I have the same problem, and a thought of using migration library only for this trivial thing makes me
tremble. Anyway, this is my attempt so far:

def add_column(engine, table_name, column):
    column_name = column.compile(dialect=engine.dialect)
    column_type = column.type.compile(engine.dialect)
    engine.execute('ALTER TABLE %s ADD COLUMN %s %s' % (table_name, column_name, column_type))

column = Column('new_column_name', String(100), primary_key=True)
add_column(engine, table_name, column)

Still, I don't know how to insert primary_key=True into raw SQL request.

See this section of the SQLAlchemy documentation:

Alembic is the latest software to offer this type of functionality and is made by the same author as SQLAlchemy.

I have a database called "ncaaf.db" built with sqlite3 and a table called "games". So I would CD into the same directory on my linux command prompt and do

sqlite3 ncaaf.db
alter table games add column q4 type float

and that is all it takes! Just make sure you update your definitions in your sqlalchemy code.

I had the same problem, I ended up just writing my own function in raw sql. If you are using SQLITE3 this might be useful.

Then if you add the column to your class definition at the same time it seems to do the trick.

import sqlite3 

def add_column(database_name, table_name, column_name, data_type):

  connection = sqlite3.connect(database_name)
  cursor = connection.cursor()

  if data_type == "Integer":
    data_type_formatted = "INTEGER"
  elif data_type == "String":
    data_type_formatted = "VARCHAR(100)"

  base_command = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}'")
  sql_command = base_command.format(table_name=table_name, column_name=column_name, data_type=data_type_formatted)

  cursor.execute(sql_command)
  connection.commit()
  connection.close()

from sqlalchemy import create_engine
engine = create_engine('sqlite:///db.sqlite3')

engine.execute('alter table table_name add column column_name String')

I've recently had this same issue so I took a point from AlexP in an earlier answer. The problem was in getting the new column into my program's metadata. Using sqlAlchemy's append_column functionality had some unexpected downstream effects ('str' object has no attribute 'dialect impl'). I corrected this by adding the column with DDL (MySQL database in this case) and then reflecting the table back from the DB into my metadata.

Code is as roughly as follows (modified slightly from what I have in order to reduce it to its minimal essence. I apologize for any mistakes - if there, they should be minor)...

try:
    # Use back quotes as a protection against SQL Injection Attacks. Can we do more?
    common.qry_engine.execute('ALTER TABLE %s ADD COLUMN %s %s' %
                              ('`' + self.tbl.schema + '`.`' + self.tbl.name + '`',
                               '`' + self.outputs[new_col] + '`', 'VARCHAR(50)'))
except exc.SQLAlchemyError as msg:
    raise GRError(desc='Unable to physically add derived column to table. Contact support.',
                  data=str(self.outputs), other_info=str(msg))

try:    # Refresh the metadata to show the new column
    self.tbl = sqlalchemy.Table(self.tbl.name, self.tbl.metadata, extend_existing=True, autoload=True)
except exc.SQLAlchemyError as msg:
    raise GRError(desc='Unable to establish metadata for new column. Contact support.',
                  data=str(self.outputs), other_info=str(msg))

Just continuing the simple way proposed by chasmani, little improvement

'''
# simple migration
# columns to add: 
# last_status_change = Column(BigInteger, default=None) 
# last_complete_phase = Column(String, default=None)  
# complete_percentage = Column(DECIMAL, default=0.0)
'''

import sqlite3

from config import APP_STATUS_DB
from sqlalchemy import types


def add_column(database_name: str, table_name: str, column_name: str, data_type: types, default=None):
    ret = False

    if default is not None:
        try:
            float(default)
            ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}' DEFAULT {default}")
        except:
            ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}' DEFAULT '{default}'")
    else:
        ddl = ("ALTER TABLE '{table_name}' ADD column '{column_name}' '{data_type}'")

    sql_command = ddl.format(table_name=table_name, column_name=column_name, data_type=data_type.__name__,
                             default=default)
    try:
        connection = sqlite3.connect(database_name)
        cursor = connection.cursor()
        cursor.execute(sql_command)
        connection.commit()
        connection.close()
        ret = True
    except Exception as e:
        print(e)
        ret = False
    return ret


add_column(APP_STATUS_DB, 'procedures', 'last_status_change', types.BigInteger)
add_column(APP_STATUS_DB, 'procedures', 'last_complete_phase', types.String)
add_column(APP_STATUS_DB, 'procedures', 'complete_percentage', types.DECIMAL, 0.0)

Yes you can Install sqlalchemy-migrate (pip install sqlalchemy-migrate) and use it in your script to call Table and Column create() method:

from sqlalchemy import String, MetaData, create_engine
from migrate.versioning.schema import Table, Column

db_engine =  create_engine(app.config.get('SQLALCHEMY_DATABASE_URI'))
db_meta = MetaData(bind=db_engine)

table = Table('tabel_name' , db_meta)
col = Column('new_column_name', String(20), default='foo')
    col.create(table)