medtagger / MedTagger

A collaborative framework for annotating medical datasets using crowdsourcing.
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[Backend Dependencies Update] Update alembic to 1.5.7 #989

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

This PR updates alembic from 1.2.1 to 1.5.7.

Changelog ### 1.5.7 ``` :released: March 11, 2021 .. change:: :tags: bug, autogenerate :tickets: 813 Adjusted the recently added :paramref:`.EnvironmentContext.configure.include_name` hook to accommodate for additional object types such as "views" that don't have a parent table, to support third party recipes and extensions. Pull request courtesy Oliver Rice. .. changelog:: ``` ### 1.5.6 ``` :released: March 5, 2021 .. change:: :tags: bug, mssql, operations :tickets: 812 Fixed bug where the "existing_type" parameter, which the MSSQL dialect requires in order to change the nullability of a column in the absence of also changing the column type, would cause an ALTER COLUMN operation to incorrectly render a second ALTER statement without the nullability if a new type were also present, as the MSSQL-specific contract did not anticipate all three of "nullability", "type_" and "existing_type" being sent at the same time. .. change:: :tags: template :ticket: 805 Add async template to Alembic to bootstrap environments that use async DBAPI. Updated the cookbook to include a migration guide on how to adapt an existing enviroment for use with DBAPI drivers. .. changelog:: ``` ### 1.5.5 ``` :released: February 20, 2021 .. change:: :tags: bug Adjusted the use of SQLAlchemy's ".copy()" internals to use "._copy()" for version 1.4.0, as this method is being renamed. .. change:: :tags: bug, environment :tickets: 797 Added new config file option ``prepend_sys_path``, which is a series of paths that will be prepended to sys.path; the default value in newly generated alembic.ini files is ".". This fixes a long-standing issue where for some reason running the alembic command line would not place the local "." path in sys.path, meaning an application locally present in "." and importable through normal channels, e.g. python interpreter, pytest, etc. would not be located by Alembic, even though the ``env.py`` file is loaded relative to the current path when ``alembic.ini`` contains a relative path. To enable for existing installations, add the option to the alembic.ini file as follows:: sys.path path, will be prepended to sys.path if present. defaults to the current working directory. prepend_sys_path = . .. seealso:: :ref:`installation` - updated documentation reflecting that local installation of the project is not necessary if running the Alembic cli from the local path. .. changelog:: ``` ### 1.5.4 ``` :released: February 3, 2021 .. change:: :tags: bug, versioning :tickets: 789 Fixed bug in versioning model where a downgrade across a revision with a dependency on another branch, yet an ancestor is also dependent on that branch, would produce an erroneous state in the alembic_version table, making upgrades impossible without manually repairing the table. .. changelog:: ``` ### 1.5.3 ``` :released: January 29, 2021 .. change:: :tags: bug, autogenerate :tickets: 786 Changed the default ordering of "CREATE" and "DROP" statements indexes and unique constraints within the autogenerate process, so that for example in an upgrade() operation, a particular index or constraint that is to be replaced such as for a casing convention change will not produce any naming conflicts. For foreign key constraint objects, this is already how constraints are ordered, and for table objects, users would normally want to use :meth:`.Operations.rename_table` in any case. .. change:: :tags: bug, autogenerate, mssql :tickets: 787 Fixed assorted autogenerate issues with SQL Server: * ignore default reflected identity on primary_key columns * improve server default comparison .. change:: :tags: bug, mysql, autogenerate :tickets: 788 Fixed issue where autogenerate rendering of ``op.alter_column()`` would fail to include MySQL ``existing_nullable=False`` if the column were part of a primary key constraint within the table metadata. .. changelog:: ``` ### 1.5.2 ``` :released: January 20, 2021 .. change:: :tags: bug, versioning, regression :tickets: 784 Fixed regression where new "loop detection" feature introduced in :ticket:`757` produced false positives for revision names that have overlapping substrings between revision number and down revision and/or dependency, if the downrev/dependency were not in sequence form. .. change:: :tags: bug, environment :tickets: 782 Fixed regression where Alembic would fail to create a transaction properly if the :class:`sqlalchemy.engine.Connection` were a so-called "branched" connection, that is, one where the ``.connect()`` method had been called to create a "sub" connection. .. changelog:: ``` ### 1.5.1 ``` :released: January 19, 2021 .. change:: :tags: bug, installation, commands :tickets: 780 Fixed installation issue where the "templates" directory was not being installed, preventing commands like "list_templates" and "init" from working. .. changelog:: ``` ### 1.5.0 ``` :released: January 18, 2021 .. change:: :tags: usecase, operations :tickets: 730 Added support for rendering of "identity" elements on :class:`.Column` objects, supported in SQLAlchemy via the :class:`.Identity` element introduced in version 1.4. Adding columns with identity is supported on PostgreSQL, MSSQL and Oracle. Changing the identity options or removing it is supported only on PostgreSQL and Oracle. .. change:: :tags: changed, environment To accommodate SQLAlchemy 1.4 and 2.0, the migration model now no longer assumes that the SQLAlchemy Connection will autocommit an individual operation. This essentially means that for databases that use non-transactional DDL (pysqlite current driver behavior, MySQL), there is still a BEGIN/COMMIT block that will surround each individual migration. Databases that support transactional DDL should continue to have the same flow, either per migration or per-entire run, depending on the value of the :paramref:`.Environment.configure.transaction_per_migration` flag. .. change:: :tags: changed, environment A :class:`.CommandError` is raised if a ``sqlalchemy.engine.Engine`` is passed to the :meth:`.MigrationContext.configure` method instead of a ``sqlalchemy.engine.Connection`` object. Previously, this would be a warning only. .. change:: :tags: bug, operations :tickets: 753 Modified the ``add_column()`` operation such that the ``Column`` object in use is shallow copied to a new instance if that ``Column`` is already attached to a ``table()`` or ``Table``. This accommodates for the change made in SQLAlchemy issue 5618 which prohibits a ``Column`` from being associated with multiple ``table()`` objects. This resumes support for using a ``Column`` inside of an Alembic operation that already refers to a parent ``table()`` or ``Table`` as well as allows operation objects just autogenerated to work. .. change:: :tags: feature, autogenerate :tickets: 650 Added new hook :paramref:`.EnvironmentContext.configure.include_name`, which complements the :paramref:`.EnvironmentContext.configure.include_object` hook by providing a means of preventing objects of a certain name from being autogenerated **before** the SQLAlchemy reflection process takes place, and notably includes explicit support for passing each schema name when :paramref:`.EnvironmentContext.configure.include_schemas` is set to True. This is most important especially for enviroments that make use of :paramref:`.EnvironmentContext.configure.include_schemas` where schemas are actually databases (e.g. MySQL) in order to prevent reflection sweeps of the entire server. .. seealso:: :ref:`autogenerate_include_hooks` - new documentation section .. change:: :tags: removed, autogenerate The long deprecated :paramref:`.EnvironmentContext.configure.include_symbol` hook is removed. The :paramref:`.EnvironmentContext.configure.include_object` and :paramref:`.EnvironmentContext.configure.include_name` hooks both achieve the goals of this hook. .. change:: :tags: bug, autogenerate :tickets: 721 Added rendering for the ``Table.prefixes`` element to autogenerate so that the rendered Python code includes these directives. Pull request courtesy Rodrigo Ce Moretto. .. change:: :tags: bug, batch :tickets: 761 Added missing "create comment" feature for columns that are altered in batch migrations. .. change:: :tags: changed :tickets: 748 Alembic 1.5.0 now supports **Python 2.7 and Python 3.6 and above**, as well as **SQLAlchemy 1.3.0 and above**. Support is removed for Python 3 versions prior to 3.6 and SQLAlchemy versions prior to the 1.3 series. .. change:: :tags: bug, batch :tickets: 773 Made an adjustment to the PostgreSQL dialect to allow it to work more effectively in batch mode, where a datatype like Boolean or non-native Enum that may have embedded rules to generate CHECK constraints will be more correctly handled in that these constraints usually will not have been generated on the PostgreSQL backend; previously it would inadvertently assume they existed unconditionally in a special PG-only "drop constraint" step. .. change:: :tags: feature, versioning :tickets: 757 The revision tree is now checked for cycles and loops between revision files when the revision environment is loaded up. Scenarios such as a revision pointing to itself, or a revision that can reach itself via a loop, are handled and will raise the :class:`.CycleDetected` exception when the environment is loaded (expressed from the Alembic commandline as a failure message and nonzero return code). Previously, these situations were silently ignored up front, and the behavior of revision traversal would either be silently incorrect, or would produce errors such as :class:`.RangeNotAncestorError`. Pull request courtesy Koichiro Den. .. change:: :tags: usecase, commands Add ``__main__.py`` file to alembic package to support invocation with ``python -m alembic``. .. change:: :tags: removed, commands Removed deprecated ``--head_only`` option to the ``alembic current`` command .. change:: :tags: removed, operations Removed legacy parameter names from operations, these have been emitting warnings since version 0.8. In the case that legacy version files have not yet been updated, these can be modified directly in order to maintain compatibility: * :meth:`.Operations.drop_constraint` - "type" (use "type_") and "name" (use "constraint_name") * :meth:`.Operations.create_primary_key` - "cols" (use "columns") and "name" (use "constraint_name") * :meth:`.Operations.create_unique_constraint` - "name" (use "constraint_name"), "source" (use "table_name") and "local_cols" (use "columns") * :meth:`.Operations.batch_create_unique_constraint` - "name" (use "constraint_name") * :meth:`.Operations.create_foreign_key` - "name" (use "constraint_name"), "source" (use "source_table"), "referent" (use "referent_table") * :meth:`.Operations.batch_create_foreign_key` - "name" (use "constraint_name"), "referent" (use "referent_table") * :meth:`.Operations.create_check_constraint` - "name" (use "constraint_name"), "source" (use "table_name") * :meth:`.Operations.batch_create_check_constraint` - "name" (use "constraint_name") * :meth:`.Operations.create_index` - "name" (use "index_name") * :meth:`.Operations.drop_index` - "name" (use "index_name"), "tablename" (use "table_name") * :meth:`.Operations.batch_drop_index` - "name" (use "index_name"), * :meth:`.Operations.create_table` - "name" (use "table_name") * :meth:`.Operations.drop_table` - "name" (use "table_name") * :meth:`.Operations.alter_column` - "name" (use "new_column_name") .. changelog:: ``` ### 1.4.3 ``` :released: September 11, 2020 .. change:: :tags: bug, sqlite, batch :tickets: 711 Added support to drop named CHECK constraints that are specified as part of a column, rather than table wide. Previously, only constraints associated with the table were considered. .. change:: :tags: bug, ops, mysql :tickets: 736 Fixed issue where the MySQL dialect would not correctly render the server default of a column in an alter operation, if the operation were programmatically generated from an autogenerate pass as it would not accommodate for the full structure of the DefaultClause construct. .. change:: :tags: bug, sqlite, batch :tickets: 697 Fixed issue where the CAST applied to a JSON column when copying a SQLite table during batch mode would cause the data to be lost, as SQLite's CAST with JSON appears to convert the data to the value "0". The CAST is now skipped in a dialect-specific manner, including for JSON columns on SQLite. Pull request courtesy Sebastián Ramírez. .. change:: :tags: bug, commands :tickets: 694 The ``alembic current`` command no longer creates an ``alembic_version`` table in the database if one does not exist already, returning no version as the current version. This allows checking for migrations in parallel without introducing race conditions. Pull request courtesy Nikolay Edigaryev. .. change:: :tags: bug, batch Fixed issue where columns in a foreign-key referenced table would be replaced with null-type columns during a batch operation; while this did not generally have any side effects, it could theoretically impact a batch operation that also targets that table directly and also would interfere with future changes to the ``.append_column()`` method to disallow implicit replacement of columns. .. change:: :tags: bug, mssql :tickets: 716 Fixed issue where the ``mssql_drop_foreign_key=True`` flag on ``op.drop_column`` would lead to incorrect syntax error due to a typo in the SQL emitted, same typo was present in the test as well so it was not detected. Pull request courtesy Oleg Shigorin. .. changelog:: ``` ### 1.4.2 ``` :released: March 19, 2020 .. change:: :tags: usecase, autogenerate :tickets: 669 Adjusted autogen comparison to accommodate for backends that support computed column reflection, dependent on SQLAlchemy version 1.3.16 or higher. This emits a warning if the SQL expression inside of a :class:`.Computed` value changes between the metadata and the database, as these expressions can't be changed without dropping and recreating the column. .. change:: :tags: bug, tests :tickets: 668 Fixed an issue that prevented the test suite from running with the recently released py.test 5.4.0. .. change:: :tags: bug, autogenerate, mysql :tickets: 671 Fixed more false-positive failures produced by the new "compare type" logic first added in :ticket:`605`, particularly impacting MySQL string types regarding flags such as "charset" and "collation". .. change:: :tags: bug, op directives, oracle :tickets: 670 Fixed issue in Oracle backend where a table RENAME with a schema-qualified name would include the schema in the "to" portion, which is rejected by Oracle. .. changelog:: ``` ### 1.4.1 ``` :released: March 1, 2020 .. change:: :tags: bug, autogenerate :tickets: 661 Fixed regression caused by the new "type comparison" logic introduced in 1.4 as part of :ticket:`605` where comparisons of MySQL "unsigned integer" datatypes would produce false positives, as the regular expression logic was not correctly parsing the "unsigned" token when MySQL's default display width would be returned by the database. Pull request courtesy Paul Becotte. .. change:: :tags: bug, environment :tickets: 663 Error message for "path doesn't exist" when loading up script environment now displays the absolute path. Pull request courtesy Rowan Hart. .. change:: :tags: bug, autogenerate :tickets: 654 Fixed regression in 1.4.0 due to :ticket:`647` where unique constraint comparison with mixed case constraint names while not using a naming convention would produce false positives during autogenerate. .. change:: :tags: bug, environment The check for matched rowcount when the alembic_version table is updated or deleted from is now conditional based on whether or not the dialect supports the concept of "rowcount" for UPDATE or DELETE rows matched. Some third party dialects do not support this concept. Pull request courtesy Ke Zhu. .. change:: :tags: bug, operations :tickets: 655 Fixed long-standing bug where an inline column CHECK constraint would not be rendered within an "ADD COLUMN" operation. The DDL compiler is now consulted for inline constraints within the :meth:`.Operations.add_column` method as is done for regular CREATE TABLE operations. .. changelog:: ``` ### 1.4.0 ``` :released: February 4, 2020 .. change:: :tags: change The internal inspection routines no longer use SQLAlchemy's ``Inspector.from_engine()`` method, which is expected to be deprecated in 1.4. The ``inspect()`` function is now used. .. change:: :tags: bug, autogenerate :tickets: 647 Adjusted the unique constraint comparison logic in a similar manner as that of :ticket:`421` did for indexes in order to take into account SQLAlchemy's own truncation of long constraint names when a naming convention is in use. Without this step, a name that is truncated by SQLAlchemy based on a unique constraint naming convention or hardcoded name will not compare properly. .. change:: :tags: feature, batch :tickets: 640 Added new parameters :paramref:`.BatchOperations.add_column.insert_before`, :paramref:`.BatchOperations.add_column.insert_after` which provide for establishing the specific position in which a new column should be placed. Also added :paramref:`.Operations.batch_alter_table.partial_reordering` which allows the complete set of columns to be reordered when the new table is created. Both operations apply only to when batch mode is recreating the whole table using ``recreate="always"``. Thanks to Marcin Szymanski for assistance with the implementation. .. change:: :tags: usecase, environment :tickets: 648 Moved the use of the ``__file__`` attribute at the base of the Alembic package into the one place that it is specifically needed, which is when the config attempts to locate the template directory. This helps to allow Alembic to be fully importable in environments that are using Python memory-only import schemes. Pull request courtesy layday. .. change:: :tags: bug, autogenerate :tickets: 605 A major rework of the "type comparison" logic is in place which changes the entire approach by which column datatypes are compared. Types are now compared based on the DDL string generated by the metadata type vs. the datatype reflected from the database. This means we compare types based on what would actually render and additionally if elements of the types change like string length, those changes are detected as well. False positives like those generated between SQLAlchemy Boolean and MySQL TINYINT should also be resolved. Thanks very much to Paul Becotte for lots of hard work and patience on this one. .. seealso:: :ref:`autogenerate_detects` - updated comments on type comparison .. changelog:: ``` ### 1.3.3 ``` :released: January 22, 2020 .. change:: :tags: bug, postgresql :tickets: 637 Fixed issue where COMMENT directives for PostgreSQL failed to correctly include an explicit schema name, as well as correct quoting rules for schema, table, and column names. Pull request courtesy Matthew Sills. .. change:: :tags: usecase, operations :tickets: 624 Added support for rendering of "computed" elements on :class:`.Column` objects, supported in SQLAlchemy via the new :class:`.Computed` element introduced in version 1.3.11. Pull request courtesy Federico Caselli. Note that there is currently no support for ALTER COLUMN to add, remove, or modify the "GENERATED ALWAYS AS" element from a column; at least for PostgreSQL, it does not seem to be supported by the database. Additionally, SQLAlchemy does not currently reliably reflect the "GENERATED ALWAYS AS" phrase from an existing column, so there is also no autogenerate support for addition or removal of the :class:`.Computed` element to or from an existing column, there is only support for adding new columns that include the :class:`.Computed` element. In the case that the :class:`.Computed` element is removed from the :class:`.Column` object in the table metadata, PostgreSQL and Oracle currently reflect the "GENERATED ALWAYS AS" expression as the "server default" which will produce an op that tries to drop the element as a default. .. changelog:: ``` ### 1.3.2 ``` :released: December 16, 2019 .. change:: :tags: bug, api, autogenerate :tickets: 635 Fixed regression introduced by :ticket:`579` where server default rendering functions began to require a dialect implementation, however the :func:`.render_python_code` convenience function did not include one, thus causing the function to fail when used in a server default context. The function now accepts a migration context argument and also creates one against the default dialect if one is not provided. .. changelog:: ``` ### 1.3.1 ``` :released: November 13, 2019 .. change:: :tags: bug, mssql :tickets: 621 Fixed bug in MSSQL dialect where the drop constraint execution steps used to remove server default or implicit foreign key constraint failed to take into account the schema name of the target table. .. changelog:: ``` ### 1.3.0 ``` :released: October 31, 2019 .. change:: :tags: feature, command :tickets: 608 Added support for ALEMBIC_CONFIG environment variable, refers to the location of the alembic configuration script in lieu of using the -c command line option. .. change:: :tags: bug, autogenerate :tickets: 131 Fixed bug in new Variant autogenerate where the order of the arguments to Variant were mistakenly reversed. .. change:: :tags: change, compatibility Some internal modifications have been made to how the names of indexes and unique constraints work to make use of new functions added in SQLAlchemy 1.4, so that SQLAlchemy has more flexibility over how naming conventions may be applied to these objects. .. changelog:: ```
Links - PyPI: https://pypi.org/project/alembic - Changelog: https://pyup.io/changelogs/alembic/ - Homepage: https://alembic.sqlalchemy.org - Docs: https://pythonhosted.org/alembic/
pyup-bot commented 3 years ago

Closing this in favor of #997