Synchronize Database models with migrations

[MoralCode]

Description
This PR resolves and reconciles the differences between the current, in-database data schema and the schema defined by the SQLAlchemy models. This is needed because, for the past few years, both the models and the migrations have had to be made manually, meaning a lack of perfect consistency between updates to the two sources can cause drift between them.

The recent changes in #3416 configured alembic to automatically compare the data models and the deployed schema and generate migrations that represent the differences. This PR reconciles the various differences that have accumulated over the years.

This PR is one step towards, but not yet a complete fix for #3388.

Notes for Reviewers
Most of the schema conflicts were resolved with relatively minor adjustments to the data models (such as specifying names for Foreign keys, adding fields to unique constraints, etc) to bring them in line with what actual deployed databases have.

There were a few places where I thought it was better to update the database instead:

• There was an index on contributors.gh_login that I dropped, since I believe gh_login has been superseded by another method of looking up contributors for a while now
• a unique constraint on the pull_request_reviews table was updated to add tool_source to its uniqueness check.
• the augur_operations.users.email_verified column was dropped since a recent maintainers call confirmed that email verification was a feature that was previously being explored as part of a password reset feature, but was ultimately dropped due to having limited utility (wasnt worth the the additional overhead of configuring sendgrid for email processing compared to a hypothetical future implementation that uses the Augur CLI to enable admins to perform password resets)

Please look over all the changes and let me know if you think any of these changes needs to be reconciled in a different way (i.e. a model change is incorrect and the database needs to change instead)

I have yet to run this on an actual augur install but plan to soon.

This change is a pretty severe blocker for other database changes I would like to make since I want to start from a relatively clean/consistent state when proposing additional migrations (including some that are important for the next release)

Signed commits

• Yes, I signed my commits.

Gen AI Disclosure

Generative AI was only used for the planning stages of this changes - for example, looking at the schemas or alembic-generated migrations and helping summarize what the differences were between the models and the database. All of these changes were understood/verified and implemented by me.

[MoralCode]

OK so it seems like the smoke tests revealed an interesting bug

Stack Trace

``` augur-1 | Traceback (most recent call last): augur-1 | File "/augur/.venv/bin/augur", line 10, in augur-1 | sys.exit(run()) augur-1 | ^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 1462, in __call__ augur-1 | return self.main(*args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 1383, in main augur-1 | rv = self.invoke(ctx) augur-1 | ^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 1850, in invoke augur-1 | return _process_result(sub_ctx.command.invoke(sub_ctx)) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 1850, in invoke augur-1 | return _process_result(sub_ctx.command.invoke(sub_ctx)) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 1246, in invoke augur-1 | return ctx.invoke(self.callback, **ctx.params) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 814, in invoke augur-1 | return callback(*args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/decorators.py", line 34, in new_func augur-1 | return f(get_current_context(), *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/augur/application/cli/__init__.py", line 45, in new_func augur-1 | return ctx.invoke(function_internet_connection, *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 814, in invoke augur-1 | return callback(*args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/decorators.py", line 34, in new_func augur-1 | return f(get_current_context(), *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/augur/application/cli/__init__.py", line 57, in new_func augur-1 | return ctx.invoke(function_db_connection, *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 814, in invoke augur-1 | return callback(*args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/decorators.py", line 34, in new_func augur-1 | return f(get_current_context(), *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/augur/application/cli/__init__.py", line 105, in new_func augur-1 | return ctx.invoke(f, *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/core.py", line 814, in invoke augur-1 | return callback(*args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/click/decorators.py", line 34, in new_func augur-1 | return f(get_current_context(), *args, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/augur/application/cli/config.py", line 105, in init_config augur-1 | config.load_config_from_dict(augmented_config) augur-1 | File "/augur/augur/application/config.py", line 316, in load_config_from_dict augur-1 | self.add_section_from_json(section_name=section_name, json_data=value) augur-1 | File "/augur/augur/application/config.py", line 282, in add_section_from_json augur-1 | writeable_config.create_section(section_name, json_data, ignore_existing=True) augur-1 | File "/augur/augur/application/config.py", line 708, in create_section augur-1 | self.add_value(section_name, key, value, ignore_existing=ignore_existing) augur-1 | File "/augur/augur/application/config.py", line 741, in add_value augur-1 | if not self.has_value(section_name, value_key): augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/augur/application/config.py", line 731, in has_value augur-1 | query = self.session.query(Config).filter(and_(Config.section_name == section_name,Config.setting_name == value_key) ) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2910, in query augur-1 | return self._query_cls(entities, self, **kwargs) augur-1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 276, in __init__ augur-1 | self._set_entities(entities) augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 288, in _set_entities augur-1 | self._raw_columns = [ augur-1 | ^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 289, in augur-1 | coercions.expect( augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/coercions.py", line 406, in expect augur-1 | insp._post_inspect augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 1253, in __get__ augur-1 | obj.__dict__[self.__name__] = result = self.fget(obj) augur-1 | ^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2707, in _post_inspect augur-1 | self._check_configure() augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2386, in _check_configure augur-1 | _configure_registries({self.registry}, cascade=True) augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 4199, in _configure_registries augur-1 | _do_configure_registries(registries, cascade) augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 4240, in _do_configure_registries augur-1 | mapper._post_configure_properties() augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2403, in _post_configure_properties augur-1 | prop.init() augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/interfaces.py", line 579, in init augur-1 | self.do_init() augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 1637, in do_init augur-1 | self._setup_join_conditions() augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 1882, in _setup_join_conditions augur-1 | self._join_condition = jc = JoinCondition( augur-1 | ^^^^^^^^^^^^^^ augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 2315, in __init__ augur-1 | self._check_foreign_cols(self.primaryjoin, True) augur-1 | File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 2958, in _check_foreign_cols augur-1 | raise sa_exc.ArgumentError(err) augur-1 | sqlalchemy.exc.ArgumentError: Could not locate any relevant foreign key columns for primary join condition 'augur_data.commits.cmt_author_platform_username = augur_data.contributors.cntrb_login' on relationship Contributor.commits. Ensure that referencing columns are associated with a ForeignKey or ForeignKeyConstraint, or are annotated in the join condition with the foreign() annotation. ```

Seems like the removal of the foreign key from the DB model is causing issues with the SQLAlchemy model given that the FK's removed from the model (which are not present in any DB i can see as far as I can tell) were in fact being relied on by other parts of the model, specifically the relationship() between commits and contributors that allows an SA model for a contributor to contain a property referencing that persons commits and vise versa.

[shlokgilda]

This needs schema='augur_data' - sequences don't inherit the table's schema automatically. Same applies to all other Sequence definitions in this file. See: https://docs.sqlalchemy.org/en/20/core/defaults.html#defining-sequences

  Sequence('chaoss_metric_status_cms_id_seq', start=1, schema='augur_data')

[shlokgilda]

Hey @MoralCode, thanks for tackling this schema drift cleanup. Found one issue that will likely cause problems:

1. The Sequence() calls are missing schema='augur_data'. Per SQLAlchemy docs:

When using tables with explicit schema names, the configured schema of the Table is not automatically shared by an embedded Sequence, instead, specify Sequence.schema

The old server_default=text("nextval('augur_data.xxx_seq'::regclass)") worked because it referenced the schema explicitly. The new Sequence('xxx_seq', start=N) will look in public schema (or whatever search_path resolves to) instead of augur_data.

Fix: Add schema='augur_data' to each Sequence:

# Instead of:
Sequence('chaoss_metric_status_cms_id_seq', start=1)

# Use:
Sequence('chaoss_metric_status_cms_id_seq', start=1, schema='augur_data')

This affects all sequence definitions in the PR.

2. Also, might be worth validating no duplicates exist for gh_login and cntrb_login before the unique constraints get added - especially on systems with manually altered DBs.

Everything else looks good.

[MoralCode]

2. Also, might be worth validating no duplicates exist for gh_login and cntrb_login before the unique constraints get added - especially on systems with manually altered DBs.

Does alembic have a mechanism to run pre-migration checks like this? (or even just a mechanism to exit early from a migration with an error if the precondition isnt met?) Would be nice to be able to have migrations be either applied or not applied, rather than potentially partially applied

[shlokgilda]

Yeah, you can just run validation queries at the start of upgrade() and raise an exception if preconditions aren't met. Alembic runs migrations in a transaction, so if it fails, the whole thing rolls back. no partial application.

def upgrade():
    conn = op.get_bind()

    result = conn.execute(text("""
        SELECT gh_login, COUNT(*) as cnt FROM augur_data.contributors
        WHERE gh_login IS NOT NULL
        GROUP BY gh_login HAVING COUNT(*) > 1
        LIMIT 5
    """))
    dupes = result.fetchall()
    if dupes:
        raise Exception(f"Cannot apply migration: found duplicate gh_login values: {dupes}")

    result = conn.execute(text("""
        SELECT cntrb_login, COUNT(*) as cnt FROM augur_data.contributors
        WHERE cntrb_login IS NOT NULL
        GROUP BY cntrb_login HAVING COUNT(*) > 1
        LIMIT 5
    """))
    dupes = result.fetchall()
    if dupes:
        raise Exception(f"Cannot apply migration: found duplicate cntrb_login values: {dupes}")

    # Actual migration operations...

The LIMIT 5 is just to keep the error message readable if there are hundreds of duplicates - can drop it or use LIMIT 1 for a simple yes/no check.

The exception aborts the transaction before any schema changes are committed.

[MoralCode]

Added schemas to sequences. Also migrated the operations and spdx schemas to use these newer sequence calls too.

gave the duplication check queries a run on our instance and.... we have about 2300 duplicates for probably historical instance reasons.

[MoralCode]

@shlokgilda problem: looking into the gh-login table duplication in our instance, im noticing that, at least for this random user i picked, it seems to actually be two separate users (one github, one gitlab) with the same username. It seems like its not possible for these colums to have a unique constraint applied to them.

also: im seeing lots of gh_* prefixed columns being used for gitlab data too...

[shlokgilda]

Ah, that's a data model issue then, not dirty data. If the same username can legitimately exist on both GitHub and GitLab as different people, then gh_login alone can't be unique.

Options:

1. Composite unique constraint. Make it unique per platform:

UniqueConstraint('gh_login', 'data_source', name='GH-UNIQUE-C', ...)
# Though this assumes data_source reliably distinguishes GitHub vs GitLab contributors.

2. Drop the unique constraint entirely - if it's not actually enforceable, don't add it. The migration 22 dropped it for a reason (maybe this exact issue?). The FK fk_commits_contributors_3 might still work if you're joining on cntrb_login which could be more reliably unique.
3. Separate the concerns - the gh_* columns are clearly meant for GitHub data, but if GitLab data is being stuffed in there too, that's a schema design issue worth documenting at minimum.

Re: GitLab data in gh_* columns - yeah that's messy. Probably happened organically when GitLab support was added? Definitely worth discussing.

Worth checking: does the code actually rely on gh_login being unique anywhere? Or was this constraint just assumed/aspirational? If nothing depends on it, simplest path is to just not add it.

[MoralCode]

3. Separate the concerns - the gh_* columns are clearly meant for GitHub data, but if GitLab data is being stuffed in there too, that's a schema design issue worth documenting at minimum.

already documented in #3469

2. The migration 22 dropped it for a reason (maybe this exact issue?)

Ah yeah thats pretty decent evidence that I resolved the conflict in this PR potentially the wrong way. Will update

[MoralCode]

Another problem: the fk_commits_contributors_3 Foreign Key depends on cntrb_login being unique.

I dont see an easy way to remove this FK cleanly, but we clearly cannot keep it because it depends on the unique constraint above that was removed

Edit: looks like this FK was also dropped in migration 22

The underlying type that exists in-database is a nullable string so thats what im using instead

[MoralCode]

ok next issue: foreign key loop in the SPDX schema between package.package_id and package_files

seems like that may be just a warning though. seems interesting that alembic is generating an empty migration rather than saying the database is up to date...

[MoralCode]

ok so that field needs to be an FK apparrently

Stack Trace

INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
augur-1         | INFO  [alembic.runtime.migration] Will assume transactional DDL.
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 28 -> 29, Add commit message table
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 29 -> 30, Add repo src id
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 30 -> 31, Update pr events unique
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 31 -> 32, Remove old OpenSSF Scorecard Unique Constraint; Add new one.
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 32 -> 33, Fix OpenSSF Scorecard Unique Constraint
augur-1         | INFO  [alembic.runtime.migration] Running upgrade 33 -> 34, Add Facade contributor full recollect to config, default to off (0) 
augur-1         | Traceback (most recent call last):
augur-1         |   File "/augur/.venv/bin/alembic", line 10, in <module>
augur-1         |     sys.exit(main())
augur-1         |              ^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/config.py", line 1033, in main
augur-1         |     CommandLine(prog=prog).main(argv=argv)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/config.py", line 1023, in main
augur-1         |     self.run_cmd(cfg, options)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/config.py", line 957, in run_cmd
augur-1         |     fn(
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/command.py", line 483, in upgrade
augur-1         |     script.run_env()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/script/base.py", line 545, in run_env
augur-1         |     util.load_python_file(self.dir, "env.py")
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/util/pyfiles.py", line 116, in load_python_file
augur-1         |     module = load_module_py(module_id, path)
augur-1         |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/util/pyfiles.py", line 136, in load_module_py
augur-1         |     spec.loader.exec_module(module)  # type: ignore
augur-1         |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "<frozen importlib._bootstrap_external>", line 940, in exec_module
augur-1         |   File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
augur-1         |   File "/augur/augur/application/schema/alembic/env.py", line 116, in <module>
augur-1         |     run_migrations_online()
augur-1         |   File "/augur/augur/application/schema/alembic/env.py", line 110, in run_migrations_online
augur-1         |     context.run_migrations()
augur-1         |   File "<string>", line 8, in run_migrations
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/runtime/environment.py", line 946, in run_migrations
augur-1         |     self.get_context().run_migrations(**kw)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/alembic/runtime/migration.py", line 627, in run_migrations
augur-1         |     step.migration_fn(**kw)
augur-1         |   File "/augur/augur/application/schema/alembic/versions/34_add_contrib_to_config.py", line 26, in upgrade
augur-1         |     config_dict = config.load_config()
augur-1         |                   ^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/augur/application/config.py", line 235, in load_config
augur-1         |     config.update(config_source.retrieve_dict())
augur-1         |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/augur/application/config.py", line 660, in retrieve_dict
augur-1         |     section_names = execute_session_query(query, 'all')
augur-1         |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/augur/application/db/util.py", line 43, in execute_session_query
augur-1         |     return catch_operational_error(func)
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/augur/application/db/util.py", line 21, in catch_operational_error
augur-1         |     return func()
augur-1         |            ^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2693, in all
augur-1         |     return self._iter().all()  # type: ignore
augur-1         |            ^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 2847, in _iter
augur-1         |     result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
augur-1         |                                                   ^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2306, in execute
augur-1         |     return self._execute_internal(
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2188, in _execute_internal
augur-1         |     result: Result[Any] = compile_state_cls.orm_execute_statement(
augur-1         |                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/context.py", line 293, in orm_execute_statement
augur-1         |     result = conn.execute(
augur-1         |              ^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1416, in execute
augur-1         |     return meth(
augur-1         |            ^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 516, in _execute_on_connection
augur-1         |     return connection._execute_clauseelement(
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1631, in _execute_clauseelement
augur-1         |     compiled_sql, extracted_params, cache_hit = elem._compile_w_cache(
augur-1         |                                                 ^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 704, in _compile_w_cache
augur-1         |     compiled_sql = self._compiler(
augur-1         |                    ^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 316, in _compiler
augur-1         |     return dialect.statement_compiler(dialect, self, **kw)
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/compiler.py", line 1426, in __init__
augur-1         |     Compiled.__init__(self, dialect, statement, **kwargs)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/compiler.py", line 867, in __init__
augur-1         |     self.string = self.process(self.statement, **compile_kwargs)
augur-1         |                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/compiler.py", line 912, in process
augur-1         |     return obj._compiler_dispatch(self, **kwargs)
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/visitors.py", line 143, in _compiler_dispatch
augur-1         |     return meth(self, **kw)  # type: ignore  # noqa: E501
augur-1         |            ^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/compiler.py", line 4585, in visit_select
augur-1         |     compile_state = select_stmt._compile_state_factory(
augur-1         |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/sql/base.py", line 687, in create_for_statement
augur-1         |     return klass.create_for_statement(statement, compiler, **kw)
augur-1         |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/context.py", line 1091, in create_for_statement
augur-1         |     _QueryEntity.to_compile_state(
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/context.py", line 2570, in to_compile_state
augur-1         |     _ColumnEntity._for_columns(
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/context.py", line 2917, in _for_columns
augur-1         |     _ORMColumnEntity(
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/context.py", line 3131, in __init__
augur-1         |     _entity._post_inspect
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 1253, in __get__
augur-1         |     obj.__dict__[self.__name__] = result = self.fget(obj)
augur-1         |                                            ^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2707, in _post_inspect
augur-1         |     self._check_configure()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2386, in _check_configure
augur-1         |     _configure_registries({self.registry}, cascade=True)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 4199, in _configure_registries
augur-1         |     _do_configure_registries(registries, cascade)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 4240, in _do_configure_registries
augur-1         |     mapper._post_configure_properties()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/mapper.py", line 2403, in _post_configure_properties
augur-1         |     prop.init()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/interfaces.py", line 579, in init
augur-1         |     self.do_init()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 1637, in do_init
augur-1         |     self._setup_join_conditions()
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 1882, in _setup_join_conditions
augur-1         |     self._join_condition = jc = JoinCondition(
augur-1         |                                 ^^^^^^^^^^^^^^
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 2315, in __init__
augur-1         |     self._check_foreign_cols(self.primaryjoin, True)
augur-1         |   File "/augur/.venv/lib/python3.11/site-packages/sqlalchemy/orm/relationships.py", line 2958, in _check_foreign_cols
augur-1         |     raise sa_exc.ArgumentError(err)
augur-1         | sqlalchemy.exc.ArgumentError: Could not locate any relevant foreign key columns for primary join condition 'augur_data.commits.cmt_author_platform_username = augur_data.contributors.cntrb_login' on relationship Contributor.commits.  Ensure that referencing columns are associated with a ForeignKey or ForeignKeyConstraint, or are annotated in the join condition with the foreign() annotation.

[MoralCode]

bumping to next release - i really want to get this right so we can start doing better database migrations