ImportError: cannot import name 'soft_unicode' from 'markupsafe'

[miltondp]

Manubot builds in Github Actions started to fail today, with this error in the Build Manuscript step:

bash build/build.sh
  shell: /bin/bash --login {0}
  env:
    GITHUB_PULL_REQUEST_SHA: 2771a1d82d807d[3](https://github.com/greenelab/clustermatch-gene-expr-manuscript/runs/5560545444?check_suite_focus=true#step:8:3)8ffb9d3661000828c1cb82b[4](https://github.com/greenelab/clustermatch-gene-expr-manuscript/runs/5560545444?check_suite_focus=true#step:8:4)9
    SPELLCHECK: true
    BUILD_DOCX: true
    TRIGGERING_SHA_7: 2771a1d
    DEFAULT_BRANCH: main
    DEFAULT_BRANCH_REF: refs/heads/main
    CONDA: /usr/share/miniconda3
    CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
Retrieving and processing reference metadata
Traceback (most recent call last):
  File "/usr/share/miniconda3/envs/manubot/bin/manubot", line 8, in <module>
    sys.exit(main())
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/manubot/command.py", line 271, in main
    function(args)
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/manubot/process/process_command.py", line 32, in cli_process
    from manubot.process.util import prepare_manuscript
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/manubot/process/util.py", line 8, in <module>
    import jinja2
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/jinja2/__init__.py", line 12, in <module>
    from .environment import Environment
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/jinja2/environment.py", line 2[5](https://github.com/greenelab/clustermatch-gene-expr-manuscript/runs/5560545444?check_suite_focus=true#step:8:5), in <module>
    from .defaults import BLOCK_END_STRING
  File "/usr/share/miniconda3/envs/manubot/lib/python3.[7](https://github.com/greenelab/clustermatch-gene-expr-manuscript/runs/5560545444?check_suite_focus=true#step:8:7)/site-packages/jinja2/defaults.py", line 3, in <module>
    from .filters import FILTERS as DEFAULT_FILTERS  # noqa: F401
  File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/jinja2/filters.py", line [13](https://github.com/greenelab/clustermatch-gene-expr-manuscript/runs/5560545444?check_suite_focus=true#step:8:13), in <module>
    from markupsafe import soft_unicode
ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/markupsafe/__init__.py)
Error: Process completed with exit code 1.

Seems to be related to this issue in markupsafe. I fixed the problem by fixing markupsafe version to 2.0.1.

[agitter]

We've seen a few users hitting that issue (#329, manubot/rootstock#459). I'm glad you were able to resolve it.

@dhimmel should we pin an issue here, in the rootstock issues, or at both locations to alert users of this error and provide advice on how to fix it?

[miltondp]

Ops, sorry I didn't see those!

[agitter]

No problem. It's a very common issue, so we should think about how to better advertise the solution.

[dhimmel]

I pinned this issue for manubot/manubot.