ARM Documentation updates #16

aliciaaevans · 2023-11-14T23:06:18Z

Add linux-aarch64 to all places the supported architectures are mentioned (still waiting for access to Mac M1 on CircleCI)
Update CI Inventory page to include CircleCI for ARM
Update Build System page to remove/modify outdated information that should mention both CircleCI and Azure
Remove references to TravisCI (unless it is still used somewhere?)
Instructions for enabling ARM platforms: additional-platforms

source/faqs.rst

source/index.rst

Yikun · 2023-11-15T15:44:30Z

I guess we also need add doc in somewhere to mention how to enbale linux-aarch64 addtional platform [1] for a package?

extra:
  additional-platforms:
    - linux-aarch64

[1] bioconda/bioconda-utils#923

Made it more general so it's accurate across multiple CI platforms

daler · 2023-11-19T03:31:29Z

I did a full pass through the docs, doing a lot of cleanup and some organization. Some highlights:

overhauled the ci-inventory page into a table. Hopefully way easier to see ALL the moving parts now.
added a section on platforms, because I was still confused about aarch64, arm64, linux-aarch64, osx-arm64, etc
added a new .. datechanged:: directive, so we can start being better about noting when something was added to the docs
updated the build-systems page to be more general (it had a lot of details about how bioconda-utils works, which is overkill)
added new aarch64 page. Added it under "developer" docs for now, since current the opt-in mechanism is not intended to be widely used
updated number of contributors
consolidated the 2 faqs into a single one
removed the cb3 page (we've been using conda-build 3 for a while now....) but ported over relevant information elsewhere

source/contributor/build-system.rst

bgruening · 2023-11-19T11:53:23Z

source/developer/aarch64.rst

+
+This is being initially approached as an opt-in process as we make sure
+all the moving parts are working correctly. A recipe can be flagged for
+building on ``linux-aarch64`` by adding the following to the


Do we intend to push containers for that as well? I would like to see this :)

Eventually, yes of course!

But not yet? Should we document that? Or should we add an additional key to enable aarch64 containers?
It would be nice to push them if we activate it in the extra section. But I guess that a different discussion.

I'm actually unclear on the current status of aarch64 containers. I know there was work on getting base images set up, so it could be that aarch64 containers are already handled. I'm still trying to catch up with the recent work though...I'm sure the answer is in there somewhere and once I figure it out I'll clarify this.

OK, looks like there was some discussion on the core chat (Oct 18) about not immediately uploading aarch64 containers. I think this will be a different discussion. I'll add a note here that containers are currently not built and uploaded.

Is the core chat public or it is only for the core team ?
I am aware only of https://app.gitter.im/#/room/#bioconda_Lobby:gitter.im but there is no discussion about containers at Oct 18 there.
Thanks!

I'd also like to join the discussion about aarch64 support! : )

Yeah, there are many discussions in many places; the one I found re: containers was indeed in a separate core team chat. However we should be better about consolidating information and discussion, ideally on a single github issue.

@Yikun @martin-g FYI, some recent PRs on pushing aarch64 images to biocontainers: bioconda/bioconda-recipes#43995, bioconda/bioconda-recipes#44457, bioconda/bioconda-utils#941 . . . largely merged into bioconda/bioconda-recipes#40550.

source/faqs.rst

daler · 2023-11-24T14:46:49Z

In thinking about @bgruening's aarch64 container question, I realized I couldn't come up with a clear answer along the lines of, "this specific thing needs to change or be updated in order to fully support aarch64 containers" or "it all looks good". So I took a deep dive into all the containers and wrote up my notes in c69024f. Hopefully this will help inform and clarify future discussions.

source/contributor/faqs.rst

source/faqs.rst

source/contributor/build-system.rst

source/developer/ci-inventory.rst

source/developer/dockerfile-inventory.rst

source/developer/repo-inventory.rst

source/faqs.rst

martin-g · 2024-01-08T13:26:42Z

source/faqs.rst

+be installed as a run dependency without having to explicitly add it as such in
+the recipe. This specification is done in the ``zlib`` recipe itself (which is
+hosted by conda-forge), so in general bioconda collaborators can just add
+``zlib`` as a build dependency.


I find this confusing.
https://github.com/bioconda/bioconda-docs/pull/16/files#diff-5a476a141b5805f24f43cab6c3548f1dd1319013abd9035ef91062a6fcd9a35bR441-R442 says that zlib should be in the requirements:host list.
Here the terminology says build dependency which sounds like requirements:build which is only for the compilers, as explained earlier.

I agree. I think "host dependency" or "host requirement" would be more clear.

Also, I'd like to share my related open PR #18 to clarify how to handle requirements like zlib that use "run exports"

@jdblischak agreed, and will get to #18 soon. I think this should be fixed over there. Any suggestions on what a better example would be?

source/faqs.rst

Co-authored-by: Martin Grigorov <[email protected]>

daler · 2024-03-04T21:58:23Z

@martin-g thanks again for all the reviews!

martin-g · 2024-03-05T07:14:38Z

@daler Thank you for all your work on Bioconda!

add aarch64 to support

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aliciaaevans mentioned this pull request Nov 14, 2023

feat: add initial support for arm builds bioconda/bioconda-recipes#40550

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daler added 20 commits November 18, 2023 15:05

add new datechanged directive

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add section on platform nomenclature

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update supported python version info

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minor tweaks to guidelines

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fix typos

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minor cleanup on bulk.rst

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clarification on repodata patching

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add Alicia to core team

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update notes on building docs

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css on datechanged directives

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overhaul and update CI inventory page

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consolidate all FAQs together into top-level

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consolidate cb3.rst into top-level faqs

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overheaul build-system.rst

c777929

Made it more general so it's accurate across multiple CI platforms

minor updates to bulk

4a7e86d

add new aarch64 page

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update number of contributors

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make CI platforms more general

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minor formatting

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clarifications in faqs

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bgruening reviewed Nov 19, 2023

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daler added 4 commits November 19, 2023 10:40

update link to galaxy's mulled-build docs

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clarifications and updates

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fix build/host/run details

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Arm/ARM clarification

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note about linux-aarch64 containers

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daler marked this pull request as ready for review November 20, 2023 15:01

Yikun approved these changes Nov 22, 2023

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add inventory of repos

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add inventory of dockerfiles/images

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daler mentioned this pull request Dec 1, 2023

Update faqs.rst: Pythons 2.7/3.6/3.7 no longer supported but 3.10 is #17

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Suggestion: Consider making Aarch64 builts ? bioconda/bioconda-recipes#23454

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Augur cannot be installed natively for ARM64 on Bioconda even though it is labeled "noarch" nextstrain/bioconda-recipes#3

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leoisl mentioned this pull request Dec 5, 2023

MBGC on OS X kowallus/mbgc#3

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Adamtaranto mentioned this pull request Jan 15, 2024

Missing Apple Silicon build of Minimap2 in Bioconda lh3/minimap2#1148

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daler and others added 8 commits March 4, 2024 15:44

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Co-authored-by: Martin Grigorov <[email protected]>

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jdblischak mentioned this pull request Mar 5, 2024

Rely on "run exports" to install zlib at runtime #18

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Build System Page Rewrite #13

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ARM Documentation updates #16

ARM Documentation updates #16

aliciaaevans commented Nov 14, 2023 •

edited by daler

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Yikun commented Nov 15, 2023

daler commented Nov 19, 2023 •

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bgruening Nov 19, 2023

daler Nov 19, 2023

bgruening Nov 19, 2023

daler Nov 20, 2023

daler Nov 20, 2023

martin-g Nov 21, 2023

Yikun Nov 22, 2023

daler Nov 22, 2023

daler Nov 26, 2023

daler commented Nov 24, 2023

martin-g Jan 8, 2024

jdblischak Jan 8, 2024

daler Mar 4, 2024

daler commented Mar 4, 2024

martin-g commented Mar 5, 2024

ARM Documentation updates #16

ARM Documentation updates #16

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aliciaaevans commented Nov 14, 2023 • edited by daler Loading

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daler commented Mar 4, 2024

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aliciaaevans commented Nov 14, 2023 •

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