nf-core modules lint fails when using new container registry

[drpatelh]

Description of the bug

Running the following command in a clone of nf-core/modules raises an error because the container isn't reachable. Presumably this is because the docker.registry isn't being factored into the check @adamrtalbot ?

$ nf-core modules lint cat/fastq


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

    nf-core/tools version 2.8 - https://nf-co.re


INFO     Linting modules repo: '.'                                                                                                                                    
INFO     Linting module: 'cat/fastq'                                                                                                                                  

╭─ [✗] 1 Module Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                           ╷                                   ╷                                                                                    │
│ Module name                               │ File path                         │ Test message                                                                       │
│╶──────────────────────────────────────────┼───────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────╴│
│ cat/fastq                                 │ modules/nf-core/cat/fastq/main.nf │ Unable to connect to container URL                                                 │
│                                           ╵                                   ╵                                                                                    │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  24 Tests Passed  │
│ [!]   0 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯
(

[adamrtalbot]

Hmmm we looked at that and fixed it. Could you print verbose here?

[adamrtalbot]

I don't get the same problem:

~/modules$ nf-core modules lint cat/fastq

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

    nf-core/tools version 2.8 - https://nf-co.re


INFO     Linting modules repo: '.'                                                                                                                                                                                  
INFO     Linting module: 'cat/fastq'                                                                                                                                                                                

╭─ [!] 1 Module Test Warning ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                           ╷                                   ╷                                                                                                                                  │
│ Module name                               │ File path                         │ Test message                                                                                                                     │
│╶──────────────────────────────────────────┼───────────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ cat/fastq                                 │ modules/nf-core/cat/fastq/main.nf │ Container versions do not match                                                                                                  │
│                                           ╵                                   ╵                                                                                                                                  │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔]  22 Tests Passed │
│ [!]   1 Test Warning │
│ [✗]   0 Tests Failed │
╰──────────────────────╯

[drpatelh]

Can you pull in the latest changes on master and re-run?

This is what I get with verbose:

$ nf-core --verbose modules lint cat/fastq

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

    nf-core/tools version 2.8 - https://nf-co.re


DEBUG    Failed checking if running in CYGWIN due to: FileNotFoundError(2, 'No such file or directory')                                                    util.py:405
DEBUG    Popen(['git', 'version'], cwd=/home/harshil/.config/nfcore/nf-core/modules, universal_newlines=False, shell=None, istream=None)                    cmd.py:976
DEBUG    Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/harshil/.config/nfcore/nf-core/modules, universal_newlines=True, shell=None, cmd.py:976
         istream=None)                                                                                                                                                
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/home/harshil/.config/nfcore/nf-core/modules, universal_newlines=False, shell=None, istream=None)         cmd.py:976
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/home/harshil/.config/nfcore/nf-core/modules, universal_newlines=False, shell=None, istream=None)     cmd.py:976
DEBUG    Using config file: /home/harshil/.config/nfcore/nf-core/modules/.nf-core.yml                                                                     utils.py:965
DEBUG    Using config file: .nf-core.yml                                                                                                                  utils.py:965
INFO     Linting modules repo: '.'                                                                                                                     __init__.py:213
INFO     Linting module: 'cat/fastq'                                                                                                                   __init__.py:217
DEBUG    Connected to URL: https://depot.galaxyproject.org/singularity/ubuntu:20.04, status_code: 200                                                   main_nf.py:326
DEBUG    Starting new HTTPS connection (1): nf-core:443                                                                                         connectionpool.py:1003
DEBUG    Unable to connect to url 'nf-core/ubuntu:20.04' due to error: HTTPSConnectionPool(host='nf-core', port=443): Max retries exceeded with url:    main_nf.py:331
         /ubuntu:20.04 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fcdbfe047c0>: Failed to establish a new                        
         connection: [Errno -2] Name or service not known'))                                                                                                          
DEBUG    Printing final results                                                                                                                        __init__.py:346

DEBUG    entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                    code.py:10
DEBUG    entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                  fence.py:10
DEBUG    entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                        blockquote.py:13
DEBUG    entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                        hr.py:14
DEBUG    entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                    list.py:97
DEBUG    entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                          reference.py:10
DEBUG    entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                        html_block.py:35
DEBUG    entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                              heading.py:13
DEBUG    entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                            lheading.py:11
DEBUG    entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                          paragraph.py:11
DEBUG    entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                    code.py:10
DEBUG    entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                  fence.py:10
DEBUG    entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                        blockquote.py:13
DEBUG    entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                        hr.py:14
DEBUG    entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                    list.py:97
DEBUG    entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                          reference.py:10
DEBUG    entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                        html_block.py:35
DEBUG    entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                              heading.py:13
DEBUG    entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                            lheading.py:11
DEBUG    entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                          paragraph.py:11
╭─ [✗] 1 Module Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                           ╷                                   ╷                                                                                    │
│ Module name                               │ File path                         │ Test message                                                                       │
│╶──────────────────────────────────────────┼───────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────╴│
│ cat/fastq                                 │ modules/nf-core/cat/fastq/main.nf │ Unable to connect to container URL                                                 │
│                                           ╵                                   ╵                                                                                    │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  24 Tests Passed  │
│ [!]   0 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯

[adamrtalbot]

Ah it's quay.io but not biocontainers. Darn, I thought I had tested this.