_coordinates=None, axes_units=None,
+    def _plot_1D_cube(self, wcs, axes=None, axes_coordinates=None, axes_units=None,
                       data_unit=None, **kwargs):
         if axes is None:
             axes = plt.subplot(projection=wcs)
@@ -153,7 +153,7 @@ def _plot_1d_cube(self, wcs, axes=None, axes_coordinates=None, axes_units=None,
 
         return axes
 
-    def _plot_2d_cube(self, wcs, axes=None, plot_axes=None, axes_coordinates=None,
+    def _plot_2D_cube(self, wcs, axes=None, plot_axes=None, axes_coordinates=None,
                       axes_units=None, data_unit=None, **kwargs):
         if axes is None:
             axes = plt.subplot(projection=wcs, slices=plot_axes)

ndcube/visualization/mpl_sequence_plotter.py

@@ -54,10 +54,7 @@ def animate(self, sequence_axis_coords=None, sequence_axis_unit=None, **kwargs):
             The unit in which the sequence_axis_coordinates should be displayed.
             If None, the default unit will be used.
         """
-        return SequenceAnimator(self._ndcube,
-                                sequence_axis_coords=sequence_axis_coords,
-                                sequence_axis_unit=sequence_axis_unit,
-                                **kwargs)
+        return SequenceAnimator(self._ndcube, sequence_axis_coords=sequence_axis_coords, sequence_axis_unit=sequence_axis_unit, **kwargs)
 
 
 class SequenceAnimator(ArrayAnimatorWCS):