Some manual testing:

sqlite-utils create-table /tmp/t.db places id integer name text country integer city integer continent integer --pk id
sqlite-utils schema /tmp/t.db

CREATE TABLE [places] (
   [id] INTEGER PRIMARY KEY,
   [name] TEXT,
   [country] INTEGER,
   [city] INTEGER,
   [continent] INTEGER
);

sqlite-utils create-table /tmp/t.db country id integer name text
sqlite-utils create-table /tmp/t.db city id integer name text
sqlite-utils create-table /tmp/t.db continent id integer name text
sqlite-utils schema /tmp/t.db

CREATE TABLE [places] (
   [id] INTEGER PRIMARY KEY,
   [name] TEXT,
   [country] INTEGER,
   [city] INTEGER,
   [continent] INTEGER
);
CREATE TABLE [country] (
   [id] INTEGER,
   [name] TEXT
);
CREATE TABLE [city] (
   [id] INTEGER,
   [name] TEXT
);
CREATE TABLE [continent] (
   [id] INTEGER,
   [name] TEXT
);

sqlite-utils transform /tmp/t.db places --add-foreign-key country country id --add-foreign-key continent continent id
sqlite-utils schema /tmp/t.db

CREATE TABLE [country] (
   [id] INTEGER,
   [name] TEXT
);
CREATE TABLE [city] (
   [id] INTEGER,
   [name] TEXT
);
CREATE TABLE [continent] (
   [id] INTEGER,
   [name] TEXT
);
CREATE TABLE "places" (
   [id] INTEGER PRIMARY KEY,
   [name] TEXT,
   [country] INTEGER REFERENCES [country]([id]),
   [city] INTEGER,
   [continent] INTEGER REFERENCES [continent]([id])
);

sqlite-utils transform /tmp/t.db places --drop-foreign-key country
sqlite-utils schema /tmp/t.db places

CREATE TABLE "places" (
   [id] INTEGER PRIMARY KEY,
   [name] TEXT,
   [country] INTEGER,
   [city] INTEGER,
   [continent] INTEGER REFERENCES [continent]([id])
)

	drop_foreign_keys: Optional[Iterable[str]] = None,
	add_foreign_keys: Optional[ForeignKeysType] = None,
	foreign_keys: Optional[ForeignKeysType] = None,

Uh oh!

CLI equivalents to transform(add_foreign_keys=) #585

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CLI equivalents to `transform(add_foreign_keys=)` #585