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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>

_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["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")