Details
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Type:
Story
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Status: Done
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Resolution: Done
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Fix Version/s: None
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Component/s: spectractor
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Labels:None
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Story Points:0.2
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Team:Architecture
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Urgent?:No
Description
Butler tests force imports of all storage classes as part of a storage class test. This generates a bunch of deprecation warnings from spectractor:
tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/tools.py:6: DeprecationWarning: `photutils.IRAFStarFinder` is a deprecated alias for `photutils.detection.IRAFStarFinder` and will be removed in the future. Instead, please use `from photutils.detection import IRAFStarFinder` to silence this warning.
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from photutils import IRAFStarFinder
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tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/tools.py:20: DeprecationWarning: Please use `maximum_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
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from scipy.ndimage.filters import maximum_filter
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tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/tools.py:21: DeprecationWarning: Please use `generate_binary_structure` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecated.
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from scipy.ndimage.morphology import generate_binary_structure, binary_erosion
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tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/tools.py:21: DeprecationWarning: Please use `binary_erosion` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecated.
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from scipy.ndimage.morphology import generate_binary_structure, binary_erosion
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tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/extractor/background.py:12: DeprecationWarning: `photutils.Background2D` is a deprecated alias for `photutils.background.Background2D` and will be removed in the future. Instead, please use `from photutils.background import Background2D` to silence this warning.
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from photutils import Background2D, SExtractorBackground
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tests/test_storageClass.py::StorageClassFactoryTestCase::testFactoryFind
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/Users/timj/work/lsstsw/stack/lsst-scipipe-6.0.0/Darwin/spectractor/g088299903b/lib/python/spectractor/extractor/background.py:12: DeprecationWarning: `photutils.SExtractorBackground` is a deprecated alias for `photutils.background.SExtractorBackground` and will be removed in the future. Instead, please use `from photutils.background import SExtractorBackground` to silence this warning.
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from photutils import Background2D, SExtractorBackground
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Please fix.
Attachments
Activity
Additional warning from test output:
spectractor/tools.py:1424: FutureWarning: use_gaussian_derivatives currently defaults to False, but will change to True in a future version. Please specify this argument explicitly to maintain the current behavior
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spectractor/fit/fitter.py:1334: OptimizeWarning: Unknown solver options: ftol
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(I'm not sure why the warnings turn up twice when the package builds via eupspkg).
I fixed a bunch of warnings. There are still lots more when you run tests but you can put them on a new ticket.
Jeremy Neveu (I've DMed you, but just re-posting here): could you take a look at the PR and just make sure you'll be OK with me up-streaming all these to you?
Approved on GitHub.
Matthias Wittgen has found that in the rubin-env 7.0.0dev python 3.11 env we have additional problems with spectractor in the use of axes vs ax parameters (seemingly from np.histogram). These deprecation warnings were not shown above.