CommandError: Can't locate revision identified by '...' when migrating using Flask-Migrate

Question

I started using Flask-Migrate today and installed it on a test project. However i am getting following error:

alembic.util.exc.CommandError: Can't locate revision identified by 'e39d16e62810'

Steps to reproduce:

1. run "python create_db.py"
2. run "flask db init"
3. add column "name" to Entry-model
4. run "flask db migrate"

EDIT: After removing migrations directory and repeating the process i am getting the same error after running "flask db migrate". I also tried using a manage.py file with flask-script --> same issue

Error:

(venv_mentz) H:\Flask-API-Test>python manage.py db migrate
INFO  [alembic.runtime.migration] Context impl SQLiteImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
Traceback (most recent call last):
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 143, in _catch_revision_errors
    yield
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 206, in get_revisions
    return self.revision_map.get_revisions(id_)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 299, in get_revisions
    return sum([self.get_revisions(id_elem) for id_elem in id_], ())
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 299, in <listcomp>
    return sum([self.get_revisions(id_elem) for id_elem in id_], ())
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 304, in get_revisions
    for rev_id in resolved_id)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 304, in <genexpr>
    for rev_id in resolved_id)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 362, in _revision_for_ident
    resolved_id)
alembic.script.revision.ResolutionError: No such revision or branch 'e39d16e62810'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "manage.py", line 14, in <module>
    manager.run()
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\flask_script\__init__.py", line 417, in run
    result = self.handle(argv[0], argv[1:])
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\flask_script\__init__.py", line 386, in handle
    res = handle(*args, **config)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\flask_script\commands.py", line 216, in __call__
    return self.run(*args, **kwargs)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\flask_migrate\__init__.py", line 197, in migrate
    version_path=version_path, rev_id=rev_id)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\command.py", line 176, in revision
    script_directory.run_env()
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 425, in run_env
    util.load_python_file(self.dir, 'env.py')
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\util\pyfiles.py", line 81, in load_python_file
    module = load_module_py(module_id, path)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\util\compat.py", line 83, in load_module_py
    spec.loader.exec_module(module)
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
  File "migrations\env.py", line 87, in <module>
    run_migrations_online()
  File "migrations\env.py", line 80, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\runtime\environment.py", line 836, in run_migrations
    self.get_context().run_migrations(**kw)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\runtime\migration.py", line 321, in run_migrations
    for step in self._migrations_fn(heads, self):
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\command.py", line 156, in retrieve_migrations
    revision_context.run_autogenerate(rev, context)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\autogenerate\api.py", line 415, in run_autogenerate
    self._run_environment(rev, migration_context, True)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\autogenerate\api.py", line 425, in _run_environment
    if set(self.script_directory.get_revisions(rev)) != \
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 206, in get_revisions
    return self.revision_map.get_revisions(id_)
  File "c:\users\marschall\appdata\local\programs\python\python36-32\Lib\contextlib.py", line 100, in __exit__
    self.gen.throw(type, value, traceback)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 174, in _catch_revision_errors
    compat.raise_from_cause(util.CommandError(resolution))
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\util\compat.py", line 194, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=exc_value)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\util\compat.py", line 187, in reraise
    raise value.with_traceback(tb)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 143, in _catch_revision_errors
    yield
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\base.py", line 206, in get_revisions
    return self.revision_map.get_revisions(id_)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 299, in get_revisions
    return sum([self.get_revisions(id_elem) for id_elem in id_], ())
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 299, in <listcomp>
    return sum([self.get_revisions(id_elem) for id_elem in id_], ())
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 304, in get_revisions
    for rev_id in resolved_id)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 304, in <genexpr>
    for rev_id in resolved_id)
  File "H:\Flask-API-Test\venv_mentz\lib\site-packages\alembic\script\revision.py", line 362, in _revision_for_ident
    resolved_id)
alembic.util.exc.CommandError: Can't locate revision identified by 'e39d16e62810'

My file structure looks like this:

app
-- views
----- __init__.py
----- main.py
-- __init__.py
-- config.py
-- models.py
instance
-- __init__.py
-- config.py
create_db.py
dev.db
run.py

My app factory:

from flask import Flask
from instance.config import app_config
from flask_migrate import Migrate

def create_app(config_name):
    """ Creates a runnable app.
        This app will be using the config with name "config_name".
    """
    app = Flask(__name__)
    # Loading the the config from instance folder with name "config_name"
    app.config.from_object(app_config[config_name])
    # Loading generic config from 'config.py'
    app.config.from_pyfile('config.py')

    # Registering this app at db
    from app.models import db
    db.init_app(app)
    migrate = Migrate(app, db)

    from app import models, views

    return app

My run.py:

""" This script runs a the app with the given configuration. """

from app import create_app

# Configuration used to run the app
config_name = 'dev'

# Creating the app by using the required configuration
app = create_app(config_name)

if __name__ == '__main__':
    app.run()

And my create_db.py file to create the database using models.py:

""" This script creates the database defined in app.models. """

from app import create_app

app = create_app('dev')
from app.models import db

# Telling SQLAlchemy what app should be used as the database model
with app.app_context():
    db.create_all()

This is my models.py:

from flask_sqlalchemy import SQLAlchemy

db = SQLAlchemy()

class Entry(db.Model):
    __tablename__ = 'Entries'
    layer_id = db.Column(db.Integer, primary_key=True)

    def __repr__(self):
        return "ID: {}; text: {}".format(self.layer_id, self.text)

EDIT: manage.py:

from flask_script import Manager
from flask_migrate import Migrate, MigrateCommand
from app import create_app
from app import models
from app.models import db

app = create_app('dev')
migrate = Migrate(app, db)
manager = Manager(app)

manager.add_command('db', MigrateCommand)

if __name__ == '__main__':
    manager.run()

Answer 1

you delete the migration directory but the version has been saved in the database, so you have to delete the version info in the dabase, run

delete from alembic_version;

in mysql shell.

As suggested by @mirekphd, If this is a developing environment or a single app for test, just delete it, Else BACKUP the data in the table.