feat: Updated SQLAlcjhemy to 2.x and introduced alembic for automatic…

… migrations (#273)

* feat: initial skeleton for alembic

* WIP

* Integrated with SQLAlchemy 2.0

* Updated dependencies

* Fixed spec file in order to copy appropriate data files in the new pyinstaller layout

* Added alembic in requirements file

* Removed circular import

* Merged develop

* fix: Modified issue with build task

* attempting to force generation of default.xpdf

* Fixed regression

* Removed file generated at runtime from the data files collected

* Fixed alembic config detection when app is running from source

* Refactor and handling database migrations

alembic.ini

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+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+# Use forward slashes (/) also on windows to provide an os agnostic path
+script_location = alembic
+
+# 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
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# 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>=3.9 or backports.zoneinfo library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# 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 alembic/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:alembic/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 = sqlite:///.appdata/database/database2.sqlite
+
+
+[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
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = --fix 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

alembic/README

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+Generic single-database configuration.

alembic/env.py

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+from logging.config import fileConfig
+
+from sqlalchemy import create_engine
+from sqlalchemy import pool
+from sqlalchemy.orm import configure_mappers
+
+from alembic import context
+from alembic.autogenerate import rewriter
+from alembic.operations import ops
+
+from bookworm.database import *
+
+
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# 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.
+
+writer = rewriter.Rewriter()
+
+@writer.rewrites(ops.MigrationScript)
+def add_imports(context, revision, op):
+    op.imports.add("import bookworm")
+    return [op]
+
+
+
+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 run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = create_engine(config.get_main_option("sqlalchemy.url"))
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=target_metadata,
+            process_revision_directives=writer
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

alembic/script.py.mako

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

alembic/versions/28099038d8d6_initial_migration.py

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+"""Initial Migration
+
+Revision ID: 28099038d8d6
+Revises: 
+Create Date: 2024-09-23 00:10:33.591108
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+import bookworm
+
+# revision identifiers, used by Alembic.
+revision: str = '28099038d8d6'
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('book',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.Column('uri', bookworm.database.models.DocumentUriDBType(length=1024), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_book_uri'), 'book', ['uri'], unique=True)
+    op.create_table('document_position_info',
+    sa.Column('last_page', sa.Integer(), nullable=True),
+    sa.Column('last_position', sa.Integer(), nullable=True),
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.Column('uri', bookworm.database.models.DocumentUriDBType(length=1024), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_document_position_info_uri'), 'document_position_info', ['uri'], unique=True)
+    op.create_table('note_tag',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_note_tag_title'), 'note_tag', ['title'], unique=True)
+    op.create_table('pinned_document',
+    sa.Column('last_opened_on', sa.DateTime(), nullable=True),
+    sa.Column('is_pinned', sa.Boolean(), nullable=True),
+    sa.Column('pinning_order', sa.Integer(), nullable=True),
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.Column('uri', bookworm.database.models.DocumentUriDBType(length=1024), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_pinned_document_uri'), 'pinned_document', ['uri'], unique=True)
+    op.create_table('quote_tag',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_quote_tag_title'), 'quote_tag', ['title'], unique=True)
+    op.create_table('recent_document',
+    sa.Column('last_opened_on', sa.DateTime(), nullable=True),
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=512), nullable=False),
+    sa.Column('uri', bookworm.database.models.DocumentUriDBType(length=1024), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_recent_document_uri'), 'recent_document', ['uri'], unique=True)
+    op.create_table('bookmark',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=255), nullable=False),
+    sa.Column('page_number', sa.Integer(), nullable=False),
+    sa.Column('position', sa.Integer(), nullable=False),
+    sa.Column('section_title', sa.String(length=1024), nullable=False),
+    sa.Column('section_identifier', sa.String(length=1024), nullable=False),
+    sa.Column('date_created', sa.DateTime(), nullable=True),
+    sa.Column('date_updated', sa.DateTime(), nullable=True),
+    sa.Column('book_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['book_id'], ['book.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('note',
+    sa.Column('content', sa.Text(), nullable=False),
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=255), nullable=False),
+    sa.Column('page_number', sa.Integer(), nullable=False),
+    sa.Column('position', sa.Integer(), nullable=False),
+    sa.Column('section_title', sa.String(length=1024), nullable=False),
+    sa.Column('section_identifier', sa.String(length=1024), nullable=False),
+    sa.Column('date_created', sa.DateTime(), nullable=True),
+    sa.Column('date_updated', sa.DateTime(), nullable=True),
+    sa.Column('book_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['book_id'], ['book.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('quote',
+    sa.Column('start_pos', sa.Integer(), nullable=False),
+    sa.Column('end_pos', sa.Integer(), nullable=False),
+    sa.Column('content', sa.Text(), nullable=False),
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=255), nullable=False),
+    sa.Column('page_number', sa.Integer(), nullable=False),
+    sa.Column('position', sa.Integer(), nullable=False),
+    sa.Column('section_title', sa.String(length=1024), nullable=False),
+    sa.Column('section_identifier', sa.String(length=1024), nullable=False),
+    sa.Column('date_created', sa.DateTime(), nullable=True),
+    sa.Column('date_updated', sa.DateTime(), nullable=True),
+    sa.Column('book_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['book_id'], ['book.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('notes_tags',
+    sa.Column('note_id', sa.Integer(), nullable=True),
+    sa.Column('note_tag_id', sa.Integer(), nullable=True),
+    sa.ForeignKeyConstraint(['note_id'], ['note.id'], ),
+    sa.ForeignKeyConstraint(['note_tag_id'], ['note_tag.id'], )
+    )
+    op.create_table('quotes_tags',
+    sa.Column('quote_id', sa.Integer(), nullable=True),
+    sa.Column('quote_tag_id', sa.Integer(), nullable=True),
+    sa.ForeignKeyConstraint(['quote_id'], ['quote.id'], ),
+    sa.ForeignKeyConstraint(['quote_tag_id'], ['quote_tag.id'], )
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('quotes_tags')
+    op.drop_table('notes_tags')
+    op.drop_table('quote')
+    op.drop_table('note')
+    op.drop_table('bookmark')
+    op.drop_index(op.f('ix_recent_document_uri'), table_name='recent_document')
+    op.drop_table('recent_document')
+    op.drop_index(op.f('ix_quote_tag_title'), table_name='quote_tag')
+    op.drop_table('quote_tag')
+    op.drop_index(op.f('ix_pinned_document_uri'), table_name='pinned_document')
+    op.drop_table('pinned_document')
+    op.drop_index(op.f('ix_note_tag_title'), table_name='note_tag')
+    op.drop_table('note_tag')
+    op.drop_index(op.f('ix_document_position_info_uri'), table_name='document_position_info')
+    op.drop_table('document_position_info')
+    op.drop_index(op.f('ix_book_uri'), table_name='book')
+    op.drop_table('book')
+    # ### end Alembic commands ###