Schema Inference

New in version 0.4.0

With simple use cases, writing a schema definition manually is pretty straight-forward with pandera. However, it can get tedious to do this with dataframes that have many columns of various data types.

To help you handle these cases, the infer_schema() function enables you to quickly infer a draft schema from a pandas dataframe or series. Below is a simple example:

import pandas as pd
import pandera as pa

from pandera import Check, Column, DataFrameSchema

df = pd.DataFrame({
    "column1": [5, 10, 20],
    "column2": ["a", "b", "c"],
    "column3": pd.to_datetime(["2010", "2011", "2012"]),
})
schema = pa.infer_schema(df)
print(schema)
 <Schema DataFrameSchema(
     columns={
         'column1': <Schema Column(name=column1, type=DataType(int64))>
         'column2': <Schema Column(name=column2, type=DataType(object))>
         'column3': <Schema Column(name=column3, type=DataType(datetime64[ns]))>
     },
     checks=[],
     coerce=True,
     dtype=None,
     index=<Schema Index(name=None, type=DataType(int64))>,
     strict=False
     name=None,
     ordered=False
 )>

These inferred schemas are rough drafts that shouldn’t be used for validation without modification. You can modify the inferred schema to obtain the schema definition that you’re satisfied with.

For DataFrameSchema objects, the following methods create modified copies of the schema:

For SeriesSchema objects:

  • set_checks()

The section below describes two workflows for persisting and modifying an inferred schema.

Schema Persistence

The schema persistence feature requires a pandera installation with the io extension. See the installation instructions for more details.

There are two ways of persisting schemas, inferred or otherwise.

Write to a Python script

You can also write your schema to a python script with to_script():

# supply a file-like object, Path, or str to write to a file. If not
# specified, to_script will output the code as a string.
schema_script = schema.to_script()
print(schema_script)
 from pandas import Timestamp
 from pandera import DataFrameSchema, Column, Check, Index, MultiIndex

 schema = DataFrameSchema(
     columns={
         "column1": Column(
             dtype=pandera.engines.numpy_engine.Int64,
             checks=[
                 Check.greater_than_or_equal_to(min_value=5.0),
                 Check.less_than_or_equal_to(max_value=20.0),
             ],
             nullable=False,
             unique=False,
             coerce=False,
             required=True,
             regex=False,
         ),
         "column2": Column(
             dtype=pandera.engines.numpy_engine.Object,
             checks=None,
             nullable=False,
             unique=False,
             coerce=False,
             required=True,
             regex=False,
         ),
         "column3": Column(
             dtype=pandera.engines.pandas_engine.DateTime,
             checks=[
                 Check.greater_than_or_equal_to(
                     min_value=Timestamp("2010-01-01 00:00:00")
                 ),
                 Check.less_than_or_equal_to(
                     max_value=Timestamp("2012-01-01 00:00:00")
                 ),
             ],
             nullable=False,
             unique=False,
             coerce=False,
             required=True,
             regex=False,
         ),
     },
     index=Index(
         dtype=pandera.engines.numpy_engine.Int64,
         checks=[
             Check.greater_than_or_equal_to(min_value=0.0),
             Check.less_than_or_equal_to(max_value=2.0),
         ],
         nullable=False,
         coerce=False,
         name=None,
     ),
     coerce=True,
     strict=False,
     name=None,
 )

As a python script, you can iterate on an inferred schema and use it to validate data once you are satisfied with your schema definition.

Write to YAML

You can also write the schema object to a yaml file with to_yaml(), and you can then read it into memory with from_yaml(). The to_yaml() and from_yaml() is a convenience method for this functionality.

# supply a file-like object, Path, or str to write to a file. If not
# specified, to_yaml will output a yaml string.
yaml_schema = schema.to_yaml()
print(yaml_schema.replace(f"{pa.__version__}", "{PANDERA_VERSION}"))
 schema_type: dataframe
 version: {PANDERA_VERSION}
 columns:
   column1:
     dtype: int64
     nullable: false
     checks:
       greater_than_or_equal_to: 5.0
       less_than_or_equal_to: 20.0
     unique: false
     coerce: false
     required: true
     regex: false
   column2:
     dtype: object
     nullable: false
     checks: null
     unique: false
     coerce: false
     required: true
     regex: false
   column3:
     dtype: datetime64[ns]
     nullable: false
     checks:
       greater_than_or_equal_to: '2010-01-01 00:00:00'
       less_than_or_equal_to: '2012-01-01 00:00:00'
     unique: false
     coerce: false
     required: true
     regex: false
 checks: null
 index:
 - dtype: int64
   nullable: false
   checks:
     greater_than_or_equal_to: 0.0
     less_than_or_equal_to: 2.0
   name: null
   coerce: false
 coerce: true
 strict: false
 unique: null

You can edit this yaml file by specifying column names under the column key. The respective values map onto key-word arguments in the Column class.

Note

Currently, only built-in Check methods are supported under the checks key.