Your message dated Mon, 13 Oct 2025 02:49:57 +0000
with message-id <[email protected]>
and subject line Bug#1114711: fixed in pymatgen 2025.10.7+dfsg1-1
has caused the Debian Bug report #1114711,
regarding pymatgen: FTBFS with NumPy 2.3
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1114711: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114711
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pymatgen
Version: 2025.2.18+dfsg1-5
Severity: important
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: pymatgen
Source-Version: 2025.10.7+dfsg1-1
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pymatgen, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated pymatgen package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 13 Oct 2025 01:29:18 +0200
Source: pymatgen
Architecture: source
Version: 2025.10.7+dfsg1-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1114711
Changes:
pymatgen (2025.10.7+dfsg1-1) unstable; urgency=medium
.
* New upstream release
- works with NumPy 2.3. Closes: #1114711
- applies debian patches CVE-2022-42964_ReDOS_vulnerability.patch
and fix-build-with-new-uncertainties.patch
- Build-Depends: python3-bibtexparser instead of python3-pybtex
- Build-Depends: pymatgen-test-files (>= 2025.10.7~)
- Build-Depends: python3-orjson
* drop Build-Depends: python3-vtk9 | python3-paraview
(crashes with vtk9 9.3.0). Keep Recommends for run-time.
* debian patch test_no_moyopy.patch skips tests using moyopy
(in analysis/test_prototypes.py), which is not (yet) packaged
* drop debian/tests/test-pymatgen-net, since network tests
(ext/test_cod.py) have been disabled upstream
* Standards-Version: 4.7.2
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Files:
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pymatgen_2025.10.7+dfsg1-1.dsc
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pymatgen_2025.10.7+dfsg1-1_source.buildinfo
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