Lint fixes.

chanzuckerberg · Aug 28, 2024 · 30e3969 · 30e3969
1 parent 2f8b26b
commit 30e3969
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Showing 107 changed files with 1,655 additions and 1,437 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -36,7 +36,6 @@ repos:
       #        pydantic-settings,
       #        click,
       #      ]
-repos:
 - repo: https://github.com/mpalmer/action-validator
   rev: v0.6.0
   hooks:

diff --git a/apiv2/database/migrations/env.py b/apiv2/database/migrations/env.py
@@ -1,11 +1,10 @@
 from logging.config import fileConfig
 
-from alembic import context
-from sqlalchemy import create_engine
 import sqlalchemy as sa
-
+from alembic import context
 from database.models import meta
 from platformics.settings import CLISettings
+from sqlalchemy import create_engine
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.

diff --git a/apiv2/database/models/alignment.py b/apiv2/database/models/alignment.py
@@ -5,27 +5,22 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import Enum, Float, ForeignKey, Integer, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import alignment_type_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.annotation_file import AnnotationFile
-    from database.models.per_section_alignment_parameters import PerSectionAlignmentParameters
     from database.models.deposition import Deposition
+    from database.models.per_section_alignment_parameters import PerSectionAlignmentParameters
+    from database.models.run import Run
     from database.models.tiltseries import Tiltseries
     from database.models.tomogram import Tomogram
-    from database.models.run import Run
+    from platformics.database.models.file import File
 
     ...
 else:
@@ -81,7 +76,8 @@ class Alignment(Base):
     )
     alignment: Mapped[str] = mapped_column(String, nullable=False)
     alignment_type: Mapped[alignment_type_enum] = mapped_column(
-        Enum(alignment_type_enum, native_enum=False), nullable=True
+        Enum(alignment_type_enum, native_enum=False),
+        nullable=True,
     )
     volume_x_dimension: Mapped[float] = mapped_column(Float, nullable=True)
     volume_y_dimension: Mapped[float] = mapped_column(Float, nullable=True)

diff --git a/apiv2/database/models/annotation.py b/apiv2/database/models/annotation.py
@@ -5,25 +5,21 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
 import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import Boolean, DateTime, Enum, Float, ForeignKey, Integer, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import annotation_method_type_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
-    from database.models.run import Run
-    from database.models.annotation_shape import AnnotationShape
     from database.models.annotation_author import AnnotationAuthor
+    from database.models.annotation_shape import AnnotationShape
     from database.models.deposition import Deposition
+    from database.models.run import Run
+    from platformics.database.models.file import File
 
     ...
 else:
@@ -79,7 +75,8 @@ class Annotation(Base):
     annotation_software: Mapped[str] = mapped_column(String, nullable=True)
     is_curator_recommended: Mapped[bool] = mapped_column(Boolean, nullable=True)
     method_type: Mapped[annotation_method_type_enum] = mapped_column(
-        Enum(annotation_method_type_enum, native_enum=False), nullable=False
+        Enum(annotation_method_type_enum, native_enum=False),
+        nullable=False,
     )
     deposition_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False)
     release_date: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable=False)

diff --git a/apiv2/database/models/annotation_author.py b/apiv2/database/models/annotation_author.py
@@ -5,21 +5,16 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from platformics.database.models.file import File
+from sqlalchemy import Boolean, ForeignKey, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.annotation import Annotation
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/annotation_file.py b/apiv2/database/models/annotation_file.py
@@ -5,24 +5,19 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import Boolean, Enum, ForeignKey, Integer, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import annotation_file_source_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.alignment import Alignment
     from database.models.annotation_shape import AnnotationShape
     from database.models.tomogram_voxel_spacing import TomogramVoxelSpacing
+    from platformics.database.models.file import File
 
     ...
 else:
@@ -44,15 +39,21 @@ class AnnotationFile(Base):
         back_populates="annotation_files",
     )
     annotation_shape_id: Mapped[int] = mapped_column(
-        Integer, ForeignKey("annotation_shape.id"), nullable=True, index=True
+        Integer,
+        ForeignKey("annotation_shape.id"),
+        nullable=True,
+        index=True,
     )
     annotation_shape: Mapped["AnnotationShape"] = relationship(
         "AnnotationShape",
         foreign_keys=annotation_shape_id,
         back_populates="annotation_files",
     )
     tomogram_voxel_spacing_id: Mapped[int] = mapped_column(
-        Integer, ForeignKey("tomogram_voxel_spacing.id"), nullable=True, index=True
+        Integer,
+        ForeignKey("tomogram_voxel_spacing.id"),
+        nullable=True,
+        index=True,
     )
     tomogram_voxel_spacing: Mapped["TomogramVoxelSpacing"] = relationship(
         "TomogramVoxelSpacing",
@@ -64,6 +65,7 @@ class AnnotationFile(Base):
     https_path: Mapped[str] = mapped_column(String, nullable=False)
     is_visualization_default: Mapped[bool] = mapped_column(Boolean, nullable=True)
     source: Mapped[annotation_file_source_enum] = mapped_column(
-        Enum(annotation_file_source_enum, native_enum=False), nullable=True
+        Enum(annotation_file_source_enum, native_enum=False),
+        nullable=True,
     )
     id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True)
diff --git a/apiv2/database/models/annotation_shape.py b/apiv2/database/models/annotation_shape.py
@@ -5,23 +5,18 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import Enum, ForeignKey, Integer
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import annotation_file_shape_type_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.annotation import Annotation
     from database.models.annotation_file import AnnotationFile
+    from platformics.database.models.file import File
 
     ...
 else:
@@ -48,6 +43,7 @@ class AnnotationShape(Base):
         foreign_keys="AnnotationFile.annotation_shape_id",
     )
     shape_type: Mapped[annotation_file_shape_type_enum] = mapped_column(
-        Enum(annotation_file_shape_type_enum, native_enum=False), nullable=True
+        Enum(annotation_file_shape_type_enum, native_enum=False),
+        nullable=True,
     )
     id: Mapped[int] = mapped_column(Integer, nullable=False, index=True, autoincrement=True, primary_key=True)
diff --git a/apiv2/database/models/dataset.py b/apiv2/database/models/dataset.py
@@ -5,25 +5,21 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
 import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import DateTime, Enum, ForeignKey, Integer, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import sample_type_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
-    from database.models.deposition import Deposition
-    from database.models.dataset_funding import DatasetFunding
     from database.models.dataset_author import DatasetAuthor
+    from database.models.dataset_funding import DatasetFunding
+    from database.models.deposition import Deposition
     from database.models.run import Run
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/dataset_author.py b/apiv2/database/models/dataset_author.py
@@ -5,21 +5,16 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from platformics.database.models.file import File
+from sqlalchemy import Boolean, ForeignKey, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.dataset import Dataset
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/dataset_funding.py b/apiv2/database/models/dataset_funding.py
@@ -5,21 +5,16 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from platformics.database.models.file import File
+from sqlalchemy import ForeignKey, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.dataset import Dataset
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/deposition.py b/apiv2/database/models/deposition.py
@@ -5,28 +5,24 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
 import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from platformics.database.models.file import File
+from sqlalchemy import DateTime, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
-    from database.models.deposition_author import DepositionAuthor
     from database.models.alignment import Alignment
     from database.models.annotation import Annotation
     from database.models.dataset import Dataset
+    from database.models.deposition_author import DepositionAuthor
+    from database.models.deposition_type import DepositionType
     from database.models.frame import Frame
     from database.models.tiltseries import Tiltseries
     from database.models.tomogram import Tomogram
-    from database.models.deposition_type import DepositionType
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/deposition_author.py b/apiv2/database/models/deposition_author.py
@@ -5,21 +5,16 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
-from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from platformics.database.models.file import File
+from sqlalchemy import Boolean, ForeignKey, Integer, String
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.deposition import Deposition
+    from platformics.database.models.file import File
 
     ...
 else:

diff --git a/apiv2/database/models/deposition_type.py b/apiv2/database/models/deposition_type.py
@@ -5,22 +5,17 @@
 Make changes to the template codegen/templates/database/models/class_name.py.j2 instead.
 """
 
-import uuid
-import uuid6
-import datetime
 from typing import TYPE_CHECKING
 
 from platformics.database.models.base import Base
-from sqlalchemy import ForeignKey, String, Float, Integer, Enum, Boolean, DateTime
-from sqlalchemy.dialects.postgresql import UUID, JSONB
+from platformics.database.models.file import File
+from sqlalchemy import Enum, ForeignKey, Integer
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from sqlalchemy.sql import func
 from support.enums import deposition_types_enum
-from platformics.database.models.file import File
 
 if TYPE_CHECKING:
-    from platformics.database.models.file import File
     from database.models.deposition import Deposition
+    from platformics.database.models.file import File
 
     ...
 else: