[Debichem-devel] Bug#1114711: pymatgen: FTBFS with NumPy 2.3

Mon Sep 8 20:44:30 BST 2025

Source: pymatgen
Version: 2025.2.18+dfsg1-5
Severity: important
User: debian-python at lists.debian.org
Usertags: numpy2.3
Tags: ftbfs, forky, sid

Dear maintainer,

During a test rebuild for NumPy 2.3, pymatgen failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:59: mcsqs executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:77: mcsqs executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_mcsqs_caller.py:89: mcsqs executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/command_line/test_vampire_caller.py:34: vampire executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:714: Only run this in CI tests
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:107: enumlib or mcsqs executable not present
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:988: could not import 'moyopy': No module named 'moyopy'
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1931: chgnet is not built against NumPy 2.0
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2003: TODO: #3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1021: PMG_MAPI_KEY environment variable not set or MP API is down. This is also the case in a PR.
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:1906: chgnet is not built against NumPy 2.0
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2015: TODO: #3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2026: TODO: #3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2035: TODO: #3958 wait for matgl resolve of torch dependency
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2668: could not import 'tblite': No module named 'tblite'
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_structure.py:2676: Pytorch and TBLite clash. https://github.com/materialsproject/pymatgen/pull/3060
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_surface.py:700: This test relies on neighbor orders and is hard coded. Disable temporarily
SKIPPED [1] .pybuild/test_python3.13/tests/core/test_xcfunc.py:56: TODO:
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:254: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:221: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:241: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:169: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:199: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:232: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:101: No FDINT
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:123: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:203: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:132: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:116: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:86: No FDINT
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:207: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:141: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:157: No x_trans.
SKIPPED [1] .pybuild/test_python3.13/tests/electronic_structure/test_boltztrap.py:43: No x_trans.
SKIPPED [19] .pybuild/test_python3.13/tests/electronic_structure/test_plotter.py: No x_trans executable found
SKIPPED [1] .pybuild/test_python3.13/tests/ext/test_optimade.py:58: MP OPTIMADE is down.
SKIPPED [1] .pybuild/test_python3.13/tests/ext/test_optimade.py:81: At least one MC OPTIMADE API is down.
SKIPPED [1] .pybuild/test_python3.13/tests/ext/test_optimade.py:40: MP OPTIMADE is down.
SKIPPED [1] .pybuild/test_python3.13/tests/ext/test_optimade.py:93: OPTIMADE providers list is down.
SKIPPED [1] .pybuild/test_python3.13/tests/io/exciting/test_inputs.py:137: inconsistent data
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_cif.py:322: non-free PF*.cif test files are not available
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_jarvis.py:12: JARVIS-tools not loaded.
SKIPPED [1] .pybuild/test_python3.13/tests/io/test_jarvis.py:20: JARVIS-tools not loaded.
SKIPPED [1] .pybuild/test_python3.13/tests/io/vasp/test_help.py:19: www.vasp.at is down
SKIPPED [1] .pybuild/test_python3.13/tests/io/vasp/test_help.py:28: www.vasp.at is down
SKIPPED [1] .pybuild/test_python3.13/tests/io/vasp/test_help.py:34: www.vasp.at is down
SKIPPED [1] .pybuild/test_python3.13/tests/io/vasp/test_inputs.py:1717: TODO: need someone to fix this
SKIPPED [1] .pybuild/test_python3.13/tests/symmetry/test_kpaths.py:21: No seek path present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:97: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:158: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:188: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:207: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:237: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:249: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:364: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:304: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:342: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:334: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:352: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:492: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:540: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:549: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:607: mcsqs not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:617: mcsqs not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:638: mcsqs not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:670: icet not installed.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:656: icet not installed.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:681: icet not installed.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_advanced_transformations.py:874: hiphive not present
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_site_transformations.py:214: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:238: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:255: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:273: enum_lib not present.
SKIPPED [1] .pybuild/test_python3.13/tests/transformations/test_standard_transformations.py:279: enum_lib not present.
= 1 failed, 2677 passed, 153 skipped, 291 deselected, 296907 warnings in 701.33s (0:11:41) =
..tot conformations = 3
..tot confs tested = 3
..below energy threshold = 3
make[1]: *** [debian/rules:115: override_dh_auto_test] Error 1
make[1]: Leaving directory '/build/reproducible-path/pymatgen-2025.2.18+dfsg1'
make: *** [debian/rules:100: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T06:14:48Z

-------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2453906/

About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.

You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/163699/

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Cheers
Timo