feat: support for osx-arm64 builds #46775

aliciaaevans · 2024-03-26T18:49:08Z

To Do:

Bioconda-Utils artifact fetching feat: fetch artifacts from GitHub Actions bioconda-utils#973
GitHub Actions and CircleCI workflow to upload to channel on merge of PR.
Include osx-arm64 in Bulk.yml GitHub Actions workflow
BiocondaBot comment artifact fetching feat: download github artifacts and condense comment bioconda-containers#79
Quick exit if the additional platform is not specified, similar to CircleCI workflow for linux-aarch64. Moved script to scripts directory and updated to be generic for any CI platform.
Update documentation OSX-Arm64 updates bioconda-docs#24
Compare CircleCI and GitHub Actions performance. Findings:
- CircleCI has better performance on a single osx-arm64 build, so that will be used for PRs and merges to master, along with linux-aarch64.
- GitHub Actions has a much longer timeout, so that will be used for osx-arm64 bulk builds along with the bulk linux-64 and osx-64 builds.
- The PR and master pipelines for GitHub Actions are manually disabled, but I added the new jobs there in case we ever need to reenable them.

.github/workflows/PR-arm.yml

aliciaaevans · 2024-03-28T21:57:18Z

bioconda/bioconda-utils#967 will avoid needing to set the SDK version in the workflow.

aliciaaevans · 2024-04-02T14:05:03Z

bioconda/bioconda-utils#967 will avoid needing to set the SDK version in the workflow.

Actually this did not fully work becauseMACOSX_DEPLOYMENT_TARGET needs to be set before run_conda_forge_build_setup is run.

aliciaaevans · 2024-04-05T15:51:59Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-04-05T15:52:21Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	bioawk-1.0-he4a0461_11.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h45fc8d7_11.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bioawk-1.0-he4a7b4a_11.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/b6aaff9f-75d6-47e7-8187-4f6efd1d4b91/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bioawk	1.0--he4a0461_11	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_11.tar.gz \| docker load`

aliciaaevans · 2024-07-02T13:36:04Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-02T13:36:28Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
linux-64	bamtools-2.5.2-hdcf5f25_4.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-64	bioawk-1.0-he4a0461_11.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bamtools-2.5.2-h447d7a5_4.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h10309d6_11.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/ee37c488-b191-4491-9477-e893ac067ca7/artifacts/0/tmp/artifacts/packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/ee37c488-b191-4491-9477-e893ac067ca7/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bamtools-2.5.2-h7f4e536_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/46f12a5c-5fe0-4c78-875b-53e09a0e5303/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/46f12a5c-5fe0-4c78-875b-53e09a0e5303/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bamtools	2.5.2--hdcf5f25_4	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bamtools:2.5.2--hdcf5f25_4.tar.gz \| docker load`
bioawk	1.0--he4a0461_11	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_11.tar.gz \| docker load`

aliciaaevans · 2024-07-02T16:16:37Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-02T16:17:00Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	bamtools-2.5.2-hdcf5f25_4.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-64	bioawk-1.0-he4a0461_11.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bamtools-2.5.2-h447d7a5_4.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h10309d6_11.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/82ea5dfb-971b-42bb-add2-c24f1aa8d169/artifacts/0/tmp/artifacts/packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/82ea5dfb-971b-42bb-add2-c24f1aa8d169/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bamtools-2.5.2-h7f4e536_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/d226436a-3716-457b-b4c7-0ad3d8bbf8c3/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/d226436a-3716-457b-b4c7-0ad3d8bbf8c3/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bamtools	2.5.2--hdcf5f25_4	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bamtools:2.5.2--hdcf5f25_4.tar.gz \| docker load`
bioawk	1.0--he4a0461_11	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_11.tar.gz \| docker load`

aliciaaevans · 2024-07-05T21:36:23Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-05T21:36:39Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	bamtools-2.5.2-hdcf5f25_4.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-64	bioawk-1.0-he4a0461_11.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bamtools-2.5.2-h447d7a5_4.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h10309d6_11.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	osx-arm64.zip	GitHub Actions	show You may also use `conda` to install after downloading and extracting the zip file. `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/14d896e0-28aa-4bc7-b170-e6ac1a0db6e7/artifacts/0/tmp/artifacts/packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/14d896e0-28aa-4bc7-b170-e6ac1a0db6e7/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bamtools-2.5.2-h7f4e536_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/e8962f6a-9b8e-42de-b26a-69ad790fbb12/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/e8962f6a-9b8e-42de-b26a-69ad790fbb12/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bamtools	2.5.2--hdcf5f25_4	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bamtools:2.5.2--hdcf5f25_4.tar.gz \| docker load`
bioawk	1.0--he4a0461_11	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_11.tar.gz \| docker load`

aliciaaevans · 2024-07-08T14:41:33Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-08T14:41:50Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	bamtools-2.5.2-hdcf5f25_4.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-64	bioawk-1.0-he4a0461_11.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bamtools-2.5.2-h447d7a5_4.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h10309d6_11.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/d1f1dd79-c173-4fc6-802d-9b68fae7c771/artifacts/0/tmp/artifacts/packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/d1f1dd79-c173-4fc6-802d-9b68fae7c771/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bamtools-2.5.2-h7f4e536_4.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/cc255e8f-fe4c-4642-a6f2-626c3eca8277/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_11.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/cc255e8f-fe4c-4642-a6f2-626c3eca8277/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bamtools	2.5.2--hdcf5f25_4	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bamtools:2.5.2--hdcf5f25_4.tar.gz \| docker load`
bioawk	1.0--he4a0461_11	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_11.tar.gz \| docker load`

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

`run_conda_forge_build_setup` from /~https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/main/.scripts/run_osx_build.sh fails to download the SDK when set to `11` instead of `11.0`. Needed for bioconda/bioconda-recipes#46775

.circleci/config.yml

.github/workflows/Bulk.yml

.github/workflows/PR.yml

.github/workflows/master.yml

This does add a little clutter from conda activate, but it could be useful for debugging some of the osx-specific stuff. Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

aliciaaevans · 2024-07-10T17:27:00Z

@BiocondaBot please fetch artifacts

BiocondaBot · 2024-07-10T17:27:20Z

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	bamtools-2.5.2-hdcf5f25_5.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
linux-64	bioawk-1.0-he4a0461_12.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the LinuxArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bamtools-2.5.2-h447d7a5_5.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-64	bioawk-1.0-h10309d6_12.tar.bz2	OSXArtifacts.zip	Azure	show You may also use `conda` to install after downloading and extracting the zip file. From the OSXArtifacts directory: `conda install -c ./packages <package name>`
osx-arm64	bamtools-2.5.2-h6057758_5.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/701a80ab-e885-4871-8c1c-e0b3791449f8/artifacts/0/tmp/artifacts/packages <package name>`
osx-arm64	bioawk-1.0-hcb76912_12.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/701a80ab-e885-4871-8c1c-e0b3791449f8/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bamtools-2.5.2-h7f4e536_5.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/894a254e-d9f0-4d55-8b9c-f52203cd94f9/artifacts/0/tmp/artifacts/packages <package name>`
linux-aarch64	bioawk-1.0-h73052cd_12.tar.bz2	repodata.json	CircleCI	show You may also use `conda` to install:`conda install -c https://output.circle-artifacts.com/output/job/894a254e-d9f0-4d55-8b9c-f52203cd94f9/artifacts/0/tmp/artifacts/packages <package name>`

Docker image(s) built:

Package	Tag	CI	Install with `docker`
bamtools	2.5.2--hdcf5f25_5	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bamtools:2.5.2--hdcf5f25_5.tar.gz \| docker load`
bioawk	1.0--he4a0461_12	Azure	show Images for Azure are in the LinuxArtifacts zip file above.`gzip -dc LinuxArtifacts/images/bioawk:1.0--he4a0461_12.tar.gz \| docker load`

aliciaaevans added the WIP label Mar 26, 2024

martin-g reviewed Mar 27, 2024

View reviewed changes

.github/workflows/PR-arm.yml Outdated Show resolved Hide resolved

.github/workflows/PR-arm.yml Outdated Show resolved Hide resolved

aliciaaevans mentioned this pull request Apr 2, 2024

feat: download github artifacts and condense comment bioconda/bioconda-containers#79

Merged

martin-g mentioned this pull request May 20, 2024

General CI failure due to Azure error No hosted parallelism has been purchased or granted #41025

Closed

aliciaaevans mentioned this pull request Jul 8, 2024

OSX-Arm64 updates bioconda/bioconda-docs#24

Merged

aliciaaevans and others added 13 commits July 9, 2024 09:42

example recipe for osx-arm64

9f1e998

test arm builds on macOS-14

d99ac26

add arch flag

0f256cc

try setting a higher sdk version

c9c2f70

check sdk versions

6860ca9

set sdk earlier

c0d311b

move logging

6f341bc

set deployment target

c9b46b5

move var setting

636bb8b

how old can we go?

eeac233

try 11.0 sdk

1d7c601

trigger on PR

8df4439

Apply suggestions from code review

c1c8812

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

aliciaaevans added 3 commits July 9, 2024 09:42

add osx-arm64 to bulk

a3cee7e

test with user friendly name

e794400

move arm jobs to existing GHA config

ef3150d

aliciaaevans force-pushed the osx-arm-builds branch from f54a430 to ef3150d Compare July 9, 2024 13:42

aliciaaevans changed the title ~~(WIP) feat: support for osx-arm64 builds~~ feat: support for osx-arm64 builds Jul 9, 2024

aliciaaevans added MacOS related osx-arm64 Related to adding osx-arm64 support and removed WIP labels Jul 9, 2024

test run_conda_forge_build_setup

16fbbf3

aliciaaevans mentioned this pull request Jul 9, 2024

fix: osx target/sdk version needs minor version bioconda/bioconda-common#57

Merged

aliciaaevans added 4 commits July 9, 2024 11:01

test run_conda_forge_build_setup on GitHub Actions

86cb5c7

debug sdk location

88afef6

try permissions

8ad3623

run_conda_forge_build_setup is working on GHA

dcd97dc

aliciaaevans commented Jul 9, 2024

View reviewed changes

.circleci/config.yml Outdated Show resolved Hide resolved

clean up

b2320e0

aliciaaevans requested a review from daler July 9, 2024 16:17

martin-g mentioned this pull request Jul 10, 2024

Update vcf-validator to 0.9.7 and add support for ARM on OSX #49075

Closed

martin-g reviewed Jul 10, 2024

View reviewed changes

aliciaaevans and others added 4 commits July 10, 2024 10:51

Try newer xcode version

0c559ad

try x flag to see how noisy it is

06eb067

bump builds

61866d8

Apply suggestions from code review

e915615

This does add a little clutter from conda activate, but it could be useful for debugging some of the osx-specific stuff. Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

aliciaaevans marked this pull request as ready for review July 10, 2024 15:57

daler approved these changes Jul 10, 2024

View reviewed changes

aliciaaevans merged commit 21fbd60 into master Jul 10, 2024
6 checks passed

aliciaaevans deleted the osx-arm-builds branch July 10, 2024 18:15

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feat: support for osx-arm64 builds #46775

feat: support for osx-arm64 builds #46775

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feat: support for osx-arm64 builds #46775

feat: support for osx-arm64 builds #46775

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