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.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
       toxdeps: tox-pypi-filter
       posargs: -n auto
       envs: |
-        - linux: py311
+        - linux: py312
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -42,15 +42,15 @@ jobs:
       posargs: -n auto
       envs: |
         - windows: py310
-        - macos: py39
+        - macos: py311
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   docs:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: "3.9"
+      default_python: "3.12"
       submodules: false
       pytest: false
       toxdeps: tox-pypi-filter
@@ -69,13 +69,12 @@ jobs:
     needs: [docs]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
     with:
-      default_python: "3.9"
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       posargs: -n auto --dist loadgroup
       envs: |
-        - linux: py39-online
+        - linux: py312-online
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -95,7 +94,7 @@ jobs:
     needs: [test]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
     with:
-      python-version: "3.10"
+      python-version: "3.12"
       test_extras: "all,tests"
       test_command: 'pytest -p no:warnings --doctest-rst -m "not mpl_image_compare" --pyargs sunpy'
       submodules: false

.pre-commit-config.yaml

@@ -1,10 +1,9 @@
-exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
 repos:
   - repo: https://github.com/myint/docformatter
     rev: v1.7.5
     hooks:
       - id: docformatter
-        args: [--in-place, --pre-summary-newline, --make-summary-multi]
+        args: ["--in-place", "--pre-summary-newline", "--make-summary-multi"]
   - repo: https://github.com/myint/autoflake
     rev: v2.3.1
     hooks:
@@ -21,25 +20,27 @@ repos:
     hooks:
       - id: ruff
         args: ["--fix", "--unsafe-fixes"]
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
-    hooks:
-      - id: prettier
+      - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
       - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
       - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
       - id: check-yaml
       - id: debug-statements
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier

CHANGELOG.rst

@@ -235,7 +235,7 @@ Features
 - :func:`aiapy.calibrate.degradation` can now accept `~astropy.time.Time` objects with length greater than 1.
   This makes it easier to compute the channel degradation over long intervals. (`#80 <https://gitlab.com/LMSAL_HUB/aia_hub/aiapy/-/merge_requests/80>`__)
 - Citation information for `aiapy` is now available from ``aiapy.__citation__``. (`#82 <https://gitlab.com/LMSAL_HUB/aia_hub/aiapy/-/merge_requests/82>`__)
-- The pointing table can now be passsed in as a keyword argument to :func:`aiapy.calibrate.update_pointing`.
+- The pointing table can now be passed in as a keyword argument to :func:`aiapy.calibrate.update_pointing`.
   Added a :func:`aiapy.calibrate.util.get_pointing_table` to retrieve the 3-hour pointing table from JSOC over a given time interval. (`#84 <https://gitlab.com/LMSAL_HUB/aia_hub/aiapy/-/merge_requests/84>`__)
 
 Bug Fixes

aiapy/__init__.py

@@ -1,5 +1,5 @@
-from pathlib import Path
 from itertools import compress
+from pathlib import Path
 
 from .version import version as __version__
 

aiapy/calibrate/__init__.py

@@ -2,8 +2,8 @@
 Subpackage for calibrating AIA imaging data.
 """
 
-from .meta import *  # NOQA
-from .prep import *  # NOQA
-from .spikes import *  # NOQA
-from .transform import *  # NOQA
-from .uncertainty import *  # NOQA
+from .meta import *  # NOQA: F403
+from .prep import *  # NOQA: F403
+from .spikes import *  # NOQA: F403
+from .transform import *  # NOQA: F403
+from .uncertainty import *  # NOQA: F403

aiapy/calibrate/meta.py

@@ -56,7 +56,7 @@ def fix_observer_location(smap):
     new_meta["hglt_obs"] = coord.lat.to(u.degree).value
     new_meta["dsun_obs"] = coord.radius.to(u.m).value
 
-    return smap._new_instance(smap.data, new_meta, plot_settings=smap.plot_settings, mask=smap.mask)
+    return smap._new_instance(smap.data, new_meta, plot_settings=smap.plot_settings, mask=smap.mask)  # NOQA: SLF001
 
 
 def update_pointing(smap, *, pointing_table=None):
@@ -104,10 +104,12 @@ def update_pointing(smap, *, pointing_table=None):
     `aiapy.calibrate.util.get_pointing_table`
     """
     if not contains_full_disk(smap):
-        raise ValueError("Input must be a full disk image.")
+        msg = "Input must be a full disk image."
+        raise ValueError(msg)
     shape_full_frame = (4096, 4096)
-    if not all(d == (s * u.pixel) for d, s in zip(smap.dimensions, shape_full_frame)):
-        raise ValueError(f"Input must be at the full resolution of {shape_full_frame}")
+    if not all(d == (s * u.pixel) for d, s in zip(smap.dimensions, shape_full_frame, strict=False)):
+        msg = f"Input must be at the full resolution of {shape_full_frame}"
+        raise ValueError(msg)
     if pointing_table is None:
         # Make range wide enough to get closest 3-hour pointing
         pointing_table = get_pointing_table(smap.date - 12 * u.h, smap.date + 12 * u.h)
@@ -134,10 +136,13 @@ def update_pointing(smap, *, pointing_table=None):
     t_obs = astropy.time.Time(t_obs)
     t_obs_in_interval = np.logical_and(t_obs >= pointing_table["T_START"], t_obs < pointing_table["T_STOP"])
     if not t_obs_in_interval.any():
-        raise IndexError(
+        msg = (
             f"No valid entries for {t_obs} in pointing table "
             f'with first T_START date of {pointing_table[0]["T_START"]} '
-            f'and a last T_STOP date of {pointing_table[-1]["T_STOP"]}.',
+            f'and a last T_STOP date of {pointing_table[-1]["T_STOP"]}.'
+        )
+        raise IndexError(
+            msg,
         )
     i_nearest = np.where(t_obs_in_interval)[0][0]
     w_str = f"{smap.wavelength.to(u.angstrom).value:03.0f}"
@@ -185,4 +190,4 @@ def update_pointing(smap, *, pointing_table=None):
     new_meta.pop("PC1_2")
     new_meta.pop("PC2_1")
     new_meta.pop("PC2_2")
-    return smap._new_instance(smap.data, new_meta, plot_settings=smap.plot_settings, mask=smap.mask)
+    return smap._new_instance(smap.data, new_meta, plot_settings=smap.plot_settings, mask=smap.mask)  # NOQA: SLF001

aiapy/calibrate/prep.py

@@ -69,10 +69,12 @@ def register(smap, *, missing=None, order=3, method="scipy"):
     # This implementation is taken directly from the `aiaprep` method in
     # sunpy.instr.aia.aiaprep under the terms of the BSD 2 Clause license.
     # See licenses/SUNPY.rst.
-    if not isinstance(smap, (AIAMap, HMIMap)):
-        raise ValueError("Input must be an AIAMap or HMIMap.")
+    if not isinstance(smap, AIAMap | HMIMap):
+        msg = "Input must be an AIAMap or HMIMap."
+        raise TypeError(msg)
     if not contains_full_disk(smap):
-        raise ValueError("Input must be a full disk image.")
+        msg = "Input must be a full disk image."
+        raise ValueError(msg)
     if smap.processing_level is None or smap.processing_level > 1:
         warnings.warn(
             "Image registration should only be applied to level 1 data",

aiapy/calibrate/spikes.py

@@ -63,9 +63,11 @@ def respike(smap, *, spikes=None):
     `fetch_spikes`
     """
     if not isinstance(smap, AIAMap):
-        raise ValueError("Input must be an AIAMap.")
+        msg = "Input must be an AIAMap."
+        raise TypeError(msg)
     if smap.meta["lvl_num"] != 1.0:
-        raise ValueError("Can only apply respike procedure to level 1 data")
+        msg = "Can only apply respike procedure to level 1 data"
+        raise ValueError(msg)
     # Approximate check to make sure the input map has not been interpolated
     # in any way. Note that the level 1 plate scales are not exactly 0.6
     # ''/pixel, but should not differ by more than 0.1%. This is only a
@@ -88,7 +90,8 @@ def respike(smap, *, spikes=None):
     # Or better yet, why can't the logic below just handle the case of
     # no spikes?
     if smap.meta["nspikes"] == 0:
-        raise ValueError("No spikes were present in the level 0 data.")
+        msg = "No spikes were present in the level 0 data."
+        raise ValueError(msg)
     if spikes is None:
         coords, values = fetch_spikes(smap, as_coords=False)
     else:
@@ -102,7 +105,7 @@ def respike(smap, *, spikes=None):
     new_meta["lvl_num"] = 0.5
     new_meta["comments"] = f"Respike applied; {values.shape[0]} hot pixels reinserted."
     new_meta["nspikes"] = 0
-    return smap._new_instance(
+    return smap._new_instance(  # NOQA: SLF001
         new_data,
         new_meta,
         plot_settings=smap.plot_settings,
@@ -151,7 +154,7 @@ def fetch_spikes(smap, *, as_coords=False):
     # If this is a cutout, need to transform the full-frame pixel
     # coordinates into the cutout pixel coordinates and then only select
     # those in the FOV of the cutout
-    if not all(d == (s * u.pixel) for d, s in zip(smap.dimensions, shape_full_frame)):
+    if not all(d == (s * u.pixel) for d, s in zip(smap.dimensions, shape_full_frame, strict=False)):
         # Construct WCS for full frame
         wcs_full_frame = copy.deepcopy(smap.wcs)
         wcs_full_frame.wcs.crval = np.array([0.0, 0.0])

aiapy/calibrate/tests/test_prep.py

@@ -95,7 +95,7 @@ def test_register_level_15(lvl_15_map):
         AiapyUserWarning,
         match="Image registration should only be applied to level 1 data",
     ):
-        register(lvl_15_map._new_instance(lvl_15_map.data, new_meta))
+        register(lvl_15_map._new_instance(lvl_15_map.data, new_meta))  # NOQA: SLF001
 
 
 @pytest.mark.parametrize(
@@ -256,7 +256,7 @@ def test_degradation_time_array():
         calibration_version=8,
     )
     assert time_correction.shape == obstime.shape
-    for o, tc in zip(obstime, time_correction):
+    for o, tc in zip(obstime, time_correction, strict=False):
         assert tc == degradation(94 * u.angstrom, o, correction_table=correction_table, calibration_version=8)
 
 

aiapy/calibrate/tests/test_spikes.py

@@ -35,7 +35,7 @@ def spikes(despiked_map):
 @pytest.mark.remote_data()
 def test_respike(respiked_map, spikes):
     coords, values = spikes
-    for x, y, v in zip(coords.x.value, coords.y.value, values):
+    for x, y, v in zip(coords.x.value, coords.y.value, values, strict=False):
         assert v == respiked_map.data[int(y), int(x)]
 
 
@@ -87,7 +87,7 @@ def test_exceptions(despiked_map, key, value, match):
 @pytest.mark.remote_data()
 def test_resample_warning(despiked_map):
     despiked_map_resample = despiked_map.resample((512, 512) * u.pixel)
-    with pytest.warns(AiapyUserWarning):
+    with pytest.warns(AiapyUserWarning, match="DEF"):
         respike(despiked_map_resample)
 
 

aiapy/calibrate/transform.py

@@ -10,10 +10,10 @@
     handles_image_nans=False,
     handles_nan_missing=True,
 )
-def _rotation_cupy(image, matrix, shift, order, missing, clip):
+def _rotation_cupy(image, matrix, shift, order, missing, clip):  # NOQA: ARG001
     """
     * Rotates using `cupyx.scipy.ndimage.affine_transform` from `cupy <https://docs.cupy.dev/en/stable/index.html>`__
-    * Coverts from a numpy array to a cupy array and then back again.
+    * Converts from a numpy array to a cupy array and then back again.
     * The ``order`` parameter is the order of the spline interpolation, and ranges
       from 0 to 5.
     * The ``mode`` parameter for :func:`~cupyx.scipy.ndimage.affine_transform` is fixed to
@@ -23,8 +23,9 @@ def _rotation_cupy(image, matrix, shift, order, missing, clip):
         import cupy
         import cupyx.scipy.ndimage
     except ImportError as e:
+        msg = "cupy or cupy-cuda* (pre-compiled for each cuda version) is required to use this rotation method."
         raise ImportError(
-            "cupy or cupy-cuda* (pre-compiled for each cuda version) is required to use this rotation method.",
+            msg,
         ) from e
     rotated_image = cupyx.scipy.ndimage.affine_transform(
         cupy.array(image).T,

aiapy/calibrate/uncertainty.py

@@ -119,7 +119,8 @@ def estimate_error(
 
     # Photometric calibration
     if include_eve and include_preflight:
-        raise ValueError("Cannot include both EVE and pre-flight correction.")
+        msg = "Cannot include both EVE and pre-flight correction."
+        raise ValueError(msg)
     calib = 0
     if include_eve:
         calib = error_table["EVEERR"]

aiapy/calibrate/util.py

@@ -72,10 +72,11 @@ def get_correction_table(*, correction_table=None):
     if isinstance(correction_table, astropy.table.QTable):
         return correction_table
     if correction_table is not None:
-        if isinstance(correction_table, (str, pathlib.Path)):
+        if isinstance(correction_table, str | pathlib.Path):
             table = QTable(astropy.io.ascii.read(correction_table))
         else:
-            raise ValueError("correction_table must be a file path, an existing table, or None.")
+            msg = "correction_table must be a file path, an existing table, or None."
+            raise ValueError(msg)
     else:
         # NOTE: the [!1=1!] disables the drms PrimeKey logic and enables
         # the query to find records that are ordinarily considered
@@ -143,7 +144,8 @@ def _select_epoch_from_correction_table(channel: u.angstrom, obstime, table, *,
     # Select the epoch for the given observation time
     obstime_in_epoch = np.logical_and(obstime >= table["T_START"], obstime < table["T_STOP"])
     if not obstime_in_epoch.any():
-        raise ValueError(f"No valid calibration epoch for {obstime}")
+        msg = f"No valid calibration epoch for {obstime}"
+        raise ValueError(msg)
     # NOTE: In some cases, there may be multiple entries for a single epoch. We want to
     # use the most up-to-date one.
     i_epoch = np.where(obstime_in_epoch)[0]
@@ -199,7 +201,8 @@ def get_pointing_table(start, end):
         # If there's no pointing information available between these times,
         # JSOC will raise a cryptic KeyError
         # (see https://github.com/LM-SAL/aiapy/issues/71)
-        raise RuntimeError(f"Could not find any pointing information between {start} and {end}")
+        msg = f"Could not find any pointing information between {start} and {end}"
+        raise RuntimeError(msg)
     table["T_START"] = Time(table["T_START"], scale="utc")
     table["T_STOP"] = Time(table["T_STOP"], scale="utc")
     for c in table.colnames:
@@ -211,9 +214,8 @@ def get_pointing_table(start, end):
             table[c].unit = "degree"
     # Remove masking on columns with pointing parameters
     for c in table.colnames:
-        if any(n in c for n in ["X0", "Y0", "IMSCALE", "INSTROT"]):
-            if hasattr(table[c], "mask"):
-                table[c] = table[c].filled(np.nan)
+        if any(n in c for n in ["X0", "Y0", "IMSCALE", "INSTROT"]) and hasattr(table[c], "mask"):
+            table[c] = table[c].filled(np.nan)
     return table
 
 
@@ -224,12 +226,13 @@ def get_error_table(error_table=None):
         os.environ["PARFIVE_DISABLE_RANGE"] = "1"
         error_table = fetch_error_table()
         os.environ.pop("PARFIVE_DISABLE_RANGE")
-    if isinstance(error_table, (str, pathlib.Path)):
+    if isinstance(error_table, str | pathlib.Path):
         table = astropy.io.ascii.read(error_table)
     elif isinstance(error_table, QTable):
         table = error_table
     else:
-        raise ValueError("error_table must be a file path, an existing table, or None.")
+        msg = f"error_table must be a file path, an existing table, or None, not {type(error_table)}"
+        raise TypeError(msg)
     table = QTable(table)
     table["DATE"] = Time(table["DATE"], scale="utc")
     table["T_START"] = Time(table["T_START"], scale="utc")

aiapy/conftest.py

@@ -11,9 +11,9 @@
 
 # Force MPL to use non-gui backends for testing.
 with contextlib.suppress(ImportError):
-    import matplotlib
+    import matplotlib as mpl
 
-    matplotlib.use("Agg")
+    mpl.use("Agg")
 
 
 @pytest.fixture()
@@ -45,8 +45,8 @@ def idl_available():
         import hissw
 
         hissw.Environment().run("")
-        return True
-    except Exception as e:  # NOQA
+        return True  # NOQA: TRY300
+    except Exception as e:  # NOQA: BLE001
         log.warning(e)
         return False