Thx Michael, Sorry about being not clear, You care right, I am using 
autogenerate. 
I read the doc, I think that's what I am looking for. Thanks.

for the missing auto inrement, I found whenever there are multiple primary 
key (foreign or not), the created tables are different.
case 1:  1 primary key,                     autoincrement + PK (same as my 
metadata)
case 2:  1 primary key + 1 or 2 foreign key (primary_key = true),         
autoincrement is not checked
case 3:  1 primary key + 1 foreign key (not primary key column),         PK 
is not checked

I am new to metadata and alembic, so there maybe some mistakes in my 
metadata. 
anyway, manually edit the scripts give me the result I want.

On Friday, June 9, 2017 at 6:52:31 PM UTC-4, Michael Bayer wrote:
>
>
>
> On Friday, June 9, 2017 at 9:00:00 AM UTC-4, ktang wrote:
>>
>> Hi,
>>
>> I have an application migrating existing mysql dbs which may have tables 
>> only in some system.
>> I am trying to use alembic to handle the migration.
>>
>> When I migrate the db to a newer version, if I don't want to drop any 
>> existing tables or columns, how can I do this (just adding stuff)?
>>
>
> I'm assuming you're talking about autogenerate.   If you are just writing 
> migration scripts by hand, you just put whatever commands you want in them 
> and that does not impact anything else that's already in the database.   If 
> you are using autogenerate, and you are comparing a model that's only a 
> subset of the real database, you can have autogenerate exclude other tables 
> by writing an "include_object" function.  Documentation for this is here: 
> http://alembic.zzzcomputing.com/en/latest/api/runtime.html?highlight=include_object#alembic.runtime.environment.EnvironmentContext.configure.params.include_object
>  
> .  You probably want to look at objects of type "table" and include based 
> on a list of names you care about.
>
>
>  
>
>>
>> And a minor issue, when I first setup alembic in my application, I 
>> generated an initial migration script which autoincrement is not set in 
>> only one of the tables while all other tables are created correctly. 
>> Is this a known issue?
>>
>
> not really, it depends on the specifics of how your Table metadata is set 
> up.  If it's just one table then there is likely something different about 
> it in your code.
>  
>

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