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[WIP] Alembic#12869

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jdavcs wants to merge 44 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom jdavcs:dev_alembic12jdavcs/galaxy:dev_alembic12Copy head branch name to clipboard

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Commits on Dec 21, 2021

• Add alembic to pyproject.toml, data package

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• Add core infrastructure for alembic

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• Add test infrastructure for alembic

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• Combine fixtures in conftest.py

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• Add type hint to fix mypy error

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• Add alembic dir to ignore list in run_tests

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• Add galaxy-specific logic to create_database

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• Simplify logic, cache database state

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• Do not override Galaxy logging: disable in alembic.

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• One does not simply use a relative path to walk into Mordor

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• Fix linting

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• Use semicolon instead of space as path separator for alembic.ini

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• Add alembic dir to ignore list in package tests

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• Reuse engine in DatabaseStateCache

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• Reuse engine for AlembicManager

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• Limit engine creation to DatabaseVerifier

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• Pass engines to DatabaseVerifier

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• Move engine_options default arg initialization to engine_factory

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• Determine combined_db_model in config, not migrations

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• Use template, encoding for db creation for galaxy db only

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• Use database_auto_migrate config setting

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• Do not load multiple metadata objects; drop test

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• Set 179 as last sqlalchemy migrate version

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• Remove migrations test from first starup workflow

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• WIP: Rewrite tests to allow postgres as test db

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• Ignore SA error when dropping migrate_version tbl (see note)

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• Modify remaining tests; leave one exposing bug

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• Fix postgres connection issue; 2 tests expected to fail

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• Add workflow for migration tests

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• Do not load db state before creating a db

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• Fix mypy error.

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• WIP: second pass at integrating; mypy not happy

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• Refactor, remove duplication, fix tests

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• WIP: temporary fix for the weird mypy error

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• Fix integration tests

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• Move triggers out of migrate directory

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• Run tests under Python 3.7

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Commits on Dec 30, 2021

• Rewrite migration algorithm, update tests

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• Fix passing config values

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• Fix tests: tsi and gxy may have different stored versions

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• Remove tmp stuff

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• Update latest version from 179 to 180

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• Cleanup postgres db when not created by test

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• Ignore mypy type error: called out of context, so attr n/a

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