Update dependencies (#429)

mgeplf · web-flow · commit 97072b073127 · 2025-10-29T14:28:02.000+01:00
* Update dependencies Package Version Latest DirectDep -------------------------- --------------- --------------- ----- alembic 1.16.5 1.17.1 Yes sqlalchemy/alembic@rel_1_16_5...rel_1_17_1 https://alembic.sqlalchemy.org/en/latest/changelog.html boto3 1.40.29 1.40.61 Yes boto/boto3@1.40.18...1.40.61 cachetools 6.2.0 6.2.1 Yes tkem/cachetools@v6.2.0...v6.2.1 https://github.com/tkem/cachetools/blob/master/CHANGELOG.rst click 8.2.1 8.3.0 Yes Not important; only for import fastapi 0.116.1 0.120.1 Yes fastapi/fastapi@0.116.0...0.120.1 https://fastapi.tiangolo.com/release-notes/ h5py 3.14.0 3.15.1 Yes Not important; only for import openai 1.101.0 2.6.1 Yes openai/openai-python@v1.101.0...v2.6.1 psycopg2 2.9.10 2.9.11 Yes psycopg/psycopg2@2.9.10...2.9.11 https://www.psycopg.org/docs/news.html pydantic 2.11.7 2.12.3 Yes pydantic/pydantic@v2.11.7...v2.12.3 https://docs.pydantic.dev/latest/changelog/ pydantic-settings 2.10.1 2.11.0 Yes pydantic/pydantic-settings@2.10.1...v2.11.0 sqlalchemy 2.0.43 2.0.44 Yes sqlalchemy/sqlalchemy@rel_2_0_43...rel_2_0_44 https://docs.sqlalchemy.org/en/20/changelog/changelog_20.html#change-2.0.45 uvicorn 0.35.0 0.38.0 Yes Kludex/uvicorn@0.37.0...0.38.0 https://uvicorn.dev/release-notes/ anyio 4.10.0 4.11.0 botocore 1.40.29 1.40.61 botocore-stubs 1.40.29 1.40.61 certifi 2025.8.3 2025.10.5 charset-normalizer 3.4.3 3.4.4 coverage 7.10.6 7.11.0 cryptography 45.0.7 46.0.3 entitysdk 0.8.4 0.8.5 httptools 0.6.4 0.7.1 idna 3.10 3.11 iniconfig 2.1.0 2.3.0 jiter 0.10.0 0.11.1 markupsafe 3.0.2 3.0.3 moto 5.1.12 5.1.15 numpy 2.3.3 2.3.4 py-partiql-parser 0.6.1 0.6.3 pydantic-core 2.33.2 2.41.4 pyright 1.1.405 1.1.407 python-dotenv 1.1.1 1.2.1 pyyaml 6.0.2 6.0.3 rich 14.1.0 14.2.0 ruff 0.13.0 0.14.2 scipy 1.16.2 1.16.3 starlette 0.47.3 0.49.1 types-awscrt 0.27.6 0.28.2 types-boto3-cloudformation 1.40.24 1.40.57 types-boto3-dynamodb 1.40.20 1.40.56 types-boto3-ec2 1.40.24 1.40.61 types-boto3-lambda 1.40.7 1.40.61 types-boto3-lite 1.40.29 1.40.61 types-boto3-rds 1.40.29 1.40.50 types-boto3-s3 1.40.26 1.40.61 types-boto3-sqs 1.40.17 1.40.61 types-cachetools 6.2.0.20250827 6.2.0.20251022 types-pyyaml 6.0.12.20250822 6.0.12.20250915 types-s3transfer 0.13.1 0.14.0 typing-inspection 0.4.1 0.4.2 uvloop 0.21.0 0.22.1 watchfiles 1.1.0 1.1.1 xmltodict 0.15.1 1.0.2 Looking at the direct dependencies: alembic: seems safe boto3: hard to tell from changelog, mainly updates to AWS apis? cachetools: according to changelog, nothing impacting us click: Not important; only for import fastapi: dependency upgrades(fix for starlette); otherwise seems safe h5py: Not important; only for import openai: lots of changes in the repo; I assume the API wasn't broken - perhaps @jankrepl can comment? psycopg2: few changes, fixed segfault and postgresql 18 pydantic: seems ok pydantic-settings: seems ok sqlalchemy: bug fixes; hard to know if we are relying on old behavior though uvicorn: looks ok
diff --git a/app/cli/curation/electrical_cell_recording.py b/app/cli/curation/electrical_cell_recording.py
@@ -52,7 +52,7 @@ def curate_assets(
     assets_dict: dict[ContentType, Asset] = {k: v[0] for k, v in assets.items()}
     # Multiple assets: keep the nwb one if any.
     if len(assets_dict) > 1:
-        if asset := assets_dict.get(ContentType.nwb, None):
+        if asset := assets_dict.get(ContentType.nwb):
             msg = (
                 f"Multiple assets {sorted(assets_dict.keys())} for ElectricalCellRecording. "
                 f"{ContentType.nwb} was kept."
diff --git a/app/routers/emodel.py b/app/routers/emodel.py
@@ -1,6 +1,5 @@
 from fastapi import APIRouter
 
-import app.service.electrical_cell_recording
 import app.service.emodel
 from app.routers.admin import router as admin_router
 
diff --git a/app/routers/legacy/model/utils.py b/app/routers/legacy/model/utils.py
@@ -142,7 +142,7 @@ def get_facets(aggs, musts, db_type, db):
         models.append(aliased(db_type))
         cur_alias = aliased(next(iter(models)))
         initial_alias = cur_alias
-        property_group = PROPERTY_MAP.get(f"{target}.{property_}", None)
+        property_group = PROPERTY_MAP.get(f"{target}.{property_}")
         facet_q = db.query(getattr(initial_alias, property_group), func.count().label("count"))
         for model, join in zip(models[1:], joins, strict=False):
             prev_alias = cur_alias
@@ -255,7 +255,7 @@ def add_predicates_to_query(query, must_terms, db_type, alias=None):  # noqa: C9
                     cur_alias = initial_alias
                 else:
                     query_map = QUERY_PATH.get(target)
-                    property_ = PROPERTY_MAP.get(f"{target}.{property_}", None)
+                    property_ = PROPERTY_MAP.get(f"{target}.{property_}")
                     if not query_map or not property_:
                         raise HTTPException(
                             status_code=500,
diff --git a/pyproject.toml b/pyproject.toml
@@ -146,6 +146,9 @@ builtins-ignorelist = ["license"]
     "S101",    # Use of `assert` detected
     "SLF001",  # private member access
 ]
+"app/db/model.py" = [
+    "A003",    # builtin-attribute-shadowing
+]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
diff --git a/uv.lock b/uv.lock

Original file line number	Diff line number	Diff line change
`@@ -146,6 +146,9 @@ builtins-ignorelist = ["license"]`
`146`	`146`	"S101", # Use of `assert` detected
`147`	`147`	`"SLF001", # private member access`
`148`	`148`	`]`
	`149`	`+"app/db/model.py" = [`
	`150`	`+ "A003", # builtin-attribute-shadowing`
	`151`	`+]`
`149`	`152`
`150`	`153`	`[tool.ruff.lint.pydocstyle]`
`151`	`154`	`convention = "google"`