Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update environment to use latest current versions #34

Merged
merged 4 commits into from
Mar 5, 2024

Conversation

bast
Copy link
Member

@bast bast commented Mar 5, 2024

This is only the conda part. I want to see whether this passes. If yes, I can also adjust the requirements.txt part.

@bast
Copy link
Member Author

bast commented Mar 5, 2024

The tests fail with:

+ snakemake --cores 1 --snakefile test/Snakefile
26
Traceback (most recent call last):
27
  File "/opt/hostedtoolcache/Python/3.11.8/x64/bin/snakemake", line 8, in <module>
28
    sys.exit(main())
29
             ^^^^^^
30
  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/snakemake/__init__.py", line 2631, in main
31
    parser = get_argument_parser()
32
             ^^^^^^^^^^^^^^^^^^^^^
33
  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/snakemake/__init__.py", line 1545, in get_argument_parser
34
    lp_solvers = pulp.list_solvers(onlyAvailable=True)
35
                 ^^^^^^^^^^^^^^^^^
36
AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?
37
Error: Process completed with exit code 1.

@bast
Copy link
Member Author

bast commented Mar 5, 2024

The pulp pin is a workaround for snakemake/snakemake#2607

@bast bast merged commit 90d559a into main Mar 5, 2024
12 checks passed
bast added a commit to coderefinery/word-count that referenced this pull request Mar 5, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant