Backports error
Opened this issue · 4 comments
Description of the bug
When running session_info.show()
when dandelion has been imported raises an error:
Cell In[2], line 2
1 #Output session Info
----> 2 session_info.show()
File ~/rds/hpc-work/conda_envs/new_bio/lib/python3.11/site-packages/session_info/main.py:209, in show(na, os, cpu, jupyter, dependencies, std_lib, private, write_req_file, req_file_name, html, excludes)
207 for mod_name in clean_modules:
208 mod_names.append(mod_name)
--> 209 mod = sys.modules[mod_name]
210 # Since modules use different attribute names to store version info,
211 # try the most common ones.
212 try:
KeyError: 'backports'
Minimal reproducible example
#Standard Imports:
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib as mpl
import scanpy as sc
import dandelion as ddl
import pingouin as pg
import session_info
#Output session Info
session_info.show()
The error message produced by the code above
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[2], line 2
1 #Output session Info
----> 2 session_info.show()
File ~/rds/hpc-work/conda_envs/new_bio/lib/python3.11/site-packages/session_info/main.py:209, in show(na, os, cpu, jupyter, dependencies, std_lib, private, write_req_file, req_file_name, html, excludes)
207 for mod_name in clean_modules:
208 mod_names.append(mod_name)
--> 209 mod = sys.modules[mod_name]
210 # Since modules use different attribute names to store version info,
211 # try the most common ones.
212 try:
KeyError: 'backports'
OS information
HPC cluster
Version information
scanpy==1.10.3 anndata==0.10.8 umap==0.5.6 numpy==2.0.2 scipy==1.14.1 pandas==2.2.3 scikit-learn==1.5.2 statsmodels==0.14.3 igraph==0.11.6 pynndescent==0.5.13
dandelion==0.3.8 pandas==2.2.3 numpy==1.26.4 matplotlib==3.9.2 networkx==3.3 scipy==1.14.1
Additional context
This is definitely caused only if importing dandelion. I have worked through each import and run session_info.show() and do not get this error until dandelion is imported.
hi there, i'm not sure what's happening since backports
is not a dependency in dandelion
but just in case, can you report back what you see with pip show backports
?
For example with anndata
:
pip show anndata
Name: anndata
Version: 0.10.9
Summary: Annotated data.
Home-page: https://github.com/scverse/anndata
Author: Philipp Angerer, Alex Wolf, Isaac Virshup, Sergei Rybakov
Author-email:
License:
Location: /opt/homebrew/Caskroom/mambaforge/base/envs/dandelion/lib/python3.11/site-packages
Requires: array-api-compat, h5py, natsort, numpy, packaging, pandas, scipy
Required-by: anndata2ri, infercnvpy, kttools, milopy, mudata, palantir, sc-dandelion, scanpy, scFates, scirpy
I use conda to manage my environment (mainly).
pip show backoports
reports WARNING: Package(s) not found: backports
conda list backports
reports:
# Name Version Build Channel
backports 1.0 pyhd8ed1ab_4 conda-forge
how about
conda-tree whoneeds backports
https://anaconda.org/conda-forge/conda-tree
anyway, it's not an issue with dandelion
:
>>> import dandelion
>>> import session_info
>>> session_info.show()
-----
dandelion 0.4.1.dev2
session_info 1.0.0
-----
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ]
macOS-14.4-arm64-arm-64bit
-----
Session information updated at 2024-10-05 08:18