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Tools for making Prefect work better for typical data science workflows

Project description

prefect DS

Tools for making Prefect work better for typical data science workflows.

Install

$ pip install prefect-ds

Usage

prefect_ds is a lightweight wrapper around Prefect, designed to make it easier to run workflows I typically encounter when doing data science — especially tasks related to analyzing large datasets and building models. Specifically, it implements the following:

PandasResultHandler

A result handler that reads to and writes from Pandas DataFrames. It should be able to handle any file type Pandas supports, and unlike built-in handlers like LocalResultHandler requires the full specification of the file path — this makes it easy to inspect task results, or use those results in other analysis. It also has support for templating, so task arguments can be injected into the filenames (useful for things like map).

>>> import os
>>> os.environ["PREFECT__LOGGING__LEVEL"] = "ERROR"

>>> import pandas as pd
>>> import time

>>> from prefect import task
>>> from prefect_ds.pandas_result_handler import PandasResultHandler 

>>> # Note the use of the task argument {id} as a template in the filename
>>> @task(result_handler=PandasResultHandler("data_{id}.csv", "csv"))
... def demo_task(id):
...     time.sleep(5)
...     return pd.DataFrame({"one": [1, 2, 3], "two": [4, 5, 6]})

Note that in order to use the templating functionality of PandasResultHandler, you will need to run your flow using the DSTaskRunner (see below for more details).

checkpoint_handler and DSTaskRunner

A state handler that implements filename-based checkpointing, in concert with the specialty result handlers in prefect_ds. It intercepts the state change from Pending to Running, runs the read method of the result handler, and if successful loads the result of that method as the result of the task, then sets the task to the Success state. Conversely, if the read method fails, the task is run as normal and instead the checkpoint_handler runs the write method of the result handler afterwards. Using the checkpoint_handler makes it much easier to cache data across Prefect runs — you don't have to explicitly persist the final flow state between runs, and you don't have to have the cache expire after a certain amount of time.

This handler combines with DSTaskRunner, an extension to Prefect's TaskRunner that implements the necessary hacks to allow for the templating of task arguments. This templating is required to handle cases like map, where without the templating the checkpoint_handler will read from/write to the same file for every iteration of the map.

>>> import contextlib

>>> from prefect import Flow
>>> from prefect.engine import FlowRunner
>>> from prefect_ds.checkpoint_handler import checkpoint_handler
>>> from prefect_ds.task_runner import DSTaskRunner

>>> with Flow("test") as flow:
...     output = demo_task(1)

>>> # First, clean up any existing task results
>>> with contextlib.suppress(FileNotFoundError):
...     os.remove("data_1.csv")

>>> # Run the flow. Since the result file doesn't exist, will run the task
>>> start = time.time()
>>> state = FlowRunner(flow=flow, task_runner_cls=DSTaskRunner).run(
...     task_runner_state_handlers=[checkpoint_handler]
... )
>>> print(f"Took more than 5 seconds: {(time.time() - start) > 5}")
Took more than 5 seconds: True

>>> # Run the flow again. Now that the result file exists, the task is short-circuited
>>> start = time.time()
>>> state = FlowRunner(flow=flow, task_runner_cls=DSTaskRunner).run(
...     task_runner_state_handlers=[checkpoint_handler]
... )
>>> print(f"Took less than 1 second: {(time.time() - start) < 1}")
Took less than 1 second: True

DSFlowRunner

An extension to Prefect's FlowRunner, which will automatically purge the results of upstream tasks once all of their downstream tasks have been run. This can be useful if your task outputs are large datasets; by default Prefect stores the results of every task for the duration of the flow, which can overwhelm your RAM if your results are all things like multi-GB Pandas DataFrames. While PandasResultHandler, checkpoint_handler, and DSTaskRunner are all designed to be used together, DSFlowRunner can have value on its own.

>>> from prefect_ds.flow_runner import DSFlowRunner

>>> @task()
... def generate_data():
...     return pd.DataFrame({"one": [1, 2, 3], "two": [4, 5, 6]})

>>> @task()
... def double_data(input_data):
...     return input_data * 2


>>> with Flow("test") as flow:
...     initial_data = generate_data()
...     two_x_data = double_data(initial_data)
...     four_x_data = double_data(two_x_data)

>>> state = DSFlowRunner(flow=flow).run(return_tasks=flow.tasks)
>>> state.result[initial_data].result # actual type is prefect_ds.result.PurgedResult

>>> state.result[two_x_data].result # another PurgedResult

>>> state.result[four_x_data].result # final result is correct, even though upstream results are gone
   one  two
0    4   16
1    8   20
2   12   24

Caveat

While these components have unit tests covering what I consider to be typical use cases, I have not attempted to comprehensively test every possible interaction with Prefect. As my understanding of Prefect is still relatively immature, I expect there are edge cases where the added functionality of prefect_ds breaks something in Prefect. I think this is especially likely with Prefect Cloud, which I have not done any testing on. If you find such a situation, please feel free to post an issue describing the problem and (ideally) including a minimum reproducible example of the bug.

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