Merge pull request #11 from fractal-analytics-platform/updates

Updates

Author: tcompa

.gitignore

@@ -1,4 +1,5 @@
 _site/
+__pycache__
 .sass-cache/
 .jekyll-cache/
 .jekyll-metadata

docs/fractal_tasks.md

@@ -20,7 +20,7 @@ hide:
 }
 </style>
 
-Here is a list of task packages which can be used in Fractal (note that not all existing packages are currently listed).
+Here is a list of task packages which can be used in Fractal. Note that not all existing packages are currently listed, see https://fractal-analytics-platform.github.io/fractal-tasks-core/all_tasks for a more complete list.
 
 <iframe src="../task-table/" class="tasks-iframe">
 </iframe>

tasks_data_retrieval/create_tasks_data.py

@@ -5,7 +5,14 @@
 from zipfile import ZipFile
 from typing import Any
 from pydantic import BaseModel
-from typing import Optional, Literal
+from typing import Optional
+from typing import Literal
+
+import sys
+
+sys.path.append(Path(__file__).parent)
+from install_instructions import get_github_install_instructions
+from install_instructions import get_pypi_install_instructions
 
 
 DOWNLOAD_FOLDER = Path(__file__).parent / "downloads"
@@ -14,7 +21,7 @@
 
 class TaskReadV2(BaseModel):
     """
-    Based on
+    Customization of
     https://github.com/fractal-analytics-platform/fractal-server/blob/main/fractal_server/app/schemas/v2/task.py
     """
 
@@ -30,6 +37,7 @@ class TaskReadV2(BaseModel):
     modality: Optional[str] = None
     authors: Optional[str] = None
     tags: list[str]
+    install_instructions: Optional[str] = None
 
     class Config:
         extra = "forbid"
@@ -117,7 +125,16 @@ def handle_pypi_project(pypi_project_url: str) -> dict[str, Any]:
     manifest = load_manifest_from_zip(wheel_path)
     Path(wheel_path).unlink()
 
-    return dict(manifest=manifest, **info)
+    install_instructions = get_pypi_install_instructions(
+        project_name=project_name,
+        version=info["version"],
+    )
+
+    return dict(
+        manifest=manifest,
+        install_instructions=install_instructions,
+        **info,
+    )
 
 
 def handle_github_repository(github_url: str) -> dict[str, Any]:
@@ -160,7 +177,16 @@ def handle_github_repository(github_url: str) -> dict[str, Any]:
     manifest = load_manifest_from_zip(wheel_path)
     Path(wheel_path).unlink()
 
-    return dict(manifest=manifest, **info)
+    install_instructions = get_github_install_instructions(
+        wheel_name=Path(wheel_path).name,
+        wheel_url=wheel_asset_browser_download_url,
+    )
+
+    return dict(
+        manifest=manifest,
+        install_instructions=install_instructions,
+        **info,
+    )
 
 
 def get_package_info(source: str) -> dict[str, Any]:
@@ -210,11 +236,7 @@ def _get_task_type(
 sources_file = Path(__file__).parent / "sources.txt"
 with sources_file.open("r") as f:
     sources = f.read().splitlines()
-sources = [
-    source
-    for source in sources
-    if not (source.startswith("#") or source == "")
-]
+sources = [source for source in sources if not (source.startswith("#") or source == "")]
 
 TASK_GROUPS = []
 for source in sources:
@@ -226,6 +248,7 @@ def _get_task_type(
         pkg_name = data["name"]
         pkg_version = data.get("version")
         authors = data["manifest"].get("authors")
+        install_instructions = data.get("install_instructions")
         pkg_task_list = data["manifest"]["task_list"]
         for task in pkg_task_list:
             new_task = dict()
@@ -236,6 +259,7 @@ def _get_task_type(
             new_task["version"] = pkg_version
             new_task["type"] = _get_task_type(task)
             new_task["authors"] = authors
+            new_task["install_instructions"] = install_instructions
             TaskReadV2(**new_task)
             task_list.append(new_task)
 
@@ -253,7 +277,12 @@ def _get_task_type(
     TASK_GROUPS.append(task_group)
 
     t_end = time.perf_counter()
-    print(f"END processing {source=} - version={pkg_version}' - added {ntasks} tasks - elapsed {t_end-t_start:.3f} s.")
+    print(
+        f"END processing {source=} - "
+        f"version={pkg_version}' - "
+        f"added {ntasks} tasks - "
+        f"elapsed {t_end-t_start:.3f} s."
+    )
     print()
 
 output_file = Path(__file__).parent / "tasks.json"

tasks_data_retrieval/install_instructions.py

@@ -0,0 +1,78 @@
+INSTALL_INSTRUCTIONS_TITLE_1 = "## How to add this task to a Fractal instance\n"
+INSTALL_INSTRUCTIONS_TITLE_2 = "## How to install this task in a Python environment\n"
+
+
+def _get_default_template_pypi() -> str:
+    lines = [
+        INSTALL_INSTRUCTIONS_TITLE_1,
+        "Trigger a _PyPI_ task collection with package `__PROJECT_NAME__` and package version `__VERSION__`.",
+        "",
+        INSTALL_INSTRUCTIONS_TITLE_2,
+        "```",
+        'pip install "__PROJECT_NAME__==__VERSION__"',
+        "```",
+    ]
+    template = "\n".join(lines) + "\n"
+    return template
+
+
+def _get_default_template_pypi_with_extra(extra: str) -> str:
+    lines = [
+        INSTALL_INSTRUCTIONS_TITLE_1,
+        f"Trigger a _PyPI_ task collection for package `__PROJECT_NAME__`, package version `__VERSION__` and package extras {extra}.",
+        "",
+        INSTALL_INSTRUCTIONS_TITLE_2,
+        "```",
+        f'pip install "__PROJECT_NAME__[{extra}]==__VERSION__"',
+        "```",
+    ]
+    template = "\n".join(lines) + "\n"
+    return template
+
+
+def _get_default_template_wheel_url() -> str:
+    lines = [
+        INSTALL_INSTRUCTIONS_TITLE_1,
+        "1. Download the wheel file from [this link](__WHEEL_URL__),",
+        "2. Trigger a _local_ task collection by uploading the wheel file.",
+        "",
+        INSTALL_INSTRUCTIONS_TITLE_2,
+        "1. Download the wheel file from [this link](__WHEEL_URL__)",
+        "2. `pip install __WHEEL_NAME__`",
+    ]
+    template = "\n".join(lines) + "\n"
+    return template
+
+
+def _get_default_template_wheel_url_with_extra(extra: str) -> str:
+    lines = [
+        INSTALL_INSTRUCTIONS_TITLE_1,
+        "1. Download the wheel file from [this link](__WHEEL_URL__),",
+        f"2. Trigger a _local_ task collection by uploading the wheel file, with package extras {extra}.",
+        "",
+        INSTALL_INSTRUCTIONS_TITLE_2,
+        "1. Download the wheel file from [this link](__WHEEL_URL__)",
+        f"2. `pip install \"__WHEEL_NAME__[{extra}]\"`",
+    ]
+    template = "\n".join(lines) + "\n"
+    return template
+
+
+def get_pypi_install_instructions(*, project_name: str, version: str) -> str:
+    instructions = _get_default_template_pypi()
+    if project_name == "fractal-tasks-core":
+        instructions = _get_default_template_pypi_with_extra(extra="fractal-tasks")
+    instructions = instructions.replace("__PROJECT_NAME__", project_name)
+    instructions = instructions.replace("__VERSION__", version)
+    print(instructions)
+    return instructions
+
+
+def get_github_install_instructions(*, wheel_name: str, wheel_url: str) -> str:
+    instructions = _get_default_template_wheel_url()
+    if wheel_name.startswith("scmultiplex"):
+        instructions = _get_default_template_wheel_url_with_extra(extra="fractal-tasks")
+    instructions = instructions.replace("__WHEEL_NAME__", wheel_name)
+    instructions = instructions.replace("__WHEEL_URL__", wheel_url)
+    print(instructions)
+    return instructions

tasks_data_retrieval/sources.txt

@@ -1,11 +1,7 @@
-https://pypi.org/project/fractal-tasks-core/
+https://pypi.org/project/fractal-tasks-core
 https://pypi.org/project/fractal-faim-ipa
 https://pypi.org/project/fractal-lif-converters
 https://pypi.org/project/operetta-compose
 https://github.com/fractal-analytics-platform/fractal-helper-tasks
 https://github.com/fmi-basel/gliberal-scMultipleX
-
-# https://github.com/Apricot-Therapeutics/APx_fractal_task_collection
-# https://github.com/fractal-analytics-platform/fractal-plantseg-tasks
-# https://github.com/m-albert/fractal-ome-zarr-hcs-stitching/archive
-# https://github.com/fractal-analytics-platform/fractal-ilastik-tasksC/archive/refs/tags/0.1.1.zip
+https://github.com/m-albert/fractal-ome-zarr-hcs-stitching