[FIXED] Import errors after updating spyder and python

Issue

-- EDIT - conda list output (top few lines)

# packages in environment at C:\ANACONDA3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py39haa95532_0
alabaster                 0.7.12             pyhd3eb1b0_0
altair                    4.1.0                    pypi_0    pypi

--

I was originally using spyder v4 and python v3.7, but needed to update python to 3.9 for some software. I removed spyder (conda remove spyder), updated python (conda install python=3.9) and reinstalled spyder (conda install spyder=4.2). Upon starting spyder I had a dependency issue, so also updated that (conda update nbconvert). Everything starts fine - I have the correct spyder and python versions.

When working previously i had a lot of packages installed with pip (pip install X). These packages are located in my anaconda directory (C:\ANACONDA3\Lib\site-packages). There were no issues with this before the updates, but now I get import errors - for example, I previously did pip install primer3 (link), and have used it successfully, but now I get:

import primer3
Traceback (most recent call last):

  Cell In[3], line 1
    import primer3

  File C:\ANACONDA3\lib\site-packages\primer3\__init__.py:40
    from .bindings import (calcHairpin, calcHomodimer, calcHeterodimer,

  File C:\ANACONDA3\lib\site-packages\primer3\bindings.py:40
    from . import thermoanalysis

ImportError: cannot import name 'thermoanalysis' from partially initialized module 'primer3' (most likely due to a circular import) (C:\ANACONDA3\lib\site-packages\primer3\__init__.py)

I have heard that pip and conda dont play that well together, but only after I had been using pip for a while - I am very much an amateur. However, seeing as they were installed into the anaconda directory, I assume that I was using the conda pip rather than a standalone local pip, and this should be fine?

Can anyone advise what the issue is/how to fix it? Whilst this has been an interesting learning experience, I have a lot of broken code now :(

Cheers! Tim

Solution

Since you have a mix of conda and pip installed packages in your base environment, the conda install python=3.9 command might have broken some of your pip installed packages. The best idea is probably to reinstall them:

pip uninstall primer3-py
pip install primer3-py

For now, for any pip installed package only (conda list includes the information if something is installed via conda or pip), that shows misbehaviour after this update, you can try the same approach. Do make sure to only do this for pip packages. Note that a lot of packages in your base came with anaconda and are managed by conda. These should all be the correct version for your new python version.

when you have some time, I would recommend the following cleanup approach:

1. Uninstall anaconda
2. Reinstall <- this will give you a clean base environment again
3. For all your projects, create and use a virtual environment created with conda

This enables you to manage different dependencies more effectively in the future. Also, if an environment breaks beyond repair, other projects are not affected and you can delete and recreate.

Answered By - FlyingTeller