snakemake.workflow.srcdir discontinued in new versions of Snakemake
karel-brinda opened this issue · comments
Extracting from #80 @shenwei356
Python versions should be limited in the range of 3.7 and 3.9. Higher versions like 3.12 caused errors like "attribute error".
There should be no issue with higher Python versions. Could you please provide the specific error message, number of line, etc?
I got this error, but didn't investigate it at all...
Traceback (most recent call last):
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/cli.py", line 1933, in args_to_api
dag_api = workflow_api.dag(
^^^^^^^^^^^^^^^^^
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/api.py", line 328, in dag
return DAGApi(
^^^^^^^
File "<string>", line 6, in __init__
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/api.py", line 438, in __post_init__
self.workflow_api._workflow.dag_settings = self.dag_settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/api.py", line 385, in _workflow
workflow.include(
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/workflow.py", line 1386, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/nfs/research/zi/mhunt/2kk/Miniphy/miniphy/workflow/Snakefile", line 48, in <module>
File "/nfs/research/zi/mhunt/Miniconda3/envs/miniphy/lib/python3.12/site-packages/snakemake/workflow.py", line 1386, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/nfs/research/zi/mhunt/2kk/Miniphy/miniphy/workflow/rules/tree.smk", line 26, in <module>
--name-internals \\
AttributeError: module 'snakemake.workflow' has no attribute 'srcdir'
make: *** [Makefile:47: all] Error 1
This seems to be an issue of Snakemake. Maybe we should require some minimal version.
Which version do you have in this environment?
It might also be possible that they removed the srcdir function from some of the latest versions.