[From nobody Thu Jul 16 00:51:08 2026 Received: (at submit) by bugs.debian.org; 24 May 2026 09:51:33 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-116.6 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_SEVERITY,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,SPF_HELO_NONE,SPF_PASS, T_PDS_OTHER_BAD_TLD,USER_IN_DKIM_WELCOMELIST,XMAILER_REPORTBUG autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 95; hammy, 150; neutral, 94; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <dparsons@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:55380) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <dparsons@debian.org>) id 1wR5Ub-002Anu-15 for submit@bugs.debian.org; Sun, 24 May 2026 09:51:33 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Date:Message-ID:Subject:To:From: Content-Transfer-Encoding:MIME-Version:Content-Type:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=iXbS9kdr73St6QeC+LNd/BFFOOwJ+r8wOC+X/V/DDxg=; b=GpGIett+WSirnVqFswmIlboW1m Lg6gOlZuY9kIssRXMvNpvqkY+OAwxBQzYwTXPCT2fzUQ/VlBH7YPrL7EwJu434qkhZBWNQye7Vo/D 5U5NLWhL+xcfeHMT6FX3qP0gebO9LSZbh55SdvRddW9yCjR4eNT9sprbTFXw0nsBi8bq6/ZFj3uJ+ iaru5dQ636xrRjnSDYaNsL8Cfe/ymBigR3bdgybyaggMk/91igTWBeZVQ1ytangdULOvjSkGEsh4j DlNdzexS+y9h+ZNa90qE1A1VFkb5B6+u7IS6P0djnn8mJPij4Yj0tgjUiQQfuKi2Gl6YscQqTrWs6 SjjSDhMQ==; Received: from authenticated-user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <dparsons@debian.org>) id 1wR5Ua-000iFe-0H; Sun, 24 May 2026 09:51:32 +0000 Received: from drew by sandy with local (Exim 4.99.2) (envelope-from <dparsons@debian.org>) id 1wR5UY-0000000CkZ1-34R7; Sun, 24 May 2026 11:51:30 +0200 Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: Drew Parsons <dparsons@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: pymatgen-core: FTBFS: test_packmol test_atoms_constraints fails Message-ID: <177961629071.3023946.12921600273416885944.reportbug@sandy> X-Mailer: reportbug 13.2.0 Date: Sun, 24 May 2026 11:51:30 +0200 X-Debian-User: dparsons Delivered-To: submit@bugs.debian.org Source: pymatgen-core Version: 2026.4.7+dfsg1-1 Severity: serious Control: forwarded -1 https://github.com/materialsproject/pymatgen-core/issues/70 test_atoms_constraints in io/test_packmol.py is fragile with different coordinates generated on different architectures e.g. https://buildd.debian.org/status/fetch.php?pkg=pymatgen-core&arch=arm64&ver=2026.4.7%2Bdfsg1-3&stamp=1779556969&raw=0 =================================== FAILURES =================================== ____________________ TestPackmolSet.test_atoms_constraints _____________________ [gw3] linux -- Python 3.14.5 /usr/bin/python3.14 self = <test_packmol.TestPackmolSet object at 0xffff67a1d0f0> def test_atoms_constraints(self): """ Test individual constraints. """ pw = PackmolBoxGen( inputfile="input.in", outputfile=Path("output.xyz"), stdoutfile=Path("stdout.txt"), control_params={"precision": 0.001}, ).get_input_set( molecules=[ { "name": "water", "number": 5, "coords": water, "constraints": ["inside sphere 0 0 0 10"], "atoms_constraints": [ {"indices": [2], "constraints": ["inside sphere 0 0 0 5"]}, {"indices": [0, 1], "constraints": ["outside sphere 0 0 0 5.5"]}, ], }, ], ) pw.write_input(f"{self.tmp_path}/with_atoms_constraints") assert os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/input.in") with open(f"{self.tmp_path}/with_atoms_constraints/input.in") as f: inp = f.read() assert ("\n atoms 3\n inside sphere 0 0 0 5\n end atoms\n") in inp assert ("\n atoms 1 2\n outside sphere 0 0 0 5.5\n end atoms\n") in inp pw.run(f"{self.tmp_path}/with_atoms_constraints") assert os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/output.xyz") assert os.path.isfile(f"{self.tmp_path}/with_atoms_constraints/stdout.txt") out = Molecule.from_file(f"{self.tmp_path}/with_atoms_constraints/output.xyz") assert out.composition.num_atoms == 15 for site in out: if site.specie.symbol == "H": > assert np.linalg.norm(site.coords) >= 5.49 E AssertionError: assert np.float64(5.483361163873123) >= 5.49 E + where np.float64(5.483361163873123) = <function norm at 0xffff7ff909b0>(array([ 3.165768, 0.049572, -4.476908])) E + where <function norm at 0xffff7ff909b0> = <module 'numpy.linalg' from '/usr/lib/python3/dist-packages/numpy/linalg/__init__.py'>.norm E + where <module 'numpy.linalg' from '/usr/lib/python3/dist-packages/numpy/linalg/__init__.py'> = np.linalg E + and array([ 3.165768, 0.049572, -4.476908]) = Site: H (3.1658, 0.0496, -4.4769).coords /build/reproducible-path/pymatgen-core-2026.4.7+dfsg1/.pybuild/test_python3.14/tests/io/test_packmol.py:427: AssertionError = 1 failed, 2507 passed, 124 skipped, 5 xfailed, 1 xpassed, 64 warnings in 251.16s (0:04:11) = The non-H case fails similarly on i386, loong64, ppc64el. Reported upstream https://github.com/materialsproject/pymatgen-core/issues/70 Severity: serious since FTBFS ]