stack trace using nf-core modules test
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bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
Attempting to test a module with nf-core modules test results in a stack trace.
Command used and terminal output
% nf-core modules test krakenuniq/build
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 4.0.2 - https://nf-co.re
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/bin/nf-core:10 in │
│ <module> │
│ │
│ 7 │
│ 8 if __name__ == '__main__': │
│ 9 │ sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) │
│ ❱ 10 │ sys.exit(run_nf_core()) │
│ 11 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/nf_core/__main__.py:130 in run_nf_core │
│ │
│ 127 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 128 │ │ stderr.print("\n") │
│ 129 │ # Launch the click cli │
│ ❱ 130 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 131 │
│ 132 │
│ 133 @tui(command="interface", help="Launch the nf-core interface") │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/rich_click/rich_command.py:402 in __call__ │
│ │
│ 399 │ │ # Include this here because I run into a false warning │
│ 400 │ │ # in the PyCharm IDE otherwise; for some reason PyCharm doesn't │
│ 401 │ │ # seem to think RichGroups are callable. (No issues with Mypy, though.) │
│ ❱ 402 │ │ return super().__call__(*args, **kwargs) │
│ 403 │ │
│ 404 │ @overload │
│ 405 │ def command(self, __func: Callable[..., Any]) -> RichCommand: ... │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/core.py:1442 in __call__ │
│ │
│ 1439 │ │
│ 1440 │ def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 1441 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1442 │ │ return self.main(*args, **kwargs) │
│ 1443 │
│ 1444 │
│ 1445 class _FakeSubclassCheck(type): │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/rich_click/rich_command.py:216 in main │
│ │
│ 213 │ │ try: │
│ 214 │ │ │ try: │
│ 215 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 216 │ │ │ │ │ rv = self.invoke(ctx) │
│ 217 │ │ │ │ │ if not standalone_mode: │
│ 218 │ │ │ │ │ │ return rv │
│ 219 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/core.py:1830 in invoke │
│ │
│ 1827 │ │ │ │ super().invoke(ctx) │
│ 1828 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1829 │ │ │ │ with sub_ctx: │
│ ❱ 1830 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1831 │ │ │
│ 1832 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1833 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/core.py:1830 in invoke │
│ │
│ 1827 │ │ │ │ super().invoke(ctx) │
│ 1828 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1829 │ │ │ │ with sub_ctx: │
│ ❱ 1830 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1831 │ │ │
│ 1832 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1833 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/core.py:1226 in invoke │
│ │
│ 1223 │ │ │ echo(style(message, fg="red"), err=True) │
│ 1224 │ │ │
│ 1225 │ │ if self.callback is not None: │
│ ❱ 1226 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1227 │ │
│ 1228 │ def shell_complete(self, ctx: Context, incomplete: str) -> list[CompletionItem]: │
│ 1229 │ │ """Return a list of completions for the incomplete value. Looks │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/core.py:794 in invoke │
│ │
│ 791 │ │ │
│ 792 │ │ with augment_usage_errors(self): │
│ 793 │ │ │ with ctx: │
│ ❱ 794 │ │ │ │ return callback(*args, **kwargs) │
│ 795 │ │
│ 796 │ def forward(self, cmd: Command, /, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 797 │ │ """Similar to :meth:`invoke` but fills in default keyword │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/click/decorators.py:34 in new_func │
│ │
│ 31 │ """ │
│ 32 │ │
│ 33 │ def new_func(*args: P.args, **kwargs: P.kwargs) -> R: │
│ ❱ 34 │ │ return f(get_current_context(), *args, **kwargs) │
│ 35 │ │
│ 36 │ return update_wrapper(new_func, f) │
│ 37 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/nf_core/__main__.py:1292 in command_modules_test │
│ │
│ 1289 │ """ │
│ 1290 │ if verbose: │
│ 1291 │ │ ctx.obj["verbose"] = verbose │
│ ❱ 1292 │ modules_test(ctx, tool, directory, no_prompts, update, once, profile) │
│ 1293 │
│ 1294 │
│ 1295 # nf-core modules lint │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/nf_core/commands_modules.py:231 in modules_test │
│ │
│ 228 │ │ │ verbose=ctx.obj["verbose"], │
│ 229 │ │ │ profile=profile, │
│ 230 │ │ ) │
│ ❱ 231 │ │ module_tester.run() │
│ 232 │ except (UserWarning, LookupError) as e: │
│ 233 │ │ log.critical(e) │
│ 234 │ │ sys.exit(1) │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/nf_core/components/components_test.py:90 in run │
│ │
│ 87 │ │
│ 88 │ def run(self) -> None: │
│ 89 │ │ """Run build steps""" │
│ ❱ 90 │ │ self.check_inputs() │
│ 91 │ │ os.environ["NFT_DIFF"] = "pdiff" # set nf-test differ to pdiff to get a better │
│ 92 │ │ os.environ["NFT_DIFF_ARGS"] = ( │
│ 93 │ │ │ "--line-numbers --expand-tabs=2" # taken from https://code.askimed.com/nf-t │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/nf_core/components/components_test.py:150 in check_inputs │
│ │
│ 147 │ │ │ │ │ "message": "Choose container software to run the test with", │
│ 148 │ │ │ │ │ "choices": ["Docker", "Singularity", "Conda"], │
│ 149 │ │ │ │ } │
│ ❱ 150 │ │ │ │ answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcor │
│ 151 │ │ │ │ profile = answer["profile"].lower() │
│ 152 │ │ │ │ os.environ["PROFILE"] = profile │
│ 153 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/questionary/prompt.py:221 in unsafe_prompt │
│ │
│ 218 │ │ if missing_args: │
│ 219 │ │ │ raise PromptParameterException(missing_args[0]) │
│ 220 │ │ │
│ ❱ 221 │ │ question = create_question_func(**_kwargs) │
│ 222 │ │ │
│ 223 │ │ answer = question.unsafe_ask(patch_stdout) │
│ 224 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/questionary/prompts/select.py:185 in select │
│ │
│ 182 │ │ │
│ 183 │ │ return tokens │
│ 184 │ │
│ ❱ 185 │ layout = common.create_inquirer_layout(ic, get_prompt_tokens, **kwargs) │
│ 186 │ │
│ 187 │ bindings = KeyBindings() │
│ 188 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/questionary/prompts/common.py:513 in create_inquirer_layout │
│ │
│ 510 │ ps: PromptSession = PromptSession( │
│ 511 │ │ get_prompt_tokens, reserve_space_for_menu=0, **kwargs │
│ 512 │ ) │
│ ❱ 513 │ _fix_unecessary_blank_lines(ps) │
│ 514 │ │
│ 515 │ validation_prompt: PromptSession = PromptSession( │
│ 516 │ │ bottom_toolbar=lambda: ic.error_message, **kwargs │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-modules-mahesh/.pixi/envs/default/lib/python3.13/site │
│ -packages/questionary/prompts/common.py:493 in _fix_unecessary_blank_lines │
│ │
│ 490 │ default_container = ps.layout.container │
│ 491 │ │
│ 492 │ default_buffer_window = ( │
│ ❱ 493 │ │ default_container.get_children()[0].content.get_children()[1].content # type: i │
│ 494 │ ) │
│ 495 │ │
│ 496 │ assert isinstance(default_buffer_window, Window) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
AttributeError: 'VSplit' object has no attribute 'content'
System information
Pixi version: 0.68.0
Nextflow version: 26.04.0
Hardware: MacBookPro18,2
Executor: local (default)
OS: Darwin 25.4.0
nf-core/tools: 4.0.2
Python version: 3.13.3
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at nf_core/main.py, particularly command_modules_test around the traceback location, and reproduce the failure with nf-core modules test krakenuniq/build. Trace the command handling to identify why it emits a stack trace; done means the command completes or reports the problem without an unhandled traceback.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, testing
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100