… jax locally

… tox with TF backend

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

…lfinder into it/keras3-pytorch

* add codecov token

* generate xml coverage report

* add timeout to testing jobs

* 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.

* Fix commit hook.

* Apply review suggestions.

* remove modular asv benchmarks

* recover old structure

* remove asv-specific lines from gitignore and manifest

* prune benchmarks

…ditional dependencies on M1 (#408)

* naive attempt at adapting to silicon mac CI

* run include guard test on Silicon CI

* double-check hdf5 is needed

* 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>

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>

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

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

* Simplify model download

* Update model cache

# Conflicts:
#	.github/workflows/test_and_deploy.yml
#	.github/workflows/test_include_guard.yaml
#	cellfinder/core/tools/prep.py

… brainmapper