feat: deptry as pre-commit and associated changes

opentargets · Dec 4, 2023 · fac4f0f · fac4f0f
1 parent 70887ca
commit fac4f0f
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Showing 5 changed files with 28 additions and 73 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -96,3 +96,9 @@ repos:
     rev: 0.3.8
     hooks:
       - id: pydoclint
+
+  - repo: https://github.com/fpgmaas/deptry.git
+    rev: 0.12.0
+    hooks:
+      - id: deptry
+        args: ["--per-rule-ignores", "DEP001=otg"]
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -43,7 +43,7 @@ markdown_extensions:
       permalink: true
 
 hooks:
-  - src/scripts/schemadocs.py
+  - src/utils/schemadocs.py
 
 repo_name: opentargets/genetics_etl_python
 repo_url: https://github.com/opentargets/genetics_etl_python

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,11 +18,12 @@ scipy = "^1.11.3"
 hydra-core = "^1.3.2"
 pyliftover = "^0.4"
 xgboost = "^1.7.3"
-scikit-learn = "^1.2.1"
 numpy = "^1.26.1"
 hail = "0.2.126"
-pyarrow = "^14.0.1"
 wandb = "^0.16.0"
+google = "^3.0.0"
+omegaconf = "^2.3.0"
+typing-extensions = "^4.8.0"
 
 [tool.poetry.dev-dependencies]
 pre-commit = "^3.5.0"
@@ -84,6 +85,9 @@ build-backend = "poetry.core.masonry.api"
 [tool.isort]
 profile = "black"
 
+[tool.deptry]
+extend_exclude = ["src/conftest.py", "src/airflow", "src/utils"]
+
 [tool.deptry.per_rule_ignores]
 DEP001 = ["otg"]
 

diff --git a/src/scripts/schemadocs.py → src/utils/schemadocs.py b/src/scripts/schemadocs.py → src/utils/schemadocs.py