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It/keras3 pytorch #396

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merged 56 commits into from
May 10, 2024
Merged

It/keras3 pytorch #396

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f23c402
replace tensorflow Tensor with keras tensor
sfmig Feb 7, 2024
d508b9f
add case for TF prep in prep_model_weights
sfmig Feb 7, 2024
559c9ab
add different backends to pyproject.toml
sfmig Feb 7, 2024
d3cb209
add backend configuration to cellfinder init file. tests passing with…
sfmig Feb 7, 2024
c8e0ac8
define extra dependencies for cellfinder with different backends. run…
sfmig Feb 8, 2024
313b988
run tox using TF and JAX backend
sfmig Feb 8, 2024
681925e
install TF in brainmapper environment before running tests in CI
sfmig Feb 8, 2024
0ff4546
add backends check to cellfinder init file
sfmig Feb 8, 2024
6ec3c33
clean up comments
sfmig Feb 8, 2024
f4857e1
fix tf-nightly import check
sfmig Feb 8, 2024
b32fab4
specify TF backend in include guard check
sfmig Feb 8, 2024
8bfa0d9
clarify comment
sfmig Feb 8, 2024
576340b
remove 'backend' from dependencies specifications
sfmig Feb 9, 2024
89339fa
Apply suggestions from code review
sfmig Feb 9, 2024
01394af
PyTorch runs utilizing multiple cores
IgorTatarnikov Feb 14, 2024
22db8f4
PyTorch fix with default models
IgorTatarnikov Apr 5, 2024
64bde71
Tests run on every push for now
IgorTatarnikov Apr 5, 2024
585e7da
Merge branch 'cellfinder-to-keras-3' into it/keras3-pytorch
IgorTatarnikov Apr 5, 2024
2934f35
Run test on torch backend only
IgorTatarnikov Apr 5, 2024
014b549
Fixed guard test to set torch as KERAS_BACKEND
IgorTatarnikov Apr 5, 2024
315dbc4
KERAS_BACKEND env variable set directly in test_include_guard.yaml
IgorTatarnikov Apr 5, 2024
4590106
Run test on python 3.11
IgorTatarnikov Apr 5, 2024
0ddb2e0
Remove tf-nightly from __init__ version check
IgorTatarnikov Apr 5, 2024
d4fed06
Merge branch 'main' into it/keras3-pytorch
IgorTatarnikov Apr 5, 2024
fe7b798
Added 3.11 to legacy tox config
IgorTatarnikov Apr 5, 2024
dcb315c
Changed legacy tox config for real this time
IgorTatarnikov Apr 5, 2024
8e77b68
Don't set the wrong max_processing value
IgorTatarnikov Apr 15, 2024
30b72f1
Torch is now set as the default backend
IgorTatarnikov Apr 16, 2024
550a126
Merge branch 'main' into it/keras3-pytorch
IgorTatarnikov Apr 16, 2024
1de446c
Tests only run with torch, updated comments
IgorTatarnikov Apr 16, 2024
f676f32
Merge branch 'cellfinder-to-keras-3' into it/keras3-pytorch
IgorTatarnikov Apr 16, 2024
e4bd665
Unpinned torch version
IgorTatarnikov Apr 16, 2024
f578095
Merge branch 'it/keras3-pytorch' of https://github.com/brainglobe/cel…
IgorTatarnikov Apr 16, 2024
560909f
Add codecov token (#403)
K-Meech Apr 18, 2024
e6a887f
Allow turning off classification or detection in GUI (#402)
matham Apr 22, 2024
b1b285c
Support single z-stack tif file for input (#397)
matham May 1, 2024
0fd0a5e
Remove modular asv benchmarks (#406)
sfmig May 1, 2024
6b529dc
Adapt CI so it covers both new and old Macs, and installs required ad…
alessandrofelder May 1, 2024
a283056
Optimize cell detection (#398) (#407)
alessandrofelder May 3, 2024
eeffd78
[pre-commit.ci] pre-commit autoupdate (#412)
pre-commit-ci[bot] May 7, 2024
8de63bd
Apply suggestions from code review
IgorTatarnikov May 8, 2024
860942c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 8, 2024
5f4882e
Simplify model download (#414)
adamltyson May 9, 2024
906f4d6
Remove jax and tf tests
IgorTatarnikov May 9, 2024
7e40ffc
Standardise the data types for inputs to all be float32
IgorTatarnikov May 9, 2024
933e5dd
Force torch to use CPU on arm based macOS during tests
IgorTatarnikov May 9, 2024
ada5f77
Added PYTORCH_MPS_HIGH_WATERMARK_RATION env variable
IgorTatarnikov May 9, 2024
546f223
Set env variables in test setup
IgorTatarnikov May 9, 2024
0546a56
Try to set the default device to cpu in the test itself
IgorTatarnikov May 9, 2024
8eb5ee3
Add device call to Conv3D to force cpu
IgorTatarnikov May 9, 2024
b995bb3
Revert changes, request one cpu left free
IgorTatarnikov May 9, 2024
78d1588
Revers the numb cores, don't use arm based mac runner
IgorTatarnikov May 9, 2024
663b69a
Merge branch 'main' into it/keras3-pytorch
IgorTatarnikov May 9, 2024
806f52b
Merged main, removed torch flags on cellfinder install for guards and…
IgorTatarnikov May 9, 2024
a38257b
Lowercase Torch
IgorTatarnikov May 9, 2024
5a1f0a8
Change cache directory
IgorTatarnikov May 9, 2024
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1 change: 1 addition & 0 deletions .github/workflows/test_and_deploy.yml
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Expand Up @@ -39,6 +39,7 @@ jobs:
runs-on: ${{ matrix.os }}
env:
PYTORCH_ENABLE_MPS_FALLBACK: "1"
PYTORCH_MPS_HIGH_WATERMARK_RATIO: "0.0"
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strategy:
matrix:
# Run all supported Python versions on linux
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