Merge pull request #327 from VariantEffect/feature/bencap/267/lint-with-ruff

Lint and Format with Ruff

Author: bencap

.flake8

@@ -61,3 +61,17 @@ jobs:
     - run: pip install poetry
     - run: poetry install --with dev --extras server
     - run: poetry run mypy src/
+
+  run-ruff-lint:
+    runs-on: ubuntu-latest
+    name: Ruff linting on Python 3.10
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev --extras server
+    - run: poetry run ruff check

.github/workflows/run-tests-on-push.yml

@@ -1,8 +1,9 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.8
     hooks:
-      - id: black
-        # Latest version of Python supported by the project
-        # See https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.9
+      # Run the linter.
+      - id: ruff
+      # Run the formatter.
+      - id: ruff-format

.pre-commit-config.yaml

@@ -1,10 +1,11 @@
 # From https://improveandrepeat.com/2021/09/python-friday-87-handling-pre-existing-tables-with-alembic-and-sqlalchemy/
 # Based on https://github.com/talkpython/data-driven-web-apps-with-flask
 
-from alembic import op
 from sqlalchemy import engine_from_config
 from sqlalchemy.engine import reflection
 
+from alembic import op
+
 
 def table_does_not_exist(table, schema=None):
     config = op.get_context().config

alembic/alembic_helpers.py

@@ -1,8 +1,7 @@
-from logging.config import fileConfig
 import os
+from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
+from sqlalchemy import engine_from_config, pool
 
 from alembic import context
 

alembic/env.py

@@ -5,9 +5,8 @@
 Create Date: 2023-08-29 12:48:18.390567
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "194cfebabe32"

alembic/versions/194cfebabe32_rename_wild_type_sequence.py

@@ -5,9 +5,8 @@
 Create Date: 2024-09-03 09:53:21.635751
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "1cee01c42909"

alembic/versions/1cee01c42909_make_index_on_contributors_unique.py

@@ -5,13 +5,10 @@
 Create Date: 2024-09-04 16:17:20.875937
 
 """
-from alembic import op
-import sqlalchemy as sa
-
 
 # revision identifiers, used by Alembic.
-revision = '1d4933b4b6f7'
-down_revision = ('76e1e55bc5c1', 'd7e6f8c3b9dc')
+revision = "1d4933b4b6f7"
+down_revision = ("76e1e55bc5c1", "d7e6f8c3b9dc")
 branch_labels = None
 depends_on = None
 

alembic/versions/1d4933b4b6f7_merge_76e1e55bc5c1_and_d7e6f8c3b9dc.py

@@ -5,20 +5,21 @@
 Create Date: 2023-06-01 14:51:04.700969
 
 """
-from typing import Optional
+
 import os
+from typing import Optional
 
 import eutils
-from eutils._internal.xmlfacades.pubmedarticleset import PubmedArticleSet
 import sqlalchemy as sa
 from eutils import EutilsNCBIError
-from mavedb.lib.exceptions import AmbiguousIdentifierError
+from eutils._internal.xmlfacades.pubmedarticleset import PubmedArticleSet
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import Session
 
 from alembic import op
-from mavedb.lib.identifiers import ExternalPublication
+from mavedb.lib.exceptions import AmbiguousIdentifierError
 from mavedb.lib.external_publications import Rxiv
+from mavedb.lib.identifiers import ExternalPublication
 from mavedb.models.publication_identifier import PublicationIdentifier
 
 # revision identifiers, used by Alembic.

alembic/versions/22e2d92d602e_add_publication_identifier_metadata_.py

@@ -5,10 +5,12 @@
 Create Date: 2024-09-09 12:25:33.180077
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
 
+from alembic import op
+
 # revision identifiers, used by Alembic.
 revision = "2b6f40ea2fb6"
 down_revision = "1cee01c42909"