Bug 2300832 - Review Request: spec2nii - Multi-format in vivo MR spectroscopy conversion to NIFTI
Summary: Review Request: spec2nii - Multi-format in vivo MR spectroscopy conversion to...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Ankur Sinha (FranciscoD)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: fedora-neuro, NeuroFedora
TreeView+ depends on / blocked
 
Reported: 2024-07-29 18:57 UTC by Ben Beasley
Modified: 2024-08-23 01:49 UTC (History)
2 users (show)

Fixed In Version:
Clone Of:
Environment:
Last Closed: 2024-08-13 02:24:05 UTC
Type: ---
Embargoed:
sanjay.ankur: fedora-review+


Attachments (Terms of Use)

Description Ben Beasley 2024-07-29 18:57:26 UTC
Spec URL: https://music.fedorapeople.org/spec2nii.spec
SRPM URL: https://music.fedorapeople.org/spec2nii-0.8.2-1.fc40.src.rpm

Description:

A program for multi-format conversion of in vivo MRS to the NIfTI-MRS format
(https://github.com/wexeee/mrs_nifti_standard).

This program was inspired by the imaging DICOM to NIfTI converter dcm2niix,
developed by Chris Rorden. All MRS(I) orientations are tested with images
converted using dcm2niix.

Fedora Account System Username: music

Until the next successful Rawhide compose, it will be necessary to pass --mock-options=--enablerepo=local to the fedora-review tool.

This is useful in its own right, and it is a dependency for BIDScoin, https://pagure.io/neuro-sig/NeuroFedora/issue/500. It will be a neuro-sig package.

Comment 1 Ankur Sinha (FranciscoD) 2024-07-31 11:03:23 UTC
Hi Ben,

Going through this now. Quick question: the pypi source does seem to include tests and upstream does run them in their CI:

https://github.com/wtclarke/spec2nii/blob/master/.github/workflows/push_pr.yml

but they're not run during the build (a missing `%bcond tests 1` perhaps?): should we try enabling them to see if they run?

Another minor note: is it worth trying to generate the man pages as part of the build (as we do using help2man) if possible so that one doesn't have to manually check/update them for each release?

I'll put it through fedora-review now and do a complete review.

Cheers,
Ankur

Comment 2 Ben Beasley 2024-07-31 15:43:20 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #1)
> Hi Ben,
> 
> Going through this now. Quick question: the pypi source does seem to include
> tests and upstream does run them in their CI:
> 
> https://github.com/wtclarke/spec2nii/blob/master/.github/workflows/push_pr.
> yml
> 
> but they're not run during the build (a missing `%bcond tests 1` perhaps?):
> should we try enabling them to see if they run?

Absolutely! I am shocked I missed that the tests were not enabled. I’ll get them working and upload a new submission.

> Another minor note: is it worth trying to generate the man pages as part of
> the build (as we do using help2man) if possible so that one doesn't have to
> manually check/update them for each release?

I could do that, but the hand-written ones are a bit nicer, I can easily have cross-references, and it’s a bit fussy to run help2man for each subcommand. Given that I don’t expect a lot of change upstream, I’m going to stick with the hand-written ones for now. If upstream were fast-moving, I would work harder at automating this. I do have that problem with uv, and I’m looking into a way to script discovery and generation of a collection of man pages for a tree of subcommands, but it’s a bit of a fussy thing to do nicely.

Comment 3 Ben Beasley 2024-07-31 19:55:09 UTC
I went through the exercise of running the tests locally, then omitted them from the final submission because the necessary data file archive was excessively large. There is at least an import-only smoke test now.

Spec URL: https://music.fedorapeople.org/20240731/spec2nii.spec
SRPM URL: https://music.fedorapeople.org/20240731/spec2nii-0.8.2-1.fc40.src.rpm

Comment 4 Fedora Review Service 2024-08-01 01:08:43 UTC
Copr build:
https://copr.fedorainfracloud.org/coprs/build/7810561
(succeeded)

Review template:
https://download.copr.fedorainfracloud.org/results/@fedora-review/fedora-review-2300832-spec2nii/fedora-rawhide-x86_64/07810561-spec2nii/fedora-review/review.txt

Found issues:

- License file VESPA_LICENSE is not marked as %license
  Read more: https://docs.fedoraproject.org/en-US/packaging-guidelines/LicensingGuidelines/#_license_text

Please know that there can be false-positives.

---
This comment was created by the fedora-review-service
https://github.com/FrostyX/fedora-review-service

If you want to trigger a new Copr build, add a comment containing new
Spec and SRPM URLs or [fedora-review-service-build] string.

Comment 5 Ankur Sinha (FranciscoD) 2024-08-12 13:46:57 UTC
This looks good now. XXX APPROVED XXX

Comment 6 Ben Beasley 2024-08-13 02:02:44 UTC
Thank you for the review!

https://release-monitoring.org/project/138096/

Comment 7 Fedora Admin user for bugzilla script actions 2024-08-13 02:03:23 UTC
The Pagure repository was created at https://src.fedoraproject.org/rpms/spec2nii

Comment 8 Fedora Update System 2024-08-13 02:20:40 UTC
FEDORA-2024-fb3846845c (spec2nii-0.8.2-1.fc41) has been submitted as an update to Fedora 41.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-fb3846845c

Comment 9 Fedora Update System 2024-08-13 02:24:05 UTC
FEDORA-2024-fb3846845c (spec2nii-0.8.2-1.fc41) has been pushed to the Fedora 41 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 10 Fedora Update System 2024-08-14 13:34:03 UTC
FEDORA-2024-2a5ccdf2c1 (spec2nii-0.8.3-1.fc40) has been submitted as an update to Fedora 40.
https://bodhi.fedoraproject.org/updates/FEDORA-2024-2a5ccdf2c1

Comment 11 Fedora Update System 2024-08-15 02:37:03 UTC
FEDORA-2024-2a5ccdf2c1 has been pushed to the Fedora 40 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf install --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-2a5ccdf2c1 \*`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-2a5ccdf2c1

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 12 Fedora Update System 2024-08-23 01:49:15 UTC
FEDORA-2024-2a5ccdf2c1 (spec2nii-0.8.3-1.fc40) has been pushed to the Fedora 40 stable repository.
If problem still persists, please make note of it in this bug report.


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