pydiverse.transform

Pipe based dataframe manipulation library that can also transform data on SQL databases

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).

To start developing, you can run the following commands:

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

# Create the environment, activate it and install the pre-commit hooks
pixi install
pixi run postinstall
pixi run pre-commit install

Testing

After installation, you should be able to run:

pixi run pytest

Testing more database backends

To facilitate easy testing, we provide a Docker Compose file to start all required servers. Just run docker compose up in the root directory of the project to start everything, and then run pytest in a new tab.

Afterwards you can run:

pixi run pytest --postgres --mssql

IBM DB2 development

The ibm_db package is only available on the following platforms: linux-64, osx-arm64, win-64.

Note

Because of this, the IBM DB2 drivers are only available in the py312ibm and py310ibm environments. You can run tests using pixi run -e py312ibm pytest --ibm_db2 -m ibm_db2.

Troubleshooting

IBM DB2 container not yet up and running

The IBM DB2 container takes a long time to start. You can find out the name of the container with docker ps (see column NAMES):

CONTAINER ID   IMAGE                                        COMMAND                  CREATED         STATUS         PORTS                                                                                 NAMES
8578e0e471ff   icr.io/db2_community/db2                     "/var/db2_setup/lib/…"   3 minutes ago   Up 3 minutes   22/tcp, 55000/tcp, 60006-60007/tcp, 0.0.0.0:50000->50000/tcp, [::]:50000->50000/tcp   pydiversepipedag-ibm_db2-1

If it is pydiversepipedag-ibm_db2-1, then you can look for Setup has completed in the log with docker logs pydiversepipedag-ibm_db2-1.

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-transform/ 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:

• bump version number in pyproject.toml (check consistency with changelog.md)
• push increased version number to main branch
• pixi run -e release hatch build
• pixi run -e release twine upload --repository testpypi dist/*
• verify with https://test.pypi.org/search/?q=pydiverse.transform

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:

• Attention: Please, only continue here, if automatic conda-forge publishing fails for longer than 24h!
• https://github.com/conda-forge/pydiverse-transform-feedstock#updating-pydiverse-transform-feedstock
• update recipe/meta.yaml
• test meta.yaml in transform repo: conda-build build ../pydiverse-transform-feedstock/recipe/meta.yaml
• commit recipe/meta.yaml to branch of fork and submit PR