Population must be a sequence

[yl030]

Hello ppanggolin team,
I installed ppanggolin through conda and when I run % ppanggolin all --fasta genomes.fasta.list

Traceback (most recent call last):
  File "/gss1/home/home/.conda/envs/ppanggolin211/bin/ppanggolin", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/site-packages/ppanggolin/main.py", line 221, in main
    ppanggolin.workflow.all.launch(args)
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/site-packages/ppanggolin/workflow/all.py", line 294, in launch
    launch_workflow(args, panrgp=True, panmodule=True)
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/site-packages/ppanggolin/workflow/all.py", line 124, in launch_workflow
    partition(pangenome,
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/site-packages/ppanggolin/nem/partition.py", line 489, in partition
    kval = evaluate_nb_partitions(organisms, output, sm_degree, free_dispersion, chunk_size, kmm,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/site-packages/ppanggolin/nem/partition.py", line 324, in evaluate_nb_partitions
    select_organisms = set(random.sample(set(organisms), chunk_size))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gss1/home/home/.conda/envs/ppanggolin211/lib/python3.12/random.py", line 413, in sample
    raise TypeError("Population must be a sequence.  "
TypeError: Population must be a sequence.  For dicts or sets, use sorted(d).

[JeanMainguy]

Hi,
Thanks for reporting the issue!
This is a known problem related to Python 3.12 compatibility. It's the same error as in issue #268, and it has been addressed in PR #273, which will be released soon.
In the meantime, you can either use an earlier version of Python or try the fix from the support_py3.12 branch. To do that, simply clone the repo and install it in your conda environment:

conda activate ppanggolin211
git clone --branch support_py3.12 https://github.com/labgem/PPanGGOLiN.git
cd PPanGGOLiN
pip install .

[yl030]

Thank you

[JeanMainguy]

Hi,
The fix has been released in version 2.1.2.
PPanGGOLIN should now work fine with Python 3.12.