virtool-workflow 7.2.2__tar.gz → 7.2.3__tar.gz

{virtool_workflow-7.2.2 → virtool_workflow-7.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: virtool-workflow
-Version: 7.2.2
+Version: 7.2.3
 Summary: A framework for developing bioinformatics workflows for Virtool.
 License: MIT
 Author: Ian Boyes
@@ -9,13 +9,13 @@ 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 (>=3.12.13,<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 (>=31.9.0,<32.0.0)
 Description-Content-Type: text/markdown

{virtool_workflow-7.2.2 → virtool_workflow-7.2.3}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "virtool-workflow"
 description = "A framework for developing bioinformatics workflows for Virtool."
-version = "7.2.2"
+version = "7.2.3"
 authors = [
     {name = "Ian Boyes"},
     {name = "Reece Hoffman"},
@@ -35,25 +35,25 @@ packages = [
 
 [tool.poetry.dependencies]
 aiofiles = "^24.1.0"
-aiohttp = "^3.12.13"
+aiohttp = "^3.12.15"
 biopython = "^1.81"
 click = "^8.2.1"
-orjson = "^3.9.9"
+orjson = "^3.11.1"
 pydantic-factories = "^1.17.3"
 pyfixtures = "^1.0.0"
-sentry-sdk = "^2.30.0"
+sentry-sdk = "^2.34.1"
 structlog-sentry = "^2.2.1"
 virtool = "^31.9.0"
 
 [tool.poetry.group.dev.dependencies]
-mypy = "^1.16.1"
+mypy = "^1.17.1"
 piccolo-theme = "^0.24.0"
 pytest = "^7.4.2"
 pytest-aiohttp = "^1.1.0"
 pytest-asyncio = "^0.21.0"
 pytest-mock = "^3.14.1"
 pytest-structlog = "^1.0"
-ruff = "^0.12.0"
+ruff = "^0.12.9"
 sphinx = "^4.0.2"
 sphinx-autobuild = "^2024.10.3"
 sphinx-nameko-theme = "^0.0.3"
@@ -86,6 +86,7 @@ select = ["ALL"]
 [tool.ruff.per-file-ignores]
 "tests/**/test_*.py" = [
     "ANN201",
+    "D205",
     "S101",
 ]
 

{virtool_workflow-7.2.2 → virtool_workflow-7.2.3}/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(),