Incompatible with `Snakemake>=8`

[votti]

Currently drop seems incompatible with the most recent Snakemake version.

Reproducible issue

• Install drop: mamba create -n drop_env_debug -c conda-forge -c bioconda drop --override-channels
• Move to a drop envrionment (eg the demo one)
• Run snakemake -n or any other snakemake command

Error:

:~/drop_demo$ snakemake -n
ImportError in file /home/vitoz/drop_demo/Snakefile, line 3:
cannot import name 'get_argument_parser' from 'snakemake' (/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/snakemake/__init__.py)
  File "/home/vitoz/drop_demo/Snakefile", line 3, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/__init__.py", line 1, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/setupDrop.py", line 2, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/__init__.py", line 1, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/DropConfig.py", line 1, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/SampleAnnotation.py", line 1, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/utils.py", line 3, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/__init__.py", line 10, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/autolink.py", line 6, in <module>
  File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/utils.py", line 12, in <module>

Workaround

Restrict snakemake version during installation: mamba create -n drop_env -c conda-forge -c bioconda drop snakemake-minimal=7.32 --override-channels

Mitigation

• Change example installation command.
• Specify dependency in drop conda release
• This seems to be a wbuild issue and I will open add an issue there as well.

[vyepez88]

many thanks! we're fixing this and let you know once it's done

[vyepez88]

Hi @votti, many thanks for your help! Really appreciate it. This should be now fixed in v 1.4.0