virtool-workflow 7.2.1__py3-none-any.whl → 7.2.3__py3-none-any.whl

virtool_workflow/__init__.py

@@ -1,6 +1,7 @@
 """
 A framework for defining Virtool workflows.
 """
+
 from virtool_workflow.decorators import step
 from virtool_workflow.runtime.run_subprocess import RunSubprocess
 from virtool_workflow.workflow import Workflow, WorkflowStep

virtool_workflow/analysis/fastqc.py

@@ -1,4 +1,5 @@
 """Utilities and fixtures for running FastQC."""
+
 from __future__ import annotations
 
 import asyncio
@@ -424,8 +425,7 @@ def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
 class FastQCRunner(Protocol):
     """A protocol describing callables that can be used to run FastQC."""
 
-    async def __call__(self, paths: ReadPaths, output_path: Path) -> dict:
-        ...
+    async def __call__(self, paths: ReadPaths, output_path: Path) -> dict: ...
 
 
 @fixture

virtool_workflow/cli.py

@@ -1,4 +1,5 @@
 """Command Line Interface to virtool_workflow"""
+
 import asyncio
 from pathlib import Path
 

virtool_workflow/runtime/hook.py

@@ -1,4 +1,5 @@
 """The :class:`Hook` class is used to hook into the workflow lifecycle."""
+
 from __future__ import annotations
 
 from asyncio import gather
@@ -119,7 +120,8 @@ class Hook:
                 return await callback(*args, **kwargs)
 
         results = await gather(
-            *[call_callback(callback) for callback in callbacks], return_exceptions=True,
+            *[call_callback(callback) for callback in callbacks],
+            return_exceptions=True,
         )
 
         for error in results:

virtool_workflow/runtime/ping.py

@@ -1,4 +1,5 @@
 """Ping the API to keep the job alive."""
+
 import asyncio
 from contextlib import asynccontextmanager
 

virtool_workflow/runtime/run.py

@@ -42,8 +42,6 @@ from virtool_workflow.runtime.sentry import configure_sentry, set_workflow_conte
 from virtool_workflow.utils import configure_logs, get_virtool_workflow_version
 from virtool_workflow.workflow import Workflow
 
-logger = get_logger("runtime")
-
 
 def configure_status_hooks():
     """Configure built-in job status hooks.
@@ -73,11 +71,13 @@ def configure_status_hooks():
         await push_status()
 
 
-async def execute(workflow: Workflow, scope: FixtureScope, events: Events):
+async def execute(workflow: Workflow, scope: FixtureScope, events: Events, logger):
     """Execute a workflow.
 
     :param workflow: The workflow to execute
     :param scope: The :class:`FixtureScope` to use for fixture injection
+    :param events: The events object for cancellation/termination
+    :param logger: The configured logger instance
 
     """
     await on_workflow_start.trigger(scope)
@@ -151,6 +151,7 @@ async def run_workflow(
     job_id: str,
     workflow: Workflow,
     events: Events,
+    logger,
 ):
     # Configure hooks here so that they can be tested when using `run_workflow`.
     configure_status_hooks()
@@ -189,7 +190,7 @@ async def run_workflow(
             scope["work_path"] = work_path
 
             async with ping_periodically(api, job_id):
-                await execute(workflow, scope, events)
+                await execute(workflow, scope, events, logger)
                 cleanup_builtin_status_hooks()
 
 
@@ -215,6 +216,7 @@ async def start_runtime(
     """
     configure_logs(bool(sentry_dsn))
 
+    logger = get_logger("runtime")
     logger.info(
         "found virtool-workflow",
         version=get_virtool_workflow_version(),
@@ -250,6 +252,7 @@ async def start_runtime(
             job_id,
             workflow,
             events,
+            logger,
         ),
     )
 

virtool_workflow/utils.py

@@ -25,6 +25,21 @@ def coerce_to_coroutine_function(func: Callable):
     return _func
 
 
+def normalize_log_level(
+    _logger: object,
+    _method_name: str,
+    event_dict: dict[str, object],
+) -> dict[str, object]:
+    """Map exception method calls to error level.
+
+    The logging module doesn't have EXCEPTION level.
+    """
+    if event_dict.get("level") == "exception":
+        event_dict["level"] = "error"
+
+    return event_dict
+
+
 def configure_logs(use_sentry: bool):
     logging.basicConfig(
         format="%(message)s",
@@ -32,17 +47,11 @@ def configure_logs(use_sentry: bool):
         level=logging.INFO,
     )
 
-    def normalize_log_level(logger, method_name, event_dict):
-        """Map EXCEPTION level to ERROR since logging module doesn't have EXCEPTION."""
-        if event_dict.get("level") == "EXCEPTION":
-            event_dict["level"] = "ERROR"
-        return event_dict
-
     processors = [
         structlog.stdlib.filter_by_level,
-        structlog.stdlib.add_logger_name,
         structlog.stdlib.add_log_level,
         normalize_log_level,
+        structlog.stdlib.add_logger_name,
         structlog.stdlib.PositionalArgumentsFormatter(),
         structlog.processors.TimeStamper(fmt="%Y-%m-%dT%H:%M:%SZ"),
         structlog.processors.StackInfoRenderer(),

virtool_workflow/workflow.py

@@ -1,4 +1,5 @@
 """Main definitions for Virtool Workflows."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass, field
@@ -9,13 +10,15 @@ 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:

{virtool_workflow-7.2.1.dist-info → virtool_workflow-7.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: virtool-workflow
-Version: 7.2.1
+Version: 7.2.3
 Summary: A framework for developing bioinformatics workflows for Virtool.
 License: MIT
 Author: Ian Boyes
@@ -9,20 +9,20 @@ Requires-Python: >=3.12.3,<3.13.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Requires-Dist: aiofiles (>=24.1.0,<25.0.0)
-Requires-Dist: aiohttp (>=3.8.1,<4.0.0)
+Requires-Dist: aiohttp (>=3.12.15,<4.0.0)
 Requires-Dist: biopython (>=1.81,<2.0)
 Requires-Dist: click (>=8.2.1,<9.0.0)
-Requires-Dist: orjson (>=3.9.9,<4.0.0)
+Requires-Dist: orjson (>=3.11.1,<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 (>=2.30.0,<3.0.0)
+Requires-Dist: sentry-sdk (>=2.34.1,<3.0.0)
 Requires-Dist: structlog-sentry (>=2.2.1,<3.0.0)
-Requires-Dist: virtool (>=31.1.3,<32.0.0)
+Requires-Dist: virtool (>=31.9.0,<32.0.0)
 Description-Content-Type: text/markdown
 
 # Virtool Workflow
 
-![Tests](https://github.com/virtool/virtool-workflow/workflows/ci/badge.svg?branch=main)
+[![CI](https://github.com/virtool/virtool-workflow/actions/workflows/ci.yml/badge.svg?branch=main&event=push)](https://github.com/virtool/virtool-workflow/actions/workflows/ci.yml)
 [![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.

{virtool_workflow-7.2.1.dist-info → virtool_workflow-7.2.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
-virtool_workflow/__init__.py,sha256=Tw0lAFudpsFyCaiR2Oz_RKYU6N-mSCmhXDftm1WT37M,308
+virtool_workflow/__init__.py,sha256=FhPRldtx5dRJftZ3pc3OMl5mWjnDqbX-qeFVQE2QApw,309
 virtool_workflow/analysis/__init__.py,sha256=eRMQhKOxijlFlYI78FzmHZoF1qYevBXycpIcmlrgFqI,57
-virtool_workflow/analysis/fastqc.py,sha256=pNorkhNVazV30fBY3KEJ6vfEskqsBzp80a_Iai8BOn8,13149
+virtool_workflow/analysis/fastqc.py,sha256=-D0_Py0e57mVmeA8VZQUB05AcgiCsAmxNQJWMvb2HXU,13142
 virtool_workflow/analysis/skewer.py,sha256=TWUfiYeUIahHbIosNYo2sqMjS4kUkoFBTspr70eRloI,7186
 virtool_workflow/analysis/trimming.py,sha256=3Dk0J322ZhBzhuplaVgxZv4l7MLu7ZhqNQHOtNi6CGM,1451
 virtool_workflow/analysis/utils.py,sha256=YU1_yInZzTNl9nKQTebUz47kUEqZ__d0k-RMLX8DWOA,1108
@@ -8,7 +8,7 @@ virtool_workflow/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 virtool_workflow/api/acquire.py,sha256=M8Wf6ck6YOPQU_0dalAYxuQbukj6c4Uat1OPhV7Gj2w,2157
 virtool_workflow/api/client.py,sha256=fXCriMv0s2L5O78fn8uIBWWPtxtPz0tUk1XHb1L7RGU,4766
 virtool_workflow/api/utils.py,sha256=Wzf1YseJKUBnUk0Ge8DMwgigWMS7Dn-VFNLlBFo6SW4,4341
-virtool_workflow/cli.py,sha256=yEl1LziABKbjc5MCOoUGLy-iuqehOou37x9ox4LA92M,1441
+virtool_workflow/cli.py,sha256=Ak--FvkVEtaaBqyuddUBXOot1cbo-W6OAJ94kgNBcFQ,1442
 virtool_workflow/data/__init__.py,sha256=L2bQ5rMpnCMuLWDMwel4-wPchfQCTHH3EEwxDqwGOsY,610
 virtool_workflow/data/analyses.py,sha256=tGUU3gLyk_4vn1Xb7FccvBc_HQzYW_AoU7Dh1OkWhAA,3105
 virtool_workflow/data/hmms.py,sha256=qHtkQO0bF6V7GGVoGDpdhXXR9RxaetWiTL3of6Pd88Y,3210
@@ -29,17 +29,17 @@ virtool_workflow/runtime/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZ
 virtool_workflow/runtime/config.py,sha256=fHkprWxxqWeEWKOobxpVvSOS5Njk5Mq32sH-p5o_d8g,546
 virtool_workflow/runtime/discover.py,sha256=-ki36Z4tV0uH_HDP4iD94KT0-JIZ8kHGciuH6wxYDdg,3016
 virtool_workflow/runtime/events.py,sha256=ZIX3veBfC_2yNTdClHJaYMPn4KAF9JZqpQ3qDq4ox_E,138
-virtool_workflow/runtime/hook.py,sha256=ZfmvDHoSE7Qwk4Rpcjyd-pYuwP55mzEddec2ngRZpsg,4328
+virtool_workflow/runtime/hook.py,sha256=zNRs6Xy2ZnGWIsAo_uFNh4ybOOWvsh6avc0A4__2FBg,4341
 virtool_workflow/runtime/path.py,sha256=J8CsNMTg4XgDtib0gVSsLNvv17q793M-ydsxN6pkHrI,562
-virtool_workflow/runtime/ping.py,sha256=Xm4udRCcldHfSV1Rjpiqr-6vE7G6kaVaZgDlzNSxdao,1434
+virtool_workflow/runtime/ping.py,sha256=OOqIY8zQujWmjMf4oFA6Ouqt1Uv7YCTPDXn2VXosKBk,1435
 virtool_workflow/runtime/redis.py,sha256=m-Dtdpbho-Qa9W5IYJCeEEZ7vv04hYu5yALsxOJr0FY,1813
-virtool_workflow/runtime/run.py,sha256=pkfNyjaDBsVHrEGqmz5Ah5FkHJN4SkCHKkEmfDO1QRU,7725
+virtool_workflow/runtime/run.py,sha256=O_XrnBPgWBfYbi70TjhN7C1hviget6kUcTGnADHmLyg,7892
 virtool_workflow/runtime/run_subprocess.py,sha256=OFHVQ2ao16X8I9nl6Nm_f3IL7rHnmLH8ixtlAFKlOLk,4790
 virtool_workflow/runtime/sentry.py,sha256=WJ9CI2fshJD5As6s3umUtJrUq4Z-hQRrSxAgbjceXrk,1326
-virtool_workflow/utils.py,sha256=9rHSlcvZsV2qE1Wo-cUDqESIATswr1zR_P8V-wP6jdk,2545
-virtool_workflow/workflow.py,sha256=W8IEFzd28wjdNNlqRrPDKyX9LeQpR6Vxy7zKeYEMQEc,2655
-virtool_workflow-7.2.1.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
-virtool_workflow-7.2.1.dist-info/METADATA,sha256=NoJWREvu-JpIz3LcAUZscYbXA-srOf--v9X94A3EygI,1759
-virtool_workflow-7.2.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-virtool_workflow-7.2.1.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
-virtool_workflow-7.2.1.dist-info/RECORD,,
+virtool_workflow/utils.py,sha256=wBeL9YSq_jYjJHjRn-b_f0eZi5LVpFO8RTQGJus-aog,2625
+virtool_workflow/workflow.py,sha256=6jUGggiLEsducXyo5owEYflzQb9qZQrAtpNS3t6z4Z4,2675
+virtool_workflow-7.2.3.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
+virtool_workflow-7.2.3.dist-info/METADATA,sha256=4FM_PM1ek-n30sB2pZkIZevBWcMARQ87BSz5yQyi930,1854
+virtool_workflow-7.2.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+virtool_workflow-7.2.3.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
+virtool_workflow-7.2.3.dist-info/RECORD,,