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@qclayssen qclayssen self-assigned this Sep 15, 2025
@qclayssen qclayssen added the enhancement New feature or request label Sep 15, 2025
@qclayssen qclayssen requested a review from scwatts September 15, 2025 00:39
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You've also bumped the version of bolt here, I think that is probably accidental

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qclayssen commented Sep 15, 2025

I did it because of how the container names work. With ghcr.io/umccr/bolt:0.2.14-gpgr, if I don't bump to ghcr.io/umccr/bolt:0.2.15-gpgr, the image gets the same name for different GPGR versions. This could be confusing and, in specific cases, cause collisions if I resume a sash workflow.

One alternative approach could be to add the tool version in the tag like ghcr.io/umccr/bolt:0.2.14-gpgr-v2.2.0 or use a hash-based suffix.

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scwatts commented Sep 15, 2025

I may misunderstand, is this PR aiming to also create the bolt 0.2.15 release? Or is it more that you're trying to bump gpgr and wanting to use the CICD to build images, which needs the workaround described to avoid name clashes?

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This PR is primarily aiming to bump GPGR to version 0.2.2. The bolt version bump to 0.2.15 is workaround for the container clashes

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scwatts commented Sep 15, 2025

Thanks for the details, I think I understand that you're wanting to bump gpgr to 2.2.0 (I believe 0.2.2 is a typo) and test this in sash

I have a couple suggestions here:

  • build the images locally as we've done here to test in sash and make any changes required if you haven't already
  • review and consider any other changes that could be included in the proposed 0.2.15 release
  • have a PR with the desired changes and then another for specifically for the release as we've done here

@qclayssen qclayssen changed the base branch from main to release/0.3.0 September 15, 2025 05:41
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qclayssen commented Sep 15, 2025

I've already tested this with the latest gpgr in bolt. It's what sash on ICA for OA v2.2.0 is currently using. No other changes are needed to support OA v2.2.0, so I was thinking of making this a small bump version so that ICA doesn't have to work on a branch.

But since it's functional, I could alternatively add this change to the bolt release/0.3.0 linked to sash v0.7.0 release. which would require more testing.

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scwatts commented Sep 15, 2025

Thanks for the extra context, this is making sense now. I see two options:

  • create the 0.2.15 release (split this PR into one for the gpgr version bump and another for the release PR)
  • include the gpgr version bump in the changes for the 0.3.0 release as you've identified

Up to you how you'd prefer to handle!

@qclayssen qclayssen changed the base branch from release/0.3.0 to main September 15, 2025 07:24
@qclayssen qclayssen changed the title bump gpgr version Release v0.2.15 Sep 15, 2025
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scwatts commented Sep 15, 2025

Taking this activity as you proceeding with 0.2.15 release option :) I'll approve the other PR shortly

CHANGELOG.md Outdated

## dev

- [14](https://github.com/umccr/bolt/pull/14) - gpgr version bump to 0.2.2
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Change to 2.2.0

RUN \
conda install --prefix /env/ \
'r-gpgr ==2.1.3' \
'r-gpgr ==2.2.0' \
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This commit shouldn't be included in this PR; the set of commits in this PR should be merged with main or rebased on main

I can rebase if you like after you make the adjustment to the CHANGELOG.md file above

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LGTM, and thanks for making those adjustments!

@qclayssen qclayssen merged commit b59abbe into main Sep 15, 2025
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3 participants