Code

It/keras3 pytorch#396

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Merged

IgorTatarnikov merged 56 commits intocellfinder-to-keras-3brainglobe/cellfinder:cellfinder-to-keras-3from it/keras3-pytorchbrainglobe/cellfinder:it/keras3-pytorchCopy head branch name to clipboardMay 10, 2024

+984-991

Commits

Commits on Feb 8, 2024

• replace tensorflow Tensor with keras tensor

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• add case for TF prep in prep_model_weights

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• add different backends to pyproject.toml

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• add backend configuration to cellfinder init file. tests passing with jax locally

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• define extra dependencies for cellfinder with different backends. run tox with TF backend

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• run tox using TF and JAX backend

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• install TF in brainmapper environment before running tests in CI

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• add backends check to cellfinder init file

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• clean up comments

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• fix tf-nightly import check

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• specify TF backend in include guard check

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• clarify comment

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Commits on Feb 9, 2024

• remove 'backend' from dependencies specifications

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• Apply suggestions from code review

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Commits on Feb 14, 2024

• PyTorch runs utilizing multiple cores

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Commits on Apr 5, 2024

• PyTorch fix with default models

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• Tests run on every push for now

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• Merge branch 'cellfinder-to-keras-3' into it/keras3-pytorch

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• Run test on torch backend only

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• Fixed guard test to set torch as KERAS_BACKEND

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• KERAS_BACKEND env variable set directly in test_include_guard.yaml

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• Run test on python 3.11

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• Remove tf-nightly from __init__ version check

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• Merge branch 'main' into it/keras3-pytorch

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• Added 3.11 to legacy tox config

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• Changed legacy tox config for real this time

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Commits on Apr 15, 2024

• Don't set the wrong max_processing value

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Commits on Apr 16, 2024

• Torch is now set as the default backend

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• Merge branch 'main' into it/keras3-pytorch

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• Tests only run with torch, updated comments

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• Merge branch 'cellfinder-to-keras-3' into it/keras3-pytorch

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• Unpinned torch version

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• Merge branch 'it/keras3-pytorch' of https://github.com/brainglobe/cellfinder into it/keras3-pytorch

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Commits on Apr 18, 2024

• Add codecov token (#403)

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Commits on Apr 22, 2024

• Allow turning off classification or detection in GUI (#402)

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Commits on May 1, 2024

• Support single z-stack tif file for input (#397)

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• Remove modular asv benchmarks (#406)

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• Adapt CI so it covers both new and old Macs, and installs required additional dependencies on M1 (#408)

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Commits on May 3, 2024

• Optimize cell detection (#398) (#407)

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Commits on May 7, 2024

• [pre-commit.ci] pre-commit autoupdate (#412)

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Commits on May 8, 2024

• Apply suggestions from code review

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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Commits on May 9, 2024

• Simplify model download (#414)

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• Remove jax and tf tests

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• Standardise the data types for inputs to all be float32

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• Force torch to use CPU on arm based macOS during tests

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• Added PYTORCH_MPS_HIGH_WATERMARK_RATION env variable

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• Set env variables in test setup

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• Try to set the default device to cpu in the test itself

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• Add device call to Conv3D to force cpu

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• Revert changes, request one cpu left free

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• Revers the numb cores, don't use arm based mac runner

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• Merge branch 'main' into it/keras3-pytorch

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• Merged main, removed torch flags on cellfinder install for guards and brainmapper

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• Lowercase Torch

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• Change cache directory

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