Update repo to python 312

.github/workflows/docs.yml

@@ -0,0 +1,100 @@
+name: docs
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.html'
+      - '**.js'
+      - '**.md'
+      - uv.lock
+      - pyproject.toml
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.js'
+      - '**.html'
+      - uv.lock
+      - pyproject.toml
+      - '**.md'
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4.2.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.21"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5.3.0
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --group docs
+
+      - name: Build docs
+        run: uv run mkdocs build
+
+      - name: Create .nojekyll file
+        run: touch site/.nojekyll
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-site
+          path: site/
+          retention-days: 1
+
+  deploy:
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4.2.2
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: docs-site
+          path: site
+
+      - name: Ensure .nojekyll exists
+        run: touch site/.nojekyll
+
+      - name: Deploy to Github pages
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
+        with:
+          branch: gh-pages
+          folder: site

.github/workflows/integration_tests.yml

@@ -36,34 +36,34 @@
 
 jobs:
   integration-tests:
-    runs-on: [self-hosted, db]
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4.2.2
         with:
           submodules: 'true'
       - name: Install uv
         uses: astral-sh/setup-uv@v5
         with:
           # Install a specific version of uv.
           version: "0.5.21"
           enable-cache: true
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version-file: ".python-version"
       - name: Install dependencies and check code
         run: |
           uv sync --dev
           source .venv/bin/activate
           coverage run -m pytest -m integration_test && coverage xml && coverage report -m
       - name: Upload coverage to Codecov
         uses: Wandalen/wretry.action@v3.8.0
         with:
           action: codecov/codecov-action@v4.0.0
           with: |
             token: ${{ secrets.CODECOV_TOKEN }}
             file: ./coverage.xml
             name: codecov-umbrella
             fail_ci_if_error: true
           attempt_limit: 5
           attempt_delay: 30000

.gitignore

@@ -26,3 +26,4 @@ multirun/
 _autosummary
 *cyclops_reports*
 *dummy_reports*
+site/

.pre-commit-config.yaml

@@ -13,6 +13,7 @@ repos:
       args: [--fix=lf]
     - id: requirements-txt-fixer
     - id: check-yaml
+      args: [--unsafe]
     - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
@@ -44,7 +45,6 @@ repos:
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
     hooks:
-    - id: nbqa-black
     - id: nbqa-ruff
       args: [--fix, --exit-non-zero-on-fix]
 

.python-version

@@ -1 +1 @@
-3.10
+3.12

cycquery/base.py

@@ -2,7 +2,7 @@
 
 import logging
 from functools import partial
-from typing import Any, Callable, Dict, List, Optional
+from typing import Any, Callable
 
 from sqlalchemy import MetaData
 from sqlalchemy.sql.selectable import Subquery
@@ -80,7 +80,7 @@ class DatasetQuerier:
         The database management system type (e.g., 'postgresql', 'mysql', 'sqlite').
     user : str, optional
         The username for the database, by default empty. Not used for SQLite.
-    pwd : str, optional
+    password : str, optional
         The password for the database, by default empty. Not used for SQLite.
     host : str, optional
         The host address of the database, by default empty. Not used for SQLite.
@@ -109,9 +109,9 @@ def __init__(
         user: str = "",
         password: str = "",
         host: str = "",
-        port: Optional[int] = None,
+        port: int | None = None,
         database: str = "",
-        schemas: Optional[List[str]] = None,
+        schemas: list[str] | None = None,
     ) -> None:
         """Initialize the querier."""
         config = DatasetQuerierConfig(
@@ -129,7 +129,7 @@ def __init__(
             return
         self._setup_table_methods()
 
-    def list_schemas(self) -> List[str]:
+    def list_schemas(self) -> list[str]:
         """List schemas in the database to query.
 
         Returns
@@ -148,7 +148,7 @@ def list_schemas(self) -> List[str]:
 
         return [schema for schema in all_schemas if schema in schemas_to_use]
 
-    def list_tables(self, schema_name: Optional[str] = None) -> List[str]:
+    def list_tables(self, schema_name: str | None = None) -> list[str]:
         """List table methods that can be queried using the database.
 
         Parameters
@@ -173,7 +173,7 @@ def list_tables(self, schema_name: Optional[str] = None) -> List[str]:
 
         return table_names
 
-    def list_columns(self, schema_name: str, table_name: str) -> List[str]:
+    def list_columns(self, schema_name: str, table_name: str) -> list[str]:
         """List columns in a table.
 
         Parameters
@@ -193,7 +193,7 @@ def list_columns(self, schema_name: str, table_name: str) -> List[str]:
             getattr(getattr(self.db, schema_name), table_name).data_.columns.keys(),
         )
 
-    def list_custom_tables(self) -> List[str]:
+    def list_custom_tables(self) -> list[str]:
         """List custom tables methods provided by the dataset API.
 
         Returns
@@ -285,10 +285,11 @@ def _setup_table_methods(self) -> None:
 
         """
         schemas = self.list_schemas()
-        meta: Dict[str, MetaData] = {}
+        meta: dict[str, MetaData] = {}
         for schema_name in schemas:
             metadata = MetaData(schema=schema_name)
-            metadata.reflect(bind=self.db.engine)
+            with self.db.engine.connect() as conn:
+                metadata.reflect(bind=conn)
             meta[schema_name] = metadata
             schema = DBSchema(schema_name, meta[schema_name])
             for table_name in meta[schema_name].tables: