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This seems to be solved in master in the meantime (works for both sqlalchemy and sqlite3 fallback):
In [1]: import pandas as pd
In [2]: import sqlite3
In [3]: import sqlalchemy
In [4]: pd.__version__
Out[4]: '0.14.1-474-g744daa7'
In [5]: con = sqlite3.connect(':memory:')
In [6]: engine = sqlalchemy.create_engine('sqlite:///:memory:')
In [7]: df = pd.DataFrame({'a':[1,2,3], 'b':[2,3,4]})
In [8]: df.to_sql('test', engine, index=False, if_exists='replace')
In [9]: df.to_sql('test', con, index=False, if_exists='replace')
In [10]: pd.read_sql_query("SELECT * FROM test WHERE a < 0", engine)
Out[10]:
Empty DataFrame
Columns: [a, b]
Index: []
In [11]: pd.read_sql_query("SELECT * FROM test WHERE a < 0", con)
Out[11]:
Empty DataFrame
Columns: [a, b]
Index: []
related to #3523
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