pyduct 0.0.1

A framework for building and running simple data engineering pipelines in Python.

PyDuct

A framework for building and running simple data engineering pipelines in Python.

In Data Science or Data Engineering you constantly hear term “data pipeline”. But there are so many meanings to this term and people often are refering to very specific tools or packages depending on their own background/needs. There are pipelines for pretty much everything and in Python alone I can think of Luigi, Airflow, scikit-learn pipelines, and Pandas pipes just off the top of my head - this article does a good job of helping you understand what is out there.

It can be quite confusing especially if you want a simple and agnostic pipeline that you can customize for your specific needs with no bells and whistles or lock-ins to libraries etc. That is where PyDuct comes in. It is for the simple data engineer who just wants to get stuff done in an ordered and repeatable way.

PyDuct is a simple data pipeline that automates a chain of transformations performed on some data.

PyDuct data pipelines are a great way of introducing automation, reproducibility, structure, and flow to your data engineering projects.

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PyDuct was made by Robert Johnson and Alexander Kozlov and Mohammadreza Khanarmuei

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What is it?

The PyDuct transformation pipelines use user defined transformation functions linked together into a TransformationPipe. The key feature of PyDuct is that the datasource passed in can be almost anything that you desire - e.g. a pandas dataframe, a geopandas dataframe, and iris datacube, a numppy array, so long as your transformation steps read and write the same object PyDuct will work for you.

Install

pip install pyduct

How to use

The TransformationPipe class accepts a list of transformation functions,'steps', to be applied sequentially. Each step contains a name and a function, applied to the input DataObject and will return a transformed DataObject. There is also a third argument in a step that is an optional dictionary of parameters to be passed to your step transformation functions.

In order to use PyDuct you need two things - a DataObject and a set of transformation steps

DataObject

In this very simplified example we will use a geopandas.GeoDataFrame as our input DataObject. To do this we will load an example data set from Kaggle on the global distribution of Volcano Eruptions: https://www.kaggle.com/datasets/texasdave/volcano-eruptions that we have stored in the repo for this package as 'volcano_data_2010.csv'

import pandas
import geopandas

Load the data and put it into a geopandas dataframe:

df1 = pandas.read_csv('../test_data/volcano_data_2010.csv')
# Keep only relevant columns
df = df1.loc[:, ("Year", "Name", "Country", "Latitude", "Longitude", "Type")]
# Create point geometries
geometry = geopandas.points_from_xy(df.Longitude, df.Latitude)
geo_df = geopandas.GeoDataFrame(df[['Year','Name','Country', 'Latitude', 'Longitude', 'Type']], geometry=geometry)
geo_df.head()

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	Year	Name	Country	Latitude	Longitude	Type	geometry
0	2010	Tungurahua	Ecuador	-1.467	-78.442	Stratovolcano	POINT (-78.44200 -1.46700)
1	2010	Eyjafjallajokull	Iceland	63.630	-19.620	Stratovolcano	POINT (-19.62000 63.63000)
2	2010	Pacaya	Guatemala	14.381	-90.601	Complex volcano	POINT (-90.60100 14.38100)
3	2010	Sarigan	United States	16.708	145.780	Stratovolcano	POINT (145.78000 16.70800)
4	2010	Karangetang [Api Siau]	Indonesia	2.780	125.480	Stratovolcano	POINT (125.48000 2.78000)

Steps

Just as an example of something to do we will define only one transformation steps to spatially subset to the Australian region. Yes, i know that this is an unrealistic example but it is just here to show you how to implement pipelines.

We must now write our transformation function - keep in mind that the function must take our DataObject as an input and return a transformed DataObject as a return... in this example that is a geopandas.GeoDataFrame

from pyproj import crs
from shapely.geometry import Polygon, MultiPolygon, box, Point

def spatialCrop(gdf: geopandas.GeoDataFrame, **kwargs):
    """
    This function will apply a sptial limit to a GeoDataFrame based on user-defined limits.
    ----------
    parameters:
        gdf (geopandas.GeoDataFrame): an input GeoDataFrame
        kwargs (dict): parameters, 
            - boundingBox (list): an iterable (lon_min, lat_min, lon_max, lat_max) of the specified region.
    Output:
        transformed_gdf (gdp.GeoDataFrame): GeoDataFrame that is spatially limited to the boundingBox.
    """
    if "boundingBox" not in kwargs:
        return gdf

    boundingBox = kwargs["boundingBox"]
    # just an example so we are doing naughty things with the CRS... look away here...
    coord_system = crs.crs.CRS('WGS 84')

    bounding = geopandas.GeoDataFrame(
        {
            'limit': ['bounding box'],
            'geometry': [
                box(boundingBox[0], boundingBox[1], boundingBox[2],
                    boundingBox[3])
            ]
        },
        crs=coord_system)
    limited_gdf = geopandas.tools.sjoin(gdf,
                                        bounding,
                                        op='intersects',
                                        how='left')
    limited_gdf = limited_gdf[limited_gdf['limit'] == 'bounding box']
    limited_gdf = limited_gdf.drop(columns=['index_right', 'limit'])

    return limited_gdf

Define a PyDuct Pipe

Now that we have a step or function and some data we can now define our transformation pipeline:

pipe = TransformationPipe(steps=[
    ('refine region', spatialCrop, {"boundingBox": [80, -50, 180, 0]})
])

Evaluate your PyDuct Pipe

This where things get interesting... we can now call evaluate on our pipe and watch the magic happen:

Input data:

geo_df

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	Year	Name	Country	Latitude	Longitude	Type	geometry
0	2010	Tungurahua	Ecuador	-1.467	-78.442	Stratovolcano	POINT (-78.44200 -1.46700)
1	2010	Eyjafjallajokull	Iceland	63.630	-19.620	Stratovolcano	POINT (-19.62000 63.63000)
2	2010	Pacaya	Guatemala	14.381	-90.601	Complex volcano	POINT (-90.60100 14.38100)
3	2010	Sarigan	United States	16.708	145.780	Stratovolcano	POINT (145.78000 16.70800)
4	2010	Karangetang [Api Siau]	Indonesia	2.780	125.480	Stratovolcano	POINT (125.48000 2.78000)
...	...	...	...	...	...	...	...
58	2018	Kilauea	United States	19.425	-155.292	Shield volcano	POINT (-155.29200 19.42500)
59	2018	Kadovar	Papua New Guinea	-3.620	144.620	Stratovolcano	POINT (144.62000 -3.62000)
60	2018	Ijen	Indonesia	-8.058	114.242	Stratovolcano	POINT (114.24200 -8.05800)
61	2018	Kilauea	United States	19.425	-155.292	Shield volcano	POINT (-155.29200 19.42500)
62	2018	Aoba	Vanuatu	-15.400	167.830	Shield volcano	POINT (167.83000 -15.40000)

63 rows × 7 columns

Evaluation:

transformed_geo_df = pipe.evaluate(geo_df)

Transformed data:

transformed_geo_df

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	Year	Name	Country	Latitude	Longitude	Type	geometry
6	2010	Merapi	Indonesia	-7.542	110.442	Stratovolcano	POINT (110.44200 -7.54200)
8	2010	Tengger Caldera	Indonesia	-7.942	112.950	Stratovolcano	POINT (112.95000 -7.94200)
9	2011	Merapi	Indonesia	-7.542	110.442	Stratovolcano	POINT (110.44200 -7.54200)
22	2013	Merapi	Indonesia	-7.542	110.442	Stratovolcano	POINT (110.44200 -7.54200)
23	2013	Paluweh	Indonesia	-8.320	121.708	Stratovolcano	POINT (121.70800 -8.32000)
25	2013	Paluweh	Indonesia	-8.320	121.708	Stratovolcano	POINT (121.70800 -8.32000)
29	2013	Okataina	New Zealand	-38.120	176.500	Lava dome	POINT (176.50000 -38.12000)
31	2014	Kelut	Indonesia	-7.930	112.308	Stratovolcano	POINT (112.30800 -7.93000)
39	2015	Manam	Papua New Guinea	-4.100	145.061	Stratovolcano	POINT (145.06100 -4.10000)
41	2015	Okataina	New Zealand	-38.120	176.500	Lava dome	POINT (176.50000 -38.12000)
45	2016	Rinjani	Indonesia	-8.420	116.470	Stratovolcano	POINT (116.47000 -8.42000)
50	2017	Dieng Volc Complex	Indonesia	-7.200	109.920	Complex volcano	POINT (109.92000 -7.20000)
52	2017	Aoba	Vanuatu	-15.400	167.830	Shield volcano	POINT (167.83000 -15.40000)
53	2017	Merapi	Indonesia	-7.542	110.442	Stratovolcano	POINT (110.44200 -7.54200)
55	2018	Kadovar	Papua New Guinea	-3.620	144.620	Stratovolcano	POINT (144.62000 -3.62000)
59	2018	Kadovar	Papua New Guinea	-3.620	144.620	Stratovolcano	POINT (144.62000 -3.62000)
60	2018	Ijen	Indonesia	-8.058	114.242	Stratovolcano	POINT (114.24200 -8.05800)
62	2018	Aoba	Vanuatu	-15.400	167.830	Shield volcano	POINT (167.83000 -15.40000)

The power of this work is in its reproducibility and scalablilty.

Credits

• Logo art from "Vecteezy.com"
• Demo data from "Kaggle.com"