From 6ffee21246f72fa19f4cabddc72e5efc0b59ac2fad7ce22e123854383d46743e Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Thu, 25 Jan 2024 22:21:44 +0000 Subject: [PATCH 1/2] Accepting request 1141606 from home:cjunghans:branches:science - Dropped 1093.patch, merged upstream - fix links in README and doc (gh#votca/votca#1091]) - fix python shebang to python3 (gh#votca/votca#1093]) - Clean-up CI (gh#votca/votca#1092], #1095) - remove reference to old webpage (gh#votca/votca#1094]) - fix doc generation without pyxtp (gh#votca/votca#1097]) - Do not run gmx tests without libgromacs (gh#votca/votca#1099]) - KS-QMMM for single-particle states (gh#votca/votca#1100]) - Spin-orbitals from ORCA in QMMM (gh#votca/votca#1101]) - better unit test for DFT embedding (gh#votca/votca#1102]) - Update to 2024 OBS-URL: https://build.opensuse.org/request/show/1141606 OBS-URL: https://build.opensuse.org/package/show/science/votca?expand=0&rev=21 --- 1093.patch | 74 ----------------------------------------------- votca-2023.tar.gz | 3 -- votca-2024.tar.gz | 3 ++ votca.changes | 15 ++++++++++ votca.spec | 9 ++---- 5 files changed, 21 insertions(+), 83 deletions(-) delete mode 100644 1093.patch delete mode 100644 votca-2023.tar.gz create mode 100644 votca-2024.tar.gz diff --git a/1093.patch b/1093.patch deleted file mode 100644 index 53e309c..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/votca-2023.tar.gz b/votca-2023.tar.gz deleted file mode 100644 index 50134c0..0000000 --- a/votca-2023.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:ac78d2eb5a6694b76878d2ab1ec86bb161765143a447cc23905cdcb2bb6743be -size 38975119 diff --git a/votca-2024.tar.gz b/votca-2024.tar.gz new file mode 100644 index 0000000..dc83fc0 --- /dev/null +++ b/votca-2024.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:be1f8ad3de2ce86f0c01014aa5358c181f128a847bc4508ba0a4bffd5c82a1cf +size 38976012 diff --git a/votca.changes b/votca.changes index b271399..7c92127 100644 --- a/votca.changes +++ b/votca.changes @@ -1,3 +1,18 @@ +------------------------------------------------------------------- +Thu Jan 25 14:33:26 UTC 2024 - Christoph Junghans + +- Dropped 1093.patch, merged upstream + - fix links in README and doc (gh#votca/votca#1091]) + - fix python shebang to python3 (gh#votca/votca#1093]) + - Clean-up CI (gh#votca/votca#1092], #1095) + - remove reference to old webpage (gh#votca/votca#1094]) + - fix doc generation without pyxtp (gh#votca/votca#1097]) + - Do not run gmx tests without libgromacs (gh#votca/votca#1099]) + - KS-QMMM for single-particle states (gh#votca/votca#1100]) + - Spin-orbitals from ORCA in QMMM (gh#votca/votca#1101]) + - better unit test for DFT embedding (gh#votca/votca#1102]) +- Update to 2024 + ------------------------------------------------------------------- Thu Nov 16 04:24:41 UTC 2023 - Christoph Junghans diff --git a/votca.spec b/votca.spec index 656df1c..2d1b974 100644 --- a/votca.spec +++ b/votca.spec @@ -25,17 +25,15 @@ %endif Name: votca -Version: 2023 +Version: 2024 Release: 0 %define uversion %{version} -%define sover 2023 +%define sover 2024 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 1093.patch -- fix python shebang -Patch0: 1093.patch BuildRequires: cmake >= 3.13 BuildRequires: eigen3-devel @@ -180,8 +178,7 @@ Provides: votca-csg-bash = %version-%release This package contains the bash completion support for votca. %prep -%setup -n %{name}-%{uversion} -q -%patch 0 -p1 +%autosetup -n %{name}-%{uversion} %build %setup_openmpi From fd18394180462fc7beb887a610aa7895f6b550fd233d3a7f98d9344557e0799e Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 31 Jan 2024 22:18:36 +0000 Subject: [PATCH 2/2] Accepting request 1143149 from home:cjunghans:branches:science - Drop python3-espressomd testing dependency, revert once gh#espressomd/espresso#4856 is fixed. - Dropped 1093.patch, merged upstream - fix links in README and doc ([gh#votca/votca#1091]) - fix python shebang to python3 ([gh#votca/votca#1093]) - Clean-up CI ([gh#votca/votca#1092], [gh#votca/votca#1095]) - remove reference to old webpage ([gh#votca/votca#1094]) - fix doc generation without pyxtp ([gh#votca/votca#1097]) - Do not run gmx tests without libgromacs ([gh#votca/votca#1099]) - KS-QMMM for single-particle states ([gh#votca/votca#1100]) - Spin-orbitals from ORCA in QMMM ([gh#votca/votca#1101]) - better unit test for DFT embedding ([gh#votca/votca#1102]) - Update to 2024 - 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]) - Add 1083.patch to fix build with boost-1.82 - don't use mpi gromacs on ix86 - Update to 2022.1 - fix PROJECT_VERSION in subdirs ([gh#votca/votca#951]) - make csg_resample and csg_stat spacing consistent ([gh#votca/votca#956]) - fix build on FreeBSD ([gh#votca/votca#959]) - update CI container names ([gh#votca/votca#961]) - Fix gw quadrature scheme ([gh#votca/votca#967]) - update install guide for spack ([gh#votca/votca#972], [gh#votca/votca#974]) - drop gmx-2021 builds from CI ([gh#votca/votca#976]) - update syntax for cmake 3.23 ([gh#votca/votca#978]) - fix CI build on Ubuntu ([gh#votca/votca#981]) - fix CI builds with icpx ([gh#votca/votca#984], [gh#votca/votca#1004]) - fix CI builds with ESPResSo 4.2.0 ([gh#votca/votca#993]) - fix localization issue ([gh#votca/votca#998], [gh#votca/votca#1000]) - update github actions to new versions ([gh#votca/votca#1007], [gh#votca/votca#1013]) - Disable gromacs on 32-bit arm since it is missing - Do not requires libint when xtp is disabled - Adjust constraints to avoid rejecting too many workers, enable parallel builds with limit_build. - Clean up specfile, remove obsolete __DATE__ mangling. - only use python3-epressomd for testing on x86_64 - Update to 2022 - fix some icpc warnings ([gh#votca/votca#934]) - only check for pytest if testing is enabled ([gh#votca/votca#930]) - exclude some builds from CI ([gh#votca/votca#940], [gh#votca/votca#942], [gh#votca/votca#944], [gh#votca/votca#945]) - update interface documentation ([gh#votca/votca#939]) - update install guide for binary packages ([gh#votca/votca#936]) - fixed sigma plot options passing ([gh#votca/votca#943]) - Also obsoletes votca-csg-apps - Update to 2022-rc.2 - fix iqm merge orbitals command ([gh#votca/votca#907]) - fix bug in basisset serialization that caused wrong Vxc values in GW ([gh#votca/votca#910]) - update performance compilation info ([gh#votca/votca#911]) - license for monorepo and all license files rst -> plain text ([gh#votca/votca#912], [gh#votca/votca#913]) - use python3 in xtp-tutorials ([gh#votca/votca#917]) - bump required boost version to 1.71 ([gh#votca/votca#915], [gh#votca/votca#916]) - clean up NOTICE files ([gh#votca/votca#919]) - rm PYTHON_INSTDIR from VOTCARC ([gh#votca/votca#924]) - update citation in xtp README ([gh#votca/votca#925]) - fix install permission of tutorials ([gh#votca/votca#926])- - Merge votca-{tools,csg,xtp} into one package OBS-URL: https://build.opensuse.org/request/show/1143149 OBS-URL: https://build.opensuse.org/package/show/science/votca?expand=0&rev=22 --- votca.changes | 24 +++++++++++++++--------- votca.spec | 3 --- 2 files changed, 15 insertions(+), 12 deletions(-) diff --git a/votca.changes b/votca.changes index 7c92127..acb3043 100644 --- a/votca.changes +++ b/votca.changes @@ -1,16 +1,22 @@ +------------------------------------------------------------------- +Wed Jan 31 20:58:32 UTC 2024 - Christoph Junghans + +- Drop python3-espressomd testing dependency, revert once + gh#espressomd/espresso#4856 is fixed. + ------------------------------------------------------------------- Thu Jan 25 14:33:26 UTC 2024 - Christoph Junghans - Dropped 1093.patch, merged upstream - - fix links in README and doc (gh#votca/votca#1091]) - - fix python shebang to python3 (gh#votca/votca#1093]) - - Clean-up CI (gh#votca/votca#1092], #1095) - - remove reference to old webpage (gh#votca/votca#1094]) - - fix doc generation without pyxtp (gh#votca/votca#1097]) - - Do not run gmx tests without libgromacs (gh#votca/votca#1099]) - - KS-QMMM for single-particle states (gh#votca/votca#1100]) - - Spin-orbitals from ORCA in QMMM (gh#votca/votca#1101]) - - better unit test for DFT embedding (gh#votca/votca#1102]) + - fix links in README and doc ([gh#votca/votca#1091]) + - fix python shebang to python3 ([gh#votca/votca#1093]) + - Clean-up CI ([gh#votca/votca#1092], [gh#votca/votca#1095]) + - remove reference to old webpage ([gh#votca/votca#1094]) + - fix doc generation without pyxtp ([gh#votca/votca#1097]) + - Do not run gmx tests without libgromacs ([gh#votca/votca#1099]) + - KS-QMMM for single-particle states ([gh#votca/votca#1100]) + - Spin-orbitals from ORCA in QMMM ([gh#votca/votca#1101]) + - better unit test for DFT embedding ([gh#votca/votca#1102]) - Update to 2024 ------------------------------------------------------------------- diff --git a/votca.spec b/votca.spec index 2d1b974..e7ce9a1 100644 --- a/votca.spec +++ b/votca.spec @@ -72,9 +72,6 @@ BuildRequires: procps BuildRequires: psmisc BuildRequires: python3-cma # only needed for testing -%ifarch x86_64 -BuildRequires: python3-espressomd -%endif BuildRequires: python3-lxml BuildRequires: python3-pytest # for hdf5