[From nobody Tue May 26 14:07:06 2026 Received: (at submit) by bugs.debian.org; 13 Oct 2025 22:41:44 +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=-107.2 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER, PDS_OTHER_BAD_TLD,SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY, 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, 76; hammy, 150; neutral, 90; 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]:44218) 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 1v8REd-00B9iN-2m for submit@bugs.debian.org; Mon, 13 Oct 2025 22:41:43 +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=ViaDkhckkUWhoBfgD0qsTaAOggXcWX7EMm5S76fSy3U=; b=Mmh995Rdi+7F+KORJqKP9cbOGR ZGA9XI7yXUURWkgGtTm0rczRK25uSyIgX9EpN90qubDtDREi6P9iqqRQhgCoz5f6GGbGibju85bz7 IgGHGEdDDreja9DPoelnU7XgpVgmH9Y1xxd3K0aq3IoT60zzUTjDO5mSLibcZOOsFicbHf/29oX+m +CaNCQbrv/5EU/dg48Z0EYqIZ6NrYIlt4lYm5Cu0Rijercf0n5lvKe3XIKyQf2wZsEKBpFl0cMThM UeWx0srchDNsG1kxw7LKCMJ8pah/NtGXdYF1sut59k7JjjDtIG+cgWxE7QGSx6rLh8hD5QAGWCwrA WZi0ixrw==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <dparsons@debian.org>) id 1v8REd-000WFF-01; Mon, 13 Oct 2025 22:41:41 +0000 Received: from drew by sandy with local (Exim 4.98.2) (envelope-from <dparsons@debian.org>) id 1v8REb-0000000BFza-0TTF; Tue, 14 Oct 2025 00:41:41 +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: test_packmol test_atoms_constraints fails on various architectures Message-ID: <176039530109.2669507.3541152463605023484.reportbug@sandy> X-Mailer: reportbug 13.2.0 Date: Tue, 14 Oct 2025 00:41:41 +0200 X-Debian-User: dparsons Delivered-To: submit@bugs.debian.org Source: pymatgen Version: 2025.10.7+dfsg1-1 Severity: serious Justification: FTBFS X-Debbugs-Cc: debian-arm@lists.debian.org, debian-loongarch@lists.debian.org, debian-powerpc@lists.debian.org User: debian-arm@lists.debian.org Usertags: arm64 User: debian-powerpc@lists.debian.org Usertags: ppc64 ppc64el User: debian-qa@lists.debian.org Usertags: i386 User: debian-loongarch@lists.debian.org Usertags: loong64 Control: forwarded -1 https://github.com/materialsproject/pymatgen/issues/4519 pymatgen 2025.10.7 FTBFS on arm64, ppc64el, i386, loong64, ppc64 in packmol tests =================================== FAILURES =================================== ____________________ TestPackmolSet.test_atoms_constraints _____________________ self = <test_packmol.TestPackmolSet object at 0xffff7443e350> 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 0xffff905acff0>(array([ 3.1658, 0.0496, -4.4769])) E + where <function norm at 0xffff905acff0> = <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([ 3.1658, 0.0496, -4.4769]) = Site: H (3.1658, 0.0496, -4.4769).coords /build/reproducible-path/pymatgen-2025.10.7+dfsg1/.pybuild/test_python3.13/tests/io/test_packmol.py:427: AssertionError ... = 1 failed, 2689 passed, 159 skipped, 294 deselected, 10 xfailed, 2 xpassed, 77 warnings in 1227.19s (0:20:27) = ]