fractal-task-tools 0.0.2__py3-none-any.whl

fractal_task_tools/task_models.py

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+from typing import Any
+from typing import Optional
+
+from pydantic import BaseModel
+from pydantic import Field
+
+
+class _BaseTask(BaseModel):
+    class Config:
+        arbitrary_types_allowed = True
+        extra = "forbid"
+
+    name: str
+    executable: str
+    meta: Optional[dict[str, Any]] = None
+    input_types: Optional[dict[str, bool]] = None
+    output_types: Optional[dict[str, bool]] = None
+    category: Optional[str] = None
+    modality: Optional[str] = None
+    tags: list[str] = Field(default_factory=list)
+    docs_info: Optional[str] = None
+
+
+class CompoundTask(_BaseTask):
+    """
+    A `CompoundTask` object must include both `executable_init` and
+    `executable` attributes, and it may include the `meta_init` and `meta`
+    attributes.
+    """
+
+    executable_init: str
+    meta_init: Optional[dict[str, Any]] = None
+
+    @property
+    def executable_non_parallel(self) -> str:
+        return self.executable_init
+
+    @property
+    def meta_non_parallel(self) -> Optional[dict[str, Any]]:
+        return self.meta_init
+
+    @property
+    def executable_parallel(self) -> str:
+        return self.executable
+
+    @property
+    def meta_parallel(self) -> Optional[dict[str, Any]]:
+        return self.meta
+
+
+class NonParallelTask(_BaseTask):
+    """
+    A `NonParallelTask` object must include the `executable` attribute, and it
+    may include the `meta` attribute.
+    """
+
+    @property
+    def executable_non_parallel(self) -> str:
+        return self.executable
+
+    @property
+    def meta_non_parallel(self) -> Optional[dict[str, Any]]:
+        return self.meta
+
+    @property
+    def executable_parallel(self) -> None:
+        return None
+
+    @property
+    def meta_parallel(self) -> None:
+        return None
+
+
+class ParallelTask(_BaseTask):
+    """
+    A `ParallelTask` object must include the `executable` attribute, and it may
+    include the `meta` attribute.
+    """
+
+    @property
+    def executable_non_parallel(self) -> None:
+        return None
+
+    @property
+    def meta_non_parallel(self) -> None:
+        return None
+
+    @property
+    def executable_parallel(self) -> str:
+        return self.executable
+
+    @property
+    def meta_parallel(self) -> Optional[dict[str, Any]]:
+        return self.meta

fractal_task_tools-0.0.2.dist-info/LICENSE

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+BSD 3-Clause License
+
+Copyright 2024 (C) Friedrich Miescher Institute for Biomedical Research and University of Zurich
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fractal_task_tools-0.0.2.dist-info/METADATA

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+Metadata-Version: 2.2
+Name: fractal-task-tools
+Version: 0.0.2
+Summary: Shared tools for Fractal tasks
+Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>
+License: BSD-3-Clause
+Project-URL: homepage, https://github.com/fractal-analytics-platform/fractal-task-tools
+Project-URL: repository, https://github.com/fractal-analytics-platform/fractal-task-tools
+Project-URL: changelog, https://github.com/fractal-analytics-platform/fractal-task-tools/blob/main/CHANGELOG.md
+Requires-Python: <3.13,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic<=2.8.2,>=2.0.0
+Requires-Dist: docstring-parser==0.15
+Provides-Extra: dev
+Requires-Dist: bumpver==2024.1130; extra == "dev"
+Requires-Dist: devtools==0.12.2; extra == "dev"
+Requires-Dist: pytest<9.0.0,>=8.3.0; extra == "dev"
+Requires-Dist: coverage<7.7.0,>=7.6.0; extra == "dev"
+
+# Fractal task tools
+
+[![PyPI version](https://img.shields.io/pypi/v/fractal-task-tools?color=gree)](https://pypi.org/project/fractal-task-tools/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![CI Status](https://github.com/fractal-analytics-platform/fractal-task-tools/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-task-tools/actions/workflows/ci_pip.yml)
+[![Coverage](https://raw.githubusercontent.com/fractal-analytics-platform/fractal-task-tools/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-task-tools/blob/python-coverage-comment-action-data/htmlcov/index.html)
+
+Fractal-task-tools provides some basic tools for building tasks for the [Fractal](https://fractal-analytics-platform.github.io/) framework.
+
+![Fractal_overview_small](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)
+
+[Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
+
+
+# Get started
+```console
+$ python -m venv venv
+
+$ source venv/bin/activate
+
+$ python -m pip install -e .
+[...]
+Successfully installed annotated-types-0.7.0 docstring-parser-0.15 fractal-task-tools-0.0.1 pydantic-2.8.2 pydantic-core-2.20.1 typing-extensions-4.12.2
+
+$ fractal-manifest create --help
+usage: fractal-manifest create [-h] --package PACKAGE [--task-list-path TASK_LIST_PATH]
+
+Create new manifest file
+
+options:
+  -h, --help            show this help message and exit
+  --package PACKAGE     Example: 'fractal_tasks_core'
+  --task-list-path TASK_LIST_PATH
+                        Dot-separated path to the `task_list.py` module, relative to the package root (default value:
+                        'dev.task_list').
+
+```
+
+# Development
+
+```console
+$ python -m venv venv
+
+$ source venv/bin/activate
+
+$ python -m pip install -e .[dev]
+[...]
+Successfully installed asttokens-2.4.1 bumpver-2024.1130 click-8.1.8 colorama-0.4.6 coverage-7.6.12 devtools-0.12.2 exceptiongroup-1.2.2 executing-2.2.0 fractal-task-tools-0.0.1 iniconfig-2.0.0 lexid-2021.1006 packaging-24.2 pluggy-1.5.0 pygments-2.19.1 pytest-8.3.5 six-1.17.0 toml-0.10.2 tomli-2.2.1
+
+$ pre-commit install
+pre-commit installed at .git/hooks/pre-commit
+```
+
+## How to make a release
+From the development environment:
+```
+bumpver update --patch --dry
+```
+
+
+## Contributors and license
+
+Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
+
+Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.

fractal_task_tools-0.0.2.dist-info/RECORD

@@ -0,0 +1,17 @@
+fractal_task_tools/__init__.py,sha256=MRGHqa12kl23-BtFENLSAtLR5nzimughL2HEce80xc0,79
+fractal_task_tools/_args_schemas.py,sha256=Ka5IAAEdC7xg03ZHMl5jFbv4Sk8JR1QKbxFl7soevlQ,7829
+fractal_task_tools/_cli.py,sha256=ikEwNVhzvr_X5PY5_s02lH7JvRcuHgjFs-hoIFQjXYo,1869
+fractal_task_tools/_create_manifest.py,sha256=Ses8N5RliTtbvaHGJwTjuE2sGyBCoJUJtcyO7JPX23w,6147
+fractal_task_tools/_descriptions.py,sha256=n7WcoIBQ4FEd16BI26iL-Sh6bEQ76jlU32JfJBF4U0A,7566
+fractal_task_tools/_package_name_tools.py,sha256=_UT2cThh742V6M0XT9m0_aByhj5fXRSjATKt_MIXFVg,819
+fractal_task_tools/_pydantic_generatejsonschema.py,sha256=qZuID7YUXOdAcL8OqsWjNFNumOIAgdJillc1lA2cHIY,3136
+fractal_task_tools/_signature_constraints.py,sha256=1ixh8acxwY5_jRdyn7KfyRDDuwqQQ2R6Zf1xlElheWY,3216
+fractal_task_tools/_task_docs.py,sha256=aEXozSKf3a7weOwJMHyTVJTvHlCKgDr1qoU-AAO3bZI,3401
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+fractal_task_tools/task_models.py,sha256=xTbdk3lf6T70o8idEWw-bdjA2dDz0KDIrBjdoh_A9Lc,2243
+fractal_task_tools-0.0.2.dist-info/LICENSE,sha256=1SGAsQ3Jm_nIU7c2TgtTZe_IOKjm9BDsrcf2r98xrdk,1584
+fractal_task_tools-0.0.2.dist-info/METADATA,sha256=07uk2zPoBCvv5Nv9Sb_k2jNsBw_2xYb-09XUwouo8Ps,4212
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+fractal_task_tools-0.0.2.dist-info/top_level.txt,sha256=2VBpiMDIBMJGOEPiHHX3njYEZGLhr4L0nu8vfkcNVzw,19
+fractal_task_tools-0.0.2.dist-info/RECORD,,

fractal_task_tools-0.0.2.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (76.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

fractal_task_tools-0.0.2.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+fractal-manifest = fractal_task_tools._cli:main

fractal_task_tools-0.0.2.dist-info/top_level.txt

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+fractal_task_tools