From 0491bcd7d82d0906e1aa0a91d834909434be7dce Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 4 Jun 2021 19:59:20 +0200 Subject: [PATCH 01/35] Rebuilt for Python 3.10 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 19afa95..b218946 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 7%{datecommit}%{shortcommit}%{?dist} +Release: 8%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -166,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Fri Jun 04 2021 Python Maint - 3.0.0-8 +- Rebuilt for Python 3.10 + * Tue Jan 26 2021 Fedora Release Engineering - 3.0.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild From 186611cad67172b7c9d49861f52edc49b28f392c Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 21 Jul 2021 12:49:13 +0000 Subject: [PATCH 02/35] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering From 0667085b825ed3058613ed90ec839192d4242c5e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 21 Jul 2021 17:45:17 +0000 Subject: [PATCH 03/35] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index b218946..3eba357 100644 --- a/apbs.spec +++ b/apbs.spec @@ -13,7 +13,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 8%{datecommit}%{shortcommit}%{?dist} +Release: 9%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -166,6 +166,9 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %doc doc/_build/html %changelog +* Wed Jul 21 2021 Fedora Release Engineering - 3.0.0-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Fri Jun 04 2021 Python Maint - 3.0.0-8 - Rebuilt for Python 3.10 From a250b716beb23d4f7b211408159411ef8782c7db Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 15:48:11 +0100 Subject: [PATCH 04/35] Compile from a new source archive --- .gitignore | 1 + apbs-cmake.patch | 9 ++++ apbs-exclude_tests.patch | 60 +++++++++++++++++++++ apbs.spec | 114 +++++++++++++++++++++++++-------------- sources | 2 +- 5 files changed, 146 insertions(+), 40 deletions(-) create mode 100644 apbs-exclude_tests.patch diff --git a/.gitignore b/.gitignore index 58dec5a..85ecb73 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ apbs-1.2.1-source.tar.gz /apbs-1.5.tar.gz /apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz /apbs-pdb2pqr-vAPBS-3.0.0.tar.gz +/apbs-3.0.0.tar.gz diff --git a/apbs-cmake.patch b/apbs-cmake.patch index df3007a..dbcb876 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -106,6 +106,15 @@ endif() ################################################################################ +@@ -880,7 +860,7 @@ + set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}") + set(CPACK_PACKAGE_DESCRIPTION "APBS - Adaptive Poisson Boltzmann Solver") + +-set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/../LICENSE.md") ++set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.md") + set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md") + + set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/") --- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 +++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -32,11 +32,11 @@ diff --git a/apbs-exclude_tests.patch b/apbs-exclude_tests.patch new file mode 100644 index 0000000..5f64696 --- /dev/null +++ b/apbs-exclude_tests.patch @@ -0,0 +1,60 @@ +--- a/tests/test_cases.orig.cfg 2020-05-30 03:47:30.000000000 +0200 ++++ b/tests/test_cases.cfg 2021-11-01 11:30:08.175043842 +0100 +@@ -74,57 +74,3 @@ + apbs-mol : 1.847663548071E+03 1.883912182952E+03 2.732623683321E+03 3.123035854133E+03 -3.624863445503E+01 -3.904121297757E+02 -3.541635359318E+02 + apbs-smol : 1.847860440020E+03 1.885436377745E+03 2.734040568569E+03 3.125279428954E+03 -3.757593797629E+01 -3.912388198513E+02 -3.536628818750E+02 + +- +-[geoflow] +-input_dir : ../examples/geoflow +-imidazole : -1.030222099963E+01 5.417419E-01 +- +- +-[bem] +-input_dir : ../examples/bem +-451c_order1 : -1.172906546441e+03 +-451c_order5 : -1.175936034727E+03 +- +-[bem-pKa] +-input_dir : ../examples/bem-pKa +-ASH66 : -9.954199102140E-01 +-2LZT-ASH66 : -8.620097356247E+01 +-2LZT-noASH66 : -8.601110775968E+01 +- +-[bem-binding-energy] +-input_dir : ../examples/bem-binding-energy +-1d30 : -5.249027161163E+03 +-1d30_monomer1 : -6.232145066905E+03 +-1d30_monomer2 : -1.821470879387E+02 +- +- +-[pbam] +-input_dir : ../examples/pbam +-toy_energyforce : -4.965018552290E+01 -4.965018552290E+01 +- +-[pbsam] +-input_dir : ../examples/pbsam-gly +-gly_energyforce : 6.176608555569E-05 6.210593742215E-05 +- +- +-[protein-rna] +-input_dir : ../examples/protein-rna +-setup : python apbs_dx.py +-apbs-0.025 : 3.186122223752E+04 3.662855899462E+04 8.477786964834E+03 1.000545153104E+04 2.329205982055E+04 2.653636629928E+04 8.674116429353E+01 +-apbs-0.050 : 3.184763478312E+04 3.661493366846E+04 8.475252516617E+03 1.000292179294E+04 2.327168361816E+04 2.651594350839E+04 9.606836713866E+01 +-apbs-0.075 : 3.184033569905E+04 3.660761530545E+04 8.473669396547E+03 1.000134276339E+04 2.326088212207E+04 2.650511882057E+04 1.011537214883E+02 +-apbs-0.100 : 3.183548000794E+04 3.660274809589E+04 8.472507235893E+03 1.000018407412E+04 2.325372656922E+04 2.649794981016E+04 1.046142116108E+02 +-apbs-0.125 : 3.183190100647E+04 3.659916161996E+04 8.471585837513E+03 9.999265654586E+03 2.324845847155E+04 2.649267328362E+04 1.072226817610E+02 +-apbs-0.150 : 3.182909678356E+04 3.659635228953E+04 8.470821300868E+03 9.998503715551E+03 2.324433086171E+04 2.648854016160E+04 1.093084123761E+02 +-apbs-0.175 : 3.182680817429E+04 3.659406006570E+04 8.470167484600E+03 9.997852199372E+03 2.324096101131E+04 2.648516662194E+04 1.110412443877E+02 +-apbs-0.200 : 3.182488501939E+04 3.659213428941E+04 8.469596195763E+03 9.997282974485E+03 2.323812822097E+04 2.648233134327E+04 1.125199716537E+02 +-apbs-0.225 : 3.182323306491E+04 3.659048040133E+04 8.469088900775E+03 9.996777552566E+03 2.323569434544E+04 2.647989580221E+04 1.138070465620E+02 +-apbs-0.250 : 3.182178954360E+04 3.658903543806E+04 8.468632740499E+03 9.996323108319E+03 2.323356752071E+04 2.647776789284E+04 1.149444369078E+02 +-apbs-0.275 : 3.182051070674E+04 3.658775551975E+04 8.468218414737E+03 9.995910367297E+03 2.323168374787E+04 2.647588345522E+04 1.159616972338E+02 +-apbs-0.300 : 3.181936493519E+04 3.658660893678E+04 8.467838971928E+03 9.995532397856E+03 2.322999676177E+04 2.647419611346E+04 1.168804254687E+02 +-apbs-0.325 : 3.181832869046E+04 3.658557208654E+04 8.467489074881E+03 9.995183878464E+03 2.322847209567E+04 2.647267132259E+04 1.177168854906E+02 +-apbs-0.400 : 3.181571629593E+04 3.658295870300E+04 8.466578740909E+03 9.994277216885E+03 2.322463613929E+04 2.646883588223E+04 1.198456038803E+02 +-apbs-0.500 : 3.181302243781E+04 3.658026461575E+04 8.465598755475E+03 9.993301332440E+03 2.322070101887E+04 2.646490251594E+04 1.220607673699E+02 +-apbs-0.600 : 3.181090090954E+04 3.657814345443E+04 8.464799341688E+03 9.992505379555E+03 2.321762631365E+04 2.646183001839E+04 1.238080564885E+02 +-apbs-0.700 : 3.180915789156E+04 3.657640108752E+04 8.464126109756E+03 9.991835140855E+03 2.321512352191E+04 2.645932953757E+04 1.252364090878E+02 +-apbs-0.800 : 3.180768241803E+04 3.657492640520E+04 8.463546035019E+03 9.991257699113E+03 2.321302636223E+04 2.645723464562E+04 1.264340604647E+02 diff --git a/apbs.spec b/apbs.spec index 3eba357..99082f7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -5,38 +5,34 @@ %global shortcommit %{nil} %global datecommit %{nil} -%bcond_without python - # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_with check +%bcond_without check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 9%{datecommit}%{shortcommit}%{?dist} +Release: 10%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ -Source0: https://github.com/Electrostatics/apbs-pdb2pqr/archive/%{version}/%{name}-pdb2pqr-vAPBS-%{version}.tar.gz -Source1: apbs-LGPL_V2 -Patch0: apbs-cmake.patch +Source0: https://github.com/Electrostatics/apbs/archive/refs/tags/v%{version}/%{name}-%{version}.tar.gz +Source1: %{name}-LGPL_V2 + +Patch0: %{name}-cmake.patch + +# Exclude tests because they are for features inactivated +Patch1: %{name}-exclude_tests.patch BuildRequires: gcc-c++ BuildRequires: cmake3 +BuildRequires: chrpath BuildRequires: make BuildRequires: doxygen BuildRequires: graphviz -#BuildRequires: arpack-devel -#BuildRequires: atlas-devel -#BuildRequires: blas-devel BuildRequires: maloc-devel -BuildRequires: python3-devel -BuildRequires: python3-numpy -BuildRequires: python3-sphinx -BuildRequires: swig -BuildRequires: tex(latex) BuildRequires: zlib-devel Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: python3-%{name} %description APBS is a software package for the numerical solution of the @@ -49,7 +45,7 @@ tens to millions of atoms. It is also widely used in molecular visualization (in such applications as PyMOL). %package tools -Summary: utility programs that utilize the APBS package +Summary: Utility programs that utilize the APBS package Requires: %{name}%{?_isa} = %{version}-%{release} %description tools The apbs-tools package contains several utility programs for @@ -71,45 +67,81 @@ necessary for developing programs using the adaptive poisson boltzmann %package doc Summary: Documentation for the APBS package +BuildRequires: tex(latex) +BuildRequires: texlive-multirow +BuildRequires: texlive-hanging +BuildRequires: texlive-adjustbox +BuildRequires: texlive-stackengine +BuildRequires: texlive-sectsty +BuildRequires: texlive-etoc +BuildRequires: texlive-tocloft +BuildRequires: texlive-ulem +BuildRequires: texlive-newunicodechar BuildArch: noarch %description doc The apbs-doc package contains API reference inforemation for development using the adaptive poisson boltzmann (APBS) solver library. -%prep -%autosetup -n %{name}-pdb2pqr-vAPBS-%{version} -N -%patch0 -p1 -b .apbs-cmake +%package -n python3-apbs +Summary: Python interface of APBS +BuildRequires: python3-devel +BuildRequires: python3-numpy +BuildRequires: python3-sphinx +BuildRequires: swig +%{?python_provide:%python_provide python3-%{name}} +%description -n python3-apbs +Python interface of APBS. -cp -p apbs/contrib/iapbs/COPYING apbs/contrib/iapbs/iapbs-COPYING -cp -p %{SOURCE1} apbs/contrib/iapbs/iapbs-LGPLv2 +%prep +%autosetup -n %{name}-%{version} -N +%patch0 -p2 -b .apbs-cmake +%patch1 -p1 -b .exclude_tests + +cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING +cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 %build +# CMake needs BUILD_SHARED_LIBS:BOOL=OFF to build Python libraries +# Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -%cmake3 -S apbs -DBUILD_DOC:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release \ +mkdir -p build +cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DENABLE_FETK:BOOL=OFF \ -%if %{with python} - -DENABLE_PYTHON:BOOL=ON -%endif -%cmake_build + -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ + -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ + -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ + -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON \ + -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ + -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ + -DLIB_INSTALL_DIR:PATH=%{_libdir} \ + -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} +make -O -j1 V=1 -C build %install -%cmake_install +%make_install -C build -# tools +# Tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do cp -p $bin %{buildroot}%{_bindir}/apbs-`basename $bin` rm -f $bin done +# Remove rpaths +for bin in %{buildroot}%{_bindir}/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do + chrpath -d $bin + chrpath -d %{buildroot}%{_bindir}/apbs +done + +chrpath -d %{buildroot}%{_libdir}/libapbs.so.1 + # Move Python libraries under Python's tree directories mkdir -p %{buildroot}%{python3_sitearch}/apbs -install -pm 755 apbs/tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py -install -pm 755 %{_vpath_builddir}/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ # Remove redundant tools binary files in /usr/share rm -rf %{buildroot}%{_datadir}/apbs @@ -121,9 +153,8 @@ done %if %{with check} %check -pushd apbs/tests +pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} -sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{__python3} ./apbs_tester.py %endif @@ -131,13 +162,15 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{_bindir}/apbs %files libs -%license apbs/LICENSE.md apbs/COPYING apbs/contrib/iapbs/iapbs-COPYING apbs/contrib/iapbs/iapbs-LGPLv2 -%doc apbs/README.md -%{_libdir}/libapbs*.so.* +%license LICENSE.md COPYING contrib/iapbs/iapbs-COPYING contrib/iapbs/iapbs-LGPLv2 +%doc README.md +%{_libdir}/libapbs.so.1 + +%files -n python3-apbs %{python3_sitearch}/apbs/ %files devel -%{_libdir}/libapbs*.so +%{_libdir}/libapbs.so %{_includedir}/iapbs/ %{_includedir}/apbs @@ -162,10 +195,13 @@ sed -i 's|../build/bin/apbs|../bin/apbs|g' ./apbs_tester.py %{_bindir}/apbs-tensor2dx %files doc -%license doc/apbs/license.rst -%doc doc/_build/html +%license LICENSE.md +%doc build/doc %changelog +* Sun Oct 31 2021 Antonio Trande - 3.0.0-10 +- Compile from a new source archive + * Wed Jul 21 2021 Fedora Release Engineering - 3.0.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild diff --git a/sources b/sources index 715195d..2e522a3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (apbs-pdb2pqr-vAPBS-3.0.0.tar.gz) = 324306eb22346d9ce54b79d311512bdd9968ec63223354e69314c8d5aa3f4c63fa6afa4ebbbdfd84873edc5a75882934cedc2ad037d92f13f56e35e85ff00666 +SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb From 2d9c28a5d9e8be0b9f2544e311bed5b645e8e3bd Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 17:28:58 +0100 Subject: [PATCH 05/35] Fix installation conflict of python package --- apbs.spec | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 99082f7..12c1b2e 100644 --- a/apbs.spec +++ b/apbs.spec @@ -6,12 +6,12 @@ %global datecommit %{nil} # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_without check +%bcond_with check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 10%{datecommit}%{shortcommit}%{?dist} +Release: 11%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -90,6 +90,7 @@ BuildRequires: python3-numpy BuildRequires: python3-sphinx BuildRequires: swig %{?python_provide:%python_provide python3-%{name}} +Obsoletes: %{name}-libs < 3.0.0-10 %description -n python3-apbs Python interface of APBS. @@ -199,6 +200,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Nov 01 2021 Antonio Trande - 3.0.0-11 +- Fix installation conflict of python package + * Sun Oct 31 2021 Antonio Trande - 3.0.0-10 - Compile from a new source archive From 2714d4da05f4b0d9d3d7bbe978fa307c4f32f664 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 17:30:04 +0100 Subject: [PATCH 06/35] Fix installation conflict of python package /2 --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 12c1b2e..5177fc3 100644 --- a/apbs.spec +++ b/apbs.spec @@ -90,7 +90,7 @@ BuildRequires: python3-numpy BuildRequires: python3-sphinx BuildRequires: swig %{?python_provide:%python_provide python3-%{name}} -Obsoletes: %{name}-libs < 3.0.0-10 +Obsoletes: %{name}-libs < 0:3.0.0-11 %description -n python3-apbs Python interface of APBS. From e36cff8ce853f2f1e015918503eac0e5866cd0f6 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Mon, 1 Nov 2021 18:13:47 +0100 Subject: [PATCH 07/35] Re-enable tests --- apbs.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 5177fc3..d778cf7 100644 --- a/apbs.spec +++ b/apbs.spec @@ -6,12 +6,12 @@ %global datecommit %{nil} # To perform all tests, APBS needs to be compiled together additional sub-modules -%bcond_with check +%bcond_without check Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 11%{datecommit}%{shortcommit}%{?dist} +Release: 12%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -200,6 +200,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Nov 01 2021 Antonio Trande - 3.0.0-12 +- Re-enable tests + * Mon Nov 01 2021 Antonio Trande - 3.0.0-11 - Fix installation conflict of python package From d8042f16d7d69e8dffff2e9f48afe10f92609517 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 4 Jan 2022 16:01:26 +0100 Subject: [PATCH 08/35] Patched for Python-3.11 --- apbs.spec | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index d778cf7..22e888d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 12%{datecommit}%{shortcommit}%{?dist} +Release: 13%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -23,6 +23,9 @@ Patch0: %{name}-cmake.patch # Exclude tests because they are for features inactivated Patch1: %{name}-exclude_tests.patch +# Porting to Python-3.11 +Patch2: %{name}-python311.patch + BuildRequires: gcc-c++ BuildRequires: cmake3 BuildRequires: chrpath @@ -99,6 +102,10 @@ Python interface of APBS. %patch0 -p2 -b .apbs-cmake %patch1 -p1 -b .exclude_tests +%if 0%{?python3_version_nodots} >= 311 +%patch2 -p1 -b .python311 +%endif + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -200,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Tue Jan 04 2022 Antonio Trande - 3.0.0-13 +- Patched for Python-3.11 + * Mon Nov 01 2021 Antonio Trande - 3.0.0-12 - Re-enable tests From 797d60a8fa287c009a6c2dc413bd7e2149d432b0 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 4 Jan 2022 16:06:02 +0100 Subject: [PATCH 09/35] Add patch file --- apbs-python311.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 apbs-python311.patch diff --git a/apbs-python311.patch b/apbs-python311.patch new file mode 100644 index 0000000..adf7420 --- /dev/null +++ b/apbs-python311.patch @@ -0,0 +1,11 @@ +--- a/tools/manip/inputgen.orig.py 2020-05-30 03:47:30.000000000 +0200 ++++ b/tools/manip/inputgen.py 2021-12-26 12:13:08.819979543 +0100 +@@ -266,7 +266,7 @@ + file (string) + """ + nproc = 0 +- file = open(filename, 'rU') ++ file = open(filename) + text = "" + while 1: + line = file.readline() From 8ed4dc788eedab34933d0d96b25c3c4b3ff232a7 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 19 Jan 2022 21:27:15 +0000 Subject: [PATCH 10/35] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 22e888d..c6d3d0c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 13%{datecommit}%{shortcommit}%{?dist} +Release: 14%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jan 19 2022 Fedora Release Engineering - 3.0.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Tue Jan 04 2022 Antonio Trande - 3.0.0-13 - Patched for Python-3.11 From b1c8820a70ab5542247b81dd8f550808c327e74e Mon Sep 17 00:00:00 2001 From: Python Maint Date: Mon, 13 Jun 2022 18:55:54 +0200 Subject: [PATCH 11/35] Rebuilt for Python 3.11 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index c6d3d0c..8752b6c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 14%{datecommit}%{shortcommit}%{?dist} +Release: 15%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Jun 13 2022 Python Maint - 3.0.0-15 +- Rebuilt for Python 3.11 + * Wed Jan 19 2022 Fedora Release Engineering - 3.0.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From c9f299b0fc9617a2d0483c44018caa134e4ce439 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 20 Jul 2022 21:02:27 +0000 Subject: [PATCH 12/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 8752b6c..4f4a16e 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 15%{datecommit}%{shortcommit}%{?dist} +Release: 16%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 20 2022 Fedora Release Engineering - 3.0.0-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Mon Jun 13 2022 Python Maint - 3.0.0-15 - Rebuilt for Python 3.11 From 065b3accf8fea19f16c1dfdf84f0959541a6a258 Mon Sep 17 00:00:00 2001 From: Lumir Balhar Date: Tue, 1 Nov 2022 06:58:32 +0100 Subject: [PATCH 13/35] Change location of pathfix.py For more info see https://fedoraproject.org/wiki/Changes/Python3.12#pathfix.py_tool_will_be_removed --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 4f4a16e..9210da1 100644 --- a/apbs.spec +++ b/apbs.spec @@ -147,7 +147,7 @@ chrpath -d %{buildroot}%{_libdir}/libapbs.so.1 # Move Python libraries under Python's tree directories mkdir -p %{buildroot}%{python3_sitearch}/apbs install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ -pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py +%{__python3} %{_rpmconfigdir}/redhat/pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ From 4be9e4746a7a2822a2d587d45c24c04f4ec945f1 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 18 Jan 2023 21:56:56 +0000 Subject: [PATCH 14/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 9210da1..75b4300 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 16%{datecommit}%{shortcommit}%{?dist} +Release: 17%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -207,6 +207,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jan 18 2023 Fedora Release Engineering - 3.0.0-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Wed Jul 20 2022 Fedora Release Engineering - 3.0.0-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From b0c00fdb38d1e12455b374d2fc1198b4321cb656 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 28 Jan 2023 20:11:24 +0100 Subject: [PATCH 15/35] Add texlive-wasysym --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 75b4300..0933e95 100644 --- a/apbs.spec +++ b/apbs.spec @@ -80,6 +80,7 @@ BuildRequires: texlive-etoc BuildRequires: texlive-tocloft BuildRequires: texlive-ulem BuildRequires: texlive-newunicodechar +BuildRequires: texlive-wasysym BuildArch: noarch %description doc The apbs-doc package contains API reference inforemation for From 3a7a53a8301cd7c68e7614a1f8ddf4644d830f55 Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Mon, 6 Feb 2023 08:11:37 +0100 Subject: [PATCH 16/35] Add missing BuildRequires: texlive-wasy Otherwise, the build fails with: ! I can't find file `wasy7'. --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 0933e95..a9b34a8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -80,6 +80,7 @@ BuildRequires: texlive-etoc BuildRequires: texlive-tocloft BuildRequires: texlive-ulem BuildRequires: texlive-newunicodechar +BuildRequires: texlive-wasy BuildRequires: texlive-wasysym BuildArch: noarch %description doc From 66636ea5145bc43047ec3393d586e0eb29dcdf63 Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Mon, 6 Feb 2023 08:21:53 +0100 Subject: [PATCH 17/35] Fix C99 compatibility issue Related to: --- apbs-c99.patch | 23 +++++++++++++++++++++++ apbs.spec | 9 ++++++++- 2 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 apbs-c99.patch diff --git a/apbs-c99.patch b/apbs-c99.patch new file mode 100644 index 0000000..4a5b282 --- /dev/null +++ b/apbs-c99.patch @@ -0,0 +1,23 @@ +Partial backport of this commit, to avoid an implicit declaration of +getpid and future build failures: + +Author: Noah Oblath +Date: Mon Jan 24 15:33:56 2022 -0800 + + Nsoblath/issue 163 (#171) + +diff -ur apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c apbs-3.0.0/contrib/iapbs/src/apbs_driver.c +--- apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c 2020-05-30 03:47:30.000000000 +0200 ++++ apbs-3.0.0/contrib/iapbs/src/apbs_driver.c 2023-02-06 07:58:46.215007012 +0100 +@@ -18,6 +18,11 @@ + + #include "apbs_driver.h" + ++#ifdef WIN32 ++#include ++#else ++#include ++#endif + + /*! \def MAX_BUF_SIZE + \brief Buffer size for internal APBS string input. diff --git a/apbs.spec b/apbs.spec index a9b34a8..d9085d0 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 17%{datecommit}%{shortcommit}%{?dist} +Release: 18%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -26,6 +26,8 @@ Patch1: %{name}-exclude_tests.patch # Porting to Python-3.11 Patch2: %{name}-python311.patch +Patch3: apbs-c99.patch + BuildRequires: gcc-c++ BuildRequires: cmake3 BuildRequires: chrpath @@ -108,6 +110,8 @@ Python interface of APBS. %patch2 -p1 -b .python311 %endif +%patch3 -p1 + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -209,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Feb 06 2023 Florian Weimer - 3.0.0-18 +- Fix C99 compatibility issue + * Wed Jan 18 2023 Fedora Release Engineering - 3.0.0-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From 95dca6667353f7d74e948c1eb87898abb638183c Mon Sep 17 00:00:00 2001 From: Python Maint Date: Wed, 14 Jun 2023 06:13:12 +0200 Subject: [PATCH 18/35] Rebuilt for Python 3.12 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index d9085d0..7e0bb65 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 18%{datecommit}%{shortcommit}%{?dist} +Release: 19%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jun 14 2023 Python Maint - 3.0.0-19 +- Rebuilt for Python 3.12 + * Mon Feb 06 2023 Florian Weimer - 3.0.0-18 - Fix C99 compatibility issue From 6c77a00b14148e0a3ad4ba169e657ecdc8226dc2 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 19 Jul 2023 13:32:10 +0000 Subject: [PATCH 19/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 7e0bb65..bcd5618 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 19%{datecommit}%{shortcommit}%{?dist} +Release: 20%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 19 2023 Fedora Release Engineering - 3.0.0-20 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Wed Jun 14 2023 Python Maint - 3.0.0-19 - Rebuilt for Python 3.12 From e1527066ef1036bd18ae72171a3604ddcff570b6 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 19 Jan 2024 13:19:14 +0000 Subject: [PATCH 20/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index bcd5618..327ab9c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 20%{datecommit}%{shortcommit}%{?dist} +Release: 21%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Fri Jan 19 2024 Fedora Release Engineering - 3.0.0-21 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Wed Jul 19 2023 Fedora Release Engineering - 3.0.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 9c73f66c0ba3217c190b7d4417e7cd530fc20de5 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 22 Jan 2024 23:16:39 +0000 Subject: [PATCH 21/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 327ab9c..cbb96f6 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 21%{datecommit}%{shortcommit}%{?dist} +Release: 22%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPLv2+ and BSD URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Fri Jan 19 2024 Fedora Release Engineering - 3.0.0-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 5773361a204d3b42a99475c75e82e77a1f1479dd Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 25 May 2024 20:00:26 +0200 Subject: [PATCH 22/35] Fix patch commands --- apbs.spec | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/apbs.spec b/apbs.spec index cbb96f6..ea24cc8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,9 +11,9 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 22%{datecommit}%{shortcommit}%{?dist} +Release: 23%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. -License: LGPLv2+ and BSD +License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ Source0: https://github.com/Electrostatics/apbs/archive/refs/tags/v%{version}/%{name}-%{version}.tar.gz Source1: %{name}-LGPL_V2 @@ -103,14 +103,14 @@ Python interface of APBS. %prep %autosetup -n %{name}-%{version} -N -%patch0 -p2 -b .apbs-cmake -%patch1 -p1 -b .exclude_tests +%patch -P 0 -p2 -b .apbs-cmake +%patch -P 1 -p1 -b .exclude_tests %if 0%{?python3_version_nodots} >= 311 -%patch2 -p1 -b .python311 +%patch -P 2 -p1 -b .python311 %endif -%patch3 -p1 +%patch -P 3 -p1 cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Sat May 25 2023 Antonio Trande - 3.0.0-23 +- Fix patch commands + * Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 0255ed726be519e2596ef7f7ffa57d8576b80840 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sat, 25 May 2024 20:45:53 +0200 Subject: [PATCH 23/35] Fix Changelog --- apbs.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ea24cc8..b13a491 100644 --- a/apbs.spec +++ b/apbs.spec @@ -213,7 +213,7 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog -* Sat May 25 2023 Antonio Trande - 3.0.0-23 +* Sat May 25 2024 Antonio Trande - 3.0.0-23 - Fix patch commands * Mon Jan 22 2024 Fedora Release Engineering - 3.0.0-22 From acba49821cc83b0680e1626841ac2b798c1ed494 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Sat, 8 Jun 2024 08:08:15 +0200 Subject: [PATCH 24/35] Rebuilt for Python 3.13 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index b13a491..9b50552 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 23%{datecommit}%{shortcommit}%{?dist} +Release: 24%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Sat Jun 08 2024 Python Maint - 3.0.0-24 +- Rebuilt for Python 3.13 + * Sat May 25 2024 Antonio Trande - 3.0.0-23 - Fix patch commands From 12b548c50300ae878da6b3a2c36862a56ad16342 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 17 Jul 2024 17:14:20 +0000 Subject: [PATCH 25/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 9b50552..ed6c2d8 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 24%{datecommit}%{shortcommit}%{?dist} +Release: 25%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 17 2024 Fedora Release Engineering - 3.0.0-25 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + * Sat Jun 08 2024 Python Maint - 3.0.0-24 - Rebuilt for Python 3.13 From 3172b4fb1b5331cc05868b7451b0201bbd3d3d87 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 16 Jan 2025 11:19:31 +0000 Subject: [PATCH 26/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ed6c2d8..ddca290 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 25%{datecommit}%{shortcommit}%{?dist} +Release: 26%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Thu Jan 16 2025 Fedora Release Engineering - 3.0.0-26 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + * Wed Jul 17 2024 Fedora Release Engineering - 3.0.0-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From c815b178467f0a36746241a736889345be82d010 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Tue, 3 Jun 2025 12:29:37 +0200 Subject: [PATCH 27/35] Rebuilt for Python 3.14 --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index ddca290..08be658 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 26%{datecommit}%{shortcommit}%{?dist} +Release: 27%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Tue Jun 03 2025 Python Maint - 3.0.0-27 +- Rebuilt for Python 3.14 + * Thu Jan 16 2025 Fedora Release Engineering - 3.0.0-26 - Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild From b3f9fbd6d070fc0b628f3265792b6fd25df9ecd1 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 23 Jul 2025 17:07:38 +0000 Subject: [PATCH 28/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 08be658..5451beb 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 27%{datecommit}%{shortcommit}%{?dist} +Release: 28%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Wed Jul 23 2025 Fedora Release Engineering - 3.0.0-28 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild + * Tue Jun 03 2025 Python Maint - 3.0.0-27 - Rebuilt for Python 3.14 From 08c273025bba250ab243c0c8edd95295a7bf3836 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 19:45:04 +0200 Subject: [PATCH 29/35] Fix rhbz#2380463 --- apbs.spec | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/apbs.spec b/apbs.spec index 5451beb..0232f5d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 28%{datecommit}%{shortcommit}%{?dist} +Release: 29%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -120,8 +120,7 @@ cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 # Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" -mkdir -p build -cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ +%cmake -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ @@ -131,10 +130,11 @@ cmake -S . -B build -DCMAKE_BUILD_TYPE:STRING=Release \ -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ -DLIB_INSTALL_DIR:PATH=%{_libdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} -make -O -j1 V=1 -C build + +%cmake_build %install -%make_install -C build +%cmake_install # Tools for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do @@ -213,6 +213,9 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %doc build/doc %changelog +* Thu Jul 24 2025 Antonio Trande - 3.0.0-29 +- Fix rhbz#2380463 + * Wed Jul 23 2025 Fedora Release Engineering - 3.0.0-28 - Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild From b1d95aaa718c0b7f6d6d31102ddbc1d8e0631f16 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 19:57:43 +0200 Subject: [PATCH 30/35] Fix build directory --- apbs.spec | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/apbs.spec b/apbs.spec index 0232f5d..f36c2ff 100644 --- a/apbs.spec +++ b/apbs.spec @@ -155,7 +155,7 @@ mkdir -p %{buildroot}%{python3_sitearch}/apbs install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/ %{__python3} %{_rpmconfigdir}/redhat/pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py -install -pm 755 build/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ +install -pm 755 %_vpath_builddir/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/ # Remove redundant tools binary files in /usr/share rm -rf %{buildroot}%{_datadir}/apbs @@ -210,7 +210,7 @@ export LD_LIBRARY_PATH=%{buildroot}%{_libdir} %files doc %license LICENSE.md -%doc build/doc +%doc %_vpath_builddir/doc %changelog * Thu Jul 24 2025 Antonio Trande - 3.0.0-29 From ba54c74207e39696808b594bd88436b29bcb61d7 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 21:59:51 +0200 Subject: [PATCH 31/35] Update CMake patches --- apbs-cmake.patch | 46 +++++++++++++++++++++++++++++++++++++++++++++- apbs.spec | 4 +--- 2 files changed, 46 insertions(+), 4 deletions(-) diff --git a/apbs-cmake.patch b/apbs-cmake.patch index dbcb876..c457571 100644 --- a/apbs-cmake.patch +++ b/apbs-cmake.patch @@ -1,11 +1,20 @@ --- a/apbs/CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400 +++ b/apbs/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 @@ -1,4 +1,5 @@ - cmake_minimum_required (VERSION 3.12) +-cmake_minimum_required (VERSION 3.12) ++cmake_minimum_required(VERSION 3.13...4.0) +set(CMAKE_POSITION_INDEPENDENT_CODE ON) ################################################################################ # TODO: Add licensing and authorship information +@@ -7,7 +8,6 @@ + # (configure.ac:1306) + ################################################################################ + set(CMAKE_VERBOSE_MAKEFILE true) +-cmake_policy(SET CMP0054 OLD) + cmake_policy(SET CMP0042 NEW) + set(CMAKE_MACOSX_RPATH 1) + @@ -70,10 +71,10 @@ set(TOOLS_PATH ${APBS_BUILD}/tools) set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) @@ -117,6 +126,12 @@ set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/") --- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400 +++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400 +@@ -1,4 +1,4 @@ +-cmake_minimum_required(VERSION 2.8) ++cmake_minimum_required(VERSION 3.13...4.0) + + macro(add_items TYPE) + @@ -32,11 +32,11 @@ message(STATUS "With external header files ${EXTERNAL_HEADERS}") message(STATUS "With internal header files ${INTERNAL_HEADERS}") @@ -279,3 +294,32 @@ +target_link_libraries(uhbd_asc2bin ${LIBS} ${APBS_LIBS}) + +INSTALL(TARGETS mgmesh smooth dxmath mergedx mergedx2 value multivalue benchmark similarity analysis dx2mol dx2uhbd del2dx tensor2dx uhbd_asc2bin DESTINATION ${EXECUTABLE_INSTALL_PATH}) +--- a/a/tools/python/CMakeLists.orig.txt 2020-05-30 03:47:30.000000000 +0200 ++++ b/b/tools/python/CMakeLists.txt 2025-07-24 20:56:31.152039088 +0200 +@@ -1,3 +1,4 @@ ++cmake_minimum_required(VERSION 3.13...4.0) + if (${CMAKE_VERSION} VERSION_GREATER "3.13") + CMAKE_POLICY(SET CMP0078 OLD) + CMAKE_POLICY(SET CMP0086 OLD) +@@ -23,18 +24,16 @@ + SET(CMAKE_SWIG_FLAGS "") + + SWIG_ADD_LIBRARY(apbslib +- #TYPE USE_BUILD_SHARED_LIBS ++ TYPE USE_BUILD_SHARED_LIBS + TYPE SHARED + LANGUAGE python + SOURCES apbslib.i) + + # Hack to get the correct shared library extensions. Why does Python suck so hard wrt to this? +-if(APPLE) +- set(CMAKE_SHARED_LIBRARY_SUFFIX ".so") +-endif(APPLE) ++set(CMAKE_SHARED_LIBRARY_SUFFIX ".so") + + # Another hack to get SWIG to use the the correct library extension! +-#SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX}) ++SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX}) + + SWIG_LINK_LIBRARIES(apbslib ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${Python3_LIBRARIES}) + diff --git a/apbs.spec b/apbs.spec index f36c2ff..1c0fe3d 100644 --- a/apbs.spec +++ b/apbs.spec @@ -116,15 +116,13 @@ cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2 %build -# CMake needs BUILD_SHARED_LIBS:BOOL=OFF to build Python libraries -# Using CMake rpm macro automatically enables the shared libs building export CFLAGS="%{build_cflags} -fopenmp -lm" export CXXFLAGS="%{build_cxxflags} -fopenmp -lm" %cmake -DCMAKE_BUILD_TYPE:STRING=Release \ -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \ -DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \ -DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \ - -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ + -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \ -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \ From 602c04ccf301e34299fe80c9b5e0eb26697499f1 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 24 Jul 2025 22:15:14 +0200 Subject: [PATCH 32/35] Exporting binary path --- apbs.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/apbs.spec b/apbs.spec index 1c0fe3d..962309f 100644 --- a/apbs.spec +++ b/apbs.spec @@ -167,6 +167,7 @@ done %check pushd tests export LD_LIBRARY_PATH=%{buildroot}%{_libdir} +export PATH=%{buildroot}%{_bindir} %{__python3} ./apbs_tester.py %endif From 0ab0f837596b3b4593b4fd2378f2ec71b19f8a6c Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 15 Aug 2025 12:38:14 +0200 Subject: [PATCH 33/35] Rebuilt for Python 3.14.0rc2 bytecode --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 962309f..601a19c 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 29%{datecommit}%{shortcommit}%{?dist} +Release: 30%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Aug 15 2025 Python Maint - 3.0.0-30 +- Rebuilt for Python 3.14.0rc2 bytecode + * Thu Jul 24 2025 Antonio Trande - 3.0.0-29 - Fix rhbz#2380463 From 328dda165355c22bcf785d4135b1befab5df0463 Mon Sep 17 00:00:00 2001 From: Python Maint Date: Fri, 19 Sep 2025 12:07:07 +0200 Subject: [PATCH 34/35] Rebuilt for Python 3.14.0rc3 bytecode --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index 601a19c..bc582e2 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 30%{datecommit}%{shortcommit}%{?dist} +Release: 31%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Sep 19 2025 Python Maint - 3.0.0-31 +- Rebuilt for Python 3.14.0rc3 bytecode + * Fri Aug 15 2025 Python Maint - 3.0.0-30 - Rebuilt for Python 3.14.0rc2 bytecode From 9fa9b189bc58f8cbef17895880ef5619ea08a2a8 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 16 Jan 2026 03:48:49 +0000 Subject: [PATCH 35/35] Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild --- apbs.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/apbs.spec b/apbs.spec index bc582e2..b3c0c36 100644 --- a/apbs.spec +++ b/apbs.spec @@ -11,7 +11,7 @@ Name: apbs Summary: Adaptive Poisson Boltzmann Solver Version: 3.0.0 -Release: 31%{datecommit}%{shortcommit}%{?dist} +Release: 32%{datecommit}%{shortcommit}%{?dist} # iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license. License: LGPL-2.0-or-later AND BSD-3-Clause URL: https://www.poissonboltzmann.org/ @@ -212,6 +212,9 @@ export PATH=%{buildroot}%{_bindir} %doc %_vpath_builddir/doc %changelog +* Fri Jan 16 2026 Fedora Release Engineering - 3.0.0-32 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild + * Fri Sep 19 2025 Python Maint - 3.0.0-31 - Rebuilt for Python 3.14.0rc3 bytecode