snakefmt corrupts heredoc string

snakefmt v0.4.0 reformats this rule:

rule one:
    output:
        out_file="out.txt",
    shell:
        r"""
cat <<'EOF'> tmp.txt

touch {output}

EOF
bash tmp.txt
        """

into:

rule one:
    output:
        out_file="out.txt",
    shell:
        r"""
        cat <<'EOF'> tmp.txt

        touch {output}

        EOF
        bash tmp.txt
        """

the reformatted indentation makes the heredoc invalid since bash expects the closing EOF at the start of the line. When execute it I get:

snakemake -p -j 1
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job      count    min threads    max threads
-----  -------  -------------  -------------
all          1              1              1
one          1              1              1
total        2              1              1

Select jobs to execute...

[Tue Oct 26 09:06:30 2021]
rule one:
    output: out.txt
    jobid: 1
    resources: tmpdir=/tmp


        cat <<'EOF'> tmp.txt

        touch out.txt

        EOF
        bash tmp.txt
        
/bin/bash: line 6: warning: here-document at line 1 delimited by end-of-file (wanted `EOF')
Waiting at most 5 seconds for missing files.

---

I tried to upgrade to snakefmt 0.4.4 using mamba. This maybe a separate issue, I get:

mamba update snakefmt # Completes OK and installs 0.4.4

snakefmt -h
Traceback (most recent call last):
  File "/home/dario/miniconda3/envs/tritume/bin/snakefmt", line 6, in <module>
    from snakefmt.snakefmt import main
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/snakefmt/snakefmt.py", line 9, in <module>
    from black import get_gitignore
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/black/__init__.py", line 48, in <module>
    from black.files import find_project_root, find_pyproject_toml, parse_pyproject_toml
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/black/files.py", line 26, in <module>
    from black.handle_ipynb_magics import jupyter_dependencies_are_installed
  File "/home/dario/miniconda3/envs/tritume/lib/python3.6/site-packages/black/handle_ipynb_magics.py", line 15, in <module>
    from typing_extensions import TypeGuard
ImportError: cannot import name 'TypeGuard'

[dariober]

@bricoletc :

some regexp capturing EOF, e.g. "<<['"]EOF

I suspect that is going to be tricky because EOF is not a special keyword. You can delimit the heredoc with any string you like (well, not any string…). Other tricky cases could be like:

shell:
    """
    python -c "
    ...some properly indented python code here. Possibly containing raw-formatted strings...?
    "
    """

Personally, I would leave the content of the strings alone and just re-align the opening and closing quotes.

[dariober]

I would be happy for r-strings to be left alone (I got the habit of always using r-strings for shell directives unless required otherwise) but I would still consider it a bug. A user may write a heredoc without r-formatting and find it broken after snakefmt.