Merge pull request #327 from VariantEffect/feature/bencap/267/lint-wi…

…th-ruff

Lint and Format with Ruff

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

@@ -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

.pre-commit-config.yaml

@@ -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

alembic/alembic_helpers.py

@@ -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/env.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/versions/194cfebabe32_rename_wild_type_sequence.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/1cee01c42909_make_index_on_contributors_unique.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/1d4933b4b6f7_merge_76e1e55bc5c1_and_d7e6f8c3b9dc.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/22e2d92d602e_add_publication_identifier_metadata_.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/2b6f40ea2fb6_add_score_range_column.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"

alembic/versions/2c8d7e2bf2fe_consolidate_publication_identifier_dois.py

@@ -5,9 +5,10 @@
 Create Date: 2024-05-16 13:06:05.561411
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "2c8d7e2bf2fe"

alembic/versions/33e99d4b90cc_add_mapped_variants_table.py

@@ -5,33 +5,39 @@
 Create Date: 2023-05-15 17:24:07.847206
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 from sqlalchemy.dialects import postgresql
 
+from alembic import op
+
 # revision identifiers, used by Alembic.
-revision = '33e99d4b90cc'
-down_revision = 'da9ba478647d'
+revision = "33e99d4b90cc"
+down_revision = "da9ba478647d"
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('mapped_variants',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('pre_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
-    sa.Column('post_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
-    sa.Column('variant_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['variant_id'], ['variants.id'], ),
-    sa.PrimaryKeyConstraint('id')
+    op.create_table(
+        "mapped_variants",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("pre_mapped", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.Column("post_mapped", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.Column("variant_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["variant_id"],
+            ["variants.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
     )
-    op.create_index(op.f('ix_mapped_variants_id'), 'mapped_variants', ['id'], unique=False)
+    op.create_index(op.f("ix_mapped_variants_id"), "mapped_variants", ["id"], unique=False)
     # ### end Alembic commands ###
 
 
 def downgrade():
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_index(op.f('ix_mapped_variants_id'), table_name='mapped_variants')
-    op.drop_table('mapped_variants')
+    op.drop_index(op.f("ix_mapped_variants_id"), table_name="mapped_variants")
+    op.drop_table("mapped_variants")
     # ### end Alembic commands ###

alembic/versions/377bb8c30bde_roles_as_enums_access_keys_can_have_.py

@@ -5,9 +5,10 @@
 Create Date: 2024-04-18 09:19:04.008237
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "377bb8c30bde"

alembic/versions/44a45d616036_make_index_on_users_unique.py

@@ -5,8 +5,8 @@
 Create Date: 2024-08-16 13:25:14.980820
 
 """
+
 from alembic import op
-import sqlalchemy as sa
 
 # revision identifiers, used by Alembic.
 revision = "44a45d616036"

alembic/versions/44d5c568f64b_simplify_reference_genome_target_.py

@@ -5,9 +5,10 @@
 Create Date: 2023-08-24 15:20:01.208691
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "44d5c568f64b"

alembic/versions/5cad62af3705_rename_pubmed_identifiers_table_to_publication_identifiers.py

@@ -5,9 +5,8 @@
 Create Date: 2023-05-09 16:18:41.360541
 
 """
-from alembic import op
-import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "5cad62af3705"

alembic/versions/60103ad1cb5b_add_target_sequence_label.py

@@ -5,9 +5,10 @@
 Create Date: 2023-08-29 16:04:44.620385
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "60103ad1cb5b"

alembic/versions/6fae83d65ee4_taxonomy.py

@@ -5,9 +5,10 @@
 Create Date: 2023-12-21 18:06:18.912925
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "6fae83d65ee4"

alembic/versions/76e1e55bc5c1_add_contributors.py

@@ -5,52 +5,75 @@
 Create Date: 2024-08-22 06:17:03.265438
 
 """
-from alembic import op
+
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
-revision = '76e1e55bc5c1'
-down_revision = '9702d32bacb3'
+revision = "76e1e55bc5c1"
+down_revision = "9702d32bacb3"
 branch_labels = None
 depends_on = None
 
 
 def upgrade():
-    op.create_table('contributors',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('orcid_id', sa.String(), nullable=False),
-    sa.Column('given_name', sa.String(), nullable=True),
-    sa.Column('family_name', sa.String(), nullable=True),
-    sa.PrimaryKeyConstraint('id')
+    op.create_table(
+        "contributors",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("orcid_id", sa.String(), nullable=False),
+        sa.Column("given_name", sa.String(), nullable=True),
+        sa.Column("family_name", sa.String(), nullable=True),
+        sa.PrimaryKeyConstraint("id"),
     )
-    op.create_index(op.f('ix_contributors_orcid_id'), 'contributors', ['orcid_id'], unique=False)
-    op.create_table('experiment_set_contributors',
-    sa.Column('experiment_set_id', sa.Integer(), nullable=False),
-    sa.Column('contributor_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
-    sa.ForeignKeyConstraint(['experiment_set_id'], ['experiment_sets.id'], ),
-    sa.PrimaryKeyConstraint('experiment_set_id', 'contributor_id')
+    op.create_index(op.f("ix_contributors_orcid_id"), "contributors", ["orcid_id"], unique=False)
+    op.create_table(
+        "experiment_set_contributors",
+        sa.Column("experiment_set_id", sa.Integer(), nullable=False),
+        sa.Column("contributor_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["contributor_id"],
+            ["contributors.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["experiment_set_id"],
+            ["experiment_sets.id"],
+        ),
+        sa.PrimaryKeyConstraint("experiment_set_id", "contributor_id"),
     )
-    op.create_table('experiment_contributors',
-    sa.Column('experiment_id', sa.Integer(), nullable=False),
-    sa.Column('contributor_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
-    sa.ForeignKeyConstraint(['experiment_id'], ['experiments.id'], ),
-    sa.PrimaryKeyConstraint('experiment_id', 'contributor_id')
+    op.create_table(
+        "experiment_contributors",
+        sa.Column("experiment_id", sa.Integer(), nullable=False),
+        sa.Column("contributor_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["contributor_id"],
+            ["contributors.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["experiment_id"],
+            ["experiments.id"],
+        ),
+        sa.PrimaryKeyConstraint("experiment_id", "contributor_id"),
     )
-    op.create_table('scoreset_contributors',
-    sa.Column('scoreset_id', sa.Integer(), nullable=False),
-    sa.Column('contributor_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['contributor_id'], ['contributors.id'], ),
-    sa.ForeignKeyConstraint(['scoreset_id'], ['scoresets.id'], ),
-    sa.PrimaryKeyConstraint('scoreset_id', 'contributor_id')
+    op.create_table(
+        "scoreset_contributors",
+        sa.Column("scoreset_id", sa.Integer(), nullable=False),
+        sa.Column("contributor_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["contributor_id"],
+            ["contributors.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["scoreset_id"],
+            ["scoresets.id"],
+        ),
+        sa.PrimaryKeyConstraint("scoreset_id", "contributor_id"),
     )
 
 
 def downgrade():
-    op.drop_table('scoreset_contributors')
-    op.drop_table('experiment_contributors')
-    op.drop_table('experiment_set_contributors')
-    op.drop_index(op.f('ix_contributors_orcid_id'), table_name='contributors')
-    op.drop_table('contributors')
+    op.drop_table("scoreset_contributors")
+    op.drop_table("experiment_contributors")
+    op.drop_table("experiment_set_contributors")
+    op.drop_index(op.f("ix_contributors_orcid_id"), table_name="contributors")
+    op.drop_table("contributors")