…emp fix)

* check if Keras present

* change TF to Keras in CI

* remove comment

* change dependencies in pyproject.toml for Keras 3.0

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

* change tensorflow dependency for cellfinder

* replace keras imports from tensorflow to just keras imports

* add keras import and reorder

* add keras and TF 2.16 to pyproject.toml

* comment out TF version check for now

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

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

* apply temp garbage collector fix

* skip troublesome test

* skip running tests on CI on windows

* remove commented out TF check

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

* remove str conversion before model.save

* raise test_detection error for sonarcloud happy

* skip running tests on windows on CI

* remove filename comment and small edits

* change some old references to TF for the import check

* change TF cached model to Keras

* replace tensorflow Tensor with keras tensor

* add case for TF prep in prep_model_weights

* add different backends to pyproject.toml

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

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

* run tox using TF and JAX backend

* install TF in brainmapper environment before running tests in CI

* add backends check to cellfinder init file

* clean up comments

* fix tf-nightly import check

* specify TF backend in include guard check

* clarify comment

* remove 'backend' from dependencies specifications

* Apply suggestions from code review

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

---------

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* use jax backend in brainmapper tests in CI

* skip TF backend on windows

* fix pip install cellfinder for brainmapper CI tests

* add keras env variable for brainmapper CLI tests

* fix prep_model_weights

* replace tensorflow Tensor with keras tensor

* add case for TF prep in prep_model_weights

* add different backends to pyproject.toml

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

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

* run tox using TF and JAX backend

* install TF in brainmapper environment before running tests in CI

* add backends check to cellfinder init file

* clean up comments

* fix tf-nightly import check

* specify TF backend in include guard check

* clarify comment

* remove 'backend' from dependencies specifications

* Apply suggestions from code review

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

* PyTorch runs utilizing multiple cores

* PyTorch fix with default models

* Tests run on every push for now

* Run test on torch backend only

* Fixed guard test to set torch as KERAS_BACKEND

* KERAS_BACKEND env variable set directly in test_include_guard.yaml

* Run test on python 3.11

* Remove tf-nightly from __init__ version check

* Added 3.11 to legacy tox config

* Changed legacy tox config for real this time

* Don't set the wrong max_processing value

* Torch is now set as the default backend

* Tests only run with torch, updated comments

* Unpinned torch version

* Add codecov token (#403)

* add codecov token

* generate xml coverage report

* add timeout to testing jobs

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

* Allow turning off classification or detection in GUI.

* Fix test.

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

for more information, see https://pre-commit.ci

* Refactor to fix code analysis errors.

* Ensure array is always 2d.

* Apply suggestions from code review

Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>

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

* Support single z-stack tif file for input.

* Fix commit hook.

* Apply review suggestions.

* Remove modular asv benchmarks (#406)

* remove modular asv benchmarks

* recover old structure

* remove asv-specific lines from gitignore and manifest

* prune benchmarks

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

* naive attempt at adapting to silicon mac CI

* run include guard test on Silicon CI

* double-check hdf5 is needed

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

* Replace coord map values with numba list/tuple for optim.

* Switch to fortran layout for faster update of last dim.

* Cache kernel.

* jit ball filter.

* Put z as first axis to speed z rolling (row-major memory).

* Unroll recursion (no perf impact either way).

* Parallelize cell cluster splitting.

* Parallelize walking for full images.

* Cleanup docs and pep8 etc.

* Add pre-commit fixes.

* Fix parallel always being selected and numba function 1st class warning.

* Run hook.

* Older python needs Union instead of |.

* Accept review suggestion.



* Address review changes.

* num_threads must be an int.

---------

Co-authored-by: Matt Einhorn <matt@einhorn.dev>

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

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0)
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.4.3](astral-sh/ruff-pre-commit@v0.3.5...v0.4.3)
- [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: sfmig <33267254+sfmig@users.noreply.github.com>

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

for more information, see https://pre-commit.ci

* Simplify model download (#414)

* Simplify model download

* Update model cache

* Remove jax and tf tests

* Standardise the data types for inputs to all be float32

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

* Added PYTORCH_MPS_HIGH_WATERMARK_RATION env variable

* Set env variables in test setup

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

* Add device call to Conv3D to force cpu

* Revert changes, request one cpu left free

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

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

* Lowercase Torch

* Change cache directory

---------

Co-authored-by: sfmig <33267254+sfmig@users.noreply.github.com>
Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Co-authored-by: Matt Einhorn <matt@einhorn.dev>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Co-authored-by: Adam Tyson <code@adamltyson.com>

# Conflicts:
#	.github/workflows/test_and_deploy.yml
#	.github/workflows/test_include_guard.yaml
#	cellfinder/core/main.py
#	cellfinder/core/tools/prep.py
#	cellfinder/core/train/train_yml.py
#	tests/core/conftest.py

…e set to cpu

…issing2