Update of Slicer issue tracker

Also Github has issue templates which could encourage detailed steps to reproduce, platform, expected behavior, etc. which would be similar to the header fields on the Mantis Tracker. ITK is also using github issue templates to encourage users to provide details about bugs/features/etc. See ITK Issue Template.

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Since mantis stores issues in a structured way (not just somewhat encouraging structure by offering a template), I find it much more efficient to locate issues in Mantis compared to GitHub.

However, I agree that probably GitHub’s issue tracker would be sufficient for Slicer, and definitely more accessible to users and developers, because most people are already familiar with GitHub, they don’t need to register yet another account, and the issue tracker integrates well with other GitHub features.

I think we should just first release Slicer-4.10.1, then move Slicer’s official repository to GitHub (still SVN is the official repository) and then switch to GitHub’s issue tracker.


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Any ETA on enabling issues in github? Even if not official yet, would be nice to report bugs/issues there.

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It would be nice to switch to github repository and issue tracker at the same time, to be able to leverage all the benefits of integration between github tools. However, there is no strict dependency, so we could start using github’s issue tracker for new issues any time.

@jcfr what is the planned date for switching to git?

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This is the next major Slicer task on my list, we should expect the transition to happen in the next few weeks.


@phcerdan would this timeline work for you? Can you submit issues to issues.slicer.org?

Yesterday, I tried to register to the bug tracking system without success, I didn’t get back an email that probably should have contained my password. Following the advice of @lassoan, I will post some issues I encountered in this thread.

Bug report
Summary: Rulers that should be hidden are always visible after loading a scene
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

  • open slicer (standard layout)
  • create a ruler somewhere
  • hide it by clicking on the eye of the ruler in the Annotations module UI
  • save the scene as mrb
  • close scene (via file menu)
  • load the mrb
    ruler is now visible in slice viewers, however the eye in the Annotations module UI is closed
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Bug report
Summary: Missing repeated question for saving scene when ending slicer
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

  • open slicer (standard layout)
  • create a ruler somewhere (or make any other edit)
  • click File --> Exit
  • the confirmation dialog appears --> click ‘Cancel exit’
  • click File --> Exit
    program ends without any further question to save the scene

This code causes the immediate exit:

(And another one in this post as I cannot post more than three consecutive posts):

Bug report
Summary: Broken marker placement cursor in non-standard layouts
Environment: 3DSlicer 4.10.2, Windows 10

Steps to reproduce:

  • open slicer (standard layout)
  • switch to another layout (e.g. Compare --> 2 viewers)
  • click on the tool button to create a fiducial
  • move cursor over the slice views
    the cursor does not change to the markup insertion cursor

this is caused by this code:

–> lines 544 and 561 should say continue;

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Hi -

I checked and your account exists on issues.slicer.org under the email you used. I had it send a password reset link so let’s see if that works.

Anyway thanks for the reports. :+1: One question: have you tried the nightly builds? The markups have gotten a lot of improvements.

I tried the issue with the ruler not being visible after loading a scene also with the nighlty build from 2019-08-29. It was the same there. Regarding the other two issues, the cited source code is unchanged to version 4.10.2 and I debugged those issues, so I assume they are still relevant.

So far no email received.
Please remove my email address from your previous post - thanks!

Sorry about that!

Not sure what’s up with that - I got the email that said your account was created. (I guess you checked your spam folder :wink:).

Anyway looks like you’ve found some good fixes. The best way forward might be to put them in the form of a github pull request so people can easily test and comment.

Regarding the rulers they have always been a bit finicky and that’s why people have been moving functionality over to markups.

Thanks for the error reports!

@jcfr I know we wanted to wait with switching to github’s issue tracker until we fully migrate Slicer to github, but it seems that the git migration takes really long time. Since Mantis has serious issues (multiple reports of people cannot sign up, we don’t get email notifications of new bugs, losing long bug reports because of server timeout, etc.), I think we could start accepting bug reports via GitHub now.

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Right now, users cannot sign up at issues.slicer.org and problems end up just reported here at the forum and if we cannot immediately address them then they may become forgotten.

Is there any objection to enabling the issue tracker for https://github.com/Slicer/Slicer/ on github?


users cannot sign up at issues.slicer.org

Could you remind me what is the problem ? We should then report the problem to @freephile so that he can have a look.

I’m not sure if it’s worth spending more time with fixing Mantis. Just a couple of issues that come to my mind:

  • Users are not familiar with Mantis but they know and use github
  • Many people already have github account and prefer not to create another just to report issues or participate in discussion on Mantis
  • Mantis is not closely integrated with github (git, projects, etc.)
  • New user sign-up is too complicated or broken (I remember several reports from the last few years)
  • Email notifications don’t work (despite all my attempts, I could not configure it to deliver email when any issue is submitted)
  • Mantis UI is not very intuitive and looks quite dated
  • Mantis needs hosting and occasional technical support, while github’s issue tracker is for free and fully self-administered through web interface

Mantis has lot more features than github’s issue tracker and offers more flexibility, but we can do without these (we don’t rely on any advanced feature in our development process).

I think we have already agreed that we transition to github’s issue tracker, the question is just when and how this should happen.

Maybe one thing that we could consider is to create placeholder github issues for the 4624 issues that we have in Mantis. These automatically generated issues could have the same headline of the original issue, content could be a link to the Mantis issue (with permalink such as issues.slicer.org/123 that could be redirected to mantis or github or anything else in the future), and the status would be closed if the Mantis issue was closed.


agreed that we transition to github’s issue tracker, the question is just when and how this should happen

I will have time to make progress on the overall transition to GitHub this week. Expect a follow up in the next few days. Once this happen, let’s also switch to GitHub issue tracker.


To elaborate: To ensure we have a lightweight source repo for future checkout (few seconds instead of minutes on a regular internet connection), we may have to rename the current one and create a new one with the same name. This week experiments will help understand what makes sense.


this is a report about a potential bug in qMRMLColorTableComboBox
(i think the github tracker is not yet active)

platform: windows
version: 3d slicer 4.10.2

steps to reproduce:

  1. start slicer
  2. load a scalar volume
  3. go to the volumes module
  4. ensure the loaded volume is the active volume
  5. the lookup table combobox provides a preview of all colormaps (as expected)
  6. close the scene without saving
  7. load the scalar volume again
  8. go to the volumes module
  9. ensure the loaded volume is the active volume
  10. the lookup table combobox does not provide previews of colormaps anymore

Thank you for reporting this. I’ve added an issue in the issue tracker: https://issues.slicer.org/view.php?id=4721