ploomber VS incubation-engineering

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Documentation: https://jupysql.ploomber.io

Note that JupySQL is a fork of ipython-sql; which is no longer actively developed. Catherine, ipython-sql's creator, was kind enough to pass the project to us (check out ipython-sql's README).

We'd love to learn what you think and what features we can ship for JupySQL to be the best SQL client! Please let us know in the comments!

For those who don't know, Jupyter has a bash kernel: https://github.com/takluyver/bash_kernel

And you can run Jupyter notebooks from the CLI with Ploomber: https://github.com/ploomber/ploomber

Develop notebook-based pipelines

Fair point. MLflow has a lot of features to cover the end-to-end dev cycle. This SQLite tracker only covers the experiment tracking part.

We have another project to cover the orchestration/pipelines aspect: https://github.com/ploomber/ploomber and we have plans to work on the rest of features. For now, we're focusing on those two.

I recommend taking a look at the ploomber open source. It helps you structure your code and parameterize it in a way that's easier to maintain and test. Our blog has lots of resources about it from testing your code to building a data science platform on AWS.

Developing end-to-end data science infrastructure can get complex. For example, many of us might have struggled to try to integrate AWS services and deal with configuration, permissions, etc. At Ploomber, we’ve worked with many companies in a wide range of industries, such as energy, entertainment, computational chemistry, and genomics, so we are constantly looking for simple solutions to get them started with Data Science in the cloud.

If you like working locally with notebooks, you can run via the free tier of ploomber, that'll allow you to get the Ram/Compute you need for the bigger models as part of the free tier. Also, it has the historical executions so you don't need to remember what you executed an hour later!

It really depends on your use cases, I've seen a lot of those tools that lock you into a certain syntax, framework or weird language (for instance Groovy). If you'd like to use core python or Jupyter notebooks I'd recommend Ploomber, the community support is really strong, there's an emphasis on observability and you can deploy it on any executor like Slurm, AWS Batch or Airflow. In addition, there's a free managed compute (cloud edition) where you can run certain bioinformatics flows like Alphafold or Cripresso2

That's what we do for lineage with https://ploomber.io/

However if you really want to optimize data currently residing in Postgres for analytical workloads, as the original comment suggests - consider moving to a dedicated OLAP DB like ClickHouse.

See results from Gitlab benchmarking ClickHouse vs TimescaleDB: https://gitlab.com/gitlab-org/incubation-engineering/apm/apm...

Key findings:

ansible: stage: configure image: alpine rules: - if: $ANSIBLE_SETUP_VM != "" && $ANSIBLE_SETUP_HOST != "" variables: ANSIBLE_HOST_KEY_CHECKING: "False" script: - apk add curl bash openssh python3 py3-pip - pip3 install ansible paramiko - ansible-galaxy collection install -r ansible/requirements.yml - curl --silent "https://gitlab.com/gitlab-org/incubation-engineering/mobile-devops/download-secure-files/-/raw/main/installer" | bash - mkdir /root/.ssh && cp .secure_files/ansible.priv /root/.ssh/id_rsa && chmod 600 /root/.ssh/id_rsa - ansible-playbook ansible/main.yml -i ansible/inventory --extra-vars vyos_host=$ANSIBLE_SETUP_VM --limit $ANSIBLE_SETUP_HOST,$ANSIBLE_SETUP_VM ```

Interesting to match with the observations from the practice of using ClickHouse[1][2] for time series:

1. Reordering to SOA helps a lot - this is the whole point of column-oriented databases.

2. Specialized codecs like Gorilla[3], DoubleDelta[4], and FPC[5] lose to simply using ZSTD[6] compression in most cases, both in compression ratio and in performance.

3. Specialized time-series DBMS like InfluxDB or TimescaleDB lose to general-purpose relational OLAP DBMS like ClickHouse [7][8][9].

[1] https://clickhouse.com/blog/optimize-clickhouse-codecs-compr...

[2] https://github.com/ClickHouse/ClickHouse

[3] https://clickhouse.com/docs/en/sql-reference/statements/crea...

[4] https://clickhouse.com/docs/en/sql-reference/statements/crea...

[5] https://clickhouse.com/docs/en/sql-reference/statements/crea...

[6] https://github.com/facebook/zstd/

[7] https://arxiv.org/pdf/2204.09795.pdf "SciTS: A Benchmark for Time-Series Databases in Scientific Experiments and Industrial Internet of Things" (2022)

[8] https://gitlab.com/gitlab-org/incubation-engineering/apm/apm... https://gitlab.com/gitlab-org/incubation-engineering/apm/apm...

[9] https://www.sciencedirect.com/science/article/pii/S187705091...

Documentation of rules is now available: https://gitlab.com/gitlab-org/incubation-engineering/ai-assist/dokter/-/blob/main/docs/overview.md