feat: nf-core modules bump-version supports specifying the toolkit #3608
Conversation
Tools like picard, fgbio, and samtools all have sub-commands. It is onerous to have to update them all individually using nf-core modules bump-version. This change allows the module name to update to have a trailing forward slash, which will be interpreted as specifying that all subcommands should be updated. E.g. nf-core modules bump-version samtools/
This comment was marked as outdated.
This comment was marked as outdated.
2753566 to
2052819
Compare
2052819 to
a5b9730
Compare
nf_core/modules/bump_versions.py
Outdated
| module: Union[str, None] = None, | ||
| all_modules: bool = False, | ||
| show_uptodate: bool = False, | ||
| _dryrun: bool = False, |
There was a problem hiding this comment.
adding dryrun was much easier to mock and test, so I went this route.
There was a problem hiding this comment.
good idea in general. I added it as a parameter
Codecov ReportAttention: Patch coverage is
☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
|
@mashehu thank-you for the review, I've added a test and improved a few others while I'm there. |
|
hinking about it: |
|
@mashehu that makes sense, but is difficult in the current state of implementation where we have a list of component names to filter against, not directories. An alternative would be to check for an exact matching component name, and if not found, append a |
|
I tried to implement the more general matching approach, could you have a look @nh13 ? |
| self, | ||
| module: Optional[str] = None, | ||
| all_modules: bool = False, | ||
| show_up_to_date: bool = False, |
There was a problem hiding this comment.
Since this method is public, the API has changed. Does this require a major version change as per semver?
There was a problem hiding this comment.
Nope, we didn't break any backwards functionality. This will be in 3.4.0
There was a problem hiding this comment.
The function signature changed, and the function is public.
There was a problem hiding this comment.
yes, but I don't know anybody who uses nf-core/tools not in CLI mode, so no breaking changes there (we are not ultra-strict semveristas here 🙂)
Tools like picard, fgbio, and samtools all have sub-commands. It is onerous to have to update them all individually using nf-core modules bump-version. This change allows the module name to update to have a trailing forward slash, which will be interpreted as specifying that all subcommands should be updated. E.g. nf-core modules bump-version samtools/
PR checklist
CHANGELOG.mdis updateddocsis updated