add deptry for opencloning-db

Author: manulera

.pre-commit-config.yaml

@@ -60,3 +60,16 @@ repos:
                 packages/opencloning/pyproject.toml|
                 pyproject.toml
             )$
+  - repo: local
+    hooks:
+      - id: deptry-opencloning-db
+        name: deptry (opencloning-db)
+        entry: uv run deptry --config packages/opencloning-db/pyproject.toml packages/opencloning-db/src
+        language: system
+        pass_filenames: false
+        files: |
+            (?x)^(
+                packages/opencloning-db/src/.*|
+                packages/opencloning-db/pyproject.toml|
+                pyproject.toml
+            )$

README.md

@@ -167,12 +167,13 @@ uv run --directory packages/opencloning-db/src python -m opencloning_db.init_db
 
 This repository uses a uv workspace. In a workspace, dependencies are resolved in one shared environment, so imports can appear to work even when a package does not declare them in its own `pyproject.toml`.
 
-To catch that for `opencloning`, pre-commit runs `deptry` against `packages/opencloning/src` using `packages/opencloning/pyproject.toml` as the source of truth for declared dependencies.
+To catch that, pre-commit runs `deptry` separately for `opencloning` and `opencloning-db`, each using that package’s `pyproject.toml` as the source of truth for declared dependencies.
 
-Run it manually from the repository root:
+Run them manually from the repository root:
 
 ```bash
 uv run deptry --config packages/opencloning/pyproject.toml packages/opencloning/src
+uv run deptry --config packages/opencloning-db/pyproject.toml packages/opencloning-db/src
 ```
 
 Current rollout note: known undeclared imports such as `pydna` are temporarily ignored and should be removed from the ignore list once dependencies are declared.

packages/opencloning-db/pyproject.toml

@@ -13,12 +13,14 @@ description = "Database for OpenCloning, a web application to generate molecular
 requires-python = ">=3.11,<4"
 dependencies = [
     "opencloning",
-    "sqlalchemy>=2.0.41,<3",
+    "fastapi>=0.135.3",
     "fastapi-pagination>=0.15.10,<0.16",
+    "opencloning-linkml>=1.0.0",
+    "pydantic[email]>=2.7.1",
+    "sqlalchemy>=2.0.41,<3",
     "PyJWT>=2.10.1,<3",
     "pwdlib[argon2]>=0.2.1,<0.3",
     "pydna>=5.5.9",
-    "email-validator>=2.3.0,<3",
 ]
 
 [tool.uv.sources]
@@ -27,12 +29,14 @@ opencloning = { workspace = true }
 [tool.poetry.dependencies]
 python = "^3.11"
 opencloning = {path = "../../opencloning", develop = true}
-sqlalchemy = "^2.0.41"
+fastapi = "^0.135.3"
 fastapi-pagination = "^0.15.10"
+opencloning-linkml = "^1.0.0"
+pydantic = {version = "^2.7.1", extras = ["email"]}
+sqlalchemy = "^2.0.41"
 PyJWT = "^2.10.1"
 pwdlib = {version = "^0.2.1", extras = ["argon2"]}
 pydna = "^5.5.9"
-email-validator = "^2.3.0"
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.0.4"
@@ -61,3 +65,6 @@ requires = ["poetry-core>=1.0.0"]
 [tool.black]
 skip-string-normalization = true
 line-length = 119
+
+[tool.deptry]
+known_first_party = ["opencloning_db"]