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pandabase links pandas DataFrames to SQL databases. Upsert, append, read, drop, describe...

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pip install pandabase

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pandabase links pandas DataFrames to SQL databases, supporting read, append, upsert, and basic database management operations.

By default, uses DataFrame.index as the primary key. By using an explicit primary key, pandabase makes rational database schemas the obvious choice, and makes it easy to maintain clean data even when it must be updated frequently.

Designed specifically for time-series datasets that need to be stored to disk permanently, but are updated over time and used primarily in-memory for computation. All supported types are nullable, great for flexible ML applications.

Tested under:

  • Python >= 3.6
  • Pandas >= 0.24, including 1.0
  • SQLAlchemy >= 1.3
  • SQLite
  • Postgres
    • requires psycopg2 and postgres >= 8

Features

  • pandabase.to_sql replaces df.to_sql
  • pandabase.read_sql replaces pd.read_sql
  • primary key support:
    • by default, uses df.index as table PK (must have name != None)
    • filter results with lowest/highest kwargs: lowest <= results.pk <= highest
    • (new in 0.4): support for multi-indexes
    • optionally, generate integer index (with parameter auto_index=True)
  • multiple insert modes: how='create_only', 'upsert', or 'append'
  • datatypes (all nullable):
    • boolean
    • int
    • float
    • datetime (UTC only)
    • string

Bonus Features

  • moderately smart insertion handles new records that 'almost correspond' with database schema automatically
  • to_sql can automatically add new columns to database as needed with kwarg: add_new_columns=True
  • supports arbitrary schemas in Postgres with kwarg: schema=name
  • comprehensive test suite (pytest)
  • companda(df1, df2) test tool: rich comparisons of DataFrames

Design Considerations

  • Minimal dependencies: Pandas (>= 0.24) & SQLAlchemy (>= 1.3) are the only requirements
  • Database is the source of truth: will coerce incoming DataFrames to fit existing schema
    • but also is reasonably smart about how new tables are created from DataFrames
  • Not horrendously slow (?)

License

MIT license

Thanks

Code partially stolen from: Dataset (nice, more general-purpose SQL interaction library) and pandas.sql

Installation

From your inside your virtual environment of choice:

~/$ pip install pandabase

For latest version:

~/$ git clone https://github.com/notsambeck/pandabase
~/$ cd pandabase
~/pandabase/$ pip install -r requirements.txt
~/pandabase/$ pip install .

Usage

# Python >= 3.6
>>> import pandas as pd
>>> import numpy as np
>>> import pandabase
>>> my_data = pd.DataFrame(index=range(7, 12), 
                           columns=['some_number'],
                           data=np.random.random((5,1)))
>>> my_data.index.name = 'my_index_name'        # index must be named to use as PK
>>> pandabase.to_sql(my_data, table_name='my_table', con='sqlite:///new_sqlite_db.sqlite', how='create_only')
Table('my_table', ...
>>> exit()

Your data is now persistently stored in a SQLite database, using my_data.index as primary key. To append or update data, replace 'create_only' with 'append' or 'upsert'. To store records without an explicit index, use 'autoindex=True'.

~/pandabase$ ls
new_sqlite_db.sqlite
>>> import pandabase
>>> df = pandabase.read_sql('my_table', con='sqlite:///new_sqlite_db.sqlite'))
>>> df
    some_number 
7   0.722416 
8   0.076045 
9   0.213118 
10  0.453716 
11  0.406995

Additional keyword arguments for pandabase.read_sql:

[lowest, highest]: minimum/maximum values for PK that will be retrieved. Can be used independently of each other.

For multi-index tables, use e.g. highest=(max_value_for_pk0, max_value_for_pk1, ), lowest=(min_value_for_pk0, min_value_for_pk1, )

Minor bug: note that selecting an empty subset of data will raise an error if type(lowest) != type(data), even if the types are comparible (e.g. float vs. int)

Using Extra Features

Companda - rich comparisons of DataFrames. call companda on two DataFrames, get a Companda object back (that evaluates to True/False).

>>> from pandabse.companda import companda
>>> df = pandabase.read_sql('my_table', con='sqlite:///new_sqlite_db.sqlite'))
>>> companda(df, df.copy())
Companda(True, message='DataFrames are equal')
>>> bool(companda(df, df.copy()))
True

>>> df2 = df.copy
>>> df2.iloc[1, 2] = -1000
>>> companda(df, df2)
Companda(False, message='Columns and indices are equal, but unequal values in columns [col_a]...')
>>> bool(companda(df, df2))
False

Table utility functions:

Under basic use cases, Pandabase can handle database administration tasks. All support schema=name kwarg in Postgres.

  • drop_db_table(table_name, con):
    • Drop table [table_name] from con - be careful with this!
  • get_db_table_names(con):
    • Get a list of table names from database.
  • get_table_column_names(con, table_name):
    • Get a list of column names from database, table.
  • describe_database(con):
    • Get a description of database content: {table_names: {table_info_dicts}}.

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