nf-core lint: Badge Warning

[sguizard]

Description of the bug

nf-core lint gives a warning about badges:
readme: README did not have a Nextflow minimum version badge.

I tried to match the badge code to the nextflowVersion, but the warning is still here.

-> nextflow.config:
nextflowVersion = '!>=21.10.3'
-> README.md (original)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
-> README.md (matching nextflow.config)
[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-!%3E%3D21.10.3-23aa62.svg)](https://www.nextflow.io/)

Command used and terminal output

╰─>$ nf-core lint

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.4.1 - https://nf-co.re


INFO     Testing pipeline: .                                                                                                                                                                          __init__.py:244

╭─ [!] 3 Pipeline Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                   │
│ readme: README did not have a Nextflow minimum version badge.                                                                                                                                                     │
│ pipeline_todos: TODO string in meta.yml: #Delete / customise this example output                                                                                                                                  │
│ pipeline_todos: TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release                                                                                                               │
│                                                                                                                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 203 Tests Passed  │
│ [?]   0 Tests Ignored │
│ [!]   3 Test Warnings │
│ [✗]   0 Tests Failed  │
╰───────────────────────╯

System information

Nextflow version: 21.10.3
Hardware: Desktop
Executor: local
OS: Kubuntu
Version of nf-core/tools: 2.4.1
Python version: 3.9.7

[fabianegli]

I believe this has been fixed in #1590

[sguizard]

It's different, here the error is on signs before the version number.
The badge shows ≥21.10.3, the config file contains !>=21.10.3.
@ewels suggests updating the regexp

tools/nf_core/lint/readme.py

Line 43 in d0ab20e

nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-%E2%89%A5([\d\.]+)-23aa62\.svg\?labelColor=000000\)\]\(https://www\.nextflow\.io/\)"

[fabianegli]

So this would then be a "lower than" Nextflow version instead of a minimal version. Couldn't "!>=" just be "<".

Changes might be warranted beyond the regex. e.g. the version check failure message text.

[ewels]

I think that the meaning of the the additional ! is that the pipeline will refuse to run with lower versions of Nextflow, instead of just throwing a warning.

For sure the best fix would be to check both the version number and the operator throughout the pipeline. But in practice it's basically always going to be either >= or !>= I think and they're super similar. So in terms of an easier fix just making the regex more flexible in this location is the simplest solution I think.

@sguizard did you update the readme badge manually or was this done by nf-core bump-version?

[sguizard]

I modified the readme manually,
The problem might also come from the sign.
The badge use ≥ and the readme use >=.

[fabianegli]

Yes, it's both, the '!' and the sign.

$ python3 -c 'from urllib.parse import quote; print(quote("!>="))'
%21%3E%3D
$ python3 -c "from urllib.parse import unquote; print(unquote('%21%3E%3D'))"
!>=
$ python3 -c 'from urllib.parse import quote; print(quote("!≥"))'
%21%E2%89%A5
$ python3 -c "from urllib.parse import unquote; print(unquote('%21%E2%89%A5'))"
!≥

[ewels]

Lets keep things simple and just tolerate all the different symbols in the regex and check only the number 👍🏻

[ErikDanielsson]

Closing due to merge of #1618