Bug 932127 – sci-chemistry/pymol-3.0.0 does not enable tests

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Agostino Sarubbo 2024-05-18 06:29:43 UTC]

https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-chemistry/pymol-3.0.0 does not enable tests.
Discovered on: amd64 (internal ref: gcc14_tinderbox)
System: GCC-14-SYSTEM (https://wiki.gentoo.org/wiki/Project:Tinderbox/Common_Issues_Helper#GCC-14)

Info about the issue:
https://wiki.gentoo.org/wiki/Project:Tinderbox/Common_Issues_Helper#QA0040

[Comment 1 Agostino Sarubbo 2024-05-18 06:29:44 UTC]

Created attachment 893194 [details]
build.log.xz

build log and emerge --info (compressed because it exceeds attachment limit, use 'xzless' to read it)

[Comment 2 Pacho Ramos 2024-09-16 07:22:48 UTC]

It seems upstream removed the script for running them:
https://salsa.debian.org/debichem-team/pymol/-/blob/master/debian/rules?ref_type=heads#L22

[Comment 3 Larry the Git Cow 2024-09-28 14:50:53 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5a1dfcc8986e29f5157bc9f706aaeb23307c4b68

commit 5a1dfcc8986e29f5157bc9f706aaeb23307c4b68
Author:     Pacho Ramos <[e-mail]>
AuthorDate: 2024-09-28 14:42:14 +0000
Commit:     Pacho Ramos <[e-mail]>
CommitDate: 2024-09-28 14:50:45 +0000

    sci-chemistry/pymol: Multiple bugfixes
    
    Upstream fixes for multiple bugs, also fixing python 3.12 and numpy2 compat,
    and fixing LTO building.
    
    Format-security patch looks to not be needed anymore (at least I couldn't
    reproduce the problem). If the problem reappears, please report the bug to
    upstream to follow its progress properly.
    
    Use icon from the pymol tarball and update desktop file.
    
    Update ebuild to try to run the tests, but keep them restricted for now as they
    keep failing.
    
    Bug: https://bugs.gentoo.org/932127
    Signed-off-by: Pacho Ramos <[e-mail]>

 .../pymol-3.0.0-SceneGetDrawFlag-indexing.patch    |  22 +++
 .../pymol/files/pymol-3.0.0-distutils-py3.12.patch |  70 ++++++++
 .../pymol/files/pymol-3.0.0-eof-maeffplugin.patch  |  22 +++
 .../files/pymol-3.0.0-lto-molfile-plugin.patch     | 187 +++++++++++++++++++++
 sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch |  35 ++++
 .../pymol/files/pymol-3.0.0-py3.12-progress.patch  |  26 +++
 sci-chemistry/pymol/pymol-3.0.0-r1.ebuild          | 123 ++++++++++++++
 7 files changed, 485 insertions(+)