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pydiverse.pipedag

Tests Docs

A pipeline orchestration library executing tasks within one python session. It takes care of SQL table (de)materialization, caching and cache invalidation. Blob storage is supported as well for example for storing model files.

This is an early stage version 0.x, however, it is already used in real projects. We are happy to receive your feedback as issues on the GitHub repo. Feel free to also comment on existing issues to extend them to your needs or to add solution ideas.

Preparing installation

To install the package locally in development mode, you will need to install pixi. For those who haven't used pixi before, it is a poetry style dependency management tool based on conda/micromamba/conda-forge package ecosystem. The conda-forge repository has well maintained packages for Linux, macOS, and Windows supporting both ARM and X86 architectures. Especially, installing psycopg2 in a portable way got much easier with pixi. In addition, pixi is really strong in creating lock files for reproducible environments (including system libraries) with many essential features missing in alternative tools like poetry (see pixi.toml).

Docker is used to test against Postgres, MS SQL Server, and DB2 database targets. The bulk of unit tests requires a Postgres test database to be up and running which can be started with docker-compose. Pixi can also help you install docker-compose if it is not already part of your docker (or alternative container runtime) installation:

pixi global install docker-compose

Installation

Currently, development on pipedag is not tested with Windows. Installing packages with pixi should work. If you are interested in contributing with Windows, please submit an issue and we will try to help you with initial setup problems.

To install pydiverse pipedag try this:

git clone https://github.com/pydiverse/pydiverse.pipedag.git
cd pydiverse.pipedag

# Create the environment, activate it and install the pre-commit hooks
pixi install  # see pixi.toml for more environments
pixi run pre-commit install

You can also use alternative environments as you find them in pixi.toml:

pixi install -e py312
pixi run -e py312 pre-commit install

Please, bear in mind, that we currently still want to be python 3.9 compatible while always supporting the newest python version available on conda-forge.

When using Pycharm, you might find it useful that we install a conda executable stub you can use for creating conda interpreters: <pydiverse.pipedag checkout>/.pixi/envs/default/libexec/conda For more information, see here.

Note

The following warning is expected when running pixi commands that solve all environments for the first time in your checkout

WARN osx-arm64 (Apple Silicon) is not supported by the pixi.toml, falling back to osx-64 (emulated with Rosetta)

It actually just applies to the py39ibm and py312ibm environments used for running IBM DB2 tests.

Testing

Most tests are based on a Postgres container running. You can launch it with a working docker-compose setup via:

docker-compose down; docker-compose up

The down command helps ensure a clean state within the databases launched.

After installation and launching docker container in the background, you should be able to run:

pixi run pytest --workers 4

You can peak in pytest.ini and github actions to see different parameters to launch more tests.

pixi run pytest --workers=auto --mssql --duckdb --snowflake --pdtransform --ibis --polars --dask --prefect

for --ibm_db2, see the IBM DB2 development on macOS section.

Example

A flow can look like this (see example/run_pipeline.py):

import tempfile

import pandas as pd
import sqlalchemy as sa

from pydiverse.pipedag import Flow, Stage, Table, materialize
from pydiverse.pipedag.context import StageLockContext
from pydiverse.pipedag.core.config import create_basic_pipedag_config
from pydiverse.pipedag.util.structlog import setup_logging


@materialize(lazy=True)
def lazy_task_1():
    return sa.select(
        sa.literal(1).label("x"),
        sa.literal(2).label("y"),
    )


@materialize(lazy=True, input_type=sa.Table)
def lazy_task_2(input1: sa.Alias, input2: sa.Alias):
    query = sa.select(
        (input1.c.x * 5).label("x5"),
        input2.c.a,
    ).select_from(input1.outerjoin(input2, input2.c.x == input1.c.x))

    return Table(query, name="task_2_out", primary_key=["a"])


@materialize(lazy=True, input_type=sa.Table)
def lazy_task_3(input1: sa.Alias):
    return sa.text(f"SELECT * FROM {input1.original.schema}.{input1.original.name}")


@materialize(lazy=True, input_type=sa.Table)
def lazy_task_4(input1: sa.Alias):
    return sa.text(f"SELECT * FROM {input1.original.schema}.{input1.original.name}")


@materialize(nout=2, version="1.0.0")
def eager_inputs():
    dfA = pd.DataFrame(
        {
            "a": [0, 1, 2, 4],
            "b": [9, 8, 7, 6],
        }
    )
    dfB = pd.DataFrame(
        {
            "a": [2, 1, 0, 1],
            "x": [1, 1, 2, 2],
        }
    )
    return Table(dfA, "dfA"), Table(dfB, "dfB_%%")


@materialize(version="1.0.0", input_type=pd.DataFrame)
def eager_task(tbl1: pd.DataFrame, tbl2: pd.DataFrame):
    return tbl1.merge(tbl2, on="x")


def main():
    with tempfile.TemporaryDirectory() as temp_dir:
        cfg = create_basic_pipedag_config(
            f"duckdb:///{temp_dir}/db.duckdb",
            disable_stage_locking=True,  # This is special for duckdb
            # Attention: If uncommented, stage and task names might be sent to the following URL.
            #   You can self-host kroki if you like:
            #   https://docs.kroki.io/kroki/setup/install/
            # kroki_url="https://kroki.io",
        ).get("default")
        with cfg:
            with Flow() as f:
                with Stage("stage_1"):
                    lazy_1 = lazy_task_1()
                    a, b = eager_inputs()
    
                with Stage("stage_2"):
                    lazy_2 = lazy_task_2(lazy_1, b)
                    lazy_3 = lazy_task_3(lazy_2)
                    eager = eager_task(lazy_1, b)
    
                with Stage("stage_3"):
                    lazy_4 = lazy_task_4(lazy_2)
                _ = lazy_3, lazy_4, eager  # unused terminal output tables
    
            # Run flow
            result = f.run()
            assert result.successful
    
            # Run in a different way for testing
            with StageLockContext():
                result = f.run()
                assert result.successful
                assert result.get(lazy_1, as_type=pd.DataFrame)["x"][0] == 1


if __name__ == "__main__":
    setup_logging()  # you can setup the logging and/or structlog libraries as you wish
    main()

Attention: sa.Alias only exists for SQLAlchemy >= 2.0. Use sa.Table or sa.sql.expression.Alias for older versions.

The with tempfile.TemporaryDirectory() is only needed to have an OS independent temporary directory available. You can also get rid of it like this:

def main():
    cfg = create_basic_pipedag_config(
        "duckdb:////tmp/pipedag/{instance_id}/db.duckdb",
        disable_stage_locking=True,  # This is special for duckdb
    ).get("default")
    ...

Example with separate database server and configuration file (i.e. Postgres in docker container)

A more realistic example can be found in example_postgres/run_pipeline.py. Please note that there are pipedag.yaml and docker-compose.yaml files in the example directory. This is also described on pydiversepipedag.readthedocs.io.

You can run this example with bash as follows:

cd example_postgres
docker-compose up

and in another terminal

cd example_postgres
pixi run python run_pipeline.py

Finally, you may connect to your localhost postgres database pipedag_default and look at tables in schemas stage_1..stage_3.

If you don't have a SQL UI at hand, you may use psql command line tool inside the docker container. Check out the NAMES column in docker ps output. If the name of your postgres container is example_postgres_1, then you can look at output tables like this:

docker exec example_postgres_1 psql --username=sa --dbname=pipedag_default -c 'select * from stage_1.dfa;'

Or more interactively:

docker exec -t -i example_postgres_1 bash
psql --username=sa --dbname=pipedag_default
\dt stage_*.*
select * from stage_2.task_2_out;

IBM DB2 development on macOS

For IBM DB2 on macOS, there are only drivers for the x86_64 architecture, not on aarch64 (see this tracking issue). For this reason, you need to have Rosetta 2 installed and create the conda environment in x86_64 mode (see here for more info about this).

softwareupdate --install-rosetta

Unfortunately, the ibm_db package is not available on conda-forge because the shipped library libdb2.dylib is compiled with GCC and not compatible with clang-based conda-forge installations (see ibmdb/db2drivers #3). Thus, we need to install GCC via homebrew in addition to the conda environment.

On Apple Silicon (M1/M2/M3/...), you need to install homebrew+gcc using Rosetta (Rosetta uses /usr/local by default):

# 
arch -x86_64 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
arch -x86_64 /usr/local/bin/brew install gcc

On Intel based Macs:

brew install gcc

Note

Because of these reasons, the IBM DB2 drivers are only available in the py312ibm and py39ibm environments. You can run tests using pixi run -e py312ibm pytest --ibm_db2.

Troubleshooting

Installing mssql odbc driver for macOS and Linux

Install via Microsoft's instructions for Linux or macOS.

In one Linux installation case, odbcinst -j revealed that it installed the configuration in /etc/unixODBC/*. But conda installed pyodbc brings its own odbcinst executable and that shows odbc config files are expected in /etc/*. Symlinks were enough to fix the problem. Try pixi run python -c 'import pyodbc;print(pyodbc.drivers())' and see whether you get more than an empty list.

Same happened for MacOS. The driver was installed in /opt/homebrew/etc/odbcinst.ini but pyodbc expected it in /etc/odbcinst.ini. This can also be solved by sudo ln -s /opt/homebrew/etc/odbcinst.ini /etc/odbcinst.ini.

Furthermore, make sure you use 127.0.0.1 instead of localhost. It seems that /etc/hosts is ignored.

Packaging and publishing to pypi and conda-forge using github actions

  • bump version number in pyproject.toml
  • set correct release date in changelog.md
  • push increased version number to main branch
  • tag commit with git tag <version>, e.g. git tag 0.7.0
  • git push --tags

The package should appear on https://pypi.org/project/pydiverse-pipedag/ in a timely manner. It is normal that it takes a few hours until the new package version is available on https://conda-forge.org/packages/.

Packaging and publishing to Pypi manually

Packages are first released on test.pypi.org:

Finally, they are published via:

  • git tag <version>
  • git push --tags
  • Attention: Please, only continue here, if automatic publishing fails for some reason!
  • pixi run -e release hatch build
  • pixi run -e release twine upload --repository pypi dist/*

Publishing package on conda-forge manually

Conda-forge packages are updated via: