fix/snakemake-dependency-pytest

[guechhouth]

Summary

Previously, the executor's tests were running against the old Snakemake version ^8.6.0. Now, they are tested against the latest version of Snakemake.

After updating the Snakemake's version, test_group_workflow was failing due to get getenv/PATH issue. Our executor plugin has getenv=False by default and the jobs did not have the right environment at EP. New Snakemake changes the scheduling internals, so the grouped jobs were more likely to run through the optimized ilp path, which resulted in a crash immediately since the PATH were missing. This could also explained why when I switched back to 8.6 version, the tests did not pass like they used to either.

Changes

• changed Snakemake in pyproject.toml from 8.6.0 to >=9.6.2
• updated the url to base classes to correct path
• overrode get_envvars() to include PATH in test_workflow() so that the environment is transferred correctly and allow the mock jobs to run

fixes #31