--containerize is broken

[mfansler]

Snakemake version

Bug appears to be introduced in v6.8.1.

Describe the bug

Inclusion of any rules with conda: specifications raises a TypeError when running snakemake --containerize.

The introduction of LocalSourceFile class in v6.8.1 appears to be incompatible with the use of os.path.relpath(env.file, os.getcwd()) in the containerize code.

Logs

Traceback (most recent call last):
  File "/opt/conda/envs/snakemake/lib/python3.9/site-packages/snakemake/__init__.py", line 602, in snakemake
    workflow.containerize()
  File "/opt/conda/envs/snakemake/lib/python3.9/site-packages/snakemake/workflow.py", line 1142, in containerize
    containerize(self)
  File "/opt/conda/envs/snakemake/lib/python3.9/site-packages/snakemake/deployment/containerize.py", line 27, in containerize
    envs = sorted(
  File "/opt/conda/envs/snakemake/lib/python3.9/site-packages/snakemake/deployment/containerize.py", line 25, in <lambda>
    relfile = lambda env: os.path.relpath(env.file, os.getcwd())
  File "/opt/conda/envs/snakemake/lib/python3.9/posixpath.py", line 456, in relpath
    path = os.fspath(path)

TypeError: expected str, bytes or os.PathLike object, not LocalSourceFile

Minimal example

Please see snakemake/snakemake-github-action#17.

Additional context

Recommended Solution

The LocalSourceCode class should implement os.PathLike, which entails implementing an __fspath__() method that returns a str. See os.PathLike.

A test case should be added to catch regression.

[johanneskoester]

Fixed with PR #1236. Thanks a lot!