[JOSS Review] tab/space bug

[gbouras13]

Re openjournals/joss-reviews#6062

After #11 copying the Snakefile, I ran:

snakemake --snakefile Snakefile -j 8 --use-conda

which yielded an error (at the bottom of this issue).

It can be fixed by replacing tab with spaces in the line

" --prob-contamination 1e-3"

in the freebayes rule in the varcall.rules file.

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/Users/a1667917/Documents/Reviews/acanthophis/Acanthophis/tests/Snakefile", line 18, in <module>
    rules.varcall.input,
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1347, in include
    code, linemap, rulecount = parse(
                               ^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1307, in parse
    for t, orig_token in automaton.consume():
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 110, in consume
    for t, orig in self.state(token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1212, in python
    for t in self.subautomaton(token.string, token=token).consume():
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 110, in consume
    for t, orig in self.state(token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 773, in block_content
    for t in self.subautomaton(
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 107, in consume
    for token in self.snakefile:
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1238, in __next__
    return next(self.tokens)
           ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/tokenize.py", line 541, in _generate_tokens_from_c_tokenizer
    raise e from None
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/tokenize.py", line 537, in _generate_tokens_from_c_tokenizer
    for info in it:
  File "<string>", line 101
    	"   --skip-coverage 100000"
    	                           ^
TabError: inconsistent use of tabs and spaces in indentation

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1371, in include
    e = update_lineno(e, self.linemaps)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/exceptions.py", line 165, in update_lineno
    ex.lineno = linemaps[ex.filename][ex.lineno]
                ~~~~~~~~^^^^^^^^^^^^^
KeyError: '<string>'

[kdm9]

Now that is a good one 😄. I can't reproduce it from the main branch:

$ git grep -n -- --skip-coverage  
acanthophis/template/workflow/rules/varcall.rules:180:        "   --skip-coverage {params.max_depth}"
$ head -n 180 acanthophis/template/workflow/rules/varcall.rules | tail -n 1 
        "   --skip-coverage {params.max_depth}"
$ head -n 180 acanthophis/template/workflow/rules/varcall.rules | tail -n 1  | xxd
00000000: 2020 2020 2020 2020 2220 2020 2d2d 736b          "   --sk
00000010: 6970 2d63 6f76 6572 6167 6520 7b70 6172  ip-coverage {par
00000020: 616d 732e 6d61 785f 6465 7074 687d 220a  ams.max_depth}".

In English, all the whitespace on that line is spaces (0x20) and not tabs (0x09) in the source code.

when you say coping, I assume you mean cp blah/Snakefile ./ and not copy-pasting within editors?

[gbouras13]

Hi @kdm9 ,

Yes, copying from the command line.

I'm getting back onto this now - will try and new pip install, will let you know how I go.

George

[kdm9]

given in your other issue there is no such error, i assume this is fixed -- please reopen if not