Switch to fractal-task-tools and deprecate current tools from fractal-tasks-core

[tcompa]

This is in principle ready, but we may want to review when to merge&release (depending on whether/when additional changes to fractal-tasks-tools are planned).

Checklist before merging

• I added an appropriate entry to CHANGELOG.md

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
fractal_tasks_core/tasks
_utils.py					22-24, 42
apply_registration_to_image.py					398
calculate_registration_image_based.py					312
cellpose_segmentation.py					612
cellvoyager_to_ome_zarr_compute.py					247
cellvoyager_to_ome_zarr_init.py					485
cellvoyager_to_ome_zarr_init_multiplex.py					532
copy_ome_zarr_hcs_plate.py					297
find_registration_consensus.py					168
illumination_correction.py					287
image_based_registration_hcs_init.py					93
import_ome_zarr.py					295
init_group_by_well_for_multiplexing.py					86
napari_workflows_wrapper.py					633
projection.py					142
Project Total

This report was generated by python-coverage-comment-action

[tcompa]

cc @jluethi @lorenzocerrone

This was the change I mentioned, about simplifying the GitHub Action step that checks that the manifest did not change: c6991ae

And here is an example where I intentionally made it fail: https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/runs/13944841477/job/39029558855

INFO:root:[check_manifest] package_name='fractal_tasks_core'
INFO:root:[check_manifest] os.getcwd()='/home/runner/work/fractal-tasks-core/fractal-tasks-core'
INFO:root:[check_manifest] package_root_dir=PosixPath('/home/runner/work/fractal-tasks-core/fractal-tasks-core/fractal_tasks_core')
INFO:root:[check_manifest] manifest_path='/home/runner/work/fractal-tasks-core/fractal-tasks-core/fractal_tasks_core/__FRACTAL_MANIFEST__.json'
ERROR:root:[check_manifest] On-disk manifest is not up to date.
ERROR:root:manifest['task_list'][0]['tags'][0] Values are different:
	Old: 'Yokogawa-fixme'
	New:'Yokogawa'
New/old manifests differ

[jluethi]

That's great!

I also reviewed the overall PR. It looks good to me overall.

The only addition: The deprecation message could be a bit more explicit:
"This function is deprecated and will be removed in a future release of fractal-tasks-core. Please migrate to fractal-task-tools for manifest building and task wrappers."

If we have a specific transition documentation ready (see comment in fractal-analytics-platform/fractal-task-tools#14), we should directly link to that.