virtool-workflow 6.0.0a7__py3-none-any.whl → 6.0.0a9__py3-none-any.whl

virtool_workflow/utils.py

@@ -1,8 +1,9 @@
 import asyncio
+import tarfile
+from collections.abc import Callable
 from functools import wraps
 from inspect import iscoroutinefunction
 from pathlib import Path
-from typing import Callable
 
 
 def coerce_to_coroutine_function(func: Callable):
@@ -19,3 +20,13 @@ def coerce_to_coroutine_function(func: Callable):
 
 async def make_directory(path: Path):
     await asyncio.to_thread(path.mkdir, exist_ok=True, parents=True)
+
+
+def untar(path: Path, target_path: Path):
+    with tarfile.open(path, "r:gz") as tar:
+        tar.extractall(target_path)
+
+
+def move_all_model_files(source_path: Path, target_path: Path):
+    for file in source_path.iterdir():
+        file.rename(target_path / file.name)

virtool_workflow/workflow.py

@@ -2,21 +2,20 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import Callable, Optional, Awaitable, Any
+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.
+    """A step-wise, long-running operation.
     """
 
     steps: list[WorkflowStep] = field(default_factory=list)
 
     def step(
-        self, step: Optional[Callable] = None, *, name: str | None = None
+        self, step: Optional[Callable] = None, *, name: str | None = None,
     ) -> Callable:
         """Decorator for adding a step to the workflow."""
         if step is None:
@@ -33,8 +32,7 @@ class Workflow:
 
 @dataclass(frozen=True)
 class WorkflowStep:
-    """
-    Metadata for a workflow step.
+    """Metadata for a workflow step.
 
     :param name: The presentation name for the step.
     :param description: The description of the step.
@@ -53,8 +51,7 @@ class WorkflowStep:
         display_name: str = None,
         description: str = None,
     ) -> WorkflowStep:
-        """
-        Create a WorkflowStep from a callable.
+        """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
@@ -82,8 +79,7 @@ class WorkflowStep:
 
 
 def _get_description_from_docstring(func: Callable[..., Any]) -> str:
-    """
-    Extract the first line of the docstring as a description for a step function.
+    """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

{virtool_workflow-6.0.0a7.dist-info → virtool_workflow-6.0.0a9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 6.0.0a7
+Version: 6.0.0a9
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT
@@ -19,7 +19,7 @@ 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 (>=1.5.7,<2.0.0)
-Requires-Dist: virtool-core (>=10.0.1,<11.0.0)
+Requires-Dist: virtool-core (>=11.0.0,<12.0.0)
 Project-URL: Repository, https://github.com/virtool/virtool-workflow
 Description-Content-Type: text/markdown
 

virtool_workflow-6.0.0a9.dist-info/RECORD

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+virtool_workflow/analysis/skewer.py,sha256=_kTCLd6XUUscgMgPVc50Xcwy1QZzxCwxbEmYgm6PQwc,7130
+virtool_workflow/analysis/trimming.py,sha256=rJG9f1mDMkivN-YcxU-_IubTUkn-oyG3NUUrhGuHWzs,1447
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virtool_workflow-6.0.0a7.dist-info/RECORD

@@ -1,46 +0,0 @@
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