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Migrate to Keras 3.0 with TF backend#373

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Merged

IgorTatarnikov merged 18 commits intocellfinder-to-keras-3brainglobe/cellfinder:cellfinder-to-keras-3from smg/keras3-tf-backendbrainglobe/cellfinder:smg/keras3-tf-backendCopy head branch name to clipboardFeb 8, 2024

+72-65

Commits

Commits on Feb 5, 2024

• remove pytest-lazy-fixture as dev dependency and skip test (with WG temp fix)

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• change tensorflow dependency for cellfinder

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• replace keras imports from tensorflow to just keras imports

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• add keras import and reorder

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Commits on Feb 6, 2024

• add keras and TF 2.16 to pyproject.toml

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• comment out TF version check for now

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• change checkpoint filename for compliance with keras 3. remove use_multiprocessing=False from fit() as it is no longer an input. test_train() passing

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• add multiprocessing parameters to cube generator constructor and remove from fit() signature (keras3 change)

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• apply temp garbage collector fix

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• skip troublesome test

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• skip running tests on CI on windows

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• remove commented out TF check

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• clean commented out code. Explicitly pass use_multiprocessing=False (as before)

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• remove str conversion before model.save

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• raise test_detection error for sonarcloud happy

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Commits on Feb 7, 2024

• skip running tests on windows on CI

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• remove filename comment and small edits

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• Merge branch 'cellfinder-to-keras-3' into smg/keras3-tf-backend

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