🐛 Snakemake-minimal error reading config file

[enryH]

Snakemake version
snakemake-minimal=7.26.0 installed using conda from bioconda.

snakemake-minimal         7.26.0             pyhdfd78af_0    bioconda

Describe the bug

Using github runners macos-latest, windows-latest and ubuntu-lastest the config file of a workflow
is not read. The introduction of the yte package for reading config files seems to cause the error.

Logs

AttributeError in file /home/runner/work/repo/workflow/Snakefile, line 6:
module 'plac' has no attribute 'flg'
  File "/home/runner/work/work/repo/workflow/Snakefile", line 6, in <module>
  File "/usr/share/miniconda3/envs/pkg/lib/python3.8/site-packages/yte/__init__.py", line 74, in <module>
Error: Process completed with exit code 1.

Minimal example

Additional context

[maarten-k]

Can you check the "plac" and "yte" versions in your environment? I think this bug is introduced in #2269

[enryH]

Yes sure

plac                      0.9.6                      py_1    conda-forge
yte                       1.5.1              pyha770c72_2    conda-forge

for the ubuntu-latest image.

[maarten-k]

It looks like that fastai, needs spacy, which needs an old version of plac.

Snakemake needs YTE which needs a modern version of plac, but YTE does not restrict the use of a minimal version number of plac This should be considered as a bug.

However, your environment file is quite big and at a certain point all dependencies become a hairball that is unmanageable. The version of programs are not fixed and unwanted behaviour might occur.( features in third-party software might disappear or change) . I advise using the integrated package manager of snakemake to trim down the size of the environment file https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management.

[enryH]

That is a fair point... I'll add rule specific dependency files to resolve this issue.

[enryH]

For me setting a minimal plac version solves the issue ( 1.0).