Please format your code with black: black snakemake tests/*.py.

brrrr, I consider this failure unrelated to the PR:

=========================== short test summary info ============================
FAILED tests/tests.py::test_paramspace - AssertionError: wrong result produced for file 'results/sep/simulations/alpha_is_2/beta_is_0.0/gamma_is_3.9.tsv':
------found------
{'alpha': np.int64(2), 'beta': np.float64(0.0), 'gamma': np.float64(3.9)}
-----expected-----
{'alpha': 2, 'beta': 0.0, 'gamma': 3.9}
-----------------
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
========= 1 failed, 22 passed, 306 deselected, 111 warnings in 51.20s ==========

But, of course, the rest will not run.

Seems like the floats are not correctly converted into plain string representations. A fix would be greatly appreciated, I don't have any time in the next days.

Already thought, that a fix might be trivial, but whether I will find the time ... Let's see.

edit: Or perhaps not so trivial - doubt that the actual code needs adaption, because np.float is quit ok and panda-ish. I'll give changing the expected results a try ...

Definitively not trivial. We could:

• change the expected results to meet the code output.
• change the test.
• change the actual code. I found the spot, it's a tiny lambda function, which could be extended.

All three options sound like tinkering to me.

Walkthrough

The recent changes enhance the validation logic for naming patterns in the Snakemake linter. By modifying the regular expression for NAME_PATTERN, the update prevents strings from ending with a '+' character, addressing potential user intent while ensuring more accurate name validation. Additionally, the change suggests accommodating simpler regex expressions for varied separator needs, promoting flexibility in file naming conventions.

Changes

Poem

🐇 In the land of code, where rabbits hop,
A regex change makes name checks pop!
No trailing '+' to cause a fright,
With patterns now clearer, everything's right!
Hopping through linting, we dance with glee,
Celebrating changes, just wait and see! 🎉

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Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

Thank you, @johanneskoester — this PR can now possibly be merged. The coderabit summarizes my intent perfectly. ;-) What do you think?

Thank you!

Thank you for the swift review!

I'm a bit confused here, as a long-running snakefile now produces a new warning:
"/path/to/snakefile:666: SyntaxWarning: invalid escape sequence '\d'"
The line number could not be easily matched back in the snakefile, but somewhere I do have such a line:

output:
    "output/outputfile_{index,\d+}.out"

This is to limit the wildcard matching to only digits. Should I ignore the warning? Should I update the rules? Should I provide more detail?

Thanks!

Thanks for reporting this!!!

You may ignore the warning. I will not. Can you please indicate the entire rule? Is there, perhaps, more detail to the warning message?

Actually, this PR only affected the linter, not the Snakemake core. So, this might be totally unrelated. But we should sort this out, before perhaps opening a full issue.

Thanks for reporting this!!!

You may ignore the warning. I will not. Can you please indicate the entire rule? Is there, perhaps, more detail to the warning message?

Actually, this PR only affected the linter, not the Snakemake core. So, this might be totally unrelated. But we should sort this out, before perhaps opening a full issue.

It's quite reproducible on my side:

FILE: snaketest

rule plus:                              
    output:                             
        "test{num,\d+}.txt"             
    shell:                              
        '''                             
        touch test{wildcards.num}.txt   
        '''                             

CONSOLE

$ snakemake -s snaketest -n -p --verbose test000.txt
snaketest:4: SyntaxWarning: invalid escape sequence '\d'
  shell:
Building DAG of jobs...
shared_storage_local_copies: True
remote_exec: False
Job stats:
job      count
-----  -------
plus         1
total        1

[Thu Aug 15 20:16:51 2024]
rule plus:
    output: test000.txt
    jobid: 0
    reason: Missing output files: test000.txt
    wildcards: num=000
    resources: tmpdir=<TBD>


        touch test000.txt

... ...

$ conda list | grep snake
# packages in environment at /home/conda/snakemake_py312:
snakemake-executor-plugin-cluster-generic 1.0.9              pyhdfd78af_0    bioconda
snakemake-interface-common 1.17.2             pyhdfd78af_0    bioconda
snakemake-interface-executor-plugins 9.2.0              pyhdfd78af_0    bioconda
snakemake-interface-report-plugins 1.0.0              pyhdfd78af_0    bioconda
snakemake-interface-storage-plugins 3.2.3              pyhdfd78af_0    bioconda
snakemake-minimal         8.18.0             pyhdfd78af_0    bioconda

The execution judging by the shell command is not affected.

Same file and command with Snakemake 8.16.0 does not show this warning.

Snakemake is a very helpful package for me. Thanks a lot !

Ah, yes, this alone is a faulty syntax expression. Try

output:
     r"test{num,\d+}.txt"

Ah, yes, this alone is a faulty syntax expression. Try

output:
     r"test{num,\d+}.txt"

That indeed fixed the warning. Thanks.

Ah, yes, this alone is a faulty syntax expression. Try

output:
     r"test{num,\d+}.txt"

Still I suggest the documentation to be refined. Currently it's still showing this misleading/faulty syntax...

ah, thanks. It's a Python thing. Will fix the docs.