plan for the GCC7 migration

[bgruening]

• label all main packages with an additional label (as conda-forge)
• merge bulk into master
• add main label to all packages with a gcc7 label
• communicate clearly to our community that now everything gets (re)build against gcc7
• communicate that we need to bump the build-number to all packages (and its dependents) if you want to have a rebuild (https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change)
• create a bot to assist users to bump builds, potentially in a single-issue
• make the bot smart enough to (re)build packages it pinning are bumped globally

[bgruening]

Thanks to @dpryan79 we have now https://bioconda.github.io/updating.html#updating-recipes-for-a-pinning-change ... the bot is in progress by @epruesse. That leaves us to the point of how we communicate this to all users.

Creating a new issue and ping /all/?

[bgruening]

I added an issue (#13578) and update the PR template (#13579) to reach more people.

[kyleabeauchamp]

Is the plan for us to wait for the old compilers to be removed and then start bumping the build number on our favorite recipes?

…

On Sun, Feb 10, 2019, 12:46 AM Björn Grüning ***@***.*** wrote: I added an issue (#13578 <#13578>) and update the PR template (#13579 <#13579>) to reach more people. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#13155 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABz_q4OOvoqn8cg1bE2P_3vtihHM3-kGks5vL9xfgaJpZM4aLSDN> .

[epruesse]

You can already start bumping. That's actually what the new bioconda-utils update-pinning command does - you hand it packages of interest and it'll bump the dependency chain as necessary.

[epruesse]

@bgruening - Does this mean I can restart autobump now?

[bgruening]

@epruesse if autobump also considers update-pinning then yes.

Let's wait for @dpryan79 to confirm and feel free to merge #13579 so we update our users.

@kyleabeauchamp: unrelated but could you add run_exports to htslib. I think this would help a lot. Would be great if we could use run_exports more in our stack.

[kyleabeauchamp]

Will take a look tonight

…

On Sun, Feb 10, 2019, 10:24 AM Björn Grüning ***@***.*** wrote: @epruesse <https://github.com/epruesse> if autobump also considers update-pinning then yes. Let's wait for @dpryan79 <https://github.com/dpryan79> to confirm and feel free to merge #13579 <#13579> so we update our users. @kyleabeauchamp <https://github.com/kyleabeauchamp>: unrelated but could you add run_exports to htslib. I think this would help a lot. Would be great if we could use run_exports more in our stack. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13155 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABz_q6RE_li-f19cmLrGwHlqrj5rmPUOks5vMGPNgaJpZM4aLSDN> .

[dpryan79]

Go for it, no need to wait for me!

[kyleabeauchamp]

I ran the update-pinning script and I get a lot of errors:

bioconda-utils update-pinning --bump-only-python recipes/ config.yml --packages deeptools
[...]

Attempting to finalize metadata for pysam
Solving environment: ...working... done
Solving environment: ...working... failed
Unsatisfiable dependencies for platform linux-64: {'bcftools==1.3.1', 'samtools==1.3.1', 'htslib==1.3.1'}

Packages requiring the following:
  No build number change needed: 12
  A rebuild for a new python version: 0
  A build number increment: 0
6 packages produced an error in conda-build: ['recipes/pysam/0.9.1', 'recipes/bcftools', 'recipes/samtools', 'recipes/pysam', 'recipes/htslib', 'recipes/pysam/0.10.0']

I also tried with --bump-only-python and got similar results. Not sure what to make of it, but I thought I'd post because I imagine others will see similar.

[kyleabeauchamp]

Regarding run_exports, I've made a WIP PR (#13586, not sure what else needs to be done.

[epruesse]

@kyleabeauchamp It works for me. Could be something with your conda setup. It does say you're in the clear for deeptools though.

[dpryan79]

@kyleabeauchamp I already rebuilt deepTools, pysam (the most recent version), and everything related to samtools/htslib. What you're seeing is due to old pysam versions depending on samtools/htslib versions that are no longer maintained in bioconda (1.3 in particular). We should really go through and see which pysam versions are still required by packages and blacklist/remove those that aren't being actively used. We can add samtools 1.3 back in if it's actually needed of course.

[epruesse]

@dpryan79 packages or recipes? I assume we only need to maintain recipes building old versions to satisfy pinnings by extant recipe versions, right?

[dpryan79]

@epruesse If there's no linking going on then we only care about packages. Pysam happens to link to htslib, though. However it's in C and not C++, so you're a better judge of whether that's an actual issue than me.