Always prettify modules.json

[muffato]

I got a bit tired of having to re-run prettier after nf-core commands because they change the layout of modules.json (especially around installed_by).

This is a patch to make prettier the default write mode for modules.json

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.43%. Comparing base (c804c1e) to head (a103084).
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[Copilot]

Pull request overview

This PR makes modules.json formatting consistent by defaulting ModulesJson.dump() to run Prettier, so that nf-core commands stop rewriting the file in a non-prettified layout (notably around installed_by).

Changes:

• Change ModulesJson.dump() default to run_prettier=True.
• Update call sites to rely on the new default (dump() instead of dump(run_prettier=True)).
• Add a changelog entry documenting the behavior change.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
nf_core/modules/modules_json.py	Switch default dump behavior to run Prettier and update internal usage.
nf_core/components/install.py	Use the new ModulesJson.dump() default during component install.
CHANGELOG.md	Document “Always prettify modules.json”.

Comments suppressed due to low confidence (1)

nf_core/modules/modules_json.py:1136

• Changing ModulesJson.dump() default to run Prettier will now invoke pre-commit run prettier on every internal call site that previously relied on the default (eg. ModulesJson.update(), remove_entry(), check_up_to_date() and others call self.dump() potentially many times in loops / recursive installs). This can significantly slow down installs/updates and make repeated writes much more expensive. Consider keeping the default False and only running Prettier once at the end of a user-facing command, or refactoring so callers that do multiple updates can disable intermediate writes / formatting and do a single prettified dump at the end.

    def dump(self, run_prettier: bool = True) -> None:
        """
        Sort the modules.json, and write it to file
        """
        # Sort the modules.json
        if self.modules_json is None:
            self.load()
        if self.modules_json is not None:
            self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
            if run_prettier:
                dump_json_with_prettier(self.modules_json_path, self.modules_json)

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[mashehu]

will make some commands slower, but can optimize for that in another PR.

[muffato]

Let me take a look and try to optimise it now.

[muffato]

New version. I'm adding run_prettier=True only to the functions that need it.
I tested installing, updating, and removing a module, patching and unpatching a module, installing, updating, and removing a sub-workflow.

[muffato]

Added support for one scenario: manual install of a module that was already installed via a sub-workflow.

[muffato]

Thank you !