What is the best approach to change primary keys in an existing Django app?

Agreed, your model is probably wrong.

The formal primary key should always be a surrogate key. Never anything else. [Strong words. Been database designer since the 1980's. Important lessoned learned is this: everything is changeable, even when the users swear on their mothers' graves that the value cannot be changed is is truly a natural key that can be taken as primary. It isn't primary. Only surrogates can be primary.]

You're doing open-heart surgery. Don't mess with schema migration. You're replacing the schema.

Unload your data into JSON files. Use Django's own internal django-admin.py tools for this. You should create one unload file for each that will be changing and each table that depends on a key which is being created. Separate files make this slightly easier to do.
Drop the tables which you are going to change from the old schema.

Tables which depend on these tables will have their FK's changed; you can either update the rows in place or -- it might be simpler -- to delete and reinsert these rows, also.
Create the new schema. This will only create the tables which are changing.
Write scripts to read and reload the data with the new keys. These are short and very similar. Each script will use json.load() to read objects from the source file; you will then create your schema objects from the JSON tuple-line objects that were built for you. You can then insert them into the database.

You have two cases.
- Tables with PK's change changed will be inserted and will get new PK's. These must be "cascaded" to other tables to assure that the other table's FK's get changed also.
- Tables with FK's that change will have to locate the row in the foreign table and update their FK reference.

Alternative.

Rename all your old tables.
Create the entire new schema.
Write SQL to migrate all the data from old schema to new schema. This will have to cleverly reassign keys as it goes.
Drop the renamed old tables.

To change primary key with south you can use south.db.create_primary_key command in datamigration. To change your custom CharField pk to standard AutoField you should do:

1) create new field in your model

class MyModel(Model):
    id = models.AutoField(null=True)

1.1) if you have a foreign key in some other model to this model, create new fake fk field on these model too (use IntegerField, it will then be converted)

class MyRelatedModel(Model):
    fake_fk = models.IntegerField(null=True)

2) create automatic south migration and migrate:

./manage.py schemamigration --auto
./manage.py migrate

3) create new datamigration

./manage.py datamigration <your_appname> fill_id

in tis datamigration fill these new id and fk fields with numbers (just enumerate them)

    for n, obj in enumerate(orm.MyModel.objects.all()):
        obj.id = n
        # update objects with foreign keys
        obj.myrelatedmodel_set.all().update(fake_fk = n)
        obj.save()

    db.delete_primary_key('my_app_mymodel')
    db.create_primary_key('my_app_mymodel', ['id'])

4) in your models set primary_key=True on your new pk field

id = models.AutoField(primary_key=True)

5) delete old primary key field (if it is not needed) create auto migration and migrate.

5.1) if you have foreign keys - delete old foreign key fields too (migrate)

6) Last step - restore fireign key relations. Create real fk field again, and delete your fake_fk field, create auto migration BUT DO NOT MIGRATE(!) - you need to modify created auto migration: instead of creating new fk and deleting fake_fk - rename column fake_fk

# in your models
class MyRelatedModel(Model):
    # delete fake_fk
    # fake_fk = models.InegerField(null=True)
    # create real fk
    mymodel = models.FoeignKey('MyModel', null=True)

# in migration
    def forwards(self, orm):
        # left this without change - create fk field
        db.add_column('my_app_myrelatedmodel', 'mymodel',
                  self.gf('django.db.models.fields.related.ForeignKey')(default=1, related_name='lots', to=orm['my_app.MyModel']),keep_default=False)

        # remove fk column and rename fake_fk
        db.delete_column('my_app_myrelatedmodel', 'mymodel_id')
        db.rename_column('my_app_myrelatedmodel', 'fake_fk', 'mymodel_id')

so previously filled fake_fk becomes a column, that contain actual relation data, and it does not get lost after all the steps above.

I managed to do this with django 1.10.4 migrations and mysql 5.5, but it wasn't easy.

I had a varchar primary key with several foreign keys. I added an id field, migrated data and foreign keys. This is how:

Adding future primary key field. I added an id = models.IntegerField(default=0) field to my main model and generated an auto migration.

Simple data migration to generate new primary keys:

def fill_ids(apps, schema_editor):
   Model = apps.get_model('<module>', '<model>')
   for id, code in enumerate(Model.objects.all()):
       code.id = id + 1
       code.save()

class Migration(migrations.Migration):
    dependencies = […]
    operations = [migrations.RunPython(fill_ids)]

Migrating existing foreign keys. I wrote a combined migration:

def change_model_fks(apps, schema_editor):
    Model = apps.get_model('<module>', '<model>')  # Our model we want to change primary key for
    FkModel = apps.get_model('<module>', '<fk_model>')  # Other model that references first one via foreign key

    mapping = {}
    for model in Model.objects.all():
        mapping[model.old_pk_field] = model.id  # map old primary keys to new

    for fk_model in FkModel.objects.all():
        if fk_model.model_id:
            fk_model.model_id = mapping[fk_model.model_id]  # change the reference
            fk_model.save()

class Migration(migrations.Migration):
    dependencies = […]
    operations = [
        # drop foreign key constraint
        migrations.AlterField(
            model_name='<FkModel>',
            name='model',
            field=models.ForeignKey('<Model>', blank=True, null=True, db_constraint=False)
        ),

        # change references
        migrations.RunPython(change_model_fks),

        # change field from varchar to integer, drop index
        migrations.AlterField(
            model_name='<FkModel>',
            name='model',
            field=models.IntegerField('<Model>', blank=True, null=True)
        ),
    ]

Swapping primary keys and restoring foreign keys. Again, a custom migration. I auto-generated the base for this migration when I a) removed primary_key=True from the old primary key and b) removed id field

class Migration(migrations.Migration):
    dependencies = […]
    operations = [
        # Drop old primary key
        migrations.AlterField(
            model_name='<Model>',
            name='<old_pk_field>',
            field=models.CharField(max_length=100),
        ),

        # Create new primary key
        migrations.RunSQL(
            ['ALTER TABLE <table> CHANGE id id INT (11) NOT NULL PRIMARY KEY AUTO_INCREMENT'],
            ['ALTER TABLE <table> CHANGE id id INT (11) NULL',
             'ALTER TABLE <table> DROP PRIMARY KEY'],
            state_operations=[migrations.AlterField(
                model_name='<Model>',
                name='id',
                field=models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID'),
            )]
        ),

        # Recreate foreign key constraints
        migrations.AlterField(
            model_name='<FkModel>',
            name='model',
            field=models.ForeignKey(blank=True, null=True, to='<module>.<Model>'),
    ]

Currently you are failing because you are adding a pk column that breaks the NOT NULL and UNIQUE requirements.

You should split the migration into several steps, separating schema migrations and data migrations:

add the new column, indexed but not primary key, with a default value (ddl migration)
migrate the data: fill the new column with the correct value (data migration)
mark the new column primary key, and remove the former pk column if it has become unnecessary (ddl migration)

I had the same problem to day and came to a solution inspired by the answers above.

My model has a "Location" table. It has a CharField called "unique_id" and I foolishly made it a primary key, last year. Of course they didn't turn out to be as unique as expected at the time. There is also a "ScheduledMeasurement" model that has a foreign key to "Location".

Now I want to correct that mistake and give Location an ordinary auto-incrementing primary key.

Steps taken:

Create a CharField ScheduledMeasurement.temp_location_unique_id and a model TempLocation, and migrations to create them. TempLocation has the structure I want Location to have.
Create a data migration that sets all the temp_location_unique_id's using the foreign key, and that copies over all the data from Location to TempLocation
Remove the foreign key and the Location table with a migration
Re-create the Location model the way I want it to be, re-create the foreign key with null=True. Renamed 'unique_id' to 'location_code'...
Create a data migration that fills in the data in Location using TempLocation, and fills in the foreign keys in ScheduledMeasurement using temp_location
Remove temp_location, TempLocation and null=True in the foreign key

And edit all the code that assumed unique_id was unique (all the objects.get(unique_id=...) stuff), and that used unique_id otherwise...

What is the best approach to change primary keys in an existing Django app?

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