Containerize Fails with Conda Envs

[mfansler]

The containerize task does not work when Conda environments are specified. I put together a demonstration repository. Error has to do with os.fspath not recognizing the type (LocalSourceFile) of the Conda environment file.

My local Snakemake v6.8 (Python 3.9.7, CentOS 7) works just fine.

---

Reproducible Example

Snakefile

rule all:
  input: "python-version.txt"

rule py_emit_version:
  output: "python-version.txt"
  conda: "envs/py39.yaml"
  shell:
    """
    python -VV > {output}
    """

envs/py39.yaml

name: py39
channels:
  - conda-forge
  - nodefaults
dependencies:
  - python=3.9

.github/workflows/snakemake-containerize.yaml

name: Snakemake Containerize

on:
  workflow_dispatch:

jobs:
  Snakemake:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2

      - name: Snakemake dry run
        uses: snakemake/snakemake-github-action@v1.23.0
        with:
          directory: '.'
          args: '-np'

      - name: Create container file
        uses: snakemake/snakemake-github-action@v1.23.0
        with:
          directory: '.'
          task: 'containerize'

      - name: Print Dockerfile
        run: |
          cat Dockerfile

Error

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

[mfansler]

This is fixed with Snakemake release v6.11.0.