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Snakemake version
6.10.0
mamba create -n snakemake -c conda-forge bioconda::snakemake=6.10
Describe the bug
When using --edit-notebook with a Snakefile with a relative notebook path, a TypeError is raised when Snakemake tries to turn that into an absolute path. It looks like the 'basedir' variable type has changed but snakemake/notebook.py was not updated to reflect this.
Logs
Traceback (most recent call last):
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 593, in _callback
raise ex
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/concurrent/futures/thread.py", line 52, in run
result = self.fn(*self.args, **self.kwargs)
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 579, in cached_or_run
run_func(*args)
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2461, in run_wrapper
raise ex
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2418, in run_wrapper
run(
File "/Users/benjolly/Documents/arsa-beech/arsa-beech-analysis/workflow/Snakefile", line 253, in __rule_seed_corr
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/notebook.py", line 233, in notebook
local_path = os.path.join(basedir, path)
File "/Users/benjolly/miniconda3/envs/snakemake/lib/python3.9/posixpath.py", line 76, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not LocalSourceFile
Snakemake version
6.10.0
mamba create -n snakemake -c conda-forge bioconda::snakemake=6.10
Describe the bug
When using --edit-notebook with a Snakefile with a relative notebook path, a TypeError is raised when Snakemake tries to turn that into an absolute path. It looks like the 'basedir' variable type has changed but snakemake/notebook.py was not updated to reflect this.
Logs
Minimal example
then
snakemake --cores 1 --edit-notebook ../results/graph.eps
(obviously need a working Jupyter environment as well)
Additional context
The text was updated successfully, but these errors were encountered: