Fractal task(s) for registering and fusing OME-Zarr HCS using multiview-stitcher.
This instructions are only relevant after you completed both the copier copy command and the git/GitLab/GitHub initialization phase - see
README
for details.
- 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- 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]"-
Enjoy developing the package.
-
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- If you add a new task, you should also add a new item to the
TASK_LISTlist, insrc/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
metaand/ormeta_inittask 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.
- Run the test suite (with somewhat verbose logging) through
python -m pytest --log-cli-level info -s- Build the package through
python -m buildThis 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.
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent