2015-09-21 16:13 GMT-07:00 Mike Bayer <mike...@zzzcomputing.com>:

>
> Are you sure you don't have any in-application event handlers or similar
> manipulating search_path?   Can you put this in your env.py and tell me
> what it says?
>
>     with connectable.connect() as connection:
>
>         row = connection.execute("show search_path").fetchone()
>         print row
>
>
> Alternatively, can you please remove the "version_table_schema" directive
> and test?  If your search_path is "public", it should not be needed.
>


I attach the new env.py, based on yours (issue persists). Output of it is:

$ alembic -c development.ini revision -m "upgrade" --autogenerate
('"$user",public',)
  Generating
  XXX/notifications/scripts/alembic/versions/519677dff97_upgrade.py ... done

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# from __future__ import with_statement
from alembic import context
from sqlalchemy import engine_from_config, pool
from logging.config import fileConfig

# 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.
fileConfig(config.config_file_name)

# add your model's MetaData object here
# for 'autogenerate' support
# from myapp import mymodel
# target_metadata = mymodel.Base.metadata

from sqlalchemy import Column, Integer, ForeignKey
from sqlalchemy.ext.declarative import declarative_base

Base = declarative_base()

class t1(Base):
    __tablename__='t1'
    __table_args__ = {'schema': 'notifications'}

    id = Column(Integer, primary_key=True)

    def __init__(self):
        pass

class t2(Base):
    __tablename__='t2'
    __table_args__ = {'schema': 'notifications'}

    id = Column(Integer, primary_key=True)
    t1id = Column('t1id', Integer, ForeignKey(t1.id))

    def __init__(self, t1id=None):
        self.t1id = t1id

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():
    """Run migrations in 'offline' mode.

    This configures the context with just a URL
    and not an Engine, though an Engine is acceptable
    here as well.  By skipping the Engine creation
    we don't even need a DBAPI to be available.

    Calls to context.execute() here emit the given string to the
    script output.

    """
    url = config.get_main_option("sqlalchemy.url")
    context.configure(
        url=url, target_metadata=target_metadata, literal_binds=True)

    with context.begin_transaction():
        context.run_migrations()


def run_migrations_online():
    """Run migrations in 'online' mode.

    In this scenario we need to create an Engine
    and associate a connection with the context.

    """
    connectable = engine_from_config(
        # config.get_section(config.config_ini_section),
        config.get_section('app:main'),
        prefix='sqlalchemy.',
        poolclass=pool.NullPool)

    with connectable.connect() as connection:
        row = connection.execute("show search_path").fetchone()
        print(row)

    with connectable.connect() as connection:
        context.configure(
            connection=connection,
            target_metadata=target_metadata,
            include_schemas=True,
        )

        with context.begin_transaction():
            context.run_migrations()

if context.is_offline_mode():
    run_migrations_offline()
else:
    run_migrations_online()

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