Merge pull request #18 from demml/migration

Update db_initializer.py

opsml/registry/sql/migration/alembic.ini

@@ -14,11 +14,12 @@ script_location = alembic
 # defaults to the current working directory.
 prepend_sys_path = .
 
+sqlalchemy.url = ""
 # 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()
+# If specified, requires the python-dateutil library that can be
+# installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to dateutil.tz.gettz()
 # leave blank for localtime
 # timezone =
 
@@ -36,10 +37,10 @@ prepend_sys_path = .
 # sourceless = false
 
 # version location specification; This defaults
-# to alembic/versions.  When using multiple version
+# to migration/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_locations = %(here)s/bar:%(here)s/bat:migration/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.
@@ -60,8 +61,6 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # are written from script.py.mako
 # output_encoding = utf-8
 
-sqlalchemy.url = ""
-
 
 [post_write_hooks]
 # post_write_hooks defines scripts or Python functions that are run
@@ -74,12 +73,6 @@ sqlalchemy.url = ""
 # 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
@@ -113,4 +106,4 @@ formatter = generic
 
 [formatter_generic]
 format = %(levelname)-5.5s [%(name)s] %(message)s
-datefmt = %H:%M:%S
+datefmt = %H:%M:%S

opsml/registry/sql/migration/alembic/env.py

@@ -1,17 +1,29 @@
+import os
 from logging.config import fileConfig
 
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 
-# 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:
+if config.attributes.get("configure_logger", True):
     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.
+
 
 def run_migrations_offline() -> None:
     """Run migrations in 'offline' mode.
@@ -47,7 +59,7 @@ def run_migrations_online() -> None:
     connection = config.attributes.get("connection")
     if connection is None:
         engine = engine_from_config(
-            config.get_section(config.config_ini_section),  # type: ignore
+            config.get_section(config.config_ini_section),
             prefix="sqlalchemy.",
             poolclass=pool.NullPool,
         )

opsml/registry/sql/migration/alembic/versions/6e3a1f978946_add_interface_types.py → opsml/registry/sql/migration/alembic/versions/c54a9fbab8dc_add_model_and_data_columns.py

@@ -1,13 +1,11 @@
-"""Add interface types
+"""update tables
 
-Revision ID: 6e3a1f978946
+Revision ID: c54a9fbab8dc
 Revises: 
-Create Date: 2024-05-02 10:44:58.659238
+Create Date: 2023-04-11 23:07:56.160420
 
 """
 
-from typing import Sequence, Union
-
 import sqlalchemy as sa
 from alembic import op
 
@@ -16,17 +14,15 @@
 from opsml.types import CommonKwargs
 
 logger = ArtifactLogger.get_logger()
-
-
 # revision identifiers, used by Alembic.
-revision: str = "6e3a1f978946"
-down_revision: Union[str, None] = None
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
+revision = "c54a9fbab8dc"
+down_revision = None
+branch_labels = None
+depends_on = None
 
 
 def upgrade() -> None:
-    logger.info("Alembic revision: Adding types to model and data registries - {}", revision)
+    logger.info("Alembic revision: Adding interface columns to model and data registries - {}", revision)
     try:
         bind = op.get_context().bind
         insp = sa.inspect(bind)