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Issue #378: Add alembic support for database migrations #387

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Issue #378: Add alembic support for database migrations #387

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Commits on Feb 4, 2022

  1. Basic infrastructure for versiondb subcommand

    @baileythegreen
    baileythegreen committed Feb 4, 2022
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  2. Add new requirement

    @baileythegreen
    baileythegreen committed Feb 4, 2022
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Commits on Feb 7, 2022

  1. Add get_version() for alembic

    @baileythegreen
    baileythegreen committed Feb 7, 2022
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Commits on Feb 9, 2022

  1. Hook pyani versiondb infrastructure to functional code

    @baileythegreen
    baileythegreen committed Feb 9, 2022
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Commits on Feb 13, 2022

  1. Add generic versions of files required for alembic to function

    @baileythegreen
    baileythegreen committed Feb 13, 2022
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  2. Alter handling of stderr and stdoutfrom alembic

    @baileythegreen
    baileythegreen committed Feb 13, 2022
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  3. Add logging and use environmental variables

    @baileythegreen
    baileythegreen committed Feb 13, 2022
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  4. Add migration script for fastANI changes to the ORM

    @baileythegreen
    baileythegreen committed Feb 13, 2022
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  5. Backup existing database before migrating

    @baileythegreen
    baileythegreen committed Feb 13, 2022
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Commits on Feb 14, 2022

  1. Use a local file to track versions in dry-run mode

    @baileythegreen
    baileythegreen committed Feb 14, 2022
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  2. Update parser to use const values instead of defaults

    @baileythegreen
    baileythegreen committed Feb 14, 2022
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  3. Update versiondb to accommodate --dry-run option

    @baileythegreen
    baileythegreen committed Feb 14, 2022
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  4. Clean up subcmd_versiondb

    @baileythegreen
    baileythegreen committed Feb 14, 2022
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  5. Add initial tests for versiondb

    @baileythegreen
    baileythegreen committed Feb 14, 2022
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Commits on Feb 23, 2022

  1. Fix test comparison value

    @baileythegreen
    baileythegreen committed Feb 23, 2022
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  2. Specify which parser arguments are optional

    @baileythegreen
    baileythegreen committed Feb 23, 2022
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  3. Abstract migration functions to one and implement dry-run

    @baileythegreen
    baileythegreen committed Feb 23, 2022
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Commits on Mar 1, 2022

  1. Add alembic_version table to database model

    @baileythegreen
    baileythegreen committed Mar 1, 2022
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  2. Add current database version to alembic_version table

    @baileythegreen
    baileythegreen committed Mar 1, 2022
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  3. Update .gitignore to ignore some testing files

    @baileythegreen
    baileythegreen committed Mar 1, 2022
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  4. Change unique constraints for comparisons table with Alembic

    @baileythegreen
    baileythegreen committed Mar 1, 2022
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  5. Groundwork for tests/test_versiondb.py

    @baileythegreen
    baileythegreen committed Mar 1, 2022
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Commits on Mar 2, 2022

  1. Add timestamp to dry-run output file name

    @baileythegreen
    baileythegreen committed Mar 2, 2022
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  2. Update migration file to allow for reflection in offline mode

    @baileythegreen
    baileythegreen committed Mar 2, 2022
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Commits on Mar 3, 2022

  1. Add empty database fixtures for tests

    @baileythegreen
    baileythegreen committed Mar 3, 2022
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  2. Update test_versiondb.py input file names

    @baileythegreen
    baileythegreen committed Mar 3, 2022
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Commits on Mar 9, 2022

  1. Add docs for versiondb

    @baileythegreen
    baileythegreen committed Mar 9, 2022
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Commits on Mar 14, 2022

  1. Add docs for versiondbAdd a directory for versionb` output files

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  2. Rework tests to look for meaningful differences between output and ta… 

    …rgets
    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  3. Update starting point for database downgrade tests

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  4. Fix errors in versiondb.py arg names

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  5. Add sqlite3 as a third-party dependency

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  6. Fix failing cli test; (failure caused by code added for alembic)

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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  7. Add sqlite installation code to config.yml

    @baileythegreen
    baileythegreen committed Mar 14, 2022
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Commits on Mar 15, 2022

  1. Test alembic command-line generation and add docstrings

    @baileythegreen
    baileythegreen committed Mar 15, 2022
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Commits on Mar 16, 2022

  1. Change how sqlite3 is installed

    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  2. Change how namespaces are retrieved to use fixtures

    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  3. Change how expected_diffs() returns values 

    This might solve problems between comparisons seen on CircleCI
    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  4. Change handling of stdout and stderr from subprocess.run calls 

    The keyword `capture_output` is not compatible with Python 3.6
    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  5. Change cleanup procedure to prevent artefacts being overwritten

    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  6. Replace remaining use of capture_output keyword; previously missed

    @baileythegreen
    baileythegreen committed Mar 16, 2022
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  7. Alter sed command to be OS-specific

    @baileythegreen
    baileythegreen committed Mar 16, 2022
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Commits on Mar 17, 2022

  1. Add targets for versiondb tests

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  2. Add target location for versiondb tests

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  3. Add alt_config file for versiondb tests

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  4. Update tests for versiondb to make diff comparison more robust

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  5. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  6. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  7. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  8. Updated config.yml

    @baileythegreen
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  9. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  10. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  11. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  12. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  13. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  14. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  15. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  16. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  17. Add default location and install instructions for sqlite3

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  18. Merge branch 'alembic_378' of https://github.com/widdowquinn/pyani in… 

    …to alembic_378
    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  19. Fix import syntax

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  20. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  21. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 17, 2022
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  22. Updated config.yml

    @baileythegreen
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  23. Updated config.yml

    @baileythegreen
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  24. Updated config.yml

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  25. Updated config.yml

    @baileythegreen
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  26. Updated config.yml

    @baileythegreen
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Commits on Mar 18, 2022

  1. Remove some dry-run specific stuff for the time being

    @baileythegreen
    baileythegreen committed Mar 18, 2022
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  2. Merge branch 'alembic_378' of https://github.com/widdowquinn/pyani in… 

    …to alembic_378
    @baileythegreen
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  3. Set create_constraint=True for compatibility between sqlalchemy ver… 

    …sions
    @baileythegreen
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Commits on Mar 19, 2022

  1. Set create_constraint flag only if sqlalchemy version is >= 1.4

    @baileythegreen
    baileythegreen committed Mar 19, 2022
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  2. Update versiondb test targets

    @baileythegreen
    baileythegreen committed Mar 19, 2022
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  3. Update versiondb test fixtures

    @baileythegreen
    baileythegreen committed Mar 19, 2022
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Commits on Mar 20, 2022

  1. Send diffs to stdout so we can debug why tests sporadically fail

    @baileythegreen
    baileythegreen committed Mar 20, 2022
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  2. Send diffs to stdout for debugging

    @baileythegreen
    baileythegreen committed Mar 20, 2022
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  3. Use sqldiff instead of diff

    @baileythegreen
    baileythegreen committed Mar 20, 2022
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Commits on Mar 28, 2022

  1. Move sqldiff specification to pyani_config.py

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  2. Remove code from earlier versions of tests

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  3. Enhance comments

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  4. Remove structures from conftest.py that are not being used after all

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  5. Add note about missing --dry-run tests

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  6. Fix typos

    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  7. sqldiff is needed for pyani versiondb, but can't install from `co… 

    …nda`
    @baileythegreen
    baileythegreen committed Mar 28, 2022
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  8. Remove references to non-existent fixtures 

    These should have been removed in 2ee0636, but were missed
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Commits on Mar 29, 2022

  1. Add alembic directories to package data for non-dev use cases

    @baileythegreen
    baileythegreen committed Mar 29, 2022
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Commits on Mar 31, 2022

  1. Update version of sqlite to 3.37.0 and abstract version into a vari… 

    …able
    @baileythegreen
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  2. Add explanations surrounding alembic tests and when they run/depend… 

    …encies
    @baileythegreen
    baileythegreen committed Mar 31, 2022
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  3. Updated config.yml

    @baileythegreen
    baileythegreen committed Mar 31, 2022
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  4. Fix typo in code explanation

    @baileythegreen
    baileythegreen committed Mar 31, 2022
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  5. Merge branch 'alembic_378' of https://github.com/widdowquinn/pyani in… 

    …to alembic_378
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  6. Skip tests requiring sqldiff when it is not installed

    @baileythegreen
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Commits on May 23, 2022

  1. Merge branch 'master' into alembic_378

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  2. Merge branch 'master' of https://github.com/widdowquinn/pyani into al… 

    …embic_378
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Commits on Jun 16, 2022

  1. Merge branch 'alembic_378' of https://github.com/widdowquinn/pyani in… 

    …to alembic_378
    @baileythegreen
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Commits on Jun 21, 2022

  1. Merge branch 'master' of https://github.com/widdowquinn/pyani into al… 

    …embic_378
    @baileythegreen
    baileythegreen committed Jun 21, 2022
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  2. Updated config.yml

    @baileythegreen
    baileythegreen committed Jun 21, 2022
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Commits on Jul 29, 2022

  1. Make changes to tests as discussed in Issue #405

    @baileythegreen
    baileythegreen committed Jul 29, 2022
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