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lorenzocerrone committed Dec 19, 2024
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7 changes: 7 additions & 0 deletions 404.html
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<!--
This file was copied by hand from
https://github.com/squidfunk/mkdocs-material/blob/master/material/404.html
(on Mon 2 Jan 14:48:33 CET 2023), and then modified.
-->

<h1>404 - Not found</h1>
145 changes: 145 additions & 0 deletions _tasks/generate_task_list.py
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import json
import logging
from pathlib import Path

import mkdocs_gen_files
import requests

logger = logging.getLogger(f"mkdocs.plugins.{__name__}")
prefix = f"[{Path(__file__).name}]"
logger.info(f"{prefix} START")


pkgs = dict()
pkgs["fractal-tasks-core"] = dict(
homepage_url="https://fractal-analytics-platform.github.io/fractal-tasks-core", # noqa
manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-tasks-core/main/fractal_tasks_core/__FRACTAL_MANIFEST__.json", # noqa
description=(
"The Fractal tasks core package is the reference implementation for "
"Fractal tasks. It contains tasks to convert Cellvoyager CV7000 and "
"CV8000 images to OME-Zarr, to make 3D projections, apply flatfield "
"illumination corrections, segment objects using Cellpose, run "
"napari workflows, calculate & apply registration and to import "
"OME-Zarrs into a Fractal workflow."
),
)

pkgs["scMultiplex"] = dict(
homepage_url="https://github.com/fmi-basel/gliberal-scMultipleX",
manifest_url="https://raw.githubusercontent.com/fmi-basel/gliberal-scMultipleX/main/src/scmultiplex/__FRACTAL_MANIFEST__.json", # noqa
description=(
"The scMultipleX package contains tasks to perform object-based "
"registration, multiplexed measurements, mesh generations and more."
),
)
pkgs["fractal-faim-ipa"] = dict(
homepage_url="https://github.com/fractal-analytics-platform/fractal-faim-ipa", # noqa
manifest_url="https://raw.githubusercontent.com/jluethi/fractal-faim-ipa/main/src/fractal_faim_ipa/__FRACTAL_MANIFEST__.json", # noqa
description=(
"Provides Fractal tasks for the conversion of Molecular Devices "
"ImageXpress microscope to OME-Zarr. This package is based on the "
"faim-ipa library developed by FAIM at FMI."
),
)
pkgs["fractal-helper-tasks"] = dict(
homepage_url="https://github.com/fractal-analytics-platform/fractal-helper-tasks", # noqa
manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-helper-tasks/main/src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json", # noqa
description=("Collection of Fractal helper tasks."),
)
pkgs["APx_fractal_task_collection"] = dict(
homepage_url="https://github.com/Apricot-Therapeutics/APx_fractal_task_collection", # noqa
manifest_url="https://raw.githubusercontent.com/Apricot-Therapeutics/APx_fractal_task_collection/main/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json", # noqa
description=(
"The APx Fractal Task Collection is mainainted by Apricot "
"Therapeutics AG, Switzerland. This is a collection of tasks intended "
"to be used in combination with the Fractal Analytics Platform "
"maintained by the BioVisionCenter Zurich (co-founded by the "
"Friedrich Miescher Institute and the University of Zurich). The "
"tasks in this collection are focused on extending Fractal's "
"capabilities of processing 2D image data, with a special focus on "
"multiplexed 2D image data. Most tasks work with 3D image data, but "
"they have not specifically been developed for this scenario."
),
)
pkgs["operetta-compose"] = dict(
homepage_url="https://github.com/leukemia-kispi/operetta-compose",
manifest_url="https://raw.githubusercontent.com/leukemia-kispi/operetta-compose/main/src/operetta_compose/__FRACTAL_MANIFEST__.json", # noqa
description=(
"Fractal tasks for the Opera/Operetta "
"microscope and drug response profiling."
),
)
pkgs["fractal-plantseg-tasks"] = dict(
homepage_url="https://github.com/fractal-analytics-platform/fractal-plantseg-tasks", # noqa
manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-plantseg-tasks/main/src/plantseg_tasks/__FRACTAL_MANIFEST__.json", # noqa
description=(
"Collection of Fractal task with the PlantSeg segmentation pipeline."
),
)
pkgs["fractal-ome-zarr-hcs-stitching"] = dict(
homepage_url="https://github.com/m-albert/fractal-ome-zarr-hcs-stitching", # noqa
manifest_url="https://raw.githubusercontent.com/m-albert/fractal-ome-zarr-hcs-stitching/main/src/fractal_ome_zarr_hcs_stitching/__FRACTAL_MANIFEST__.json", # noqa
description=(
"Fractal task(s) for registering and fusing OME-Zarr HCS using "
"multiview-stitcher."
),
)
pkgs["fractal-lif-converters"] = dict(
homepage_url="https://github.com/fractal-analytics-platform/fractal-lif-converters", # noqa
manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-lif-converters/refs/heads/main/src/fractal_lif_converters/__FRACTAL_MANIFEST__.json", # noqa
description=("OME-Zarr converters for Leica Lif files built using bioio"),
)
pkgs["fractal-ilastik-tasks"] = dict(
homepage_url="https://github.com/fractal-analytics-platform/fractal-ilastik-tasks", # noqa
manifest_url="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-ilastik-tasks/refs/heads/main/src/ilastik_tasks/__FRACTAL_MANIFEST__.json", # noqa
description=(
"Collection of Fractal task to run Headless ilastik workflows. Early "
"prototype version, feedback is welcome."
),
)
# pkgs["abbott"] = dict(
# homepage_url="https://github.com/MaksHess/abbott",
# manifest_url="https://raw.githubusercontent.com/MaksHess/abbott/main/src/abbott/__FRACTAL_MANIFEST__.json", # noqa
# description=(
# "Work in progress task package to provide 3D registration methods "
# "based on Elastix."
# ),
# )

script_path = __file__
script_dir = Path(script_path).parent
markdown_file = script_dir / "_all.md"
logger.info(f"{prefix} Writing output to {markdown_file}")

with mkdocs_gen_files.open(markdown_file.as_posix(), "w") as md:
for package_name, package in pkgs.items():
homepage_url = package["homepage_url"]
manifest_url = package["manifest_url"]
description = package.get("description", None)
r = requests.get(manifest_url)
if not r.status_code == 200:
error_msg = f"Something wrong with the request to {manifest_url}"
logger.error(f"{prefix} {error_msg}")
raise ValueError(error_msg)
manifest = json.loads(r.content.decode("utf-8"))
task_list = manifest["task_list"]
md.write(f"## `{package_name}`\n")
md.write(f"**Package:** `{package_name}`\n\n")
md.write(f"**Home page:** {homepage_url}\n\n")
if description is not None:
md.write(f"**Description:** {description}\n\n")
md.write("**Tasks:**\n\n")
for task in task_list:
name = task["name"]
docs_link = task.get("docs_link")
if package_name == "fractal-tasks-core":
md.write(f"* [{name}]({docs_link})\n")
else:
md.write(f"* {name}\n")
num_tasks = len(task_list)
logger.info(
f"{prefix} Processed {package_name}, found {num_tasks} tasks"
)
md.write("\n\n")

logger.info(f"{prefix} END")
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