From a9371a9d88d6ed33e4032f0ef87290590515616d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 21 Jan 2023 06:30:13 +0000 Subject: [PATCH 01/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index d5579d3..bd03ff8 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2022.1 %global uversion %{version} %global sover 2022 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -253,6 +253,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jan 21 2023 Fedora Release Engineering - 2022.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Wed Dec 21 2022 Christoph Junghans - 2022.1-1 - Version bump to v2022.1 From fd0e40a3e661d0bddb496372d5e811080f5661c2 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 3 Feb 2023 10:45:55 -0700 Subject: [PATCH 02/33] Version bump to v2023-rc.1 (bug #2166654) --- .gitignore | 1 + sources | 2 +- votca.spec | 14 ++++++++------ 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index a9369ce..5e2642d 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ /votca-2022-rc.2.tar.gz /votca-2022.tar.gz /votca-2022.1.tar.gz +/votca-2023-rc.1.tar.gz diff --git a/sources b/sources index c6010d7..933eb75 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2022.1.tar.gz) = dda5cbf1835440abd1b0b511275e10e5facfa9f133062ae082cca4f5654e4af0be0b574b87c70004c0d07920519927bac5620b89ce073de9985bdf792f0dd21a +SHA512 (votca-2023-rc.1.tar.gz) = 68ceecb3a466262b23cdebadb9e0a4f6e36230d0bdf36538a89b258da1bf63f3a45aae537a6f65c5de15871aa3b827589f035a6bfd97a04612c8ca89a17520b1 diff --git a/votca.spec b/votca.spec index bd03ff8..328f1e2 100644 --- a/votca.spec +++ b/votca.spec @@ -1,8 +1,8 @@ Name: votca -Version: 2022.1 -%global uversion %{version} -%global sover 2022 -Release: 2%{?dist} +Version: 2023~rc1 +%global uversion 2023-rc.1 +%global sover 2023 +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -205,8 +205,7 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %install %cmake_install # Install bash completion file -mkdir -p %{buildroot}%{_datadir}/bash-completion/completions -mv %{buildroot}%{_datadir}/votca/rc/csg-completion.bash %{buildroot}%{_datadir}/bash-completion/completions/votca +%__install -D -m0644 %{__cmake_builddir}/csg/scripts/csg-completion.bash %{buildroot}%{_datadir}/bash-completion/completions/votca %fdupes %{buildroot}%{_prefix} @@ -253,6 +252,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Fri Feb 03 2023 Christoph Junghans - 2023-1 +- Version bump to v2023-rc.1 (bug #2166654) + * Sat Jan 21 2023 Fedora Release Engineering - 2022.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From 9d7fafa3f76b93b7a420fefebbcc4f9ca503b06d Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 3 Feb 2023 20:02:32 -0700 Subject: [PATCH 03/33] fix build on ppc64le --- 1039.patch | 23 +++++++++++++++++++++++ votca.spec | 2 ++ 2 files changed, 25 insertions(+) create mode 100644 1039.patch diff --git a/1039.patch b/1039.patch new file mode 100644 index 0000000..420d4fd --- /dev/null +++ b/1039.patch @@ -0,0 +1,23 @@ +From 7bff1111840d261ed7ae4985150ef8c36ed3ea58 Mon Sep 17 00:00:00 2001 +From: Christoph Junghans +Date: Fri, 3 Feb 2023 19:57:27 -0700 +Subject: [PATCH] increase tolerance for diabatization test + +--- + CHANGELOG.rst | 2 ++ + xtp/src/tests/test_diabatization.cc | 2 +- + 2 files changed, 3 insertions(+), 1 deletion(-) + +diff --git a/xtp/src/tests/test_diabatization.cc b/xtp/src/tests/test_diabatization.cc +index d2ac16c10e..891d065b90 100644 +--- a/xtp/src/tests/test_diabatization.cc ++++ b/xtp/src/tests/test_diabatization.cc +@@ -237,7 +237,7 @@ BOOST_AUTO_TEST_CASE(FCD_coupling_test) { + + double J_ref = 0.00071879817182406039; + double J = coupling * votca::tools::conv::hrt2ev; +- BOOST_CHECK_CLOSE(J_ref, J, 1e-4); ++ BOOST_CHECK_CLOSE(J_ref, J, 1e-3); + + libint2::finalize(); + } diff --git a/votca.spec b/votca.spec index 328f1e2..4d29e27 100644 --- a/votca.spec +++ b/votca.spec @@ -7,6 +7,7 @@ Summary: Versatile Object-oriented Toolkit for Coarse-graining Applicatio License: ASL 2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz +Patch0: 1039.patch %global with_xtp 1 # libint2 used by xtp is broken on 32-bit archs @@ -186,6 +187,7 @@ This package contains bash completion support for the VOTCA package. %prep %setup -q -n %{name}-%{uversion} +%patch0 -p1 # we don't have an espressopp package in Fedora yet rm -rf csg-tutorials/spce/ibi_espressopp From b3ec12cb15eda91aabf74504c0b580cd19345d32 Mon Sep 17 00:00:00 2001 From: Jonathan Wakely Date: Mon, 20 Feb 2023 22:19:13 +0000 Subject: [PATCH 04/33] Rebuilt for Boost 1.81 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 4d29e27..66356b5 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2023~rc1 %global uversion 2023-rc.1 %global sover 2023 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -254,6 +254,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Mon Feb 20 2023 Jonathan Wakely - 2023~rc1-2 +- Rebuilt for Boost 1.81 + * Fri Feb 03 2023 Christoph Junghans - 2023-1 - Version bump to v2023-rc.1 (bug #2166654) From 533dfd0e17b4fd1277eb0f49a22ccbff6f8965d9 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jul 2023 17:52:21 +0000 Subject: [PATCH 05/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 66356b5..450929f 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2023~rc1 %global uversion 2023-rc.1 %global sover 2023 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -254,6 +254,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jul 22 2023 Fedora Release Engineering - 2023~rc1-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Mon Feb 20 2023 Jonathan Wakely - 2023~rc1-2 - Rebuilt for Boost 1.81 From 69d8f991dda1f9ba41440ac9e669c9acb5562837 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 27 Jul 2023 13:29:19 -0600 Subject: [PATCH 06/33] Version bump to v2023-rc.2 --- .gitignore | 1 + 1039.patch | 23 ----------------------- sources | 2 +- votca.spec | 11 ++++++----- 4 files changed, 8 insertions(+), 29 deletions(-) delete mode 100644 1039.patch diff --git a/.gitignore b/.gitignore index 5e2642d..08184df 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ /votca-2022.tar.gz /votca-2022.1.tar.gz /votca-2023-rc.1.tar.gz +/votca-2023-rc.2.tar.gz diff --git a/1039.patch b/1039.patch deleted file mode 100644 index 420d4fd..0000000 --- a/1039.patch +++ /dev/null @@ -1,23 +0,0 @@ -From 7bff1111840d261ed7ae4985150ef8c36ed3ea58 Mon Sep 17 00:00:00 2001 -From: Christoph Junghans -Date: Fri, 3 Feb 2023 19:57:27 -0700 -Subject: [PATCH] increase tolerance for diabatization test - ---- - CHANGELOG.rst | 2 ++ - xtp/src/tests/test_diabatization.cc | 2 +- - 2 files changed, 3 insertions(+), 1 deletion(-) - -diff --git a/xtp/src/tests/test_diabatization.cc b/xtp/src/tests/test_diabatization.cc -index d2ac16c10e..891d065b90 100644 ---- a/xtp/src/tests/test_diabatization.cc -+++ b/xtp/src/tests/test_diabatization.cc -@@ -237,7 +237,7 @@ BOOST_AUTO_TEST_CASE(FCD_coupling_test) { - - double J_ref = 0.00071879817182406039; - double J = coupling * votca::tools::conv::hrt2ev; -- BOOST_CHECK_CLOSE(J_ref, J, 1e-4); -+ BOOST_CHECK_CLOSE(J_ref, J, 1e-3); - - libint2::finalize(); - } diff --git a/sources b/sources index 933eb75..fdb3bc9 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2023-rc.1.tar.gz) = 68ceecb3a466262b23cdebadb9e0a4f6e36230d0bdf36538a89b258da1bf63f3a45aae537a6f65c5de15871aa3b827589f035a6bfd97a04612c8ca89a17520b1 +SHA512 (votca-2023-rc.2.tar.gz) = 983c9139c584541809c11c2299eb94d26a35ff59087771e4fc333d13285cae20c56ed636c8649342274f47760c2b2b40a2e2a030e9f60fc0bad0709c550045c3 diff --git a/votca.spec b/votca.spec index 450929f..1af2fdc 100644 --- a/votca.spec +++ b/votca.spec @@ -1,13 +1,12 @@ Name: votca -Version: 2023~rc1 -%global uversion 2023-rc.1 +Version: 2023~rc2 +%global uversion 2023-rc.2 %global sover 2023 -Release: 3%{?dist} +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz -Patch0: 1039.patch %global with_xtp 1 # libint2 used by xtp is broken on 32-bit archs @@ -187,7 +186,6 @@ This package contains bash completion support for the VOTCA package. %prep %setup -q -n %{name}-%{uversion} -%patch0 -p1 # we don't have an espressopp package in Fedora yet rm -rf csg-tutorials/spce/ibi_espressopp @@ -254,6 +252,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Wed Jul 26 2023 Christoph Junghans - 2023~rc2-1 +- Version bump to v2023-rc.2 + * Sat Jul 22 2023 Fedora Release Engineering - 2023~rc1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From c18c3adcabf46d196fffd4a55db97cd36bdcda5b Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sun, 12 Nov 2023 12:57:58 -0700 Subject: [PATCH 07/33] Rebuild for gromacs-2023 --- votca.spec | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/votca.spec b/votca.spec index 1af2fdc..94423d3 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2023~rc2 %global uversion 2023-rc.2 %global sover 2023 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -18,7 +18,9 @@ Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{na %global with_gmx 1 # no gromacs package on 32-bit archs -%ifarch %ix86 %arm +# and since gmx-2023 also s390x +# same for espressomd +%ifarch %ix86 %arm s390x %global with_gmx 0 %endif @@ -46,12 +48,13 @@ BuildRequires: libint2-devel # mpi packages only used for testing %if %{with_gmx} BuildRequires: gromacs-openmpi -%endif -# not available on 32-bit archs -%ifnarch s390x i686 armv7hl -BuildRequires: python3-espresso-openmpi -%endif +# only needed to run gromacs BuildRequires: openmpi-devel +BuildRequires: python3-espresso-openmpi +%else +%global _openmpi_load %{nil} +%global _openmpi_unload %{nil} +%endif #used for testing only %if %{with_gmx} @@ -252,6 +255,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sun Nov 12 2023 Christoph Junghans - 2023~rc2-2 +- Rebuild for gromacs-2023 + * Wed Jul 26 2023 Christoph Junghans - 2023~rc2-1 - Version bump to v2023-rc.2 From ff1bdc4a6aec3fa894128fe6306b80948a1317a0 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 15 Nov 2023 21:17:52 -0700 Subject: [PATCH 08/33] Version bump to v2023 --- .gitignore | 1 + 1093.patch | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 2 +- votca.spec | 11 +++++--- 4 files changed, 84 insertions(+), 4 deletions(-) create mode 100644 1093.patch diff --git a/.gitignore b/.gitignore index 08184df..efc267f 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ /votca-2022.1.tar.gz /votca-2023-rc.1.tar.gz /votca-2023-rc.2.tar.gz +/votca-2023.tar.gz diff --git a/1093.patch b/1093.patch new file mode 100644 index 0000000..a9c3122 --- /dev/null +++ b/1093.patch @@ -0,0 +1,74 @@ +From e1e568942fef46f63cfae0317a72f86cf4bddf46 Mon Sep 17 00:00:00 2001 +From: Christoph Junghans +Date: Wed, 15 Nov 2023 19:56:20 -0700 +Subject: [PATCH] py: fix all shebangs + +--- + tools/scripts/extract_xml_metadata.py | 2 +- + xtp-tutorials/pyxtp/scripts/run_energy.py | 2 +- + xtp-tutorials/pyxtp/scripts/run_gradient.py | 2 +- + xtp-tutorials/pyxtp/scripts/run_mapchecker.py | 2 +- + xtp-tutorials/pyxtp/scripts/run_optimization.py | 2 +- + xtp/src/pyxtp/pyxtp/capture_standard_output.py | 2 +- + 6 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/tools/scripts/extract_xml_metadata.py b/tools/scripts/extract_xml_metadata.py +index 413fb81f07..fde43f5ec3 100755 +--- a/tools/scripts/extract_xml_metadata.py ++++ b/tools/scripts/extract_xml_metadata.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + # + # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) + # +diff --git a/xtp-tutorials/pyxtp/scripts/run_energy.py b/xtp-tutorials/pyxtp/scripts/run_energy.py +index bf585b91e8..dbc8d2b9d0 100644 +--- a/xtp-tutorials/pyxtp/scripts/run_energy.py ++++ b/xtp-tutorials/pyxtp/scripts/run_energy.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + """Example to compute energies using XTP.""" + from pyxtp import xtp, Visualization + from ase import Atoms +diff --git a/xtp-tutorials/pyxtp/scripts/run_gradient.py b/xtp-tutorials/pyxtp/scripts/run_gradient.py +index 30bfbf0472..16aa6c8730 100644 +--- a/xtp-tutorials/pyxtp/scripts/run_gradient.py ++++ b/xtp-tutorials/pyxtp/scripts/run_gradient.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + """Example to perform a gradient calculation.""" + from pyxtp import xtp + from ase import Atoms +diff --git a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py +index 41db246465..f53783ce68 100755 +--- a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py ++++ b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + """Examples to show xtp_binds usage.""" + from pyxtp import xtp_binds + from pathlib import Path +diff --git a/xtp-tutorials/pyxtp/scripts/run_optimization.py b/xtp-tutorials/pyxtp/scripts/run_optimization.py +index 3a624e35b5..c4301b43af 100644 +--- a/xtp-tutorials/pyxtp/scripts/run_optimization.py ++++ b/xtp-tutorials/pyxtp/scripts/run_optimization.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + """Example to optimize the geometry of CO""" + from pyxtp import xtp + from ase.io import write +diff --git a/xtp/src/pyxtp/pyxtp/capture_standard_output.py b/xtp/src/pyxtp/pyxtp/capture_standard_output.py +index 5cc5e14c2d..ec5514ac33 100644 +--- a/xtp/src/pyxtp/pyxtp/capture_standard_output.py ++++ b/xtp/src/pyxtp/pyxtp/capture_standard_output.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/env python3 + """Examples to show xtp_binds usage.""" + import io + from contextlib import redirect_stdout diff --git a/sources b/sources index fdb3bc9..70f3d0e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2023-rc.2.tar.gz) = 983c9139c584541809c11c2299eb94d26a35ff59087771e4fc333d13285cae20c56ed636c8649342274f47760c2b2b40a2e2a030e9f60fc0bad0709c550045c3 +SHA512 (votca-2023.tar.gz) = eb8a3c8629991f3bfcd5dc5cca0d21f6c8a246d259868d8ba9866d7e9922ef8cf31ff652209ff930cb2ce7f402df7fb70652c70c97075771519301756305d9ff diff --git a/votca.spec b/votca.spec index 94423d3..809f1c6 100644 --- a/votca.spec +++ b/votca.spec @@ -1,12 +1,13 @@ Name: votca -Version: 2023~rc2 -%global uversion 2023-rc.2 +Version: 2023 +%global uversion %{version} %global sover 2023 -Release: 2%{?dist} +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz +Patch0: 1093.patch %global with_xtp 1 # libint2 used by xtp is broken on 32-bit archs @@ -189,6 +190,7 @@ This package contains bash completion support for the VOTCA package. %prep %setup -q -n %{name}-%{uversion} +%patch 0 -p1 # we don't have an espressopp package in Fedora yet rm -rf csg-tutorials/spce/ibi_espressopp @@ -255,6 +257,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Thu Nov 16 2023 Christoph Junghans - 2023-1 +- Version bump to v2023 + * Sun Nov 12 2023 Christoph Junghans - 2023~rc2-2 - Rebuild for gromacs-2023 From 55adc3a82008d36302e9e2b8b50723887941c03b Mon Sep 17 00:00:00 2001 From: Jonathan Wakely Date: Thu, 18 Jan 2024 05:23:59 +0000 Subject: [PATCH 09/33] Rebuilt for Boost 1.83 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 809f1c6..3fe42ae 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2023 %global uversion %{version} %global sover 2023 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -257,6 +257,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Thu Jan 18 2024 Jonathan Wakely - 2023-2 +- Rebuilt for Boost 1.83 + * Thu Nov 16 2023 Christoph Junghans - 2023-1 - Version bump to v2023 From e9ad59a144d6d3164b17b292158bd2433b5358fe Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 24 Jan 2024 21:39:54 -0700 Subject: [PATCH 10/33] Version bump to v2024 (bug#2260025) --- .gitignore | 1 + 1093.patch | 74 ------------------------------------------------------ sources | 2 +- votca.spec | 27 +++++++++----------- 4 files changed, 14 insertions(+), 90 deletions(-) delete mode 100644 1093.patch diff --git a/.gitignore b/.gitignore index efc267f..1c73cdc 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ /votca-2023-rc.1.tar.gz /votca-2023-rc.2.tar.gz /votca-2023.tar.gz +/votca-2024.tar.gz diff --git a/1093.patch b/1093.patch deleted file mode 100644 index a9c3122..0000000 --- a/1093.patch +++ /dev/null @@ -1,74 +0,0 @@ -From e1e568942fef46f63cfae0317a72f86cf4bddf46 Mon Sep 17 00:00:00 2001 -From: Christoph Junghans -Date: Wed, 15 Nov 2023 19:56:20 -0700 -Subject: [PATCH] py: fix all shebangs - ---- - tools/scripts/extract_xml_metadata.py | 2 +- - xtp-tutorials/pyxtp/scripts/run_energy.py | 2 +- - xtp-tutorials/pyxtp/scripts/run_gradient.py | 2 +- - xtp-tutorials/pyxtp/scripts/run_mapchecker.py | 2 +- - xtp-tutorials/pyxtp/scripts/run_optimization.py | 2 +- - xtp/src/pyxtp/pyxtp/capture_standard_output.py | 2 +- - 6 files changed, 6 insertions(+), 6 deletions(-) - -diff --git a/tools/scripts/extract_xml_metadata.py b/tools/scripts/extract_xml_metadata.py -index 413fb81f07..fde43f5ec3 100755 ---- a/tools/scripts/extract_xml_metadata.py -+++ b/tools/scripts/extract_xml_metadata.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - # - # Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org) - # -diff --git a/xtp-tutorials/pyxtp/scripts/run_energy.py b/xtp-tutorials/pyxtp/scripts/run_energy.py -index bf585b91e8..dbc8d2b9d0 100644 ---- a/xtp-tutorials/pyxtp/scripts/run_energy.py -+++ b/xtp-tutorials/pyxtp/scripts/run_energy.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - """Example to compute energies using XTP.""" - from pyxtp import xtp, Visualization - from ase import Atoms -diff --git a/xtp-tutorials/pyxtp/scripts/run_gradient.py b/xtp-tutorials/pyxtp/scripts/run_gradient.py -index 30bfbf0472..16aa6c8730 100644 ---- a/xtp-tutorials/pyxtp/scripts/run_gradient.py -+++ b/xtp-tutorials/pyxtp/scripts/run_gradient.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - """Example to perform a gradient calculation.""" - from pyxtp import xtp - from ase import Atoms -diff --git a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py -index 41db246465..f53783ce68 100755 ---- a/xtp-tutorials/pyxtp/scripts/run_mapchecker.py -+++ b/xtp-tutorials/pyxtp/scripts/run_mapchecker.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - """Examples to show xtp_binds usage.""" - from pyxtp import xtp_binds - from pathlib import Path -diff --git a/xtp-tutorials/pyxtp/scripts/run_optimization.py b/xtp-tutorials/pyxtp/scripts/run_optimization.py -index 3a624e35b5..c4301b43af 100644 ---- a/xtp-tutorials/pyxtp/scripts/run_optimization.py -+++ b/xtp-tutorials/pyxtp/scripts/run_optimization.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - """Example to optimize the geometry of CO""" - from pyxtp import xtp - from ase.io import write -diff --git a/xtp/src/pyxtp/pyxtp/capture_standard_output.py b/xtp/src/pyxtp/pyxtp/capture_standard_output.py -index 5cc5e14c2d..ec5514ac33 100644 ---- a/xtp/src/pyxtp/pyxtp/capture_standard_output.py -+++ b/xtp/src/pyxtp/pyxtp/capture_standard_output.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/env python3 - """Examples to show xtp_binds usage.""" - import io - from contextlib import redirect_stdout diff --git a/sources b/sources index 70f3d0e..8495f27 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2023.tar.gz) = eb8a3c8629991f3bfcd5dc5cca0d21f6c8a246d259868d8ba9866d7e9922ef8cf31ff652209ff930cb2ce7f402df7fb70652c70c97075771519301756305d9ff +SHA512 (votca-2024.tar.gz) = 765bb5e76493a4bb5d00d62911f33d576ba3a3e72ccdf03d5fb66b67fafa12a133da3b19d6883f76f0354be30ecefd3c6537643854c5fe44646db270ba1fa5ff diff --git a/votca.spec b/votca.spec index 3fe42ae..bd10455 100644 --- a/votca.spec +++ b/votca.spec @@ -1,27 +1,22 @@ Name: votca -Version: 2023 +Version: 2024 %global uversion %{version} -%global sover 2023 -Release: 2%{?dist} +%global sover 2024 +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz -Patch0: 1093.patch + +# https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval +ExcludeArch: %{ix86} %global with_xtp 1 -# libint2 used by xtp is broken on 32-bit archs -# https://github.com/evaleev/libint/issues/196 -# https://github.com/votca/xtp/issues/652 -%ifarch %ix86 %arm -%global with_xtp 0 -%endif %global with_gmx 1 -# no gromacs package on 32-bit archs -# and since gmx-2023 also s390x +# no gromacs package on s390x # same for espressomd -%ifarch %ix86 %arm s390x +%ifarch s390x %global with_gmx 0 %endif @@ -189,8 +184,7 @@ Provides: votca-csg-bash = %version-%release This package contains bash completion support for the VOTCA package. %prep -%setup -q -n %{name}-%{uversion} -%patch 0 -p1 +%autosetup -p1 -n %{name}-%{uversion} # we don't have an espressopp package in Fedora yet rm -rf csg-tutorials/spce/ibi_espressopp @@ -257,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Wed Jan 24 2024 Christoph Junghans - 2024-1 +- Version bump to v2024 (bug#2260025) + * Thu Jan 18 2024 Jonathan Wakely - 2023-2 - Rebuilt for Boost 1.83 From 694eef8cdfbce4b7dbe03bd5e7e4621e9b45433a Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 1 Feb 2024 06:48:51 -0700 Subject: [PATCH 11/33] Rebuilt to gromacs-2024 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index bd10455..491f0ef 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2024 %global uversion %{version} %global sover 2024 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Thu Feb 01 2024 Christoph Junghans - 2024-2 +- Rebuilt to gromacs-2024 + * Wed Jan 24 2024 Christoph Junghans - 2024-1 - Version bump to v2024 (bug#2260025) From acfd10ae76567fbb81462040b515f3bacf19dfcb Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 20 Jul 2024 09:00:59 +0000 Subject: [PATCH 12/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 491f0ef..10762cf 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2024 %global uversion %{version} %global sover 2024 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jul 20 2024 Fedora Release Engineering - 2024-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + * Thu Feb 01 2024 Christoph Junghans - 2024-2 - Rebuilt to gromacs-2024 From 4505e1e5d7597cca0b2d3370ed2a217f6066a129 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sat, 20 Jul 2024 14:06:58 -0600 Subject: [PATCH 13/33] Version bump to v2024.1 (bug #2298540) --- .gitignore | 1 + sources | 2 +- votca.spec | 7 +++++-- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 1c73cdc..ed31b05 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ /votca-2023-rc.2.tar.gz /votca-2023.tar.gz /votca-2024.tar.gz +/votca-2024.1.tar.gz diff --git a/sources b/sources index 8495f27..2a38a4c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2024.tar.gz) = 765bb5e76493a4bb5d00d62911f33d576ba3a3e72ccdf03d5fb66b67fafa12a133da3b19d6883f76f0354be30ecefd3c6537643854c5fe44646db270ba1fa5ff +SHA512 (votca-2024.1.tar.gz) = ed54d6883f3ae3cc25b518d178a78352ca4920c1796da55ec69688796c7cff24cf13623cce6af463c0d3e70cee0797a88958d3268a416915921cb4af3aeb98f0 diff --git a/votca.spec b/votca.spec index 10762cf..0781324 100644 --- a/votca.spec +++ b/votca.spec @@ -1,8 +1,8 @@ Name: votca -Version: 2024 +Version: 2024.1 %global uversion %{version} %global sover 2024 -Release: 3%{?dist} +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: ASL 2.0 URL: http://www.votca.org @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jul 20 2024 Christoph Junghans - 2024.1-1 +- Version bump to v2024.1 (bug #2298540) + * Sat Jul 20 2024 Fedora Release Engineering - 2024-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From d41a68a451df6af75ded5fd9c7b1b7e01b136469 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miroslav=20Such=C3=BD?= Date: Wed, 24 Jul 2024 18:08:59 +0200 Subject: [PATCH 14/33] convert ASL 2.0 license to SPDX This is part of https://fedoraproject.org/wiki/Changes/SPDX_Licenses_Phase_4 --- votca.spec | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/votca.spec b/votca.spec index 0781324..0f15b1c 100644 --- a/votca.spec +++ b/votca.spec @@ -2,9 +2,10 @@ Name: votca Version: 2024.1 %global uversion %{version} %global sover 2024 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications -License: ASL 2.0 +# Automatically converted from old format: ASL 2.0 - review is highly recommended. +License: Apache-2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz @@ -251,6 +252,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Wed Jul 24 2024 Miroslav Suchý - 2024.1-2 +- convert license to SPDX + * Sat Jul 20 2024 Christoph Junghans - 2024.1-1 - Version bump to v2024.1 (bug #2298540) From 38a7086daada1b120eed8efca9ef89622f5620ca Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sun, 29 Sep 2024 15:44:21 -0600 Subject: [PATCH 15/33] Version bump to v2024.2 (bug #2315578) --- .gitignore | 1 + sources | 2 +- votca.spec | 8 +++++--- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index ed31b05..9d27553 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ /votca-2023.tar.gz /votca-2024.tar.gz /votca-2024.1.tar.gz +/votca-2024.2.tar.gz diff --git a/sources b/sources index 2a38a4c..20e9e26 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2024.1.tar.gz) = ed54d6883f3ae3cc25b518d178a78352ca4920c1796da55ec69688796c7cff24cf13623cce6af463c0d3e70cee0797a88958d3268a416915921cb4af3aeb98f0 +SHA512 (votca-2024.2.tar.gz) = 39266ac0a106248df36f5d36ea4a0443e72051ea109a48c483640f81a8903da69f551c986899dfdcc305c27c46afb235651cd7df42af2f573888b756bde45f95 diff --git a/votca.spec b/votca.spec index 0f15b1c..a277d94 100644 --- a/votca.spec +++ b/votca.spec @@ -1,10 +1,9 @@ Name: votca -Version: 2024.1 +Version: 2024.2 %global uversion %{version} %global sover 2024 -Release: 2%{?dist} +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications -# Automatically converted from old format: ASL 2.0 - review is highly recommended. License: Apache-2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz @@ -252,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sun Sep 29 2024 Christoph Junghans - 2024.2-1 +- Version bump to v2024.2 (bug #2315578) + * Wed Jul 24 2024 Miroslav Suchý - 2024.1-2 - convert license to SPDX From 57dadd01af82608c39c9a79e11af666a6f5821d6 Mon Sep 17 00:00:00 2001 From: Susi Lehtola Date: Sat, 12 Oct 2024 17:20:13 +0000 Subject: [PATCH 16/33] Bump spec to rebuild against libxc 7 --- votca.spec | 3 +++ 1 file changed, 3 insertions(+) diff --git a/votca.spec b/votca.spec index a277d94..79ea027 100644 --- a/votca.spec +++ b/votca.spec @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Oct 12 2024 Susi Lehtola - 2024.2-2 +- Rebuild against libxc 7.0.0 in rawhide. + * Sun Sep 29 2024 Christoph Junghans - 2024.2-1 - Version bump to v2024.2 (bug #2315578) From 0e0979210ddfc0a90dbc044451fec6140c4a93ad Mon Sep 17 00:00:00 2001 From: Susi Lehtola Date: Sat, 12 Oct 2024 17:25:01 +0000 Subject: [PATCH 17/33] forgot to bump release --- votca.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 79ea027..19bb9d0 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2024.2 %global uversion %{version} %global sover 2024 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org From 40cd9f33deea23627839f8a810c71147c5271000 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Fri, 25 Oct 2024 17:32:59 -0600 Subject: [PATCH 18/33] Rebuild for hdf5 1.14.5 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 19bb9d0..22e9ee3 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2024.2 %global uversion %{version} %global sover 2024 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Fri Oct 25 2024 Orion Poplawski - 2024.2-3 +- Rebuild for hdf5 1.14.5 + * Sat Oct 12 2024 Susi Lehtola - 2024.2-2 - Rebuild against libxc 7.0.0 in rawhide. From 4137298ee739e4dc3b01943792a6806d6b0f88af Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sun, 19 Jan 2025 14:37:37 +0000 Subject: [PATCH 19/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 22e9ee3..2dc355d 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2024.2 %global uversion %{version} %global sover 2024 -Release: 3%{?dist} +Release: 4%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -251,6 +251,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sun Jan 19 2025 Fedora Release Engineering - 2024.2-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + * Fri Oct 25 2024 Orion Poplawski - 2024.2-3 - Rebuild for hdf5 1.14.5 From fb2a9da2cd8a8f14adb5159b1e258469c6a9cb91 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Tue, 25 Feb 2025 12:40:23 -0700 Subject: [PATCH 20/33] Add s390x fix --- votca.spec | 3 +++ 1 file changed, 3 insertions(+) diff --git a/votca.spec b/votca.spec index 2dc355d..e44898c 100644 --- a/votca.spec +++ b/votca.spec @@ -56,7 +56,10 @@ BuildRequires: python3-espresso-openmpi %if %{with_gmx} BuildRequires: gromacs %endif +# no lammps on s390x as mpi is broken +%ifnarch s390x BuildRequires: lammps +%endif BuildRequires: python3-cma BuildRequires: python3-pytest BuildRequires: gnuplot From 368932e009d1cc1629bbdb25cb3bffc9bc70e761 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 28 Mar 2025 12:00:07 -0600 Subject: [PATCH 21/33] Version bump to v2025 (bug #2355797) --- .gitignore | 1 + sources | 2 +- votca.spec | 9 ++++++--- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 9d27553..fd80c82 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ /votca-2024.tar.gz /votca-2024.1.tar.gz /votca-2024.2.tar.gz +/votca-2025.tar.gz diff --git a/sources b/sources index 20e9e26..91d7081 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2024.2.tar.gz) = 39266ac0a106248df36f5d36ea4a0443e72051ea109a48c483640f81a8903da69f551c986899dfdcc305c27c46afb235651cd7df42af2f573888b756bde45f95 +SHA512 (votca-2025.tar.gz) = 64abab25e4b1a71eb0ab19e2f2d930fa4cbe3de60c813d1caebe6a9f482bf088b4cfce8d45e432fa1d64bfc83e842cb700d263f1d9f1c1a9412646ed95931bdc diff --git a/votca.spec b/votca.spec index e44898c..1fbb8f2 100644 --- a/votca.spec +++ b/votca.spec @@ -1,8 +1,8 @@ Name: votca -Version: 2024.2 +Version: 2025 %global uversion %{version} -%global sover 2024 -Release: 4%{?dist} +%global sover 2025 +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -254,6 +254,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Fri Mar 28 2025 Christoph Junghans - 2025-1 +- Version bump to v2025 (bug #2355797) + * Sun Jan 19 2025 Fedora Release Engineering - 2024.2-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild From 53e82516b40e404b51a8bb7deaea36ca7afb4cd9 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 25 Jul 2025 20:13:49 +0000 Subject: [PATCH 22/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 1fbb8f2..c36831e 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2025 %global uversion %{version} %global sover 2025 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -254,6 +254,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Fri Jul 25 2025 Fedora Release Engineering - 2025-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild + * Fri Mar 28 2025 Christoph Junghans - 2025-1 - Version bump to v2025 (bug #2355797) From 926bcdeb1d2accd11f2ebce28b67afba831f57e8 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 14 Aug 2025 06:48:26 -0600 Subject: [PATCH 23/33] Rebuilt for gromacs-2025 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index c36831e..130ec91 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2025 %global uversion %{version} %global sover 2025 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -254,6 +254,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Thu Aug 14 2025 Christoph Junghans - 2025-3 +- Rebuilt for gromacs-2025 + * Fri Jul 25 2025 Fedora Release Engineering - 2025-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild From d181fd7d52ec46ec472818afb631fbb3c571359d Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 3 Oct 2025 14:15:30 -0600 Subject: [PATCH 24/33] Version bump to v2025.1 Fixes: rhbz#2401325 --- .gitignore | 1 + sources | 2 +- votca.spec | 8 ++++++-- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index fd80c82..4098c32 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,4 @@ /votca-2024.1.tar.gz /votca-2024.2.tar.gz /votca-2025.tar.gz +/votca-2025.1.tar.gz diff --git a/sources b/sources index 91d7081..fd5de8c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2025.tar.gz) = 64abab25e4b1a71eb0ab19e2f2d930fa4cbe3de60c813d1caebe6a9f482bf088b4cfce8d45e432fa1d64bfc83e842cb700d263f1d9f1c1a9412646ed95931bdc +SHA512 (votca-2025.1.tar.gz) = 4b199d54a555fe6c640aa8e01fa60ba57d4b26f639521572558b79eb0f741c236e93c8341fb7a28b92122f41912a9901305dd57d15c0fdcd67d89d3f0bc00801 diff --git a/votca.spec b/votca.spec index 130ec91..46c6939 100644 --- a/votca.spec +++ b/votca.spec @@ -1,8 +1,8 @@ Name: votca -Version: 2025 +Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 3%{?dist} +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -254,6 +254,10 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Fri Oct 03 2025 Christoph Junghans - 2025.1-1 +- Version bump to v2025.1 +- Fixes: rhbz#2401325 + * Thu Aug 14 2025 Christoph Junghans - 2025-3 - Rebuilt for gromacs-2025 From 02cfed9ecedb4a296c2daf0bde5593aad5fb7fc9 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sun, 2 Nov 2025 10:56:55 -0700 Subject: [PATCH 25/33] Add support for eigen3 v5 --- 1189.diff | 85 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ votca.spec | 7 ++++- 2 files changed, 91 insertions(+), 1 deletion(-) create mode 100644 1189.diff diff --git a/1189.diff b/1189.diff new file mode 100644 index 0000000..841c98a --- /dev/null +++ b/1189.diff @@ -0,0 +1,85 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 71f2601c2..b35b5a89a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -110,7 +110,7 @@ find_package(Boost 1.71.0 REQUIRED + COMPONENTS program_options filesystem regex timer) + set_package_properties(Boost PROPERTIES TYPE REQUIRED PURPOSE "Extended C++ libraries") + +-find_package(Eigen3 3.3.0 NO_MODULE REQUIRED) ++find_package(Eigen3 NO_MODULE REQUIRED) + set_package_properties(Eigen3 PROPERTIES TYPE REQUIRED PURPOSE "C++ vector data structures") + message(STATUS "Found Eigen3: ${Eigen3_DIR}") + +diff --git a/xtp/include/votca/xtp/glink.h b/xtp/include/votca/xtp/glink.h +index 4b6887228..3e50c8e3f 100644 +--- a/xtp/include/votca/xtp/glink.h ++++ b/xtp/include/votca/xtp/glink.h +@@ -19,6 +19,9 @@ + #ifndef VOTCA_XTP_GLINK_H + #define VOTCA_XTP_GLINK_H + ++// Standard includes ++#include ++ + // Local VOTCA includes + #include "eigen.h" + +diff --git a/xtp/include/votca/xtp/openmp_cuda.h b/xtp/include/votca/xtp/openmp_cuda.h +index 53d9052c2..bc78b752b 100644 +--- a/xtp/include/votca/xtp/openmp_cuda.h ++++ b/xtp/include/votca/xtp/openmp_cuda.h +@@ -21,6 +21,9 @@ + #ifndef VOTCA_XTP_OPENMP_CUDA_H + #define VOTCA_XTP_OPENMP_CUDA_H + ++// Standard includes ++#include ++ + // Local VOTCA includes + #include "eigen.h" + +diff --git a/xtp/include/votca/xtp/qmstate.h b/xtp/include/votca/xtp/qmstate.h +index c616239b6..e2e0ecabf 100644 +--- a/xtp/include/votca/xtp/qmstate.h ++++ b/xtp/include/votca/xtp/qmstate.h +@@ -22,6 +22,7 @@ + #define VOTCA_XTP_QMSTATE_H + + // Standard includes ++#include + #include + + // VOTCA includes +diff --git a/xtp/src/libxtp/espfit.cc b/xtp/src/libxtp/espfit.cc +index acaf44630..47d3ecdbe 100644 +--- a/xtp/src/libxtp/espfit.cc ++++ b/xtp/src/libxtp/espfit.cc +@@ -192,9 +192,15 @@ StaticSegment Espfit::FitPartialCharges(const Orbitals& orbitals, + << flush; + Eigen::VectorXd charges; + if (do_svd_) { ++#if EIGEN_VERSION_AT_LEAST(3,5,0) ++ Eigen::JacobiSVD svd; ++ svd.setThreshold(conditionnumber_); ++ svd.compute(Amat); ++#else + Eigen::JacobiSVD svd; + svd.setThreshold(conditionnumber_); + svd.compute(Amat, Eigen::ComputeThinU | Eigen::ComputeThinV); ++#endif + charges = svd.solve(Bvec); + XTP_LOG(Log::info, log_) << TimeStamp() << " SVD Done. " << flush; + if ((Bvec.size() - svd.nonzeroSingularValues()) != 0) { +diff --git a/xtp/src/libxtp/symmetric_matrix.cc b/xtp/src/libxtp/symmetric_matrix.cc +index e48593113..e2eac3c87 100644 +--- a/xtp/src/libxtp/symmetric_matrix.cc ++++ b/xtp/src/libxtp/symmetric_matrix.cc +@@ -18,6 +18,7 @@ + */ + + // Standard includes ++#include + #include + + // Local VOTCA includes diff --git a/votca.spec b/votca.spec index 46c6939..dff1ebd 100644 --- a/votca.spec +++ b/votca.spec @@ -2,11 +2,13 @@ Name: votca Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz +# add support for Eigen3 v5, merged upstream, drop in next version bump +Patch0: https://github.com/votca/votca/pull/1189.diff # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval ExcludeArch: %{ix86} @@ -254,6 +256,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sun Nov 02 2025 Christoph Junghans - 2025.1-2 +- Add support for eigen3 v5 + * Fri Oct 03 2025 Christoph Junghans - 2025.1-1 - Version bump to v2025.1 - Fixes: rhbz#2401325 From 8ed5a2c9c200f3ff99a3c77b4f9e36c19e387e54 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 17 Jan 2026 20:03:39 +0000 Subject: [PATCH 26/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index dff1ebd..2fd20e5 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -256,6 +256,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jan 17 2026 Fedora Release Engineering - 2025.1-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild + * Sun Nov 02 2025 Christoph Junghans - 2025.1-2 - Add support for eigen3 v5 From 06314249a6e5bc094f7df491ef5174536049a4ca Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sun, 18 Jan 2026 12:24:13 -0700 Subject: [PATCH 27/33] Fix build with boost-1.90 Fixes: rhbz#2429731 --- ...266b0bec5501d18c47e7b1430dce80c526b6.patch | 584 ++++++++++++++++++ votca.spec | 8 +- 2 files changed, 591 insertions(+), 1 deletion(-) create mode 100644 c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch diff --git a/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch b/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch new file mode 100644 index 0000000..32df74b --- /dev/null +++ b/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch @@ -0,0 +1,584 @@ +From c5aa266b0bec5501d18c47e7b1430dce80c526b6 Mon Sep 17 00:00:00 2001 +From: "B. Baumeier" +Date: Thu, 15 Jan 2026 09:43:40 +0100 +Subject: [PATCH] explicit referencing to boost::format + +--- + csg/src/tools/csg_dlptopol.cc | 7 +++-- + csg/src/tools/csg_gmxtopol.cc | 3 +-- + xtp/src/libxtp/davidsonsolver.cc | 7 ++--- + xtp/src/libxtp/gwbse/bse.cc | 17 ++++++------ + xtp/src/libxtp/gwbse/gwbse.cc | 17 ++++++------ + xtp/src/libxtp/job.cc | 14 +++++----- + xtp/src/libxtp/jobcalculators/eqm.cc | 28 +++++++++----------- + xtp/src/libxtp/jobcalculators/iqm.cc | 38 +++++++++++++-------------- + xtp/src/libxtp/parallelxjobcalc.cc | 10 +++---- + xtp/src/libxtp/tools/diabatization.cc | 17 ++++++------ + 10 files changed, 72 insertions(+), 86 deletions(-) + +diff --git a/csg/src/tools/csg_dlptopol.cc b/csg/src/tools/csg_dlptopol.cc +index d068c791f7..e1549ce005 100644 +--- a/csg/src/tools/csg_dlptopol.cc ++++ b/csg/src/tools/csg_dlptopol.cc +@@ -27,7 +27,6 @@ + + using namespace votca::csg; + using namespace std; +-using boost::format; + + /** + \brief class for writing dlpoly topology files +@@ -158,8 +157,8 @@ bool DLPTopolApp::EvaluateTopology(Topology *top, Topology *) { + + stringstream ss_bp1, ss_bp2; + +- ss_bp1 << format("%8s%8s") % bead_name1 % bead_name2; +- ss_bp2 << format("%8s%8s") % bead_name2 % bead_name1; ++ ss_bp1 << boost::format("%8s%8s") % bead_name1 % bead_name2; ++ ss_bp2 << boost::format("%8s%8s") % bead_name2 % bead_name1; + + bool is_new_pair = true; + +@@ -234,7 +233,7 @@ void DLPTopolApp::WriteMoleculeAtoms(ostream &out, const Molecule &cg) { + btype = btype.substr( + 0, btype.find_first_of("#")); // skip #index of atom from its type + +- out << format("%8s %10f %10f 1 0 1 %10d %8s %8s %10d \n") % ++ out << boost::format("%8s %10f %10f 1 0 1 %10d %8s %8s %10d \n") % + btype % b->getMass() % b->getQ() % (i + 1) % btype % bname % + (i + 1); + //% b->getType()->getName() % b->getMass() % b->getQ() % (i+1) % +diff --git a/csg/src/tools/csg_gmxtopol.cc b/csg/src/tools/csg_gmxtopol.cc +index f041c199cd..a1459a8ef1 100644 +--- a/csg/src/tools/csg_gmxtopol.cc ++++ b/csg/src/tools/csg_gmxtopol.cc +@@ -27,7 +27,6 @@ + + using namespace votca::csg; + using namespace std; +-using boost::format; + + class GmxTopolApp : public CsgApplication { + public: +@@ -77,7 +76,7 @@ void GmxTopolApp::WriteAtoms(ostream &out, Molecule &cg) { + out << "; nr type resnr residue atom cgnr charge mass\n"; + for (votca::Index i = 0; i < cg.BeadCount(); ++i) { + Bead *b = cg.getBead(i); +- out << format("%d %s 1 RES %s %d %f %f\n") % (i + 1) % b->getType() % ++ out << boost::format("%d %s 1 RES %s %d %f %f\n") % (i + 1) % b->getType() % + b->getName() % (i + 1) % b->getQ() % b->getMass(); + } + out << endl; +diff --git a/xtp/src/libxtp/davidsonsolver.cc b/xtp/src/libxtp/davidsonsolver.cc +index e4a340754f..96ed03bc64 100644 +--- a/xtp/src/libxtp/davidsonsolver.cc ++++ b/xtp/src/libxtp/davidsonsolver.cc +@@ -23,9 +23,6 @@ + #include "votca/xtp/davidsonsolver.h" + #include "votca/xtp/eigen.h" + +-using boost::format; +-using std::flush; +- + namespace votca { + namespace xtp { + +@@ -95,7 +92,7 @@ void DavidsonSolver::printIterationData( + double percent_converged = 100 * double(converged_roots) / double(neigen); + XTP_LOG(Log::error, log_) + << TimeStamp() +- << format(" %1$4d %2$12d \t %3$4.2e \t %4$5.2f%% converged") % i_iter_ % ++ << boost::format(" %1$4d %2$12d \t %3$4.2e \t %4$5.2f%% converged") % i_iter_ % + proj.search_space() % rep.res_norm().head(neigen).maxCoeff() % + percent_converged + << std::flush; +@@ -544,7 +541,7 @@ void DavidsonSolver::storeNotConvergedData( + percent_converged *= 100.; + XTP_LOG(Log::error, log_) + << TimeStamp() << "- Warning : Davidson " +- << format("%1$5.2f%%") % percent_converged << " converged after " ++ << boost::format("%1$5.2f%%") % percent_converged << " converged after " + << i_iter_ << " iterations." << std::flush; + info_ = Eigen::ComputationInfo::NoConvergence; + } +diff --git a/xtp/src/libxtp/gwbse/bse.cc b/xtp/src/libxtp/gwbse/bse.cc +index 11ad3ba1ad..300887dda1 100644 +--- a/xtp/src/libxtp/gwbse/bse.cc ++++ b/xtp/src/libxtp/gwbse/bse.cc +@@ -34,7 +34,6 @@ + #include "votca/xtp/rpa.h" + #include "votca/xtp/vc2index.h" + +-using boost::format; + using std::flush; + + namespace votca { +@@ -276,7 +275,7 @@ void BSE::printFragInfo(const std::vector >& frags, + double dq = frag.value().H[state] + frag.value().E[state]; + double qeff = dq + frag.value().Gs; + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " Fragment %1$4d -- hole: %2$5.1f%% electron: " + "%3$5.1f%% dQ: %4$+5.2f Qeff: %5$+5.2f") % + int(frag.getId()) % (100.0 * frag.value().H[state]) % +@@ -292,7 +291,7 @@ void BSE::PrintWeights(const Eigen::VectorXd& weights) const { + double weight = weights(i_bse); + if (weight > opt_.min_print_weight) { + XTP_LOG(Log::error, log_) +- << format(" HOMO-%1$-3d -> LUMO+%2$-3d : %3$3.1f%%") % ++ << boost::format(" HOMO-%1$-3d -> LUMO+%2$-3d : %3$3.1f%%") % + (opt_.homo - vc.v(i_bse)) % (vc.c(i_bse) - opt_.homo - 1) % + (100.0 * weight) + << flush; +@@ -329,7 +328,7 @@ void BSE::Analyze_singlets(std::vector > fragments, + + double osc = oscs[i]; + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " S = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " + "= %4$+1.4f = %5$+1.4f = %6$+1.4f") % + (i + 1) % (hrt2ev * energies(i)) % +@@ -341,7 +340,7 @@ void BSE::Analyze_singlets(std::vector > fragments, + + const Eigen::Vector3d& trdip = orb.TransitionDipoles()[i]; + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " TrDipole length gauge[e*bohr] dx = %1$+1.4f dy = " + "%2$+1.4f dz = %3$+1.4f |d|^2 = %4$+1.4f f = %5$+1.4f") % + trdip[0] % trdip[1] % trdip[2] % (trdip.squaredNorm()) % osc +@@ -379,7 +378,7 @@ void BSE::Analyze_triplets(std::vector > fragments, + } + + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " T = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " + "= %4$+1.4f = %5$+1.4f") % + (i + 1) % (tools::conv::hrt2ev * energies(i)) % +@@ -392,7 +391,7 @@ void BSE::Analyze_triplets(std::vector > fragments, + if (fragments.size() > 0) { + printFragInfo(fragments, i); + } +- XTP_LOG(Log::error, log_) << format(" ") << flush; ++ XTP_LOG(Log::error, log_) << boost::format(" ") << flush; + } + + return; +@@ -597,7 +596,7 @@ void BSE::Perturbative_DynamicalScreening(const QMStateType& type, + for (Index i = 0; i < opt_.nmax; ++i) { + double osc = oscs[i]; + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " S(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " + "nm f " + "= %4$+1.4f") % +@@ -614,7 +613,7 @@ void BSE::Perturbative_DynamicalScreening(const QMStateType& type, + << flush; + for (Index i = 0; i < opt_.nmax; ++i) { + XTP_LOG(Log::error, log_) +- << format( ++ << boost::format( + " T(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " + "nm ") % + (i + 1) % (hrt2ev * BSEenergies_dynamic(i)) % +diff --git a/xtp/src/libxtp/gwbse/gwbse.cc b/xtp/src/libxtp/gwbse/gwbse.cc +index 86ffe9d42b..14ab4a45f6 100644 +--- a/xtp/src/libxtp/gwbse/gwbse.cc ++++ b/xtp/src/libxtp/gwbse/gwbse.cc +@@ -38,7 +38,6 @@ + #include "votca/xtp/vxc_grid.h" + #include "votca/xtp/vxc_potential.h" + +-using boost::format; + using std::flush; + namespace votca { + namespace xtp { +@@ -427,7 +426,7 @@ void GWBSE::addoutput(tools::Property& summary) { + gwbse_summary.setAttribute("units", "eV"); + gwbse_summary.setAttribute( + "DFTEnergy", +- (format("%1$+1.6f ") % (orbitals_.getDFTTotalEnergy() * hrt2ev)).str()); ++ (boost::format("%1$+1.6f ") % (orbitals_.getDFTTotalEnergy() * hrt2ev)).str()); + + tools::Property& dft_summary = gwbse_summary.add("dft", ""); + dft_summary.setAttribute("HOMO", gwopt_.homo); +@@ -438,16 +437,16 @@ void GWBSE::addoutput(tools::Property& summary) { + level_summary.setAttribute("number", state + gwopt_.qpmin); + level_summary.add( + "dft_energy", +- (format("%1$+1.6f ") % ++ (boost::format("%1$+1.6f ") % + (orbitals_.MOs().eigenvalues()(state + gwopt_.qpmin) * hrt2ev)) + .str()); + level_summary.add( + "gw_energy", +- (format("%1$+1.6f ") % (orbitals_.QPpertEnergies()(state) * hrt2ev)) ++ (boost::format("%1$+1.6f ") % (orbitals_.QPpertEnergies()(state) * hrt2ev)) + .str()); + + level_summary.add("qp_energy", +- (format("%1$+1.6f ") % ++ (boost::format("%1$+1.6f ") % + (orbitals_.QPdiag().eigenvalues()(state) * hrt2ev)) + .str()); + } +@@ -458,7 +457,7 @@ void GWBSE::addoutput(tools::Property& summary) { + tools::Property& level_summary = singlet_summary.add("level", ""); + level_summary.setAttribute("number", state + 1); + level_summary.add( +- "omega", (format("%1$+1.6f ") % ++ "omega", (boost::format("%1$+1.6f ") % + (orbitals_.BSESinglets().eigenvalues()(state) * hrt2ev)) + .str()); + if (orbitals_.hasTransitionDipoles()) { +@@ -467,9 +466,9 @@ void GWBSE::addoutput(tools::Property& summary) { + double f = 2 * dipoles.squaredNorm() * + orbitals_.BSESinglets().eigenvalues()(state) / 3.0; + +- level_summary.add("f", (format("%1$+1.6f ") % f).str()); ++ level_summary.add("f", (boost::format("%1$+1.6f ") % f).str()); + tools::Property& dipol_summary = level_summary.add( +- "Trdipole", (format("%1$+1.4f %2$+1.4f %3$+1.4f") % dipoles.x() % ++ "Trdipole", (boost::format("%1$+1.4f %2$+1.4f %3$+1.4f") % dipoles.x() % + dipoles.y() % dipoles.z()) + .str()); + dipol_summary.setAttribute("unit", "e*bohr"); +@@ -483,7 +482,7 @@ void GWBSE::addoutput(tools::Property& summary) { + tools::Property& level_summary = triplet_summary.add("level", ""); + level_summary.setAttribute("number", state + 1); + level_summary.add( +- "omega", (format("%1$+1.6f ") % ++ "omega", (boost::format("%1$+1.6f ") % + (orbitals_.BSETriplets().eigenvalues()(state) * hrt2ev)) + .str()); + } +diff --git a/xtp/src/libxtp/job.cc b/xtp/src/libxtp/job.cc +index d5cef59b56..d01f8895aa 100644 +--- a/xtp/src/libxtp/job.cc ++++ b/xtp/src/libxtp/job.cc +@@ -31,7 +31,7 @@ + + namespace votca { + namespace xtp { +-using boost::format; ++ + Job::Job(const tools::Property &prop) { + + // DEFINED BY USER +@@ -124,23 +124,23 @@ void Job::ToStream(std::ofstream &ofs) const { + "\t\t"); + std::string tab = "\t"; + ofs << tab << "\n"; +- ofs << tab << tab << (format("%1$d\n") % id_).str(); +- ofs << tab << tab << (format("%1$s\n") % tag_).str(); ++ ofs << tab << tab << (boost::format("%1$d\n") % id_).str(); ++ ofs << tab << tab << (boost::format("%1$s\n") % tag_).str(); + ofs << iomXML << input_; + ofs << tab << tab +- << (format("%1$s\n") % ConvertStatus(status_)).str(); ++ << (boost::format("%1$s\n") % ConvertStatus(status_)).str(); + + if (has_host_) { +- ofs << tab << tab << (format("%1$s\n") % host_).str(); ++ ofs << tab << tab << (boost::format("%1$s\n") % host_).str(); + } + if (has_time_) { +- ofs << tab << tab << (format("\n") % time_).str(); ++ ofs << tab << tab << (boost::format("\n") % time_).str(); + } + if (has_output_) { + ofs << iomXML << output_; + } + if (has_error_) { +- ofs << tab << tab << (format("%1$s\n") % error_).str(); ++ ofs << tab << tab << (boost::format("%1$s\n") % error_).str(); + } + ofs << tab << "\n"; + return; +diff --git a/xtp/src/libxtp/jobcalculators/eqm.cc b/xtp/src/libxtp/jobcalculators/eqm.cc +index 93e0a77cfe..2158f3ffc9 100644 +--- a/xtp/src/libxtp/jobcalculators/eqm.cc ++++ b/xtp/src/libxtp/jobcalculators/eqm.cc +@@ -30,8 +30,6 @@ + // Local private VOTCA includes + #include "eqm.h" + +-using boost::format; +- + namespace votca { + namespace xtp { + +@@ -76,7 +74,7 @@ void EQM::WriteJobFile(const Topology& top) { + tools::Property Input; + tools::Property& pInput = Input.add("input", ""); + tools::Property& pSegment = +- pInput.add("segment", (format("%1$s") % segment.getId()).str()); ++ pInput.add("segment", (boost::format("%1$s") % segment.getId()).str()); + pSegment.setAttribute("type", segment.getType()); + pSegment.setAttribute("id", segment.getId()); + Job job(id, tag, Input, Job::AVAILABLE); +@@ -136,8 +134,8 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + std::string frame_dir = + "frame_" + boost::lexical_cast(top.getStep()); + std::string orb_file = +- (format("%1%_%2%%3%") % "molecule" % segId % ".orb").str(); +- std::string mol_dir = (format("%1%%2%%3%") % "molecule" % "_" % segId).str(); ++ (boost::format("%1%_%2%%3%") % "molecule" % segId % ".orb").str(); ++ std::string mol_dir = (boost::format("%1%%2%%3%") % "molecule" % "_" % segId).str(); + std::string package_append = "workdir_" + Identify(); + std::string work_dir = + (arg_path / eqm_work_dir / package_append / frame_dir / mol_dir) +@@ -154,10 +152,10 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + XTP_LOG(Log::error, pLog) << "Running DFT" << std::flush; + Logger dft_logger(votca::Log::current_level); + dft_logger.setMultithreading(false); +- dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); +- dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); +- dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); +- dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); ++ dft_logger.setPreface(Log::info, (boost::format("\nDFT INF ...")).str()); ++ dft_logger.setPreface(Log::error, (boost::format("\nDFT ERR ...")).str()); ++ dft_logger.setPreface(Log::warning, (boost::format("\nDFT WAR ...")).str()); ++ dft_logger.setPreface(Log::debug, (boost::format("\nDFT DBG ...")).str()); + std::string package = package_options_.get(".name").as(); + std::unique_ptr qmpackage = QMPackageFactory().Create(package); + qmpackage->setLog(&dft_logger); +@@ -198,7 +196,7 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + std::string DIR = eqm_work_dir + "/molecules/" + frame_dir; + std::filesystem::create_directories(DIR); + std::string gbw_file = +- (format("%1%_%2%%3%") % "molecule" % segId % ".gbw").str(); ++ (boost::format("%1%_%2%%3%") % "molecule" % segId % ".gbw").str(); + std::string GBWFILE = DIR + "/" + gbw_file; + XTP_LOG(Log::error, pLog) + << "Copying MO data to " << gbw_file << std::flush; +@@ -230,10 +228,10 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + GWBSE gwbse = GWBSE(orbitals); + Logger gwbse_logger(votca::Log::current_level); + gwbse_logger.setMultithreading(false); +- gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); +- gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); +- gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); +- gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); ++ gwbse_logger.setPreface(Log::info, (boost::format("\nGWBSE INF ...")).str()); ++ gwbse_logger.setPreface(Log::error, (boost::format("\nGWBSE ERR ...")).str()); ++ gwbse_logger.setPreface(Log::warning, (boost::format("\nGWBSE WAR ...")).str()); ++ gwbse_logger.setPreface(Log::debug, (boost::format("\nGWBSE DBG ...")).str()); + gwbse.setLogger(&gwbse_logger); + gwbse.Initialize(gwbse_options_); + gwbse.Evaluate(); +@@ -254,7 +252,7 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + std::string ESPDIR = + "MP_FILES/" + frame_dir + "/" + esp2multipole.GetStateString(); + StaticSegment seg2 = esp2multipole.Extractingcharges(orbitals); +- std::string mps_file = (format("%1%_%2%_%3%.mps") % segType % segId % ++ std::string mps_file = (boost::format("%1%_%2%_%3%.mps") % segType % segId % + esp2multipole.GetStateString()) + .str(); + std::filesystem::create_directories(ESPDIR); +diff --git a/xtp/src/libxtp/jobcalculators/iqm.cc b/xtp/src/libxtp/jobcalculators/iqm.cc +index 533be1bb5c..f154e1a4d4 100644 +--- a/xtp/src/libxtp/jobcalculators/iqm.cc ++++ b/xtp/src/libxtp/jobcalculators/iqm.cc +@@ -36,8 +36,6 @@ + // Local private VOTCA includes + #include "iqm.h" + +-using boost::format; +- + namespace votca { + namespace xtp { + +@@ -211,23 +209,23 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + + // set the folders + std::string pair_dir = +- (format("%1%%2%%3%%4%%5%") % "pair" % "_" % ID_A % "_" % ID_B).str(); ++ (boost::format("%1%%2%%3%%4%%5%") % "pair" % "_" % ID_A % "_" % ID_B).str(); + + std::filesystem::path arg_path, arg_pathA, arg_pathB, arg_pathAB; + + std::string orbFileA = + (arg_pathA / eqm_work_dir / "molecules" / frame_dir / +- (format("%1%_%2%%3%") % "molecule" % ID_A % ".orb").str()) ++ (boost::format("%1%_%2%%3%") % "molecule" % ID_A % ".orb").str()) + .generic_string(); + ; + std::string orbFileB = + (arg_pathB / eqm_work_dir / "molecules" / frame_dir / +- (format("%1%_%2%%3%") % "molecule" % ID_B % ".orb").str()) ++ (boost::format("%1%_%2%%3%") % "molecule" % ID_B % ".orb").str()) + .generic_string(); + ; + std::string orbFileAB = + (arg_pathAB / iqm_work_dir / "pairs_iqm" / frame_dir / +- (format("%1%%2%%3%%4%%5%") % "pair_" % ID_A % "_" % ID_B % ".orb").str()) ++ (boost::format("%1%%2%%3%%4%%5%") % "pair_" % ID_A % "_" % ID_B % ".orb").str()) + .generic_string(); + ; + std::string orb_dir = +@@ -287,10 +285,10 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + + Logger dft_logger(Log::current_level); + dft_logger.setMultithreading(false); +- dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); +- dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); +- dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); +- dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); ++ dft_logger.setPreface(Log::info, (boost::format("\nDFT INF ...")).str()); ++ dft_logger.setPreface(Log::error, (boost::format("\nDFT ERR ...")).str()); ++ dft_logger.setPreface(Log::warning, (boost::format("\nDFT WAR ...")).str()); ++ dft_logger.setPreface(Log::debug, (boost::format("\nDFT DBG ...")).str()); + std::string package = dftpackage_options_.get("name").as(); + std::unique_ptr qmpackage = QMPackageFactory().Create(package); + qmpackage->setLog(&dft_logger); +@@ -316,12 +314,12 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + << "Copying monomer .gbw files to pair folder" << std::flush; + std::string gbwFileA = + (arg_pathA / eqm_work_dir / "molecules" / frame_dir / +- (format("%1%_%2%%3%") % "molecule" % ID_A % ".gbw").str()) ++ (boost::format("%1%_%2%%3%") % "molecule" % ID_A % ".gbw").str()) + .generic_string(); + ; + std::string gbwFileB = + (arg_pathB / eqm_work_dir / "molecules" / frame_dir / +- (format("%1%_%2%%3%") % "molecule" % ID_B % ".gbw").str()) ++ (boost::format("%1%_%2%%3%") % "molecule" % ID_B % ".gbw").str()) + .generic_string(); + ; + std::string gbwFileA_workdir = +@@ -451,10 +449,10 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + XTP_LOG(Log::error, pLog) << "Running GWBSE" << std::flush; + Logger gwbse_logger(Log::current_level); + gwbse_logger.setMultithreading(false); +- gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); +- gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); +- gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); +- gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); ++ gwbse_logger.setPreface(Log::info, (boost::format("\nGWBSE INF ...")).str()); ++ gwbse_logger.setPreface(Log::error, (boost::format("\nGWBSE ERR ...")).str()); ++ gwbse_logger.setPreface(Log::warning, (boost::format("\nGWBSE WAR ...")).str()); ++ gwbse_logger.setPreface(Log::debug, (boost::format("\nGWBSE DBG ...")).str()); + GWBSE gwbse = GWBSE(orbitalsAB); + gwbse.setLogger(&gwbse_logger); + gwbse.Initialize(gwbse_options_); +@@ -507,13 +505,13 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { + Logger bsecoupling_logger(Log::current_level); + bsecoupling_logger.setMultithreading(false); + bsecoupling_logger.setPreface(Log::info, +- (format("\nBSECOU INF ...")).str()); ++ (boost::format("\nBSECOU INF ...")).str()); + bsecoupling_logger.setPreface(Log::error, +- (format("\nBSECOU ERR ...")).str()); ++ (boost::format("\nBSECOU ERR ...")).str()); + bsecoupling_logger.setPreface(Log::warning, +- (format("\nBSECOU WAR ...")).str()); ++ (boost::format("\nBSECOU WAR ...")).str()); + bsecoupling_logger.setPreface(Log::debug, +- (format("\nBSECOU DBG ...")).str()); ++ (boost::format("\nBSECOU DBG ...")).str()); + bsecoupling.setLogger(&bsecoupling_logger); + bsecoupling.Initialize(bsecoupling_options_); + bsecoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); +diff --git a/xtp/src/libxtp/parallelxjobcalc.cc b/xtp/src/libxtp/parallelxjobcalc.cc +index fe8b0402c4..ed48189937 100644 +--- a/xtp/src/libxtp/parallelxjobcalc.cc ++++ b/xtp/src/libxtp/parallelxjobcalc.cc +@@ -28,8 +28,6 @@ + // Local VOTCA includes + #include "votca/xtp/parallelxjobcalc.h" + +-using boost::format; +- + namespace votca { + namespace xtp { + +@@ -124,13 +122,13 @@ void ParallelXJobCalc::CustomizeLogger(QMThread &thread) { + log.setMultithreading(maverick_); + + log.setPreface(Log::info, +- (format("\nT%1$02d INF ...") % thread.getId()).str()); ++ (boost::format("\nT%1$02d INF ...") % thread.getId()).str()); + log.setPreface(Log::error, +- (format("\nT%1$02d ERR ...") % thread.getId()).str()); ++ (boost::format("\nT%1$02d ERR ...") % thread.getId()).str()); + log.setPreface(Log::warning, +- (format("\nT%1$02d WAR ...") % thread.getId()).str()); ++ (boost::format("\nT%1$02d WAR ...") % thread.getId()).str()); + log.setPreface(Log::debug, +- (format("\nT%1$02d DBG ...") % thread.getId()).str()); ++ (boost::format("\nT%1$02d DBG ...") % thread.getId()).str()); + } + + // REGISTER PARALLEL CALCULATORS +diff --git a/xtp/src/libxtp/tools/diabatization.cc b/xtp/src/libxtp/tools/diabatization.cc +index f9e7e256bb..33ae5eef9f 100644 +--- a/xtp/src/libxtp/tools/diabatization.cc ++++ b/xtp/src/libxtp/tools/diabatization.cc +@@ -17,7 +17,6 @@ + + #include "diabatization.h" + +-using boost::format; + using std::flush; + + namespace votca { +@@ -145,11 +144,11 @@ bool Diabatization::Run() { + // Printing Output + if (!isQMMM_) { + XTP_LOG(Log::error, log_) +- << format("Diabatic Energy 1: %1$+1.12f eV") % ++ << boost::format("Diabatic Energy 1: %1$+1.12f eV") % + (diabatic_H(0, 0) * votca::tools::conv::hrt2ev) + << flush; + XTP_LOG(Log::error, log_) +- << format("Diabatic Energy 2: %1$+1.12f eV") % ++ << boost::format("Diabatic Energy 2: %1$+1.12f eV") % + (diabatic_H(1, 1) * votca::tools::conv::hrt2ev) + << flush; + E1_ = E1ad; +@@ -178,7 +177,7 @@ bool Diabatization::Run() { + J = coupling.second * votca::tools::conv::hrt2ev; + + XTP_LOG(Log::error, log_) +- << format("Unprojected diabatic Coupling: %1$+1.12f eV") % (J_unproj) ++ << boost::format("Unprojected diabatic Coupling: %1$+1.12f eV") % (J_unproj) + << flush; + std::pair Ead = GMHDiabatization.adiabatic_energies(); + +@@ -214,26 +213,26 @@ bool Diabatization::Run() { + + // print output + XTP_LOG(Log::error, log_) +- << format("Internal adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % ++ << boost::format("Internal adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % + (E1ad * votca::tools::conv::hrt2ev) % + (E2ad * votca::tools::conv::hrt2ev) + << flush; + + XTP_LOG(Log::error, log_) +- << format("Diabatic Coupling: %1$+1.12f eV ") % (J) << flush; ++ << boost::format("Diabatic Coupling: %1$+1.12f eV ") % (J) << flush; + if (isQMMM_) { + + XTP_LOG(Log::error, log_) +- << format("QMMM adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % ++ << boost::format("QMMM adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % + (E1_ * votca::tools::conv::hrt2ev) % + (E2_ * votca::tools::conv::hrt2ev) + << flush; + + XTP_LOG(Log::error, log_) +- << format("QMMM correction factor: %1$+1.12f ") % (QMMM_correction) ++ << boost::format("QMMM correction factor: %1$+1.12f ") % (QMMM_correction) + << flush; + XTP_LOG(Log::error, log_) +- << format("Diabatic Coupling with QMMM: %1$+1.12f eV ") % (J_QMMM) ++ << boost::format("Diabatic Coupling with QMMM: %1$+1.12f eV ") % (J_QMMM) + << flush; + } + diff --git a/votca.spec b/votca.spec index 2fd20e5..c7822a7 100644 --- a/votca.spec +++ b/votca.spec @@ -2,13 +2,15 @@ Name: votca Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 3%{?dist} +Release: 4%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz # add support for Eigen3 v5, merged upstream, drop in next version bump Patch0: https://github.com/votca/votca/pull/1189.diff +# fix build with boost-1.90, merged upstream, drop in next version bump +Patch1: c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval ExcludeArch: %{ix86} @@ -256,6 +258,10 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sun Jan 18 2026 Christoph Junghans - 2025.1-4 +- Fix build with boost-1.90 +- Fixes: rhbz#2429731 + * Sat Jan 17 2026 Fedora Release Engineering - 2025.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild From dc670d9d9818718bfa8c50d0fca23be75d1d78c2 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sat, 31 Jan 2026 10:01:49 -0700 Subject: [PATCH 28/33] Rebuild for gromacs-2026 Fixes: rhbz#2432566 --- votca.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index c7822a7..711b14e 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 4%{?dist} +Release: 5%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -258,6 +258,10 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Sat Jan 31 2026 Christoph Junghans - 2025.1-5 +- Rebuild for gromacs-2026 +- Fixes: rhbz#2432566 + * Sun Jan 18 2026 Christoph Junghans - 2025.1-4 - Fix build with boost-1.90 - Fixes: rhbz#2429731 From 75df220c2b3a6273d3bdffb20d2d50deeb9bed09 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 23 Feb 2026 20:42:16 -0700 Subject: [PATCH 29/33] BR cmake instead of cmake3 --- votca.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/votca.spec b/votca.spec index 711b14e..10471f5 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2025.1 %global uversion %{version} %global sover 2025 -Release: 5%{?dist} +Release: 6%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -26,7 +26,7 @@ ExcludeArch: %{ix86} BuildRequires: gcc-c++ BuildRequires: fdupes -BuildRequires: cmake3 +BuildRequires: cmake BuildRequires: expat-devel BuildRequires: fftw-devel BuildRequires: eigen3-devel @@ -258,6 +258,9 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Tue Feb 24 2026 Orion Poplawski - 2025.1-6 +- BR cmake instead of cmake3 + * Sat Jan 31 2026 Christoph Junghans - 2025.1-5 - Rebuild for gromacs-2026 - Fixes: rhbz#2432566 From 9d8c7be04d3450e3f8d7e6e21b2535f33f9109b4 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Mon, 9 Mar 2026 15:16:08 -0600 Subject: [PATCH 30/33] Version bump to v2026 Fixes: rhbz#2445810 --- .gitignore | 1 + 1189.diff | 85 --- ...266b0bec5501d18c47e7b1430dce80c526b6.patch | 584 ------------------ sources | 2 +- votca.spec | 32 +- 5 files changed, 11 insertions(+), 693 deletions(-) delete mode 100644 1189.diff delete mode 100644 c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch diff --git a/.gitignore b/.gitignore index 4098c32..1d7c121 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ /votca-2024.2.tar.gz /votca-2025.tar.gz /votca-2025.1.tar.gz +/votca-2026.tar.gz diff --git a/1189.diff b/1189.diff deleted file mode 100644 index 841c98a..0000000 --- a/1189.diff +++ /dev/null @@ -1,85 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 71f2601c2..b35b5a89a 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -110,7 +110,7 @@ find_package(Boost 1.71.0 REQUIRED - COMPONENTS program_options filesystem regex timer) - set_package_properties(Boost PROPERTIES TYPE REQUIRED PURPOSE "Extended C++ libraries") - --find_package(Eigen3 3.3.0 NO_MODULE REQUIRED) -+find_package(Eigen3 NO_MODULE REQUIRED) - set_package_properties(Eigen3 PROPERTIES TYPE REQUIRED PURPOSE "C++ vector data structures") - message(STATUS "Found Eigen3: ${Eigen3_DIR}") - -diff --git a/xtp/include/votca/xtp/glink.h b/xtp/include/votca/xtp/glink.h -index 4b6887228..3e50c8e3f 100644 ---- a/xtp/include/votca/xtp/glink.h -+++ b/xtp/include/votca/xtp/glink.h -@@ -19,6 +19,9 @@ - #ifndef VOTCA_XTP_GLINK_H - #define VOTCA_XTP_GLINK_H - -+// Standard includes -+#include -+ - // Local VOTCA includes - #include "eigen.h" - -diff --git a/xtp/include/votca/xtp/openmp_cuda.h b/xtp/include/votca/xtp/openmp_cuda.h -index 53d9052c2..bc78b752b 100644 ---- a/xtp/include/votca/xtp/openmp_cuda.h -+++ b/xtp/include/votca/xtp/openmp_cuda.h -@@ -21,6 +21,9 @@ - #ifndef VOTCA_XTP_OPENMP_CUDA_H - #define VOTCA_XTP_OPENMP_CUDA_H - -+// Standard includes -+#include -+ - // Local VOTCA includes - #include "eigen.h" - -diff --git a/xtp/include/votca/xtp/qmstate.h b/xtp/include/votca/xtp/qmstate.h -index c616239b6..e2e0ecabf 100644 ---- a/xtp/include/votca/xtp/qmstate.h -+++ b/xtp/include/votca/xtp/qmstate.h -@@ -22,6 +22,7 @@ - #define VOTCA_XTP_QMSTATE_H - - // Standard includes -+#include - #include - - // VOTCA includes -diff --git a/xtp/src/libxtp/espfit.cc b/xtp/src/libxtp/espfit.cc -index acaf44630..47d3ecdbe 100644 ---- a/xtp/src/libxtp/espfit.cc -+++ b/xtp/src/libxtp/espfit.cc -@@ -192,9 +192,15 @@ StaticSegment Espfit::FitPartialCharges(const Orbitals& orbitals, - << flush; - Eigen::VectorXd charges; - if (do_svd_) { -+#if EIGEN_VERSION_AT_LEAST(3,5,0) -+ Eigen::JacobiSVD svd; -+ svd.setThreshold(conditionnumber_); -+ svd.compute(Amat); -+#else - Eigen::JacobiSVD svd; - svd.setThreshold(conditionnumber_); - svd.compute(Amat, Eigen::ComputeThinU | Eigen::ComputeThinV); -+#endif - charges = svd.solve(Bvec); - XTP_LOG(Log::info, log_) << TimeStamp() << " SVD Done. " << flush; - if ((Bvec.size() - svd.nonzeroSingularValues()) != 0) { -diff --git a/xtp/src/libxtp/symmetric_matrix.cc b/xtp/src/libxtp/symmetric_matrix.cc -index e48593113..e2eac3c87 100644 ---- a/xtp/src/libxtp/symmetric_matrix.cc -+++ b/xtp/src/libxtp/symmetric_matrix.cc -@@ -18,6 +18,7 @@ - */ - - // Standard includes -+#include - #include - - // Local VOTCA includes diff --git a/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch b/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch deleted file mode 100644 index 32df74b..0000000 --- a/c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch +++ /dev/null @@ -1,584 +0,0 @@ -From c5aa266b0bec5501d18c47e7b1430dce80c526b6 Mon Sep 17 00:00:00 2001 -From: "B. Baumeier" -Date: Thu, 15 Jan 2026 09:43:40 +0100 -Subject: [PATCH] explicit referencing to boost::format - ---- - csg/src/tools/csg_dlptopol.cc | 7 +++-- - csg/src/tools/csg_gmxtopol.cc | 3 +-- - xtp/src/libxtp/davidsonsolver.cc | 7 ++--- - xtp/src/libxtp/gwbse/bse.cc | 17 ++++++------ - xtp/src/libxtp/gwbse/gwbse.cc | 17 ++++++------ - xtp/src/libxtp/job.cc | 14 +++++----- - xtp/src/libxtp/jobcalculators/eqm.cc | 28 +++++++++----------- - xtp/src/libxtp/jobcalculators/iqm.cc | 38 +++++++++++++-------------- - xtp/src/libxtp/parallelxjobcalc.cc | 10 +++---- - xtp/src/libxtp/tools/diabatization.cc | 17 ++++++------ - 10 files changed, 72 insertions(+), 86 deletions(-) - -diff --git a/csg/src/tools/csg_dlptopol.cc b/csg/src/tools/csg_dlptopol.cc -index d068c791f7..e1549ce005 100644 ---- a/csg/src/tools/csg_dlptopol.cc -+++ b/csg/src/tools/csg_dlptopol.cc -@@ -27,7 +27,6 @@ - - using namespace votca::csg; - using namespace std; --using boost::format; - - /** - \brief class for writing dlpoly topology files -@@ -158,8 +157,8 @@ bool DLPTopolApp::EvaluateTopology(Topology *top, Topology *) { - - stringstream ss_bp1, ss_bp2; - -- ss_bp1 << format("%8s%8s") % bead_name1 % bead_name2; -- ss_bp2 << format("%8s%8s") % bead_name2 % bead_name1; -+ ss_bp1 << boost::format("%8s%8s") % bead_name1 % bead_name2; -+ ss_bp2 << boost::format("%8s%8s") % bead_name2 % bead_name1; - - bool is_new_pair = true; - -@@ -234,7 +233,7 @@ void DLPTopolApp::WriteMoleculeAtoms(ostream &out, const Molecule &cg) { - btype = btype.substr( - 0, btype.find_first_of("#")); // skip #index of atom from its type - -- out << format("%8s %10f %10f 1 0 1 %10d %8s %8s %10d \n") % -+ out << boost::format("%8s %10f %10f 1 0 1 %10d %8s %8s %10d \n") % - btype % b->getMass() % b->getQ() % (i + 1) % btype % bname % - (i + 1); - //% b->getType()->getName() % b->getMass() % b->getQ() % (i+1) % -diff --git a/csg/src/tools/csg_gmxtopol.cc b/csg/src/tools/csg_gmxtopol.cc -index f041c199cd..a1459a8ef1 100644 ---- a/csg/src/tools/csg_gmxtopol.cc -+++ b/csg/src/tools/csg_gmxtopol.cc -@@ -27,7 +27,6 @@ - - using namespace votca::csg; - using namespace std; --using boost::format; - - class GmxTopolApp : public CsgApplication { - public: -@@ -77,7 +76,7 @@ void GmxTopolApp::WriteAtoms(ostream &out, Molecule &cg) { - out << "; nr type resnr residue atom cgnr charge mass\n"; - for (votca::Index i = 0; i < cg.BeadCount(); ++i) { - Bead *b = cg.getBead(i); -- out << format("%d %s 1 RES %s %d %f %f\n") % (i + 1) % b->getType() % -+ out << boost::format("%d %s 1 RES %s %d %f %f\n") % (i + 1) % b->getType() % - b->getName() % (i + 1) % b->getQ() % b->getMass(); - } - out << endl; -diff --git a/xtp/src/libxtp/davidsonsolver.cc b/xtp/src/libxtp/davidsonsolver.cc -index e4a340754f..96ed03bc64 100644 ---- a/xtp/src/libxtp/davidsonsolver.cc -+++ b/xtp/src/libxtp/davidsonsolver.cc -@@ -23,9 +23,6 @@ - #include "votca/xtp/davidsonsolver.h" - #include "votca/xtp/eigen.h" - --using boost::format; --using std::flush; -- - namespace votca { - namespace xtp { - -@@ -95,7 +92,7 @@ void DavidsonSolver::printIterationData( - double percent_converged = 100 * double(converged_roots) / double(neigen); - XTP_LOG(Log::error, log_) - << TimeStamp() -- << format(" %1$4d %2$12d \t %3$4.2e \t %4$5.2f%% converged") % i_iter_ % -+ << boost::format(" %1$4d %2$12d \t %3$4.2e \t %4$5.2f%% converged") % i_iter_ % - proj.search_space() % rep.res_norm().head(neigen).maxCoeff() % - percent_converged - << std::flush; -@@ -544,7 +541,7 @@ void DavidsonSolver::storeNotConvergedData( - percent_converged *= 100.; - XTP_LOG(Log::error, log_) - << TimeStamp() << "- Warning : Davidson " -- << format("%1$5.2f%%") % percent_converged << " converged after " -+ << boost::format("%1$5.2f%%") % percent_converged << " converged after " - << i_iter_ << " iterations." << std::flush; - info_ = Eigen::ComputationInfo::NoConvergence; - } -diff --git a/xtp/src/libxtp/gwbse/bse.cc b/xtp/src/libxtp/gwbse/bse.cc -index 11ad3ba1ad..300887dda1 100644 ---- a/xtp/src/libxtp/gwbse/bse.cc -+++ b/xtp/src/libxtp/gwbse/bse.cc -@@ -34,7 +34,6 @@ - #include "votca/xtp/rpa.h" - #include "votca/xtp/vc2index.h" - --using boost::format; - using std::flush; - - namespace votca { -@@ -276,7 +275,7 @@ void BSE::printFragInfo(const std::vector >& frags, - double dq = frag.value().H[state] + frag.value().E[state]; - double qeff = dq + frag.value().Gs; - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " Fragment %1$4d -- hole: %2$5.1f%% electron: " - "%3$5.1f%% dQ: %4$+5.2f Qeff: %5$+5.2f") % - int(frag.getId()) % (100.0 * frag.value().H[state]) % -@@ -292,7 +291,7 @@ void BSE::PrintWeights(const Eigen::VectorXd& weights) const { - double weight = weights(i_bse); - if (weight > opt_.min_print_weight) { - XTP_LOG(Log::error, log_) -- << format(" HOMO-%1$-3d -> LUMO+%2$-3d : %3$3.1f%%") % -+ << boost::format(" HOMO-%1$-3d -> LUMO+%2$-3d : %3$3.1f%%") % - (opt_.homo - vc.v(i_bse)) % (vc.c(i_bse) - opt_.homo - 1) % - (100.0 * weight) - << flush; -@@ -329,7 +328,7 @@ void BSE::Analyze_singlets(std::vector > fragments, - - double osc = oscs[i]; - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " S = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " - "= %4$+1.4f = %5$+1.4f = %6$+1.4f") % - (i + 1) % (hrt2ev * energies(i)) % -@@ -341,7 +340,7 @@ void BSE::Analyze_singlets(std::vector > fragments, - - const Eigen::Vector3d& trdip = orb.TransitionDipoles()[i]; - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " TrDipole length gauge[e*bohr] dx = %1$+1.4f dy = " - "%2$+1.4f dz = %3$+1.4f |d|^2 = %4$+1.4f f = %5$+1.4f") % - trdip[0] % trdip[1] % trdip[2] % (trdip.squaredNorm()) % osc -@@ -379,7 +378,7 @@ void BSE::Analyze_triplets(std::vector > fragments, - } - - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " T = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f nm " - "= %4$+1.4f = %5$+1.4f") % - (i + 1) % (tools::conv::hrt2ev * energies(i)) % -@@ -392,7 +391,7 @@ void BSE::Analyze_triplets(std::vector > fragments, - if (fragments.size() > 0) { - printFragInfo(fragments, i); - } -- XTP_LOG(Log::error, log_) << format(" ") << flush; -+ XTP_LOG(Log::error, log_) << boost::format(" ") << flush; - } - - return; -@@ -597,7 +596,7 @@ void BSE::Perturbative_DynamicalScreening(const QMStateType& type, - for (Index i = 0; i < opt_.nmax; ++i) { - double osc = oscs[i]; - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " S(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " - "nm f " - "= %4$+1.4f") % -@@ -614,7 +613,7 @@ void BSE::Perturbative_DynamicalScreening(const QMStateType& type, - << flush; - for (Index i = 0; i < opt_.nmax; ++i) { - XTP_LOG(Log::error, log_) -- << format( -+ << boost::format( - " T(dynamic) = %1$4d Omega = %2$+1.12f eV lamdba = %3$+3.2f " - "nm ") % - (i + 1) % (hrt2ev * BSEenergies_dynamic(i)) % -diff --git a/xtp/src/libxtp/gwbse/gwbse.cc b/xtp/src/libxtp/gwbse/gwbse.cc -index 86ffe9d42b..14ab4a45f6 100644 ---- a/xtp/src/libxtp/gwbse/gwbse.cc -+++ b/xtp/src/libxtp/gwbse/gwbse.cc -@@ -38,7 +38,6 @@ - #include "votca/xtp/vxc_grid.h" - #include "votca/xtp/vxc_potential.h" - --using boost::format; - using std::flush; - namespace votca { - namespace xtp { -@@ -427,7 +426,7 @@ void GWBSE::addoutput(tools::Property& summary) { - gwbse_summary.setAttribute("units", "eV"); - gwbse_summary.setAttribute( - "DFTEnergy", -- (format("%1$+1.6f ") % (orbitals_.getDFTTotalEnergy() * hrt2ev)).str()); -+ (boost::format("%1$+1.6f ") % (orbitals_.getDFTTotalEnergy() * hrt2ev)).str()); - - tools::Property& dft_summary = gwbse_summary.add("dft", ""); - dft_summary.setAttribute("HOMO", gwopt_.homo); -@@ -438,16 +437,16 @@ void GWBSE::addoutput(tools::Property& summary) { - level_summary.setAttribute("number", state + gwopt_.qpmin); - level_summary.add( - "dft_energy", -- (format("%1$+1.6f ") % -+ (boost::format("%1$+1.6f ") % - (orbitals_.MOs().eigenvalues()(state + gwopt_.qpmin) * hrt2ev)) - .str()); - level_summary.add( - "gw_energy", -- (format("%1$+1.6f ") % (orbitals_.QPpertEnergies()(state) * hrt2ev)) -+ (boost::format("%1$+1.6f ") % (orbitals_.QPpertEnergies()(state) * hrt2ev)) - .str()); - - level_summary.add("qp_energy", -- (format("%1$+1.6f ") % -+ (boost::format("%1$+1.6f ") % - (orbitals_.QPdiag().eigenvalues()(state) * hrt2ev)) - .str()); - } -@@ -458,7 +457,7 @@ void GWBSE::addoutput(tools::Property& summary) { - tools::Property& level_summary = singlet_summary.add("level", ""); - level_summary.setAttribute("number", state + 1); - level_summary.add( -- "omega", (format("%1$+1.6f ") % -+ "omega", (boost::format("%1$+1.6f ") % - (orbitals_.BSESinglets().eigenvalues()(state) * hrt2ev)) - .str()); - if (orbitals_.hasTransitionDipoles()) { -@@ -467,9 +466,9 @@ void GWBSE::addoutput(tools::Property& summary) { - double f = 2 * dipoles.squaredNorm() * - orbitals_.BSESinglets().eigenvalues()(state) / 3.0; - -- level_summary.add("f", (format("%1$+1.6f ") % f).str()); -+ level_summary.add("f", (boost::format("%1$+1.6f ") % f).str()); - tools::Property& dipol_summary = level_summary.add( -- "Trdipole", (format("%1$+1.4f %2$+1.4f %3$+1.4f") % dipoles.x() % -+ "Trdipole", (boost::format("%1$+1.4f %2$+1.4f %3$+1.4f") % dipoles.x() % - dipoles.y() % dipoles.z()) - .str()); - dipol_summary.setAttribute("unit", "e*bohr"); -@@ -483,7 +482,7 @@ void GWBSE::addoutput(tools::Property& summary) { - tools::Property& level_summary = triplet_summary.add("level", ""); - level_summary.setAttribute("number", state + 1); - level_summary.add( -- "omega", (format("%1$+1.6f ") % -+ "omega", (boost::format("%1$+1.6f ") % - (orbitals_.BSETriplets().eigenvalues()(state) * hrt2ev)) - .str()); - } -diff --git a/xtp/src/libxtp/job.cc b/xtp/src/libxtp/job.cc -index d5cef59b56..d01f8895aa 100644 ---- a/xtp/src/libxtp/job.cc -+++ b/xtp/src/libxtp/job.cc -@@ -31,7 +31,7 @@ - - namespace votca { - namespace xtp { --using boost::format; -+ - Job::Job(const tools::Property &prop) { - - // DEFINED BY USER -@@ -124,23 +124,23 @@ void Job::ToStream(std::ofstream &ofs) const { - "\t\t"); - std::string tab = "\t"; - ofs << tab << "\n"; -- ofs << tab << tab << (format("%1$d\n") % id_).str(); -- ofs << tab << tab << (format("%1$s\n") % tag_).str(); -+ ofs << tab << tab << (boost::format("%1$d\n") % id_).str(); -+ ofs << tab << tab << (boost::format("%1$s\n") % tag_).str(); - ofs << iomXML << input_; - ofs << tab << tab -- << (format("%1$s\n") % ConvertStatus(status_)).str(); -+ << (boost::format("%1$s\n") % ConvertStatus(status_)).str(); - - if (has_host_) { -- ofs << tab << tab << (format("%1$s\n") % host_).str(); -+ ofs << tab << tab << (boost::format("%1$s\n") % host_).str(); - } - if (has_time_) { -- ofs << tab << tab << (format("\n") % time_).str(); -+ ofs << tab << tab << (boost::format("\n") % time_).str(); - } - if (has_output_) { - ofs << iomXML << output_; - } - if (has_error_) { -- ofs << tab << tab << (format("%1$s\n") % error_).str(); -+ ofs << tab << tab << (boost::format("%1$s\n") % error_).str(); - } - ofs << tab << "\n"; - return; -diff --git a/xtp/src/libxtp/jobcalculators/eqm.cc b/xtp/src/libxtp/jobcalculators/eqm.cc -index 93e0a77cfe..2158f3ffc9 100644 ---- a/xtp/src/libxtp/jobcalculators/eqm.cc -+++ b/xtp/src/libxtp/jobcalculators/eqm.cc -@@ -30,8 +30,6 @@ - // Local private VOTCA includes - #include "eqm.h" - --using boost::format; -- - namespace votca { - namespace xtp { - -@@ -76,7 +74,7 @@ void EQM::WriteJobFile(const Topology& top) { - tools::Property Input; - tools::Property& pInput = Input.add("input", ""); - tools::Property& pSegment = -- pInput.add("segment", (format("%1$s") % segment.getId()).str()); -+ pInput.add("segment", (boost::format("%1$s") % segment.getId()).str()); - pSegment.setAttribute("type", segment.getType()); - pSegment.setAttribute("id", segment.getId()); - Job job(id, tag, Input, Job::AVAILABLE); -@@ -136,8 +134,8 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - std::string frame_dir = - "frame_" + boost::lexical_cast(top.getStep()); - std::string orb_file = -- (format("%1%_%2%%3%") % "molecule" % segId % ".orb").str(); -- std::string mol_dir = (format("%1%%2%%3%") % "molecule" % "_" % segId).str(); -+ (boost::format("%1%_%2%%3%") % "molecule" % segId % ".orb").str(); -+ std::string mol_dir = (boost::format("%1%%2%%3%") % "molecule" % "_" % segId).str(); - std::string package_append = "workdir_" + Identify(); - std::string work_dir = - (arg_path / eqm_work_dir / package_append / frame_dir / mol_dir) -@@ -154,10 +152,10 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - XTP_LOG(Log::error, pLog) << "Running DFT" << std::flush; - Logger dft_logger(votca::Log::current_level); - dft_logger.setMultithreading(false); -- dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); -- dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); -- dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); -- dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); -+ dft_logger.setPreface(Log::info, (boost::format("\nDFT INF ...")).str()); -+ dft_logger.setPreface(Log::error, (boost::format("\nDFT ERR ...")).str()); -+ dft_logger.setPreface(Log::warning, (boost::format("\nDFT WAR ...")).str()); -+ dft_logger.setPreface(Log::debug, (boost::format("\nDFT DBG ...")).str()); - std::string package = package_options_.get(".name").as(); - std::unique_ptr qmpackage = QMPackageFactory().Create(package); - qmpackage->setLog(&dft_logger); -@@ -198,7 +196,7 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - std::string DIR = eqm_work_dir + "/molecules/" + frame_dir; - std::filesystem::create_directories(DIR); - std::string gbw_file = -- (format("%1%_%2%%3%") % "molecule" % segId % ".gbw").str(); -+ (boost::format("%1%_%2%%3%") % "molecule" % segId % ".gbw").str(); - std::string GBWFILE = DIR + "/" + gbw_file; - XTP_LOG(Log::error, pLog) - << "Copying MO data to " << gbw_file << std::flush; -@@ -230,10 +228,10 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - GWBSE gwbse = GWBSE(orbitals); - Logger gwbse_logger(votca::Log::current_level); - gwbse_logger.setMultithreading(false); -- gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); -- gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); -- gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); -- gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); -+ gwbse_logger.setPreface(Log::info, (boost::format("\nGWBSE INF ...")).str()); -+ gwbse_logger.setPreface(Log::error, (boost::format("\nGWBSE ERR ...")).str()); -+ gwbse_logger.setPreface(Log::warning, (boost::format("\nGWBSE WAR ...")).str()); -+ gwbse_logger.setPreface(Log::debug, (boost::format("\nGWBSE DBG ...")).str()); - gwbse.setLogger(&gwbse_logger); - gwbse.Initialize(gwbse_options_); - gwbse.Evaluate(); -@@ -254,7 +252,7 @@ Job::JobResult EQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - std::string ESPDIR = - "MP_FILES/" + frame_dir + "/" + esp2multipole.GetStateString(); - StaticSegment seg2 = esp2multipole.Extractingcharges(orbitals); -- std::string mps_file = (format("%1%_%2%_%3%.mps") % segType % segId % -+ std::string mps_file = (boost::format("%1%_%2%_%3%.mps") % segType % segId % - esp2multipole.GetStateString()) - .str(); - std::filesystem::create_directories(ESPDIR); -diff --git a/xtp/src/libxtp/jobcalculators/iqm.cc b/xtp/src/libxtp/jobcalculators/iqm.cc -index 533be1bb5c..f154e1a4d4 100644 ---- a/xtp/src/libxtp/jobcalculators/iqm.cc -+++ b/xtp/src/libxtp/jobcalculators/iqm.cc -@@ -36,8 +36,6 @@ - // Local private VOTCA includes - #include "iqm.h" - --using boost::format; -- - namespace votca { - namespace xtp { - -@@ -211,23 +209,23 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - - // set the folders - std::string pair_dir = -- (format("%1%%2%%3%%4%%5%") % "pair" % "_" % ID_A % "_" % ID_B).str(); -+ (boost::format("%1%%2%%3%%4%%5%") % "pair" % "_" % ID_A % "_" % ID_B).str(); - - std::filesystem::path arg_path, arg_pathA, arg_pathB, arg_pathAB; - - std::string orbFileA = - (arg_pathA / eqm_work_dir / "molecules" / frame_dir / -- (format("%1%_%2%%3%") % "molecule" % ID_A % ".orb").str()) -+ (boost::format("%1%_%2%%3%") % "molecule" % ID_A % ".orb").str()) - .generic_string(); - ; - std::string orbFileB = - (arg_pathB / eqm_work_dir / "molecules" / frame_dir / -- (format("%1%_%2%%3%") % "molecule" % ID_B % ".orb").str()) -+ (boost::format("%1%_%2%%3%") % "molecule" % ID_B % ".orb").str()) - .generic_string(); - ; - std::string orbFileAB = - (arg_pathAB / iqm_work_dir / "pairs_iqm" / frame_dir / -- (format("%1%%2%%3%%4%%5%") % "pair_" % ID_A % "_" % ID_B % ".orb").str()) -+ (boost::format("%1%%2%%3%%4%%5%") % "pair_" % ID_A % "_" % ID_B % ".orb").str()) - .generic_string(); - ; - std::string orb_dir = -@@ -287,10 +285,10 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - - Logger dft_logger(Log::current_level); - dft_logger.setMultithreading(false); -- dft_logger.setPreface(Log::info, (format("\nDFT INF ...")).str()); -- dft_logger.setPreface(Log::error, (format("\nDFT ERR ...")).str()); -- dft_logger.setPreface(Log::warning, (format("\nDFT WAR ...")).str()); -- dft_logger.setPreface(Log::debug, (format("\nDFT DBG ...")).str()); -+ dft_logger.setPreface(Log::info, (boost::format("\nDFT INF ...")).str()); -+ dft_logger.setPreface(Log::error, (boost::format("\nDFT ERR ...")).str()); -+ dft_logger.setPreface(Log::warning, (boost::format("\nDFT WAR ...")).str()); -+ dft_logger.setPreface(Log::debug, (boost::format("\nDFT DBG ...")).str()); - std::string package = dftpackage_options_.get("name").as(); - std::unique_ptr qmpackage = QMPackageFactory().Create(package); - qmpackage->setLog(&dft_logger); -@@ -316,12 +314,12 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - << "Copying monomer .gbw files to pair folder" << std::flush; - std::string gbwFileA = - (arg_pathA / eqm_work_dir / "molecules" / frame_dir / -- (format("%1%_%2%%3%") % "molecule" % ID_A % ".gbw").str()) -+ (boost::format("%1%_%2%%3%") % "molecule" % ID_A % ".gbw").str()) - .generic_string(); - ; - std::string gbwFileB = - (arg_pathB / eqm_work_dir / "molecules" / frame_dir / -- (format("%1%_%2%%3%") % "molecule" % ID_B % ".gbw").str()) -+ (boost::format("%1%_%2%%3%") % "molecule" % ID_B % ".gbw").str()) - .generic_string(); - ; - std::string gbwFileA_workdir = -@@ -451,10 +449,10 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - XTP_LOG(Log::error, pLog) << "Running GWBSE" << std::flush; - Logger gwbse_logger(Log::current_level); - gwbse_logger.setMultithreading(false); -- gwbse_logger.setPreface(Log::info, (format("\nGWBSE INF ...")).str()); -- gwbse_logger.setPreface(Log::error, (format("\nGWBSE ERR ...")).str()); -- gwbse_logger.setPreface(Log::warning, (format("\nGWBSE WAR ...")).str()); -- gwbse_logger.setPreface(Log::debug, (format("\nGWBSE DBG ...")).str()); -+ gwbse_logger.setPreface(Log::info, (boost::format("\nGWBSE INF ...")).str()); -+ gwbse_logger.setPreface(Log::error, (boost::format("\nGWBSE ERR ...")).str()); -+ gwbse_logger.setPreface(Log::warning, (boost::format("\nGWBSE WAR ...")).str()); -+ gwbse_logger.setPreface(Log::debug, (boost::format("\nGWBSE DBG ...")).str()); - GWBSE gwbse = GWBSE(orbitalsAB); - gwbse.setLogger(&gwbse_logger); - gwbse.Initialize(gwbse_options_); -@@ -507,13 +505,13 @@ Job::JobResult IQM::EvalJob(const Topology& top, Job& job, QMThread& opThread) { - Logger bsecoupling_logger(Log::current_level); - bsecoupling_logger.setMultithreading(false); - bsecoupling_logger.setPreface(Log::info, -- (format("\nBSECOU INF ...")).str()); -+ (boost::format("\nBSECOU INF ...")).str()); - bsecoupling_logger.setPreface(Log::error, -- (format("\nBSECOU ERR ...")).str()); -+ (boost::format("\nBSECOU ERR ...")).str()); - bsecoupling_logger.setPreface(Log::warning, -- (format("\nBSECOU WAR ...")).str()); -+ (boost::format("\nBSECOU WAR ...")).str()); - bsecoupling_logger.setPreface(Log::debug, -- (format("\nBSECOU DBG ...")).str()); -+ (boost::format("\nBSECOU DBG ...")).str()); - bsecoupling.setLogger(&bsecoupling_logger); - bsecoupling.Initialize(bsecoupling_options_); - bsecoupling.CalculateCouplings(orbitalsA, orbitalsB, orbitalsAB); -diff --git a/xtp/src/libxtp/parallelxjobcalc.cc b/xtp/src/libxtp/parallelxjobcalc.cc -index fe8b0402c4..ed48189937 100644 ---- a/xtp/src/libxtp/parallelxjobcalc.cc -+++ b/xtp/src/libxtp/parallelxjobcalc.cc -@@ -28,8 +28,6 @@ - // Local VOTCA includes - #include "votca/xtp/parallelxjobcalc.h" - --using boost::format; -- - namespace votca { - namespace xtp { - -@@ -124,13 +122,13 @@ void ParallelXJobCalc::CustomizeLogger(QMThread &thread) { - log.setMultithreading(maverick_); - - log.setPreface(Log::info, -- (format("\nT%1$02d INF ...") % thread.getId()).str()); -+ (boost::format("\nT%1$02d INF ...") % thread.getId()).str()); - log.setPreface(Log::error, -- (format("\nT%1$02d ERR ...") % thread.getId()).str()); -+ (boost::format("\nT%1$02d ERR ...") % thread.getId()).str()); - log.setPreface(Log::warning, -- (format("\nT%1$02d WAR ...") % thread.getId()).str()); -+ (boost::format("\nT%1$02d WAR ...") % thread.getId()).str()); - log.setPreface(Log::debug, -- (format("\nT%1$02d DBG ...") % thread.getId()).str()); -+ (boost::format("\nT%1$02d DBG ...") % thread.getId()).str()); - } - - // REGISTER PARALLEL CALCULATORS -diff --git a/xtp/src/libxtp/tools/diabatization.cc b/xtp/src/libxtp/tools/diabatization.cc -index f9e7e256bb..33ae5eef9f 100644 ---- a/xtp/src/libxtp/tools/diabatization.cc -+++ b/xtp/src/libxtp/tools/diabatization.cc -@@ -17,7 +17,6 @@ - - #include "diabatization.h" - --using boost::format; - using std::flush; - - namespace votca { -@@ -145,11 +144,11 @@ bool Diabatization::Run() { - // Printing Output - if (!isQMMM_) { - XTP_LOG(Log::error, log_) -- << format("Diabatic Energy 1: %1$+1.12f eV") % -+ << boost::format("Diabatic Energy 1: %1$+1.12f eV") % - (diabatic_H(0, 0) * votca::tools::conv::hrt2ev) - << flush; - XTP_LOG(Log::error, log_) -- << format("Diabatic Energy 2: %1$+1.12f eV") % -+ << boost::format("Diabatic Energy 2: %1$+1.12f eV") % - (diabatic_H(1, 1) * votca::tools::conv::hrt2ev) - << flush; - E1_ = E1ad; -@@ -178,7 +177,7 @@ bool Diabatization::Run() { - J = coupling.second * votca::tools::conv::hrt2ev; - - XTP_LOG(Log::error, log_) -- << format("Unprojected diabatic Coupling: %1$+1.12f eV") % (J_unproj) -+ << boost::format("Unprojected diabatic Coupling: %1$+1.12f eV") % (J_unproj) - << flush; - std::pair Ead = GMHDiabatization.adiabatic_energies(); - -@@ -214,26 +213,26 @@ bool Diabatization::Run() { - - // print output - XTP_LOG(Log::error, log_) -- << format("Internal adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % -+ << boost::format("Internal adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % - (E1ad * votca::tools::conv::hrt2ev) % - (E2ad * votca::tools::conv::hrt2ev) - << flush; - - XTP_LOG(Log::error, log_) -- << format("Diabatic Coupling: %1$+1.12f eV ") % (J) << flush; -+ << boost::format("Diabatic Coupling: %1$+1.12f eV ") % (J) << flush; - if (isQMMM_) { - - XTP_LOG(Log::error, log_) -- << format("QMMM adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % -+ << boost::format("QMMM adiabatic energies: %1$+1.12f eV and %2$+1.12f eV") % - (E1_ * votca::tools::conv::hrt2ev) % - (E2_ * votca::tools::conv::hrt2ev) - << flush; - - XTP_LOG(Log::error, log_) -- << format("QMMM correction factor: %1$+1.12f ") % (QMMM_correction) -+ << boost::format("QMMM correction factor: %1$+1.12f ") % (QMMM_correction) - << flush; - XTP_LOG(Log::error, log_) -- << format("Diabatic Coupling with QMMM: %1$+1.12f eV ") % (J_QMMM) -+ << boost::format("Diabatic Coupling with QMMM: %1$+1.12f eV ") % (J_QMMM) - << flush; - } - diff --git a/sources b/sources index fd5de8c..fc97924 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (votca-2025.1.tar.gz) = 4b199d54a555fe6c640aa8e01fa60ba57d4b26f639521572558b79eb0f741c236e93c8341fb7a28b92122f41912a9901305dd57d15c0fdcd67d89d3f0bc00801 +SHA512 (votca-2026.tar.gz) = 2c4c924dbb0072aa885ec64062a26c607cea2f99f6aeb58c048b347c7b6a55f6d674cb7baec7c687e8d79949255f736ffae72630a03f24dcd3c323ab3cb154d4 diff --git a/votca.spec b/votca.spec index 10471f5..170833b 100644 --- a/votca.spec +++ b/votca.spec @@ -1,16 +1,12 @@ Name: votca -Version: 2025.1 +Version: 2026 %global uversion %{version} -%global sover 2025 -Release: 6%{?dist} +%global sover 2026 +Release: 1%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz -# add support for Eigen3 v5, merged upstream, drop in next version bump -Patch0: https://github.com/votca/votca/pull/1189.diff -# fix build with boost-1.90, merged upstream, drop in next version bump -Patch1: c5aa266b0bec5501d18c47e7b1430dce80c526b6.patch # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval ExcludeArch: %{ix86} @@ -34,7 +30,6 @@ BuildRequires: boost-devel %if %{with_gmx} BuildRequires: gromacs-devel %endif -BuildRequires: perl-generators BuildRequires: hdf5-devel BuildRequires: python3 %if %{with_xtp} @@ -109,6 +104,7 @@ Obsoletes: votca-tools-devel <= 2022~rc1 Provides: votca-tools-devel = %version-%release Obsoletes: votca-xtp-devel <= 2022~rc1 Provides: votca-xtp-devel = %version-%release +Obsoletes: votca-csg-tutorials <= 2025.1 %description devel %{votca_desc} @@ -140,14 +136,6 @@ Provides: votca-csg-common = %version-%release This package contains architecture independent data files for the VOTCA package. -%package csg-tutorials -Summary: Architecture independent csg tutorial files for VOTCA -BuildArch: noarch -Requires: %{name} = %{version}-%{release} - -%description csg-tutorials -%{votca_desc} - This package contains architecture independent csg tutorial files for the VOTCA package. @@ -193,9 +181,6 @@ This package contains bash completion support for the VOTCA package. %prep %autosetup -p1 -n %{name}-%{uversion} -# we don't have an espressopp package in Fedora yet -rm -rf csg-tutorials/spce/ibi_espressopp - %build # load openmpi, so that cmake can find mdrun_openmpi for testing only %_openmpi_load @@ -211,7 +196,7 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %install %cmake_install # Install bash completion file -%__install -D -m0644 %{__cmake_builddir}/csg/scripts/csg-completion.bash %{buildroot}%{_datadir}/bash-completion/completions/votca +%__install -D -m0644 %{__cmake_builddir}/csg/src/tools//csg-completion.bash %{buildroot}%{_datadir}/bash-completion/completions/votca %fdupes %{buildroot}%{_prefix} @@ -233,9 +218,6 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %exclude %{_datadir}/votca/*-tutorials/ %exclude %{_datadir}/votca/xtp/ -%files csg-tutorials -%{_datadir}/votca/csg-tutorials/ - %if %{with_xtp} %files xtp-tutorials %{_datadir}/votca/xtp-tutorials/ @@ -258,6 +240,10 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %{_datadir}/bash-completion/completions/votca %changelog +* Mon Mar 09 2026 Christoph Junghans - 2026-1 +- Version bump to v2026 +- Fixes: rhbz#2445810 + * Tue Feb 24 2026 Orion Poplawski - 2025.1-6 - BR cmake instead of cmake3 From 2ee54e132b94b7e75d5e272e684f384952854014 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Mon, 9 Mar 2026 16:51:25 -0600 Subject: [PATCH 31/33] Version bump to v2026 Drop s390x and some clean up Fixes: rhbz#2445810 --- votca.spec | 36 +++--------------------------------- 1 file changed, 3 insertions(+), 33 deletions(-) diff --git a/votca.spec b/votca.spec index 170833b..4348cdd 100644 --- a/votca.spec +++ b/votca.spec @@ -9,16 +9,11 @@ URL: http://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz # https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval -ExcludeArch: %{ix86} +# no gromacs package on s390x +ExcludeArch: %{ix86} s390x %global with_xtp 1 - %global with_gmx 1 -# no gromacs package on s390x -# same for espressomd -%ifarch s390x -%global with_gmx 0 -%endif BuildRequires: gcc-c++ BuildRequires: fdupes @@ -40,29 +35,12 @@ BuildRequires: libecpint-devel BuildRequires: libint2-devel %endif -# mpi packages only used for testing -%if %{with_gmx} -BuildRequires: gromacs-openmpi -# only needed to run gromacs -BuildRequires: openmpi-devel -BuildRequires: python3-espresso-openmpi -%else -%global _openmpi_load %{nil} -%global _openmpi_unload %{nil} -%endif - #used for testing only %if %{with_gmx} BuildRequires: gromacs %endif -# no lammps on s390x as mpi is broken -%ifnarch s390x -BuildRequires: lammps -%endif BuildRequires: python3-cma BuildRequires: python3-pytest -BuildRequires: gnuplot -BuildRequires: psmisc Requires: %{name}-common = %{version}-%{release} Requires: %{name}-libs%{?_isa} = %{version}-%{release} @@ -182,16 +160,10 @@ This package contains bash completion support for the VOTCA package. %autosetup -p1 -n %{name}-%{uversion} %build -# load openmpi, so that cmake can find mdrun_openmpi for testing only -%_openmpi_load -# not a 100% sure why this is needed, but otherwise espressomd cannot be found -export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" - %{cmake} -DCMAKE_BUILD_TYPE=Release -DINSTALL_RC_FILES=OFF -DENABLE_TESTING=ON -DBUILD_CSGAPPS=ON \ -DBUILD_XTP=%{with_xtp} \ -DENABLE_REGRESSION_TESTING=ON -DHDF5_C_COMPILER_EXECUTABLE=/usr/bin/h5cc -DINJECT_MARCH_NATIVE=OFF %cmake_build -%_openmpi_unload %install %cmake_install @@ -201,10 +173,7 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %fdupes %{buildroot}%{_prefix} %check -%_openmpi_load -export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %ctest -%_openmpi_unload %files %{_bindir}/{votca,csg,xtp}_* @@ -242,6 +211,7 @@ export PYTHONPATH="${MPI_PYTHON3_SITEARCH}${PYTHONPATH:+:}${PYTHONPATH}" %changelog * Mon Mar 09 2026 Christoph Junghans - 2026-1 - Version bump to v2026 +- Drop s390x and some clean up - Fixes: rhbz#2445810 * Tue Feb 24 2026 Orion Poplawski - 2025.1-6 From 643a1c894d057046efe57df37b0160c641c3ea66 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Thu, 16 Apr 2026 19:30:45 -0600 Subject: [PATCH 32/33] Rebuild for hdf5 2.1 --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index 4348cdd..cfc7a8f 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2026 %global uversion %{version} %global sover 2026 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -209,6 +209,9 @@ This package contains bash completion support for the VOTCA package. %{_datadir}/bash-completion/completions/votca %changelog +* Fri Apr 17 2026 Orion Poplawski - 2026-2 +- Rebuild for hdf5 2.1 + * Mon Mar 09 2026 Christoph Junghans - 2026-1 - Version bump to v2026 - Drop s390x and some clean up From f41afab2d6c7851d0d9d97c47416fda5c69bcfde Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 17 Jul 2026 08:37:44 +0000 Subject: [PATCH 33/33] Rebuilt for https://fedoraproject.org/wiki/Fedora_45_Mass_Rebuild --- votca.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/votca.spec b/votca.spec index cfc7a8f..abad731 100644 --- a/votca.spec +++ b/votca.spec @@ -2,7 +2,7 @@ Name: votca Version: 2026 %global uversion %{version} %global sover 2026 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 URL: http://www.votca.org @@ -209,6 +209,9 @@ This package contains bash completion support for the VOTCA package. %{_datadir}/bash-completion/completions/votca %changelog +* Fri Jul 17 2026 Fedora Release Engineering - 2026-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_45_Mass_Rebuild + * Fri Apr 17 2026 Orion Poplawski - 2026-2 - Rebuild for hdf5 2.1