ENH: Support native osx-arm64 conda install

[corneliusroemer]

Context

Now that bioconda supports osx-arm64, we can finally try to make a native environment, which will speed up local builds by around a factor of 2.

There's quite a lot of work to do: all our dependencies will need to be supported by osx-arm64, but it should be doable!

This issue is a tracker, to help us see what's still missing.

Tasks

• Migrate all bioconda dependencies to osx-arm64:

  • snakemake-minimal
  • pathogen-embed
  • nextstrain-cli
  • snakemake
  • bx-python: Build bx-python for osx-arm64 bioconda/bioconda-recipes#49092
  • treetime
  • evofr
  • bcbio-gff
  • pango_aliasor
  • epiweeks
  • pyfastx: Build pyfastx for osx-arm64 bioconda/bioconda-recipes#49093
  • nextclade: Build nextclade for osx-arm64 bioconda/bioconda-recipes#49095
  • nextclade2: Build nextclade2 for osx-arm64 bioconda/bioconda-recipes#49097
  • iqtree: Build Iqtree for osx-arm64 bioconda/bioconda-recipes#49090
  • fasttree: Build fasttree for osx-arm64 bioconda/bioconda-recipes#49100
  • auspice: Build auspice for osx-arm64 bioconda/bioconda-recipes#49103
  • csvtk: Builds csvtk for osx-arm64 bioconda/bioconda-recipes#49094
  • nextalign: Build nextalign for osx-arm64 bioconda/bioconda-recipes#49096
  • seqkit: Build seqkit for osx-arm64 bioconda/bioconda-recipes#49099
  • mafft: Add macOS arm64 build conda-forge/mafft-feedstock#3
  • raxml: Build raxml for osx-arm64 bioconda/bioconda-recipes#49098
  • vcftools: Build vcftools for osx-arm64 bioconda/bioconda-recipes#49102
  • augur: blocked on xopen, blocked on python-isal, blocked on isa-l, unless we make python-isal optional for xopen which should be doable
  • xopen: fighting here Manually migrate for osx-arm64, bump to v2.0.2 conda-forge/xopen-feedstock#45
  • gzip: Manual osx-arm64 migration conda-forge/gzip-feedstock#9

• Ensure conda-forge packages are available under osx-arm64

• feat: Make osx-arm64 version of conda-base #80

[jameshadfield]

Are we still missing tsv-utils which is osx-64/linux-64?

conda-base/src/recipe.yaml

Line 83 in 224ad39

- tsv-utils

[corneliusroemer]

@jameshadfield no 😀 I migrated it to conda-forge a few days ago as it's of general utility and not bio limited. check it out at conda-forge/tsv-utils

[victorlin]

There are two stages here - the first one is making sure that dependencies can be installed natively which looked like a big undertaking, thank you for taking care of that!

Next, we have to update the build to produce the package for osx-arm64. I think this is what needs to be done:

1. Use osx-arm64 here:

   conda-base/devel/conda-subdir

   Lines 17 to 18 in e5090a8

   	Darwin/arm64)
   	echo "osx-64";;

2. Use macos-14 here:

   conda-base/.github/workflows/ci.yaml

   Lines 29 to 36 in e5090a8

   	build-and-test:
   	needs: generate-version
   	strategy:
   	fail-fast: false
   	matrix:
   	os:
   	- ubuntu-22.04
   	- macos-12

For (2) I think we'll want to append to the list rather than replace macos-12 so that there will still be a native package for Intel Macs.

[corneliusroemer]

Nice @victorlin - I didn't see this comment of yours just now but came to the same conclusions when trying a PR. I've made one here:

• feat: Make osx-arm64 version of conda-base #80

It turns out that gzip isn't yet available for osx-arm64. We could potentially drop that for osx-arm64 as gzip is available from the system on macOS arm64.

But I made a migration pr to conda-forge anyways:

• Manual osx-arm64 migration conda-forge/gzip-feedstock#9

[victorlin]

@corneliusroemer let me know if you need any help pushing #80 through. I've prioritized task under my name at our biweekly priorities meetings because it seems close to done, and I think it'd be great to take advantage of all the work that you and others have done to make it possible.