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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. | ||
--> | ||
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<h1>404 - Not found</h1> |
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import json | ||
import logging | ||
from pathlib import Path | ||
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import mkdocs_gen_files | ||
import requests | ||
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logger = logging.getLogger(f"mkdocs.plugins.{__name__}") | ||
prefix = f"[{Path(__file__).name}]" | ||
logger.info(f"{prefix} START") | ||
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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." | ||
), | ||
) | ||
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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." | ||
# ), | ||
# ) | ||
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script_path = __file__ | ||
script_dir = Path(script_path).parent | ||
markdown_file = script_dir / "_all.md" | ||
logger.info(f"{prefix} Writing output to {markdown_file}") | ||
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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") | ||
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logger.info(f"{prefix} END") |
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