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py-alphafold: update to 2.2.4, update dependencies#33876

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adamjstewart merged 2 commits intospack:developfrom
aweits:alphafold_update
Dec 2, 2022
Merged

py-alphafold: update to 2.2.4, update dependencies#33876
adamjstewart merged 2 commits intospack:developfrom
aweits:alphafold_update

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@aweits aweits commented Nov 13, 2022

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spackbot-app bot commented Nov 13, 2022

Hi @aweits! I noticed that the following package(s) don't yet have maintainers:

  • openmm
  • py-etils

Are you interested in adopting any of these package(s)? If so, simply add the following to the package class:

    maintainers = ["aweits"]

If not, could you contact the developers of this package and see if they are interested? You can quickly see who has worked on a package with spack blame:

$ spack blame openmm

Thank you for your help! Please don't add maintainers without their consent.

You don't have to be a Spack expert or package developer in order to be a "maintainer," it just gives us a list of users willing to review PRs or debug issues relating to this package. A package can have multiple maintainers; just add a list of GitHub handles of anyone who wants to volunteer.

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Can you try enabling jax in CI? Just uncomment in share/spack/gitlab/cloud_pipelines/stacks/ml-*/spack.yaml

@spackbot-app spackbot-app bot added core PR affects Spack core functionality gitlab Issues related to gitlab integration labels Nov 13, 2022
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Protobuf changes look a little sus. Most other changes are prob right but I don't see where you're getting the dependency version ranges from so it's hard to review. Can you add comments to those packages whenever it isn't as simple as checking the root setup.py file for a list of deps?

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Mostly meta comments and non-required suggestions, I think this is basically good to go.

remove_linked_tree(self.tmp_path)
remove_linked_tree(self.buildtmp)

def patch(self):
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Any reason to drop the patch method? I think it helps to logically separate patching from installation. Unless the multi-build system refactor broke this somehow.

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the multi-build system has yielded some surprising behavior here - not sure I like this solution, but see all the references to "wrapped_package_object" perhaps @alalazo has some words of wisdom?

@aweits aweits force-pushed the alphafold_update branch 2 times, most recently from 19a6819 to 1a366c4 Compare November 24, 2022 23:13
adamjstewart
adamjstewart previously approved these changes Nov 25, 2022
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aweits commented Dec 2, 2022

any objection to merging as-is?

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We need to get CI passing first. Either rebase or keep pinging spackbot to rerun the pipeline

@adamjstewart adamjstewart enabled auto-merge (squash) December 2, 2022 20:49
@adamjstewart adamjstewart merged commit 588d2e2 into spack:develop Dec 2, 2022
@aweits aweits deleted the alphafold_update branch December 5, 2022 15:43
luke-dt pushed a commit to dantaslab/spack that referenced this pull request Dec 5, 2022
* py-alphafold: update to 2.2.4, update dependencies

* style
amd-toolchain-support pushed a commit to amd-toolchain-support/spack that referenced this pull request Feb 16, 2023
* py-alphafold: update to 2.2.4, update dependencies

* style
@adamjstewart adamjstewart mentioned this pull request Feb 17, 2023
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2 participants