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python312Packages.pymatgen: disable test that crashes on Darwin#422968

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K900 merged 1 commit intoNixOS:masterfrom
sarahec:pymatgen-darwin-bad-test
Jul 11, 2025
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python312Packages.pymatgen: disable test that crashes on Darwin#422968
K900 merged 1 commit intoNixOS:masterfrom
sarahec:pymatgen-darwin-bad-test

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@sarahec sarahec commented Jul 6, 2025 •
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Test failure on Darwin: worker 'gw1' crashed while running 'tests/io/abinit/test_abitimer.py::TestAbinitTimer::test_timer'

Test disabled. This is one of many tests that all access the same MacOS graphics routine and fail due to sandboxing and/or headless builds (Hydra).

Discovered in nixpkgs-review of #421308

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • Nixpkgs 25.11 Release Notes (or backporting 25.05 Nixpkgs Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
  • NixOS 25.11 Release Notes (or backporting 25.05 NixOS Release notes)
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other contributing documentation in corresponding paths.

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@ofborg ofborg bot added the 6.topic: darwin Running or building packages on Darwin label Jul 6, 2025
@nixpkgs-ci nixpkgs-ci bot added the 6.topic: python Python is a high-level, general-purpose programming language. label Jul 6, 2025
@nix-owners nix-owners bot requested a review from PsyanticY July 6, 2025 16:19
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sarahec commented Jul 6, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 422968
Commit: 300e743cb0cbe3e34c68d111f878480f9dc54219

aarch64-darwin

✅ 4 packages built:
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.sumo
  • python312Packages.sumo.dist

@nixpkgs-ci nixpkgs-ci bot added 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 0 This PR does not cause any packages to rebuild on Linux. labels Jul 6, 2025
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ethancedwards8 commented Jul 6, 2025

nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 422968
Commit: 300e743cb0cbe3e34c68d111f878480f9dc54219

aarch64-darwin

✅ 4 packages built:
  • python312Packages.pymatgen
  • python312Packages.pymatgen.dist
  • python312Packages.sumo
  • python312Packages.sumo.dist

ethancedwards8
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Approved automatically following the successful run of nixpkgs-review.

@nixpkgs-ci nixpkgs-ci bot added the 12.approvals: 1 This PR was reviewed and approved by one person. label Jul 6, 2025
@Pandapip1 Pandapip1 added the 1.severity: blocker This is preventing another PR or issue from being completed label Jul 7, 2025
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Pandapip1 commented Jul 7, 2025

Blocking #421308

@Pandapip1 Pandapip1 added 12.approvals: 2 This PR was reviewed and approved by two persons. and removed 12.approvals: 1 This PR was reviewed and approved by one person. labels Jul 7, 2025
@sarahec sarahec force-pushed the pymatgen-darwin-bad-test branch from 300e743 to 1cec9b8 Compare July 7, 2025 23:30
@sarahec sarahec force-pushed the pymatgen-darwin-bad-test branch from 1cec9b8 to 72ba52b Compare July 7, 2025 23:59
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sarahec commented Jul 8, 2025

Filed materialsproject/pymatgen#4452 and added a link.

@sarahec sarahec requested a review from jonhermansen July 8, 2025 02:10
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I'm so sorry @sarahec , ok I got it sorted now. I tested your branch out. The tests fail on x86_64-darwin with the commit before your patch. The tests succeed with your commit applied.

When I said "I see the same issue", I meant that I got the same exact test failure that you did, with the sandbox enabled.

Your fix works for me. 👍

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jonhermansen commented Jul 8, 2025 •
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BTW, I tried building the package with python3.11 and it failed in a completely different way. Figured I'd mention it, because I tried it.

@nixpkgs-ci nixpkgs-ci bot added 12.approvals: 3+ This PR was reviewed and approved by three or more persons. and removed 12.approvals: 2 This PR was reviewed and approved by two persons. labels Jul 8, 2025
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sarahec commented Jul 8, 2025

BTW, I tried building the package with python3.11 and it failed in a completely different way. Figured I'd mention it, because I tried it.

Yeah, Python 3.11 isn't officially supported anymore (in nixpkgs).

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Pandapip1 commented Jul 8, 2025

How are you even building it with python 3.11? The attrset is gone!

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jonhermansen commented Jul 8, 2025 •
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How are you even building it with python 3.11? The attrset is gone!

nix-build -I nixpkgs=. -A python311Packages.pymatgen

Should I not do that? Or, is it not doing what I think it's doing?

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Pandapip1 commented Jul 9, 2025

Well, that attrset has been removed in the latest master it seems, so you don't have to worry about it not working because it no longer exists.

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jonhermansen commented Jul 9, 2025

Well, that attrset has been removed in the latest master it seems, so you don't have to worry about it not working because it no longer exists.

I worked off of @sarahec's history, so whatever was there, I tried it 😅

@K900 K900 merged commit 6bf134f into NixOS:master Jul 11, 2025
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sarahec commented Jul 11, 2025

@K900 Thank you

@sarahec sarahec deleted the pymatgen-darwin-bad-test branch July 11, 2025 16:40
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nixos-discourse commented Jul 14, 2025

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-already-reviewed/2617/2450

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@jonhermansen jonhermansen jonhermansen approved these changes

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1.severity: blocker This is preventing another PR or issue from being completed 6.topic: darwin Running or building packages on Darwin 6.topic: python Python is a high-level, general-purpose programming language. 10.rebuild-darwin: 1-10 This PR causes between 1 and 10 packages to rebuild on Darwin. 10.rebuild-linux: 0 This PR does not cause any packages to rebuild on Linux. 12.approvals: 3+ This PR was reviewed and approved by three or more persons.

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