Add tables and set up alembic

alembic.ini

@@ -0,0 +1,108 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = migrations
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python-dateutil library that can be
+# installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to dateutil.tz.gettz()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the
+# "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to migrations/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:migrations/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+version_path_separator = os  # Use os.pathsep. Default configuration used for new projects.
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+sqlalchemy.url = driver://user:pass@localhost/dbname
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

app/conftest.py

@@ -0,0 +1 @@
+"""The application-level conftest."""

app/database.py

@@ -0,0 +1,83 @@
+"""
+Database models and session.
+
+The database is a SQLite database, and is stored in the root
+of the project as `db.sqlite3`.
+
+The database is managed using Alembic, and migrations
+are stored in the `migrations/` directory.
+
+The module defines the following models:
+
+- `Repo`: A repository that is being tracked.
+- `Dependency`: A dependency of a repository.
+- `RepoDependency`: A relationship between a repository and a dependency.
+
+The database is accessed asynchronously using SQLAlchemy's async API.
+"""
+from collections.abc import AsyncGenerator
+from pathlib import PurePath
+from typing import Final
+
+from sqlalchemy import ForeignKey, String
+from sqlalchemy.ext.asyncio import (
+    AsyncAttrs,
+    AsyncSession,
+    async_sessionmaker,
+    create_async_engine,
+)
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
+
+DB_PATH: Final[PurePath] = PurePath(__file__).parent.parent / "db.sqlite3"
+
+SQLALCHEMY_DATABASE_URL: Final[str] = f"sqlite+aiosqlite:///{DB_PATH}"
+
+engine = create_async_engine(SQLALCHEMY_DATABASE_URL)
+
+async_session_maker = async_sessionmaker(engine, expire_on_commit=False)
+
+
+async def get_async_session() -> AsyncGenerator[AsyncSession, None]:
+    """Get an async session."""
+    async with async_session_maker() as session:
+        yield session
+
+
+class Base(AsyncAttrs, DeclarativeBase):
+    """Declarative base for database models."""
+
+    pass
+
+
+class Repo(Base):
+    """A repository that is being tracked."""
+
+    __tablename__ = "repo"
+    id: Mapped[int] = mapped_column(primary_key=True)
+    url: Mapped[str] = mapped_column(nullable=False, unique=True)
+    dependencies: Mapped[list["Dependency"]] = relationship(
+        "Dependency", secondary="repo_dependency", back_populates="repos"
+    )
+
+
+class Dependency(Base):
+    """A dependency of a repository."""
+
+    __tablename__ = "dependency"
+    id: Mapped[int] = mapped_column(primary_key=True)
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    repos: Mapped[list["Repo"]] = relationship(
+        "Repo", secondary="repo_dependency", back_populates="dependencies"
+    )
+
+
+class RepoDependency(Base):
+    """A relationship between a repository and a dependency."""
+
+    __tablename__ = "repo_dependency"
+    repo_id: Mapped[int] = mapped_column(
+        ForeignKey(Repo.id, ondelete="CASCADE"), primary_key=True
+    )
+    dependency_id: Mapped[int] = mapped_column(
+        ForeignKey(Dependency.id, ondelete="CASCADE"), primary_key=True
+    )

app/settings.py

@@ -0,0 +1 @@
+"""The application settings."""

app/tests/__init__.py

@@ -0,0 +1 @@
+"""The application tests."""

migrations/README

@@ -0,0 +1 @@
+Generic single-database configuration with an async dbapi.

migrations/env.py

@@ -0,0 +1,100 @@
+import asyncio
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy import pool
+from sqlalchemy.engine import Connection
+from sqlalchemy.ext.asyncio import async_engine_from_config
+
+from app.database import SQLALCHEMY_DATABASE_URL, Base
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Overriding the sqlalchemy.url value from the alembic.ini file
+# with the value from the app's database.py file.
+# This is needed because the alembic.ini file is used by the
+# Alembic CLI to run migrations, but the app's database.py file
+# is used by the app itself to connect to the database.
+# The app's database.py file is the source of truth for the
+# database connection URL.
+
+config.set_main_option("sqlalchemy.url", SQLALCHEMY_DATABASE_URL)
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+target_metadata = Base.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def do_run_migrations(connection: Connection) -> None:
+    context.configure(connection=connection, target_metadata=target_metadata)
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+async def run_async_migrations() -> None:
+    """In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    connectable = async_engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    async with connectable.connect() as connection:
+        await connection.run_sync(do_run_migrations)
+
+    await connectable.dispose()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode."""
+
+    asyncio.run(run_async_migrations())
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

migrations/versions/7ee6dc0ae743_add_repo_dependency_and_repodependency_.py

@@ -0,0 +1,51 @@
+"""Add Repo, Dependency, and RepoDependency tables
+
+Revision ID: 7ee6dc0ae743
+Revises:
+Create Date: 2023-07-28 22:41:31.438931
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "7ee6dc0ae743"
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "dependency",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sa.String(length=255), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "repo",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("url", sa.String(), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("url"),
+    )
+    op.create_table(
+        "repo_dependency",
+        sa.Column("repo_id", sa.Integer(), nullable=False),
+        sa.Column("dependency_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["dependency_id"], ["dependency.id"], ondelete="CASCADE"
+        ),
+        sa.ForeignKeyConstraint(["repo_id"], ["repo.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("repo_id", "dependency_id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("repo_dependency")
+    op.drop_table("repo")
+    op.drop_table("dependency")
+    # ### end Alembic commands ###

pyproject.toml

@@ -89,6 +89,10 @@ extend-select = [
     "NPY", # numpy-specific rules
     "Q", # flake8-quotes
 ]
+[tool.ruff.per-file-ignores]
+# Ignore missing docstrings in migrations and alembic files
+"**/migrations/*.py" = ["D"]
+"**/migrations/env.py" = ["ERA001"]
 
 [tool.ruff.pydocstyle]
 convention = "numpy"