diff --git a/1083.patch b/1083.patch deleted file mode 100644 index 2b948ba..0000000 --- a/1083.patch +++ /dev/null @@ -1,44 +0,0 @@ -diff --git a/xtp/src/libxtp/calculators/kmclifetime.cc b/xtp/src/libxtp/calculators/kmclifetime.cc -index f6a1093ff..56730bce9 100644 ---- a/xtp/src/libxtp/calculators/kmclifetime.cc -+++ b/xtp/src/libxtp/calculators/kmclifetime.cc -@@ -21,7 +21,7 @@ - - // Third party includes - #include --#include -+#include - - // VOTCA includes - #include -@@ -290,7 +290,7 @@ void KMCLifetime::RunVSSM() { - - // determine where it will jump to - ResetForbiddenlist(forbiddendests); -- boost::progress_display progress(insertions_); -+ boost::timer::progress_display progress(insertions_); - - while (true) { - // LEVEL 2 -diff --git a/xtp/src/libxtp/calculators/neighborlist.cc b/xtp/src/libxtp/calculators/neighborlist.cc -index ce18af288..0b4bcc61b 100644 ---- a/xtp/src/libxtp/calculators/neighborlist.cc -+++ b/xtp/src/libxtp/calculators/neighborlist.cc -@@ -17,7 +17,7 @@ - - // Third party includes - #include --#include -+#include - - // Local private VOTCA includes - #include "neighborlist.h" -@@ -124,7 +124,7 @@ bool Neighborlist::Evaluate(Topology& top) { - - top.NBList().Cleanup(); - -- boost::progress_display progress(segs.size()); -+ boost::timer::progress_display progress(segs.size()); - // cache approx sizes - std::vector approxsize = std::vector(segs.size(), 0.0); - #pragma omp parallel for diff --git a/1093.patch b/1093.patch new file mode 100644 index 0000000..53e309c --- /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/votca-2022.1.tar.gz b/votca-2022.1.tar.gz deleted file mode 100644 index d3747e0..0000000 --- a/votca-2022.1.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:4710a7552f94789936324d76d2e0830b576de8d3f1c605748e2d20947d018100 -size 61692029 diff --git a/votca-2023.tar.gz b/votca-2023.tar.gz new file mode 100644 index 0000000..50134c0 --- /dev/null +++ b/votca-2023.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ac78d2eb5a6694b76878d2ab1ec86bb161765143a447cc23905cdcb2bb6743be +size 38975119 diff --git a/votca.changes b/votca.changes index 4734090..b271399 100644 --- a/votca.changes +++ b/votca.changes @@ -1,3 +1,62 @@ +------------------------------------------------------------------- +Thu Nov 16 04:24:41 UTC 2023 - Christoph Junghans + +- Drop 1083.patch - merged upstream +- Add 1093.patch from upstream to fix python shebang +- Update to 2023 + - fix pyxtp option restart ([gh#votca/votca#1074]) + - fix Changelog check ([gh#votca/votca#1070]) + - add python bindings for xtp ([gh#votca/votca#1061]) + - replaced pointers in MD2QM mapping ([gh#votca/votca#1075]) + - fixed typo in esp2multipole option ([gh#votca/votca#1076]) + - update MKL detection to MKL config ([gh#votca/votca#1053]) + - remove geometry optimization ([gh#votca/votca#1077]) + - remove all references to old pdf manual ([gh#votca/votca#1081]) + - replaced deprecated boost::progress headers ([gh#votca/votca#1083]) + - drop intel classic builds from CI ([gh#votca/votca#1085]) + - disable some libint2 warning and CI clean up ([gh#votca/votca#1088]) + - fix population analysis for embedded DFT ([gh#votca/votca#1089]) + - fix pyxtp xtp-tutorials ([gh#votca/votca#1090]) + - add note on gmx build for install ([gh#votca/votca#1052]) + - fix typos in esp2multipole options ([gh#votca/votca#1054]) + - Used sharedable lock in xtp ([gh#votca/votca#1057]) + - Make votca tests compile without OpenMP ([gh#votca/votca#1065]) + - increase tolerance for diabatization test ([gh#votca/votca#1039], + [gh#votca/votca#1043]) + - removed boost::filesystem ([gh#votca/votca#1041]) + - clean up C++ defines ([gh#votca/votca#1044]) + - drop gmx-2022 builds from CI ([gh#votca/votca#1046]) + - update ccaching in CI ([gh#votca/votca#1048], [gh#votca/votca#1050]) + - add support for gmx-2023 api ([gh#votca/votca#1059]) + - updated formatting ([gh#votca/votca#1062]) + - remove stable branch workflow ([gh#votca/votca#1066]) + - Refactor changelog actions ([gh#votca/votca#1068]) + - fix CI build with icpx ([gh#votca/votca#1018]) + - implemented projection-based DFT embedding ([gh#votca/votca#964]) + - Added LMO energy output and cube file generation ([gh#votca/votca#970]) + - fix typos in csg-tutorials xml files ([gh#votca/votca#980]) + - unitary optimization for localization of orbitals ([gh#votca/votca#971]) + - separate option for density max convergence tolerance in qmmm + ([gh#votca/votca#987]) + - Correct ECP charges added in Orca Molden reader ([gh#votca/votca#990]) + - Implemented truncated basis for embedded DFT ([gh#votca/votca#991]) + - Implemented ER diabatization for BSE ([gh#votca/votca#988]) + - update esp++ spce tutorial to py3 ([gh#votca/votca#997]) + - Truncated GW-in-DFT embedded in static/polar MM implemeted + ([gh#votca/votca#1003]) + - reducing XTP tutorial size ([gh#votca/votca#1020], [gh#votca/votca#1025]) + - Clean up 3body Stillinger-Weber implement, docs and tutorial + ([gh#votca/votca#1012]) + - fixed options handling in xtp_autogen_mapping ([gh#votca/votca#1024]) + - Major CMake refactor ([gh#votca/votca#950], [gh#votca/votca#1022]) + - Fix all doxygen warnings ([gh#votca/votca#1026]) + - basis and auxbasis are written to QMMM checkpoint file + ([gh#votca/votca#1030]) + - iterations_max can now be zero ([gh#votca/votca#1033]) + - add an XML check to csg_inverse ([gh#votca/votca#1031]) + - fix propane/imc and add propane/imc-ibiintra to csg-tutorials + ([gh#votca/votca#821]) + ------------------------------------------------------------------- Mon Nov 13 23:26:43 UTC 2023 - Christoph Junghans diff --git a/votca.spec b/votca.spec index e3ed67e..656df1c 100644 --- a/votca.spec +++ b/votca.spec @@ -25,17 +25,17 @@ %endif Name: votca -Version: 2022.1 +Version: 2023 Release: 0 %define uversion %{version} -%define sover 2022 +%define sover 2023 Summary: Versatile Object-oriented Toolkit for Coarse-graining Applications License: Apache-2.0 Group: Productivity/Scientific/Chemistry URL: https://www.votca.org Source0: https://github.com/votca/votca/archive/v%{uversion}.tar.gz#/%{name}-%{uversion}.tar.gz -# PATCH-FIX-UPSTREAM 1083.patch -- based on upsteam PR 1083, fix build with boost-1.82 -Patch0: 1083.patch +# PATCH-FIX-UPSTREAM 1093.patch -- fix python shebang +Patch0: 1093.patch BuildRequires: cmake >= 3.13 BuildRequires: eigen3-devel @@ -196,7 +196,7 @@ This package contains the bash completion support for votca. %install %cmake_install -sed -i '1s@env @@' %{buildroot}/%{_bindir}/votca_{compare,help2doc} \ +sed -i '1s@env @@' \ %{buildroot}/%{_datadir}/votca/scripts/inverse/{iie,cma_processor,table_smooth_at_cut_off}.py \ %{buildroot}/%{_datadir}/votca/csg-tutorials/LJ1-LJ2/imc/svd.py \ %{buildroot}/%{_datadir}/votca/csg-tutorials/spce/ibi*/spce.py @@ -207,7 +207,7 @@ sed -i '1s@env @@' %{buildroot}/%{_bindir}/xtp_* %{buildroot}/%{_datadir}/votca/ # Move bash completion file to correct location mkdir -p %{buildroot}%{_datadir}/bash_completion.d -cp %{buildroot}%{_datadir}/votca/rc/csg-completion.bash %{buildroot}%{_datadir}/bash_completion.d/votca +cp %{__builddir}/csg/scripts/csg-completion.bash %{buildroot}%{_datadir}/bash_completion.d/votca %fdupes %{buildroot}%{_prefix}