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Minyus / pipelinex

PipelineX: Python package to build ML pipelines for experimentation with Kedro, MLflow, and more

Home Page:https://pipelinex.readthedocs.io/

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PipelineX

PipelineX: Python package to build ML pipelines for experimentation with Kedro, MLflow, and more

Python version PyPI version License Documentation

PipelineX Overview

PipelineX is a Python package to build ML pipelines for experimentation with Kedro, MLflow, and more

PipelineX provides the following options which can be used independently or together.

  • HatchDict: Python in YAML/JSON

    HatchDict is a Python dict parser that enables you to include Python objects in YAML/JSON files.

    Note: HatchDict can be used with or without Kedro.

  • Flex-Kedro: Kedro plugin for flexible config

    • Flex-Kedro-Pipeline: Kedro plugin for quicker pipeline set up

    • Flex-Kedro-Context: Kedro plugin for YAML lovers

  • MLflow-on-Kedro: Kedro plugin for MLflow users

    MLflow-on-Kedro provides integration of Kedro with MLflow with Kedro DataSets and Hooks.

    Note: You do not need to install MLflow if you do not use.

  • Kedro-Extras: Kedro plugin to use various Python packages

    Kedro-Extras provides Kedro DataSets, decorators, and wrappers to use various Python packages such as:

    Note: You do not need to install Python packages you do not use.

Please refer here to find out how PipelineX differs from other pipeline/workflow packages: Airflow, Luigi, Gokart, Metaflow, and Kedro.

Install PipelineX

[Option 1] Install from the PyPI

pip install pipelinex

[Option 2] Development install

This is recommended only if you want to modify the source code of PipelineX.

git clone https://github.com/Minyus/pipelinex.git
cd pipelinex
python setup.py develop

Prepare development environment for PipelineX

You can install packages and organize development environment with pipenv. Refer the pipenv document to install pipenv. Once you installed pipenv, you can use pipenv to install and organize your environment.

# install dependent libraries
$ pipenv install

# install development libraries
$ pipenv install --dev

# install pipelinex
$ pipenv run install

# install pipelinex via setup.py
$ pipenv run install_dev

# lint python code
$ pipenv run lint

# format python code
$ pipenv run fmt

# sort imports
$ pipenv run sort

# apply mypy to python code
$ pipenv run vet

# get into shell
$ pipenv shell

# run test
$ pipenv run test

Prepare Docker environment for PipelineX

git clone https://github.com/Minyus/pipelinex.git
cd pipelinex
docker build --tag pipelinex .
docker run --rm -it pipelinex

Getting Started with PipelineX

Kedro (0.17-0.18) Starter projects

Kedro starters (Cookiecutter templates) to use Kedro, Scikit-learn, MLflow, and PipelineX are available at: kedro-starters-sklearn

Iris dataset is included and used, but you can easily change to Kaggle Titanic dataset.

Example/Demo Projects tested with Kedro 0.16

HatchDict: Python in YAML/JSON

API document

Open In Colab

Python objects in YAML/JSON

Introduction to YAML

YAML is a common text format used for application config files.

YAML's most notable advantage is allowing users to mix 2 styles, block style and flow style.

Example:

import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml="""
block_style_demo:
  key1: value1
  key2: value2
flow_style_demo: {key1: value1, key2: value2}
"""
parameters = yaml.safe_load(params_yaml)

print("### 2 styles in YAML ###")
pprint(parameters)
### 2 styles in YAML ###
{'block_style_demo': {'key1': 'value1', 'key2': 'value2'},
 'flow_style_demo': {'key1': 'value1', 'key2': 'value2'}}

To store highly nested (hierarchical) dict or list, YAML is more conveinient than hard-coding in Python code.

  • YAML's block style, which uses indentation, allows users to omit opening and closing symbols to specify a Python dict or list ({} or []).

  • YAML's flow style, which uses opening and closing symbols, allows users to specify a Python dict or list within a single line.

So simply using YAML with Python will be the best way for Machine Learning experimentation?

Let's check out the next example.

Example:

import yaml
from pprint import pprint  # pretty-print for clearer look


# Read parameters dict from a YAML file in actual use
params_yaml = """
model_kind: LogisticRegression
model_params:
  C: 1.23456
  max_iter: 987
  random_state: 42
"""
parameters = yaml.safe_load(params_yaml)

print("### Before ###")
pprint(parameters)

model_kind = parameters.get("model_kind")
model_params_dict = parameters.get("model_params")

if model_kind == "LogisticRegression":
    from sklearn.linear_model import LogisticRegression
    model = LogisticRegression(**model_params_dict)

elif model_kind == "DecisionTree":
    from sklearn.tree import DecisionTreeClassifier
    model = DecisionTreeClassifier(**model_params_dict)

elif model_kind == "RandomForest":
    from sklearn.ensemble import RandomForestClassifier
    model = RandomForestClassifier(**model_params_dict)

else:
    raise ValueError("Unsupported model_kind.")

print("\n### After ###")
print(model)
### Before ###
{'model_kind': 'LogisticRegression',
 'model_params': {'C': 1.23456, 'max_iter': 987, 'random_state': 42}}

### After ###
LogisticRegression(C=1.23456, class_weight=None, dual=False, fit_intercept=True,
                   intercept_scaling=1, l1_ratio=None, max_iter=987,
                   multi_class='warn', n_jobs=None, penalty='l2',
                   random_state=42, solver='warn', tol=0.0001, verbose=0,
                   warm_start=False)

This way is inefficient as we need to add import and if statements for the options in the Python code in addition to modifying the YAML config file.

Any better way?

Python tags in YAML

PyYAML provides UnsafeLoader which can load Python objects without import.

Example usage of !!python/object

import yaml
# You do not need `import sklearn.linear_model` using PyYAML's UnsafeLoader


# Read parameters dict from a YAML file in actual use
params_yaml = """
model:
  !!python/object:sklearn.linear_model.LogisticRegression
  C: 1.23456
  max_iter: 987
  random_state: 42
"""

parameters = yaml.unsafe_load(params_yaml)  # unsafe_load required

model = parameters.get("model")

print("### model object by PyYAML's UnsafeLoader ###")
print(model)
### model object by PyYAML's UnsafeLoader ###
LogisticRegression(C=1.23456, class_weight=None, dual=None, fit_intercept=None,
                   intercept_scaling=None, l1_ratio=None, max_iter=987,
                   multi_class=None, n_jobs=None, penalty=None, random_state=42,
                   solver=None, tol=None, verbose=None, warm_start=None)

Example usage of !!python/name

import yaml

# Read parameters dict from a YAML file in actual use
params_yaml = """
numpy_array_func: 
  !!python/name:numpy.array
"""

try:
    parameters = yaml.unsafe_load(params_yaml)  # unsafe_load required for PyYAML 5.1 or later
except:
    parameters = yaml.load(params_yaml)

numpy_array_func = parameters.get("numpy_array_func")

import numpy

assert numpy_array_func == numpy.array

PyYAML's !!python/object and !!python/name, however, has the following problems.

  • !!python/object or !!python/name are too long to write.
  • Positional (unnamed) arguments are apparently not supported.

Any better way?

PipelineX provides the solution.

Alternative to Python tags in YAML

PipelineX's HatchDict provides an easier syntax, as follows, to convert Python dictionaries read from YAML or JSON files to Python objects without import.

  • Use = key to specify the package, module, and class/function with . separator in foo_package.bar_module.baz_class format.
  • [Optional] Use _ key to specify (list of) positional (unnamed) arguments if any.
  • [Optional] Add keyword arguments (kwargs) if any.

To return an object instance like PyYAML's !!python/object, feed positional and/or keyword arguments. If it has no arguments, just feed null (known as None in Python) to _ key.

To return an uninstantiated (raw) object like PyYAML's !!python/name, just feed = key without any arguments.

Example alternative to !!python/object specifying keyword arguments:

from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look
# You do not need `import sklearn.linear_model` using PipelineX's HatchDict

# Read parameters dict from a YAML file in actual use
params_yaml="""
model:
  =: sklearn.linear_model.LogisticRegression
  C: 1.23456
  max_iter: 987
  random_state: 42
"""
parameters = yaml.safe_load(params_yaml)

model_dict = parameters.get("model")

print("### Before ###")
pprint(model_dict)

model = HatchDict(parameters).get("model")

print("\n### After ###")
print(model)
### Before ###
{'=': 'sklearn.linear_model.LogisticRegression',
 'C': 1.23456,
 'max_iter': 987,
 'random_state': 42}

### After ###
LogisticRegression(C=1.23456, class_weight=None, dual=False, fit_intercept=True,
                   intercept_scaling=1, l1_ratio=None, max_iter=987,
                   multi_class='warn', n_jobs=None, penalty='l2',
                   random_state=42, solver='warn', tol=0.0001, verbose=0,
                   warm_start=False)

Example alternative to !!python/object specifying both positional and keyword arguments:

from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look

params_yaml = """
metrics:
  - =: functools.partial
    _:
      =: sklearn.metrics.roc_auc_score
    multiclass: ovr
"""
parameters = yaml.safe_load(params_yaml)

metrics_dict = parameters.get("metrics")

print("### Before ###")
pprint(metrics_dict)

metrics = HatchDict(parameters).get("metrics")

print("\n### After ###")
print(metrics)
### Before ###
[{'=': 'functools.partial',
  '_': {'=': 'sklearn.metrics.roc_auc_score'},
  'multiclass': 'ovr'}]

### After ###
[functools.partial(<function roc_auc_score at 0x16bcf19d0>, multiclass='ovr')]

Example alternative to !!python/name:

from pipelinex import HatchDict
import yaml

# Read parameters dict from a YAML file in actual use
params_yaml="""
numpy_array_func:
  =: numpy.array
"""
parameters = yaml.safe_load(params_yaml)

numpy_array_func = HatchDict(parameters).get("numpy_array_func")

import numpy

assert numpy_array_func == numpy.array

This import-less Python object supports nested objects (objects that receives object arguments) by recursive depth-first search.

For more examples, please see Use with PyTorch.

This import-less Python object feature, inspired by the fact that Kedro uses load_obj for file I/O (DataSet), uses load_obj copied from kedro.utils which dynamically imports Python objects using importlib, a Python standard library.

Anchor-less aliasing in YAML/JSON

Aliasing in YAML

To avoid repeating, YAML natively provides Anchor&Alias Anchor&Alias feature, and Jsonnet provides Variable feature to JSON.

Example:

import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml="""
train_params:
  train_batch_size: &batch_size 32
  val_batch_size: *batch_size
"""
parameters = yaml.safe_load(params_yaml)

train_params_dict = parameters.get("train_params")

print("### Conversion by YAML's Anchor&Alias feature ###")
pprint(train_params_dict)
### Conversion by YAML's Anchor&Alias feature ###
{'train_batch_size': 32, 'val_batch_size': 32}

Unfortunately, YAML and Jsonnet require a medium to share the same value.

This is why PipelineX provides anchor-less aliasing feature.

Alternative to aliasing in YAML

You can directly look up another value in the same YAML/JSON file using "$" key without an anchor nor variable.

To specify the nested key (key in a dict of dict), use "." as the separator.

Example:

from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml="""
train_params:
  train_batch_size: 32
  val_batch_size: {$: train_params.train_batch_size}
"""
parameters = yaml.safe_load(params_yaml)

train_params_dict = parameters.get("train_params")

print("### Before ###")
pprint(train_params_dict)

train_params = HatchDict(parameters).get("train_params")

print("\n### After ###")
pprint(train_params)
### Before ###
{'train_batch_size': 32,
 'val_batch_size': {'$': 'train_params.train_batch_size'}}

### After ###
{'train_batch_size': 32, 'val_batch_size': 32}

Python expression in YAML/JSON

Strings wrapped in parentheses are evaluated as a Python expression.

from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml = """
train_params:
  param1_tuple_python: (1, 2, 3)
  param1_tuple_yaml: !!python/tuple [1, 2, 3]
  param2_formula_python: (2 + 3)
  param3_neg_inf_python: (float("-Inf"))
  param3_neg_inf_yaml: -.Inf
  param4_float_1e9_python: (1e9)
  param4_float_1e9_yaml: 1.0e+09
  param5_int_1e9_python: (int(1e9))
"""
parameters = yaml.load(params_yaml)

train_params_raw = parameters.get("train_params")

print("### Before ###")
pprint(train_params_raw)

train_params_converted = HatchDict(parameters).get("train_params")

print("\n### After ###")
pprint(train_params_converted)
### Before ###
{'param1_tuple_python': '(1, 2, 3)',
 'param1_tuple_yaml': (1, 2, 3),
 'param2_formula_python': '(2 + 3)',
 'param3_neg_inf_python': '(float("-Inf"))',
 'param3_neg_inf_yaml': -inf,
 'param4_float_1e9_python': '(1e9)',
 'param4_float_1e9_yaml': 1000000000.0,
 'param5_int_1e9_python': '(int(1e9))'}

### After ###
{'param1_tuple_python': (1, 2, 3),
 'param1_tuple_yaml': (1, 2, 3),
 'param2_formula_python': 5,
 'param3_neg_inf_python': -inf,
 'param3_neg_inf_yaml': -inf,
 'param4_float_1e9_python': 1000000000.0,
 'param4_float_1e9_yaml': 1000000000.0,
 'param5_int_1e9_python': 1000000000}

Introduction to Kedro

Why the unified data interface framework is needed

Machine Learning projects involves with loading and saving various data in various ways such as:

  • files in local/network file system, Hadoop Distributed File System (HDFS), Amazon S3, Google Cloud Storage
    • e.g. CSV, JSON, YAML, pickle, images, models, etc.
  • databases
    • Postgresql, MySQL etc.
  • Spark
  • REST API (HTTP(S) requests)

It is often the case that many Machine Learning Engineers code both data loading/saving and data transformation mixed in the same Python module or Jupyter notebook during experimentation/prototyping phase and suffer later on because:

  • During experimentation/prototyping, we often want to save the intermediate data after each transformation.
  • In production environments, we often want to skip saving data to minimize latency and storage space.
  • To benchmark the performance or troubleshoot, we often want to switch the data source.
    • e.g. read image files in local storage or download images through REST API

The proposed solution is the unified data interface.

Here is a simple demo example to predict survival on the Titanic.

Pipeline visualized by Kedro-viz

Common code to define the tasks/operations/transformations:

# Define tasks

def train_model(model, df, cols_features, col_target):
    # train a model here
    return model

def run_inference(model, df, cols_features):
    # run inference here
    return df

It is notable that you do not need to add any Kedro-related code here to use Kedro later on.

Furthermore, you do not need to add any MLflow-related code here to use MLflow later on as Kedro hooks provided by PipelineX can handle behind the scenes.

This advantage enables you to keep your pipelines for experimentation/prototyping/benchmarking production-ready.

  1. Plain code:
# Configure: can be written in a config file (YAML, JSON, etc.)

train_data_filepath = "data/input/train.csv"
train_data_load_args = {"float_precision": "high"}

test_data_filepath = "data/input/test.csv"
test_data_load_args = {"float_precision": "high"}

pred_data_filepath = "data/load/pred.csv"
pred_data_save_args = {"index": False, "float_format": "%.16e"}

model_kind = "LogisticRegression"
model_params_dict = {
  "C": 1.23456
  "max_iter": 987
  "random_state": 42
}

# Run tasks

import pandas as pd

if model_kind == "LogisticRegression":
    from sklearn.linear_model import LogisticRegression
    model = LogisticRegression(**model_params_dict)

train_df = pd.read_csv(train_data_filepath, **train_data_load_args)
model = train_model(model, train_df)

test_df = pd.read_csv(test_data_filepath, **test_data_load_args)
pred_df = run_inference(model, test_df)
pred_df.to_csv(pred_data_filepath, **pred_data_save_args)
  1. Following the data interface framework, objects with _load, and _save methods, proposed by Kedro and supported by PipelineX:
# Define a data interface: better ones such as "CSVDataSet" are provided by Kedro

import pandas as pd
from pathlib import Path


class CSVDataSet:
    def __init__(self, filepath, load_args={}, save_args={}):
        self._filepath = filepath
        self._load_args = {}
        self._load_args.update(load_args)
        self._save_args = {"index": False}
        self._save_args.update(save_args)

    def _load(self) -> pd.DataFrame:
        return pd.read_csv(self._filepath, **self._load_args)

    def _save(self, data: pd.DataFrame) -> None:
        save_path = Path(self._filepath)
        save_path.parent.mkdir(parents=True, exist_ok=True)
        data.to_csv(str(save_path), **self._save_args)


# Configure data interface: can be written in catalog config file using Kedro

train_dataset = CSVDataSet(
    filepath="data/input/train.csv",
    load_args={"float_precision": "high"},
    # save_args={"float_format": "%.16e"},  # You can set save_args for future use
)

test_dataset = CSVDataSet(
    filepath="data/input/test.csv",
    load_args={"float_precision": "high"},
    # save_args={"float_format": "%.16e"},  # You can set save_args for future use
)

pred_dataset = CSVDataSet(
    filepath="data/load/pred.csv",
    # load_args={"float_precision": "high"},  # You can set load_args for future use
    save_args={"float_format": "%.16e"},
)

model_kind = "LogisticRegression"
model_params_dict = {
  "C": 1.23456
  "max_iter": 987
  "random_state": 42
}
cols_features = [
  "Pclass",  # The passenger's ticket class
  "Parch",  # # of parents / children aboard the Titanic
]
col_target = "Survived"  # Column used as the target: whether the passenger survived or not


# Run tasks: can be configured as a pipeline using Kedro
# and can be written in parameters config file using PipelineX

if model_kind == "LogisticRegression":
    from sklearn.linear_model import LogisticRegression
    model = LogisticRegression(**model_params_dict)

train_df = train_dataset._load()
model = train_model(model, train_df, cols_features, col_target)

test_df = test_dataset._load()
pred_df = run_inference(model, test_df, cols_features)

pred_dataset._save(pred_df)

Just following the data interface framework might be somewhat beneficial in the long run, but not enough.

Let's see what Kedro and PipelineX can do.

Kedro overview

Kedro is a Python package to develop pipelines consisting of:

Kedro pipelines can be run sequentially or in parallel.

Regarding Kedro, please see:

Here is a simple example Kedro project.

#  catalog.yml

train_df:
  type: pandas.CSVDataSet # short for kedro.extras.datasets.pandas.CSVDataSet
  filepath: data/input/train.csv
  load_args:
    float_precision: high
  # save_args: # You can set save_args for future use
  # float_format": "%.16e"

test_df:
  type: pandas.CSVDataSet # short for kedro.extras.datasets.pandas.CSVDataSet
  filepath: data/input/test.csv
  load_args:
    float_precision: high
  # save_args: # You can set save_args for future use
  # float_format": "%.16e"

pred_df:
  type: pandas.CSVDataSet # short for kedro.extras.datasets.pandas.CSVDataSet
  filepath: data/load/pred.csv
  # load_args: # You can set load_args for future use
  # float_precision: high
  save_args:
    float_format: "%.16e"
# parameters.yml

model:
  !!python/object:sklearn.linear_model.LogisticRegression
  C: 1.23456
  max_iter: 987
  random_state: 42
cols_features: # Columns used as features in the Titanic data table
  - Pclass # The passenger's ticket class
  - Parch # # of parents / children aboard the Titanic
col_target: Survived # Column used as the target: whether the passenger survived or not
# pipeline.py

from kedro.pipeline import Pipeline, node

from my_module import train_model, run_inference

def create_pipeline(**kwargs):
    return Pipeline(
        [
            node(
                func=train_model,
                inputs=["params:model", "train_df", "params:cols_features", "params:col_target"],
                outputs="model",
            ),
            node(
                func=run_inference,
                inputs=["model", "test_df", "params:cols_features"],
                outputs="pred_df",
            ),
        ]
    )
# run.py

from kedro.runner import SequntialRunner

# Set up ProjectContext here

context = ProjectContext()
context.run(pipeline_name="__default__", runner=SequentialRunner())

Kedro pipelines can be visualized using kedro-viz.

Kedro pipelines can be productionized using:

  • kedro-airflow: converts a Kedro pipeline into Airflow Python operators.
  • kedro-docker: builds a Docker image that can run a Kedro pipeline
  • kedro-argo: converts a Kedro pipeline into an Argo (backend of Kubeflow) pipeline

Flex-Kedro: Kedro plugin for flexible config

API document

Flex-Kedro provides more options to configure Kedro projects flexibly and thus quickly by KFlex-Kedro-Pipeline and Flex-Kedro-Context features.

Flex-Kedro-Pipeline: Kedro plugin for quicker pipeline set up

If you want to define Kedro pipelines quickly, you can consider to use pipelinex.FlexiblePipeline instead of kedro.pipeline.Pipeline. pipelinex.FlexiblePipeline adds the following options to kedro.pipeline.Pipeline.

Dict for nodes

To define each node, dict can be used instead of kedro.pipeline.node.

Example:

pipelinex.FlexiblePipeline(
    nodes=[dict(func=task_func1, inputs="my_input", outputs="my_output")]
)

will be equivalent to:

kedro.pipeline.Pipeline(
    nodes=[
        kedro.pipeline.node(func=task_func1, inputs="my_input", outputs="my_output")
    ]
)

Sequential nodes

For sub-pipelines consisting of nodes of only single input and single output, you can optionally use Sequential API similar to PyTorch (torch.nn.Sequential) and Keras (tf.keras.Sequential)

Example:

pipelinex.FlexiblePipeline(
    nodes=[
        dict(
            func=[task_func1, task_func2, task_func3],
            inputs="my_input",
            outputs="my_output",
        )
    ]
)

will be equivalent to:

kedro.pipeline.Pipeline(
    nodes=[
        kedro.pipeline.node(
            func=task_func1, inputs="my_input", outputs="my_output__001"
        ),
        kedro.pipeline.node(
            func=task_func2, inputs="my_output__001", outputs="my_output__002"
        ),
        kedro.pipeline.node(
            func=task_func3, inputs="my_output__002", outputs="my_output"
        ),
    ]
)

Decorators without using the method

  • Optionally specify the Python function decorator(s) to apply to multiple nodes under the pipeline using decorator argument instead of using decorate method of kedro.pipeline.Pipeline.

    Example:

    pipelinex.FlexiblePipeline(
    nodes=[
        kedro.pipeline.node(func=task_func1, inputs="my_input", outputs="my_output")
    ],
    decorator=[task_deco, task_deco],
)

    will be equivalent to:

    kedro.pipeline.Pipeline(
    nodes=[
        kedro.pipeline.node(func=task_func1, inputs="my_input", outputs="my_output")
    ]
).decorate(task_deco, task_deco)

  • Optionally specify the default python module (path of .py file) if you do not want to repeat the same (deep and/or long) Python module (e.g. foo.bar.my_task1, foo.bar.my_task2, etc.)

Flex-Kedro-Context: Kedro plugin for YAML lovers

If you want to take advantage of YAML more than Kedro supports, you can consider to use pipelinex.FlexibleContext instead of kedro.framework.context.KedroContext. pipelinex.FlexibleContext adds preprocess of parameters.yml and catalog.yml to kedro.framework.context.KedroContext to provide flexibility. This option is for YAML lovers only. If you don't like YAML very much, skip this one.

Define Kedro pipelines in parameters.yml

You can define the inter-task dependency (DAG) for Kedro pipelines in parameters.yml using PIPELINES key. To define each Kedro pipeline, you can use the kedro.pipeline.Pipeline or its variant such as pipelinex.FlexiblePipeline as shown below.

# parameters.yml

PIPELINES:
  __default__:
    =: pipelinex.FlexiblePipeline
    module: # Optionally specify the default Python module so you can omit the module name to which functions belongs
    decorator: # Optionally specify function decorator(s) to apply to each node
    nodes:
      - inputs: ["params:model", train_df, "params:cols_features", "params:col_target"]
        func: sklearn_demo.train_model
        outputs: model

      - inputs: [model, test_df, "params:cols_features"]
        func: sklearn_demo.run_inference
        outputs: pred_df

Configure Kedro run config in parameters.yml

You can specify the run config in parameters.yml using RUN_CONFIG key instead of specifying the args for kedro run command for every run.

You can still set the args for kedro run to overwrite.

In addition to the args for kedro run, you can opt to run only missing nodes (skip tasks which have already been run to resume pipeline using the intermediate data files or databases.) by only_missing key.

# parameters.yml

RUN_CONFIG:
  pipeline_name: __default__
  runner: SequentialRunner # Set to "ParallelRunner" to run in parallel
  only_missing: False # Set True to run only missing nodes
  tags: # None
  node_names: # None
  from_nodes: # None
  to_nodes: # None
  from_inputs: # None
  load_versions: # None

Use HatchDict feature in parameters.yml

You can use HatchDict feature in parameters.yml.

# parameters.yml

model:
  =: sklearn.linear_model.LogisticRegression
  C: 1.23456
  max_iter: 987
  random_state: 42
cols_features: # Columns used as features in the Titanic data table
  - Pclass # The passenger's ticket class
  - Parch # # of parents / children aboard the Titanic
col_target: Survived # Column used as the target: whether the passenger survived or not

Enable caching for Kedro DataSets in catalog.yml

Enable caching using cached key set to True if you do not want Kedro to load the data from disk/database which were in the memory. (kedro.io.CachedDataSet is used under the hood.)

Use HatchDict feature in catalog.yml

You can use HatchDict feature in catalog.yml.

MLflow-on-Kedro: Kedro plugin for MLflow users

API document

How to use MLflow from Kedro projects

Kedro DataSet and Hooks (callbacks) are provided to use MLflow without adding any MLflow-related code in the node (task) functions.

  • pipelinex.MLflowDataSet

    Kedro Dataset that saves data to or loads data from MLflow depending on dataset argument as follows.

    • If set to "p", the value will be saved/loaded as an MLflow parameter (string).

    • If set to "m", the value will be saved/loaded as an MLflow metric (numeric).

    • If set to "a", the value will be saved/loaded based on the data type.

      • If the data type is either {float, int}, the value will be saved/loaded as an MLflow metric.

      • If the data type is either {str, list, tuple, set}, the value will be saved/load as an MLflow parameter.

      • If the data type is dict, the value will be flattened with dot (".") as the separator and then saved/loaded as either an MLflow metric or parameter based on each data type as explained above.

    • If set to either {"json", "csv", "xls", "parquet", "png", "jpg", "jpeg", "img", "pkl", "txt", "yml", "yaml"}, the backend dataset instance will be created accordingly to save/load as an MLflow artifact.

    • If set to a Kedro DataSet object or a dictionary, it will be used as the backend dataset to save/load as an MLflow artifact.

    • If set to None (default), MLflow logging will be skipped.

    Regarding all the options, please see the API document

  • Kedro Hooks

    Regarding all the options, please see the API document

MLflow-ready Kedro projects can be generated by the Kedro starters (Cookiecutter template) which include the following example config:

# catalog.yml

# Write a pickle file & upload to MLflow
model:
  type: pipelinex.MLflowDataSet
  dataset: pkl

# Write a csv file & upload to MLflow
pred_df: 
  type: pipelinex.MLflowDataSet
  dataset: csv

# Write an MLflow metric
score:
  type: pipelinex.MLflowDataSet
  dataset: m  
# catalog.py (alternative to catalog.yml)

catalog_dict = {
  "model": MLflowDataSet(dataset="pkl"),  # Write a pickle file & upload to MLflow
  "pred_df": MLflowDataSet(dataset="csv"),  # Write a csv file & upload to MLflow
  "score": MLflowDataSet(dataset="m"),  # Write an MLflow metric
}
# mlflow_config.py

import pipelinex

mlflow_hooks = (
    pipelinex.MLflowBasicLoggerHook(
        uri="sqlite:///mlruns/sqlite.db",
        experiment_name="experiment_001",
        artifact_location="./mlruns/experiment_001",
        offset_hours=0,
    ),
    pipelinex.MLflowCatalogLoggerHook(
        auto=True,
    ),
    pipelinex.MLflowArtifactsLoggerHook(
        filepaths_before_pipeline_run=["conf/base/parameters.yml"],
        filepaths_after_pipeline_run=[
            "info.log",
            "errors.log",
        ],
    ),
    pipelinex.MLflowEnvVarsLoggerHook(
        param_env_vars=["HOSTNAME"],
        metric_env_vars=[],
    ),
    pipelinex.MLflowTimeLoggerHook(),
)

Logged metrics shown in MLflow's UI

Gantt chart for execution time, generated using Plotly, shown in MLflow's UI

Comparison with kedro-mlflow package

Both PipelineX's MLflow-on-Kedro and kedro-mlflow provide integration of MLflow to Kedro. Here are the comparisons.

  • Features supported by both PipelineX and kedro-mlflow

    • Kedro DataSets and Hooks to log (save/upload) artifacts, parameters, and metrics to MLflow.
    • Truncate MLflow parameter values to 250 characters to avoid error due to MLflow parameter length limit.
    • Dict values can be flattened using dot (".") as the separator to log each value inside the dict separately.

  • Features supported by only PipelineX

    • [Time logging] Option to log execution time for each task (Kedro node) as MLflow metrics
    • [Gantt logging] Option to log Gantt chart HTML file that visualizes execution time using Plotly as an MLflow artifact (inspired by Apache Airflow)
    • [Automatic backend Kedro DataSets for common artifacts] Option to specify a common file extension ({"json", "csv", "xls", "parquet", "png", "jpg", "jpeg", "img", "pkl", "txt", "yml", "yaml"}) so the Kedro DataSet object will be created behind the scene instead of manually specifying a Kedro DataSet including filepath in the catalog (inspired by Kedro Wings).
    • [Automatic logging for MLflow parameters and metrics] Option to log each dataset not listed in the catalog as MLflow parameter or metric, instead of manually specifying a Kedro DataSet in the catalog.
      • If the data type is either {float, int}, the value will be saved/loaded as an MLflow metric.
      • If the data type is either {str, list, tuple, set}, the value will be saved/load as an MLflow parameter.
      • If the data type is dict, the value will be flattened with dot (".") as the separator and then saved/loaded as either an MLflow metric or parameter based on each data type as explained above.
      • For example, "data_loading_config": {"train": {"batch_size": 32}} will be logged as MLflow metric of "data_loading_config.train.batch_size": 32
    • [Flexible config per DataSet] For each Kedro DataSet, it is possible to configure differently. For example, a dict value can be logged as an MLflow parameter (string) as is while another one can be logged as an MLflow metric after being flattened.
    • [Direct artifact logging] Option to specify the paths of any data to log as MLflow artifacts after Kedro pipeline runs without using a Kedro DataSet, which is useful if you want to save local files (e.g. info/warning/error log files, intermediate model weights saved by Machine Learning packages such as PyTorch and TensorFlow, etc.)
    • [Environment Variable logging] Option to log Environment Variables
    • [Downloading] Option to download MLflow artifacts, params, metrics from an existing MLflow experiment run using the Kedro DataSet
    • [Up to date] Support for Kedro 0.17.x (released in Dec 2020) or later

  • Features provided by only kedro-mlflow

    • A wrapper for MLflow's log_model
    • Configure MLflow logging in a YAML file
    • Option to use MLflow tag or raise error if MLflow parameter values exceed 250 characters

Kedro-Extras: Kedro plugin to use various Python packages

API document

Kedro-Extras provides Kedro DataSets and decorators not available in kedro.extras.

Contributors who are willing to help preparing the test code and send pull request to Kedro following Kedro's CONTRIBUTING.md are welcomed.

Additional Kedro datasets (data interface sets)

pipelinex.extras.datasets provides the following Kedro Datasets (data interface sets) mainly for Computer Vision applications using PyTorch/torchvision, OpenCV, and Scikit-image.

Additional function decorators for benchmarking

Open In Colab

pipelinex.extras.decorators provides Python decorators for benchmarking.

  • log_time

    • logs the duration time of a function (difference of timestamp before and after running the function).
    • Slightly modified version of Kedro's log_time

  • mem_profile

    • logs the peak memory usage during running the function.
    • memory_profiler needs to be installed.
    • Slightly modified version of Kedro's mem_profile

  • nvml_profile

    • logs the difference of NVIDIA GPU usage before and after running the function.
    • pynvml or py3nvml needs to be installed.
from pipelinex import log_time
from pipelinex import mem_profile  # Need to install memory_profiler for memory profiling
from pipelinex import nvml_profile  # Need to install pynvml for NVIDIA GPU profiling
from time import sleep
import logging

logging.basicConfig(level=logging.INFO)

@nvml_profile
@mem_profile
@log_time
def foo_func(i=1):
    sleep(0.5)  # Needed to avoid the bug reported at https://github.com/pythonprofilers/memory_profiler/issues/216
    return "a" * i

output = foo_func(100_000_000)
INFO:pipelinex.decorators.decorators:Running 'foo_func' took 549ms [0.549s]
INFO:pipelinex.decorators.memory_profiler:Running 'foo_func' consumed 579.02MiB memory at peak time
INFO:pipelinex.decorators.nvml_profiler:Ran: 'foo_func', NVML returned: {'_Driver_Version': '418.67', '_NVML_Version': '10.418.67', 'Device_Count': 1, 'Devices': [{'_Name': 'Tesla P100-PCIE-16GB', 'Total_Memory': 17071734784, 'Free_Memory': 17071669248, 'Used_Memory': 65536, 'GPU_Utilization_Rate': 0, 'Memory_Utilization_Rate': 0}]}, Used memory diff: [0]

Use with PyTorch

Open In Colab

To develop a simple neural network, it is convenient to use Sequential API (e.g. torch.nn.Sequential, tf.keras.Sequential).

  • Hardcoded:
from torch.nn import Sequential, Conv2d, ReLU

model = Sequential(
    Conv2d(in_channels=3, out_channels=16, kernel_size=[3, 3]),
    ReLU(),
)

print("### model object by hard-coding ###")
print(model)
### model object by hard-coding ###
Sequential(
  (0): Conv2d(3, 16, kernel_size=[3, 3], stride=(1, 1))
  (1): ReLU()
)
  • Using import-less Python object feature:
from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml="""
model:
  =: torch.nn.Sequential
  _:
    - {=: torch.nn.Conv2d, in_channels: 3, out_channels: 16, kernel_size: [3, 3]}
    - {=: torch.nn.ReLU, _: }
"""
parameters = yaml.safe_load(params_yaml)

model_dict = parameters.get("model")

print("### Before ###")
pprint(model_dict)

model = HatchDict(parameters).get("model")

print("\n### After ###")
print(model)
### Before ###
{'=': 'torch.nn.Sequential',
 '_': [{'=': 'torch.nn.Conv2d',
        'in_channels': 3,
        'kernel_size': [3, 3],
        'out_channels': 16},
       {'=': 'torch.nn.ReLU', '_': None}]}

### After ###
Sequential(
  (0): Conv2d(3, 16, kernel_size=[3, 3], stride=(1, 1))
  (1): ReLU()
)

In addition to Sequential, TensorFLow/Keras provides modules to merge branches such as tf.keras.layers.Concatenate, but PyTorch provides only functional interface such as torch.cat.

PipelineX provides modules to merge branches such as ModuleConcat, ModuleSum, and ModuleAvg.

  • Hardcoded:
from torch.nn import Sequential, Conv2d, AvgPool2d, ReLU
from pipelinex import ModuleConcat

model = Sequential(
    ModuleConcat(
        Conv2d(in_channels=3, out_channels=16, kernel_size=[3, 3], stride=[2, 2], padding=[1, 1]),
        AvgPool2d(kernel_size=[3, 3], stride=[2, 2], padding=[1, 1]),
    ),
    ReLU(),
)
print("### model object by hard-coding ###")
print(model)
### model object by hard-coding ###
Sequential(
  (0): ModuleConcat(
    (0): Conv2d(3, 16, kernel_size=[3, 3], stride=[2, 2], padding=[1, 1])
    (1): AvgPool2d(kernel_size=[3, 3], stride=[2, 2], padding=[1, 1])
  )
  (1): ReLU()
)
  • Using import-less Python object feature:
from pipelinex import HatchDict
import yaml
from pprint import pprint  # pretty-print for clearer look

# Read parameters dict from a YAML file in actual use
params_yaml="""
model:
  =: torch.nn.Sequential
  _:
    - =: pipelinex.ModuleConcat
      _:
        - {=: torch.nn.Conv2d, in_channels: 3, out_channels: 16, kernel_size: [3, 3], stride: [2, 2], padding: [1, 1]}
        - {=: torch.nn.AvgPool2d, kernel_size: [3, 3], stride: [2, 2], padding: [1, 1]}
    - {=: torch.nn.ReLU, _: }
"""
parameters = yaml.safe_load(params_yaml)

model_dict = parameters.get("model")

print("### Before ###")
pprint(model_dict)

model = HatchDict(parameters).get("model")

print("\n### After ###")
print(model)
### Before ###
{'=': 'torch.nn.Sequential',
 '_': [{'=': 'pipelinex.ModuleConcat',
        '_': [{'=': 'torch.nn.Conv2d',
               'in_channels': 3,
               'kernel_size': [3, 3],
               'out_channels': 16,
               'padding': [1, 1],
               'stride': [2, 2]},
              {'=': 'torch.nn.AvgPool2d',
               'kernel_size': [3, 3],
               'padding': [1, 1],
               'stride': [2, 2]}]},
       {'=': 'torch.nn.ReLU', '_': None}]}

### After ###
Sequential(
  (0): ModuleConcat(
    (0): Conv2d(3, 16, kernel_size=[3, 3], stride=[2, 2], padding=[1, 1])
    (1): AvgPool2d(kernel_size=[3, 3], stride=[2, 2], padding=[1, 1])
  )
  (1): ReLU()
)

Use with PyTorch Ignite

Wrappers of PyTorch Ignite provides most of features available in Ignite, including integration with MLflow, in an easy declarative way.

In addition, the following optional features are available in PipelineX.

  • Use only partial samples in dataset (Useful for quick preliminary check before using the whole dataset)
  • Time limit for training (Useful for code-only (Kernel-only) Kaggle competitions with time limit)

Here are the arguments for NetworkTrain:

loss_fn (callable): Loss function used to train.
    Accepts an instance of loss functions at https://pytorch.org/docs/stable/nn.html#loss-functions
epochs (int, optional): Max epochs to train
seed (int, optional): Random seed for training.
optimizer (torch.optim, optional): Optimizer used to train.
    Accepts optimizers at https://pytorch.org/docs/stable/optim.html
optimizer_params (dict, optional): Parameters for optimizer.
train_data_loader_params (dict, optional): Parameters for data loader for training.
    Accepts args at https://pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader
val_data_loader_params (dict, optional): Parameters for data loader for validation.
    Accepts args at https://pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader
evaluation_metrics (dict, optional): Metrics to compute for evaluation.
    Accepts dict of metrics at https://pytorch.org/ignite/metrics.html
evaluate_train_data (str, optional): When to compute evaluation_metrics using training dataset.
    Accepts events at https://pytorch.org/ignite/engine.html#ignite.engine.Events
evaluate_val_data (str, optional): When to compute evaluation_metrics using validation dataset.
    Accepts events at https://pytorch.org/ignite/engine.html#ignite.engine.Events
progress_update (bool, optional): Whether to show progress bar using tqdm package
scheduler (ignite.contrib.handle.param_scheduler.ParamScheduler, optional): Param scheduler.
    Accepts a ParamScheduler at
    https://pytorch.org/ignite/contrib/handlers.html#module-ignite.contrib.handlers.param_scheduler
scheduler_params (dict, optional): Parameters for scheduler
model_checkpoint (ignite.handlers.ModelCheckpoint, optional): Model Checkpoint.
    Accepts a ModelCheckpoint at https://pytorch.org/ignite/handlers.html#ignite.handlers.ModelCheckpoint
model_checkpoint_params (dict, optional): Parameters for ModelCheckpoint at
    https://pytorch.org/ignite/handlers.html#ignite.handlers.ModelCheckpoint
early_stopping_params (dict, optional): Parameters for EarlyStopping at
    https://pytorch.org/ignite/handlers.html#ignite.handlers.EarlyStopping
time_limit (int, optioinal): Time limit for training in seconds.
train_dataset_size_limit (int, optional): If specified, only the subset of training dataset is used.
    Useful for quick preliminary check before using the whole dataset.
val_dataset_size_limit (int, optional): If specified, only the subset of validation dataset is used.
    useful for qucik preliminary check before using the whole dataset.
cudnn_deterministic (bool, optional): Value for torch.backends.cudnn.deterministic.
    See https://pytorch.org/docs/stable/notes/randomness.html for details.
cudnn_benchmark (bool, optional): Value for torch.backends.cudnn.benchmark.
    See https://pytorch.org/docs/stable/notes/randomness.html for details.
mlflow_logging (bool, optional): If True and MLflow is installed, MLflow logging is enabled.

Please see the example code using MNIST dataset prepared based on the original code.

It is also possible to use:

It is planned to port some code used with PyTorch Ignite to PyTorch Ignite repository once test and example codes are prepared.

Use with OpenCV

A challenge of image processing is that the parameters and algorithms that work with an image often do not work with another image. You will want to output intermediate images from each image processing pipeline step for visual check during development, but you will not want to output all the intermediate images to save time and disk space in production.

Wrappers of OpenCV and ImagesLocalDataSet are the solution. You can concentrate on developping your image processing pipeline for an image (3-D or 2-D numpy array), and it will run for all the images in a folder.

If you are devepping an image processing pipeline consisting of 5 steps and you have 10 images, for example, you can check 10 generated images in each of 5 folders, 50 images in total, during development.

Story behind PipelineX

When I was working on a Deep Learning project, it was very time-consuming to develop the pipeline for experimentation. I wanted 2 features.

First one was an option to resume the pipeline using the intermediate data files instead of running the whole pipeline. This was important for rapid Machine/Deep Learning experimentation.

Second one was modularity, which means keeping the 3 components, task processing, file/database access, and DAG definition, independent. This was important for efficient software engineering.

After this project, I explored for a long-term solution. I researched about 3 Python packages for pipeline development, Airflow, Luigi, and Kedro, but none of these could be a solution.

Luigi provided resuming feature, but did not offer modularity. Kedro offered modularity, but did not provide resuming feature.

After this research, I decided to develop my own package that works on top of Kedro. Besides, I added syntactic sugars including Sequential API similar to Keras and PyTorch to define DAG. Furthermore, I added integration with MLflow, PyTorch, Ignite, pandas, OpenCV, etc. while working on more Machine/Deep Learning projects.

After I confirmed my package worked well with the Kaggle competition, I released it as PipelineX.

Author

Yusuke Minami @Minyus

Contributors are welcome!

How to contribute

Please see CONTRIBUTING.md for details.

Contributor list

About

PipelineX: Python package to build ML pipelines for experimentation with Kedro, MLflow, and more

https://pipelinex.readthedocs.io/

pipelineexperimentationmachine-learningdeep-learningdata-sciencedata-engineering

License:Other

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