It/keras3 pytorch #396
It/keras3 pytorch #396
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… tox with TF backend
Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
* 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>
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Looking good @IgorTatarnikov ! Mainly minor comments or questions in the review. Some higher-level comments below.
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I know you say in the description that docs are not required atm, but maybe a quick edit to the README is useful so that we don't forget when we return to this. Could be just stating the need to install a backend, the need to configure the backend (via env variable for example) if developing, how to run tests locally with all backends etc.
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I ran the tests locally using
toxwith the three backends and got some errors fortorchthat seem to relate to Apple chips. I wrote some more details and a possible workaround in the review. -
The comparison with the previous performance looks great! Not the focus of this review, but I was thinking for the blogpost it would be more relevant to compare the
torchimplementation and the previous TF implementation more explicitly. Right now the comparison is more like: given an implementation, how does default model compare to retrained model.
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
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Description
What is this PR
Why is this PR needed?
Migrating away from tensorflow backend.
What does this PR do?
Makes torch the default backend, CI tests will only run with a torch backend on python 3.9, 3.10 and 3.11.
References
Please reference any existing issues/PRs that relate to this PR.
How has this PR been tested?
Tested locally and on CI.
Is this a breaking change?
Hopefully not? If people want to continue using a tensorflow installation all they have to do is run
export KERAS_BACKEND="tensorflow"and make suretensorflow>=2.16.1Does this PR require an update to the documentation?
Not this one. The PR from
cellfinder-to-keras-3tomainwill definitely need extra documentation. Might be worth timing the release of the next version with a blog post explaining the changes.Checklist: