virtool-workflow 0.0.0__py3-none-any.whl

virtool_workflow/workflow.py

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+"""Main definitions for Virtool Workflows."""
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Any, Awaitable, Callable, Optional
+
+from virtool_workflow.utils import coerce_to_coroutine_function
+
+
+@dataclass
+class Workflow:
+    """A step-wise, long-running operation.
+    """
+
+    steps: list[WorkflowStep] = field(default_factory=list)
+
+    def step(
+        self, step: Optional[Callable] = None, *, name: str | None = None,
+    ) -> Callable:
+        """Decorator for adding a step to the workflow."""
+        if step is None:
+
+            def _decorator(func: Callable):
+                self.step(func, name=name)
+
+            return _decorator
+
+        step = WorkflowStep.from_callable(step, display_name=name)
+        self.steps.append(step)
+        return step
+
+
+@dataclass(frozen=True)
+class WorkflowStep:
+    """Metadata for a workflow step.
+
+    :param name: The presentation name for the step.
+    :param description: The description of the step.
+    :param call: The async step function.
+    """
+
+    display_name: str
+    description: str
+    function: Callable[..., Awaitable[Any]]
+
+    @classmethod
+    def from_callable(
+        cls,
+        func: Callable[..., Any],
+        *,
+        display_name: str = None,
+        description: str = None,
+    ) -> WorkflowStep:
+        """Create a WorkflowStep from a callable.
+
+        :param func: The callable to be used.
+        :param display_name: The display name to be used, if None then a display name
+            will be created based on the function name of `call`.
+        :param description: A text description of the step. If None then the docstring
+            `call` will be used.
+        """
+        func = coerce_to_coroutine_function(func)
+
+        display_name = display_name or func.__name__.replace("_", " ").title()
+
+        try:
+            description = description or _get_description_from_docstring(func)
+        except ValueError:
+            description = ""
+
+        return cls(
+            display_name=display_name,
+            description=description,
+            function=func,
+        )
+
+    async def __call__(self, *args, **kwargs):
+        return await self.function(*args, **kwargs)
+
+
+def _get_description_from_docstring(func: Callable[..., Any]) -> str:
+    """Extract the first line of the docstring as a description for a step function.
+
+    :param func: The step function to get the description for
+    :raise ValueError: When `call` does not have a docstring
+    """
+    if func.__doc__ is None:
+        raise ValueError(f"{func} does not have a docstring")
+
+    return func.__doc__.strip().split("\n")[0]

virtool_workflow-0.0.0.dist-info/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Canadian Food Inspection Agency
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

virtool_workflow-0.0.0.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: virtool-workflow
+Version: 0.0.0
+Summary: A framework for developing bioinformatics workflows for Virtool.
+License: MIT
+Author: Ian Boyes
+Maintainer: Ian Boyes
+Requires-Python: >=3.12.3,<3.13.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Dist: aiofiles (>=0.7.0,<0.8.0)
+Requires-Dist: aiohttp (>=3.8.1,<4.0.0)
+Requires-Dist: biopython (>=1.81,<2.0)
+Requires-Dist: click (>=8.1.7,<9.0.0)
+Requires-Dist: orjson (>=3.9.9,<4.0.0)
+Requires-Dist: pydantic-factories (>=1.17.3,<2.0.0)
+Requires-Dist: pyfixtures (>=1.0.0,<2.0.0)
+Requires-Dist: sentry-sdk (>=2.3.1,<3.0.0)
+Requires-Dist: structlog-sentry (>=2.2.1,<3.0.0)
+Requires-Dist: virtool (>=31.1.3,<32.0.0)
+Description-Content-Type: text/markdown
+
+# Virtool Workflow
+
+![Tests](https://github.com/virtool/virtool-workflow/workflows/ci/badge.svg?branch=main)
+[![PyPI version](https://badge.fury.io/py/virtool-workflow.svg)](https://badge.fury.io/py/virtool-workflow)
+
+A framework for developing bioinformatic workflows in Python.
+
+```python
+from virtool_workflow import step
+
+
+@step
+def step_function():
+    ...
+
+
+@step
+def step_function_2():
+    ...
+```
+
+## Contributing
+
+### Commits
+
+We require specific commit formatting. Any commit that does not follow the guidelines
+will be squashed at our discretion.
+
+Read our [commit and release](https://dev.virtool.ca/en/latest/commits_releases.html)
+documentation for more information.
+
+### Tests
+
+Run tests with:
+
+```shell
+# Bring up Redis and the test container.
+docker compose up -d
+
+# Run tests in the test container.
+docker compose exec test poetry run pytest
+```
+
+Run specific tests like:
+
+```shell
+docker compose exec test poetry run pytest tests/test_status.py
+```
+

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virtool_workflow-0.0.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: poetry-core 2.1.3
+Root-Is-Purelib: true
+Tag: py3-none-any

virtool_workflow-0.0.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+run-workflow=virtool_workflow.cli:cli_main
+