fractal-ome-zarr-hcs-stitching

Fractal task(s) for registering and fusing OME-Zarr HCS using multiview-stitcher.

Development instructions

This instructions are only relevant after you completed both the copier copy command and the git/GitLab/GitHub initialization phase - see README for details.

1. It is recommended to work from an isolated Python virtual environment:

   # Create the virtual environment in the folder venv
   python -m venv venv
   # Activate the Python virtual environment
   source venv/bin/activate
   # Deactivate the virtual environment, when you don't need it any more
   deactivate

2. You can install your package locally as in:

   # Install only fractal_ome_zarr_hcs_stitching:
   python -m pip install -e .
   # Install both fractal_ome_zarr_hcs_stitching and development dependencies (e.g. pytest):
   python -m pip install -e ".[dev]"

3. Enjoy developing the package.

4. The template already includes a sample task ("Thresholding Task"). Whenever you change its input parameters or docstring, re-run

   python src/fractal_ome_zarr_hcs_stitching/dev/create_manifest.py
   git add src/fractal_ome_zarr_hcs_stitching/__FRACTAL_MANIFEST__.json
   git commit -m'Update `__FRACTAL_MANIFEST__.json`'
   git push origin main

5. If you add a new task, you should also add a new item to the TASK_LIST list, in src/fractal_ome_zarr_hcs_stitching/dev/task_list.py. Here is an example:

   
   from fractal_tasks_core.dev.task_models import NonParallelTask
   from fractal_tasks_core.dev.task_models import ParallelTask
   from fractal_tasks_core.dev.task_models import CompoundTask

TASK_LIST = [ NonParallelTask( name="My non-parallel task", executable="my_non_parallel_task.py", meta={"cpus_per_task": 1, "mem": 4000}, ), ParallelTask( name="My parallel task", executable="my_parallel_task.py", meta={"cpus_per_task": 1, "mem": 4000}, ), CompoundTask( name="My compound task", executable_init="my_task_init.py", executable="my_actual_task.py", meta_init={"cpus_per_task": 1, "mem": 4000}, meta={"cpus_per_task": 2, "mem": 12000}, ), ]

Notes:

* After adding a task, you should also update the manifest (see point 4 above).
* The minimal example above also includes the `meta` and/or `meta_init` task properties; these are optional, and you can remove them if not needed.
* More details on Fractal tasks will be soon available at https://fractal-analytics-platform.github.io.

6. Run the test suite (with somewhat verbose logging) through
```console
python -m pytest --log-cli-level info -s

7. Build the package through

   python -m build

   This command will create the release distribution files in the dist folder. The wheel one (ending with .whl) is the one you can use to collect your tasks within Fractal.