Merck / Merck/BioPhi

Specify pandas version

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#40 1 comment 0 reactions 0 assignees View on GitHub

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Dominant language
Python
Stars
265
Forks
65
PR merge metrics
No merged PRs in 30d

Description

Upgrading to pandas 2.0 makes the program raise a HumannessTaskError:

  • If you submit a light sequence it will say it expected a heavy sequence
  • If you submit a heavy sequence it will say it expected a light sequence

Traced the error back to pandas 2.0 and the following AttributeError in SQLAlchemy:

AttributeError: 'Connection' object has no attribute 'exec_driver_sql'

Reverting to pandas 1.5.2 solved the issue

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the HumannessTaskError with pandas 2.0, then inspect the project's dependency declarations and the SQLAlchemy database interaction implicated by the AttributeError. The issue is done when both light and heavy sequence submissions behave correctly with the supported pandas version, without the reported connection error.

Written by the indexing model from the issue text.

Assessment

Tech stack
pandas, python, sqlalchemy
Domain
backend, databases
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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