The Open-source Framework for Precision Data Testing¶
Data validation for scientists, engineers, and analysts seeking correctness.
pandera is a Union.ai
open source project that provides a flexible and expressive API for performing data
validation on dataframe-like objects to make data processing pipelines more readable
and robust.
Dataframes contain information that pandera explicitly validates at runtime.
This is useful in production-critical data pipelines or reproducible research
settings. With pandera, you can:
Define a schema once and use it to validate different dataframe types including pandas, polars, dask, modin, and pyspark.pandas.
Check the types and properties of columns in a
pd.DataFrameor values in apd.Series.Perform more complex statistical validation like hypothesis testing.
Parse data to standardize the preprocessing steps needed to produce valid data.
Seamlessly integrate with existing data analysis/processing pipelines via function decorators.
Define dataframe models with the class-based API with pydantic-style syntax and validate dataframes using the typing syntax.
Synthesize data from schema objects for property-based testing with pandas data structures.
Lazily Validate dataframes so that all validation rules are executed before raising an error.
Integrate with a rich ecosystem of python tools like pydantic, fastapi and mypy.
Install¶
Install with pip:
pip install pandera
Or conda:
conda install -c conda-forge pandera
Extras¶
Installing additional functionality:
pip install 'pandera[hypotheses]' # hypothesis checks
pip install 'pandera[io]' # yaml/script schema io utilities
pip install 'pandera[strategies]' # data synthesis strategies
pip install 'pandera[mypy]' # enable static type-linting of pandas
pip install 'pandera[fastapi]' # fastapi integration
pip install 'pandera[dask]' # validate dask dataframes
pip install 'pandera[pyspark]' # validate pyspark dataframes
pip install 'pandera[modin]' # validate modin dataframes
pip install 'pandera[modin-ray]' # validate modin dataframes with ray
pip install 'pandera[modin-dask]' # validate modin dataframes with dask
pip install 'pandera[geopandas]' # validate geopandas geodataframes
pip install 'pandera[polars]' # validate polars dataframes
conda install -c conda-forge pandera-hypotheses # hypothesis checks
conda install -c conda-forge pandera-io # yaml/script schema io utilities
conda install -c conda-forge pandera-strategies # data synthesis strategies
conda install -c conda-forge pandera-mypy # enable static type-linting of pandas
conda install -c conda-forge pandera-fastapi # fastapi integration
conda install -c conda-forge pandera-dask # validate dask dataframes
conda install -c conda-forge pandera-pyspark # validate pyspark dataframes
conda install -c conda-forge pandera-modin # validate modin dataframes
conda install -c conda-forge pandera-modin-ray # validate modin dataframes with ray
conda install -c conda-forge pandera-modin-dask # validate modin dataframes with dask
conda install -c conda-forge pandera-geopandas # validate geopandas geodataframes
conda install -c conda-forge pandera-polars # validate polars dataframes
Quick Start¶
import pandas as pd
import pandera as pa
# data to validate
df = pd.DataFrame({
"column1": [1, 4, 0, 10, 9],
"column2": [-1.3, -1.4, -2.9, -10.1, -20.4],
"column3": ["value_1", "value_2", "value_3", "value_2", "value_1"],
})
# define schema
schema = pa.DataFrameSchema({
"column1": pa.Column(int, checks=pa.Check.le(10)),
"column2": pa.Column(float, checks=pa.Check.lt(-1.2)),
"column3": pa.Column(str, checks=[
pa.Check.str_startswith("value_"),
# define custom checks as functions that take a series as input and
# outputs a boolean or boolean Series
pa.Check(lambda s: s.str.split("_", expand=True).shape[1] == 2)
]),
})
validated_df = schema(df)
print(validated_df)
column1 column2 column3
0 1 -1.3 value_1
1 4 -1.4 value_2
2 0 -2.9 value_3
3 10 -10.1 value_2
4 9 -20.4 value_1
You can pass the built-in python types that are supported by
pandas, or strings representing the
legal pandas datatypes,
or pandera’s DataType:
schema = pa.DataFrameSchema({
# built-in python types
"int_column": pa.Column(int),
"float_column": pa.Column(float),
"str_column": pa.Column(str),
# pandas dtype string aliases
"int_column2": pa.Column("int64"),
"float_column2": pa.Column("float64"),
# pandas > 1.0.0 support native "string" type
"str_column2": pa.Column("str"),
# pandera DataType
"int_column3": pa.Column(pa.Int),
"float_column3": pa.Column(pa.Float),
"str_column3": pa.Column(pa.String),
})
For more details on data types, see DataType
Dataframe Model¶
pandera also provides an alternative API for expressing schemas inspired
by dataclasses and
pydantic. The equivalent
DataFrameModel for the above
DataFrameSchema would be:
from pandera.typing import Series
class Schema(pa.DataFrameModel):
column1: int = pa.Field(le=10)
column2: float = pa.Field(lt=-1.2)
column3: str = pa.Field(str_startswith="value_")
@pa.check("column3")
def column_3_check(cls, series: Series[str]) -> Series[bool]:
"""Check that column3 values have two elements after being split with '_'"""
return series.str.split("_", expand=True).shape[1] == 2
Schema.validate(df)
| column1 | column2 | column3 | |
|---|---|---|---|
| 0 | 1 | -1.3 | value_1 |
| 1 | 4 | -1.4 | value_2 |
| 2 | 0 | -2.9 | value_3 |
| 3 | 10 | -10.1 | value_2 |
| 4 | 9 | -20.4 | value_1 |
Informative Errors¶
If the dataframe does not pass validation checks, pandera provides
useful error messages. An error argument can also be supplied to
Check for custom error messages.
In the case that a validation Check is violated:
simple_schema = pa.DataFrameSchema({
"column1": pa.Column(
int, pa.Check(lambda x: 0 <= x <= 10, element_wise=True,
error="range checker [0, 10]"))
})
# validation rule violated
fail_check_df = pd.DataFrame({
"column1": [-20, 5, 10, 30],
})
try:
simple_schema(fail_check_df)
except pa.errors.SchemaError as exc:
print(exc)
Column 'column1' failed element-wise validator number 0: <Check <lambda>: range checker [0, 10]> failure cases: -20, 30
And in the case of a mis-specified column name:
# column name mis-specified
wrong_column_df = pd.DataFrame({
"foo": ["bar"] * 10,
"baz": [1] * 10
})
try:
simple_schema(wrong_column_df)
except pa.errors.SchemaError as exc:
print(exc)
column 'column1' not in dataframe. Columns in dataframe: ['foo', 'baz']
Error Reports¶
If the dataframe is validated lazily with lazy=True, errors will be aggregated
into an error report. The error report groups DATA and SCHEMA errors to
to give an overview of error sources within a dataframe. Take the following schema
and dataframe:
schema = pa.DataFrameSchema({"id": pa.Column(int, pa.Check.lt(10))}, name="MySchema", strict=True)
df = pd.DataFrame({"id": [1, None, 30], "extra_column": [1, 2, 3]})
try:
schema.validate(df, lazy=True)
except pa.errors.SchemaErrors as exc:
print(exc)
{
"SCHEMA": {
"COLUMN_NOT_IN_SCHEMA": [
{
"schema": "MySchema",
"column": "MySchema",
"check": "column_in_schema",
"error": "column 'extra_column' not in DataFrameSchema {'id': <Schema Column(name=id, type=DataType(int64))>}"
}
],
"SERIES_CONTAINS_NULLS": [
{
"schema": "MySchema",
"column": "id",
"check": "not_nullable",
"error": "non-nullable series 'id' contains null values:1 NaNName: id, dtype: float64"
}
],
"WRONG_DATATYPE": [
{
"schema": "MySchema",
"column": "id",
"check": "dtype('int64')",
"error": "expected series 'id' to have type int64, got float64"
}
]
},
"DATA": {
"DATAFRAME_CHECK": [
{
"schema": "MySchema",
"column": "id",
"check": "less_than(10)",
"error": "Column 'id' failed element-wise validator number 0: less_than(10) failure cases: 30.0"
}
]
}
}
Validating the above dataframe will result in data level errors, namely the id
column having a value which fails a check, as well as schema level errors, such as the
extra column and the None value.
This error report can be useful for debugging, with each item in the various
lists corresponding to a SchemaError
Contributing¶
All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome.
A detailed overview on how to contribute can be found in the contributing guide on GitHub.
Issues¶
Submit issues, feature requests or bugfixes on github.
Need Help?¶
There are many ways of getting help with your questions. You can ask a question on Github Discussions page or reach out to the maintainers and pandera community on Discord
How to Cite¶
If you use pandera in the context of academic or industry research, please
consider citing the paper and/or software package.
Paper¶
@InProceedings{ niels_bantilan-proc-scipy-2020,
author = { {N}iels {B}antilan },
title = { pandera: {S}tatistical {D}ata {V}alidation of {P}andas {D}ataframes },
booktitle = { {P}roceedings of the 19th {P}ython in {S}cience {C}onference },
pages = { 116 - 124 },
year = { 2020 },
editor = { {M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut and {D}avid {S}hupe },
doi = { 10.25080/Majora-342d178e-010 }
}
Software Package¶
License and Credits¶
pandera is licensed under the MIT license.
and is written and maintained by Niels Bantilan (mailto:niels@pandera.ci)