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Python, poetry, and pandas

From: Sébastien Lerique
Subject: Python, poetry, and pandas
Date: Wed, 10 Mar 2021 16:38:38 +0900

Dear all,

In the course of trying out poetry for data science projects on guix, I am running into the problem of some poetry-installed packages not finding their desired libraries. (See example below with pandas.) I suppose this is because poetry will download pre-built binary wheels which have pre-coded library paths.

If this is the problem, would there be any clean way to wrap those binary wheels, or patch poetry-on-guix to mandatorily rebuild binaries? (Would that make sense?)

(I am aware that python-pandas is packaged for guix, but some packages I will need down the road might not be; this project is also in collaboration with non guix users, so I am looking for a workflow which will work for them too.)

(I am also aware of guix-jupyter, but that is another topic I'd like to return to later as it needs some more bugsquashing for usability.)

Happy hacking!

$ poetry new poetry-test

Created package poetry_test in poetry-test
$ cd poetry-test/
$ poetry add pandas
Creating virtualenv poetry-test-vOWX4_Vr-py3.8 in /home/sl/.cache/pypoetry/virtualenvs
Using version ^1.2.3 for pandas

Updating dependencies
Resolving dependencies... (0.2s)

Writing lock file

Package operations: 4 installs, 9 updates, 0 removals

• Updating pyparsing (2.4.6 /home/sl/.guix-profile/lib/python3.8/site-packages -> 2.4.7) • Updating six (1.14.0 /home/sl/.guix-profile/lib/python3.8/site-packages -> 1.15.0) • Updating attrs (19.3.0 /home/sl/.guix-profile/lib/python3.8/site-packages -> 20.3.0) • Updating more-itertools (8.2.0 /home/sl/.guix-profile/lib/python3.8/site-packages -> 8.7.0) • Updating numpy (1.17.3 /home/sl/.guix-profile/lib/python3.8/site-packages -> 1.20.1) • Updating packaging (20.0 /home/sl/.guix-profile/lib/python3.8/site-packages -> 20.9)
 • Installing pluggy (0.13.1)
 • Installing py (1.10.0)
• Updating python-dateutil (2.8.1 /home/sl/.guix-profile/lib/python3.8/site-packages -> 2.8.1) • Updating pytz (2020.4 /home/sl/.guix-profile/lib/python3.8/site-packages -> 2021.1) • Updating wcwidth (0.1.8 /home/sl/.guix-profile/lib/python3.8/site-packages -> 0.2.5)
 • Installing pandas (1.2.3)
 • Installing pytest (5.4.3)
$ poetry run which python
$ poetry run python
Python 3.8.2 (default, Jan  1 1970, 00:00:01)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
import pandas
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/", line 51, in <module>
   from pandas.core.api import (
File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/", line 31, in <module>
   from pandas.core.groupby import Grouper, NamedAgg
File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/groupby/", line 1, in <module> from pandas.core.groupby.generic import DataFrameGroupBy, NamedAgg, SeriesGroupBy File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/groupby/", line 65, in <module>
   from pandas.core.frame import DataFrame
File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/", line 119, in <module> from pandas.core import algorithms, common as com, generic, nanops, ops File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/", line 111, in <module> from pandas.core.window import Expanding, ExponentialMovingWindow, Rolling, Window File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/window/", line 1, in <module>
   from pandas.core.window.ewm import (  # noqa:F401
File "/home/sl/.cache/pypoetry/virtualenvs/poetry-test-vOWX4_Vr-py3.8/lib/python3.8/site-packages/pandas/core/window/", line 9, in <module>
   import pandas._libs.window.aggregations as window_aggregations
ImportError: cannot open shared object file: No such file or directory


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