Error running `resqui` against kallisto GitHub Repo

[kmpf]

Hi there,

I did run:

resqui -u git@github.com:pachterlab/kallisto.git -v

and got this error:

Loading default configuration.
GitHub API token ✖
Repository URL: https://github.com/pachterlab/kallisto.git
Project name: kallisto
Author: Pall Melsted
Email: pmelsted@gmail.com
Version: v0.52.0
Branch, tag or commit hash: 4e9f29cf3b021260415430c057a22469ca081391
Checking indicators ...
  has_license/HowFairIs (0.0s): Traceback (most recent call last):
  File "~/miniconda3/bin/resqui", line 7, in <module>
    sys.exit(resqui())
             ~~~~~~^^
  File "~/miniconda3/lib/python3.13/site-packages/resqui/cli.py", line 209, in resqui
    results = getattr(plugin_instance, plugin_method)(url, branch_hash_or_tag)
  File "~/miniconda3/lib/python3.13/site-packages/resqui/plugins/howfairis.py", line 31, in has_license
    result = self.executor.execute(script)
  File "~/miniconda3/lib/python3.13/site-packages/resqui/executors/python.py", line 62, in execute
    return subprocess.run(
           ~~~~~~~~~~~~~~^
        [f"{self.temp_dir}/bin/python", "-c", script],
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<2 lines>...
        env=env,
        ^^^^^^^^
    )
    ^
  File "~/miniconda3/lib/python3.13/subprocess.py", line 554, in run
    with Popen(*popenargs, **kwargs) as process:
         ~~~~~^^^^^^^^^^^^^^^^^^^^^^
  File "/home/hubert/miniconda3/lib/python3.13/subprocess.py", line 1039, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                        pass_fds, cwd, env,
                        ^^^^^^^^^^^^^^^^^^^
    ...<5 lines>...
                        gid, gids, uid, umask,
                        ^^^^^^^^^^^^^^^^^^^^^^
                        start_new_session, process_group)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "~/miniconda3/lib/python3.13/subprocess.py", line 1908, in _execute_child
    env_list.append(k + b'=' + os.fsencode(v))
                               ~~~~~~~~~~~^^^
  File "<frozen os>", line 850, in fsencode
TypeError: expected str, bytes or os.PathLike object, not NoneType

What did I do wrong? Some options missing in the call?

Also the error message does not really help me to identify the error.

[vuillaut]

Hi

Please retry using

resqui -u https://github.com/pachterlab/kallisto -t <GITUB_TOKEN> 

[tamasgal]

Indeed, it looks like an older version of resqui which does not print an explicit error that the GitHub token is missing (the red GitHub API token ✖ is the only indicator)

As @vuillaut suggested, either rerun with a token or update to get a more descriptive error and then rerun with a token 😉

[kmpf]

Thanks for your replies. Just to clarify, I do not have any privilegs for the repository I want to analyse. That is the use case I am mainly interested in. Of course I could fork the project and then provide the API token, but that looks like overkill to me. Is there a way resqui can be used for my use case?

Or did I get something wrong? Sorry, for the confusion.

[kmpf]

Additional info: The version I was using for the above mentioned error was resqui-0.1.8.dev2+g182a1021f from the main branch of the repo. But I received a similar error using v0.1.7. In both cases the error was a python stacktrace.

[tamasgal]

There is a confusion. You need to generate your own API token which the plugins can use to access the otherwise limited GitHub API. No need to fork anything, you can use that key for multiple projects.

[kmpf]

Thanks for the clarification. By using one of my personal access token, it ran without errors. Which is most important to me. Still the issue with the error message remains. Should I open a new issue for that and close this one?

[tamasgal]

The unclear error was fixed in #40 after it was reported in #39 but i did not get any feedback and therefor not merged it.

I just merged that into main, can you try with that again and check if it's better now?

[kmpf]

Looks nice now:

$ resqui -u https://github.com/pachterlab/kallisto
Loading default configuration.
GitHub API token ✖
Repository URL: https://github.com/pachterlab/kallisto
Project name: kallisto
Author: Pall Melsted
Email: pmelsted@gmail.com
Version: v0.52.0
Branch, tag or commit hash: 4e9f29cf3b021260415430c057a22469ca081391
Checking indicators ...
  has_license/HowFairIs |⚠️  missing GITHUB_ACTION_TOKEN (skipping its indicators)
  has_citation/CFFConvert (0.3s): ✖
  has_ci_tests/OpenSSFScorecard |⚠️  missing GITHUB_ACTION_TOKEN (skipping its indicators)
  human_code_review_requirement/OpenSSFScorecard |⚠️  missing GITHUB_ACTION_TOKEN (skipping its indicators)
  has_published_package/OpenSSFScorecard |⚠️  missing GITHUB_ACTION_TOKEN (skipping its indicators)
  has_no_security_leak/Gitleaks (10.7s): ✖
Summary has been written to resqui_summary.json
Publishing summary ✖ Missing authentication token

Thanks a lot for fixing. I close the issue.