<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/7e371114824c7481acbeeb360021d31a7a091285">https://github.com/macports/macports-ports/commit/7e371114824c7481acbeeb360021d31a7a091285</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 7e371114824 apbs: update to 3.4.1
</span>7e371114824 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 7e371114824c7481acbeeb360021d31a7a091285
</span>Author: jwhowarth <howarth.mailing.lists@gmail.com>
AuthorDate: Sat May 11 07:51:09 2024 -0400
<span style='display:block; white-space:pre;color:#404040;'> apbs: update to 3.4.1
</span>---
science/apbs/Portfile | 150 ++++++++++-----------
science/apbs/files/cmake-maloc.patch | 62 +++++++++
.../apbs/files/disable_python_cmake_check.patch | 31 +++++
science/apbs/files/open-U-obsolete.patch | 11 ++
science/apbs/files/patch-CMakeLists.txt.diff | 27 ----
science/apbs/files/patch-Eigen-include-path.diff | 22 ---
.../files/patch-contrib-tabipb-CMakeLists.txt.diff | 31 -----
science/apbs/files/patch-pbsolvercz.cpp.diff | 11 --
science/apbs/files/patch-testfiles.patch | 62 +++++++++
science/apbs/files/patch-tests-apbs_tester.py.diff | 11 --
science/apbs/files/python3.patch | 16 +++
.../apbs/files/wrong-path-for-interpreter.patch | 64 +++++++++
12 files changed, 316 insertions(+), 182 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/Portfile b/science/apbs/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ff7431c461c..46579db31f1 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -2,11 +2,9 @@
</span>
PortSystem 1.0
PortGroup compiler_blacklist_versions 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup cmake 1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup mpi 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup cmake 1.1
</span> PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-cmake.out_of_source yes
</span> name apbs
categories science
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -20,64 +18,90 @@ long_description APBS is a software package for the numerical \
</span> electrostatic interactions between molecular \
solutes over a wide range of length scales.
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup Electrostatics apbs-pdb2pqr d4e78c62e6a07f92c26924318d83a159fa6af063
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version 1.4.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage http://www.poissonboltzmann.org
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-worksrcdir ${worksrcdir}/apbs
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# stealth update; remove for next version
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-dist_subdir ${name}/${version}_1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 09ffa6a90c190eb4e584934519c8cbd6229fc7b8 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 3c3e6914a1a69c27d54d9d9ea7ffd1072e3bc82209971289f0a8a7964fcdf82b \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 37120958
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 3.4.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://www.poissonboltzmann.org
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+set FETK_version 1.9.3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup Electrostatics apbs ${version} v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.tarball_from releases
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+extract.mkdir no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites https://github.com/Electrostatics/apbs/archive/refs/tags/v${version}:apbs \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ https://github.com/Electrostatics/FETK/archive/refs/tags/${FETK_version}:FETK
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+distfiles apbs-${version}.tar.gz:apbs FETK-${FETK_version}.tar.gz:FETK
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums apbs-${version}.tar.gz \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rmd160 17de250c3887ff68f89a873c5a0be19f6ab38813 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 85806314 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ FETK-${FETK_version}.tar.gz \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rmd160 25cf57754a0b817e76e19b8de93617e554302661 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 2ce7ab04cba4403f4208c3ecf1c81a0a18aae6a77d22da0ffa5f64c2da7c6f28 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 27757348
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+worksrcdir ${workpath}/apbs-${version}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Test support requires python3 but the
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# building the apbs python module with swig
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# is unnecessary for apbs's use in pymol.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+platform darwin {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {${os.major} < 19} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ depends_test port:python312
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set python ${prefix}/bin/python3.12
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ } else {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set python /usr/bin/python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span>
depends_lib port:maloc \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- port:readline
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# dependencies are not managed correctly within this code, so errors such as from -lapbs_geoflow might occur
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# how to solve: first 'make apbs_geoflow', then 'make all'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-use_parallel_build no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:superlu \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:SuiteSparse
</span>
configure.optflags -O3 -ffast-math
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.args-append -DENABLE_OPENMP:BOOL=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.cppflags-append -I${worksrcpath}/include -Wno-error=implicit-int -Wno-error=incompatible-function-pointer-types
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Follow Debian's approach of not building those
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# features like BEM, GEOFLOW or PBAM that only
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# exist in apbs's github without tagged releases yet.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append -DAPBS_STATIC_BUILD=ON \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DBUILD_SHARED_LIBS=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DBUILD_TOOLS=ON \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DENABLE_OPENMP:BOOL=OFF \
</span> -DENABLE_BEM=OFF \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- -DCMAKE_C_COMPILER_ARG1:STRING="-I${worksrcpath}/include ${configure.cflags}" \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- -DCMAKE_CXX_COMPILER_ARG1:STRING="-I${worksrcpath}/include ${configure.cxxflags} -stdlib=libc++"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# otherwise obsolete subport installation will fail on patch phase and not get to pre-configure error about replacement
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-if {${subport} eq ${name}} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles patch-CMakeLists.txt.diff patch-Eigen-include-path.diff patch-contrib-tabipb-CMakeLists.txt.diff patch-pbsolvercz.cpp.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[mpi_variant_isset]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patchfiles-append patch-tests-apbs_tester.py.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DENABLE_GEOFLOW=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DENABLE_PBAM=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DBUILD_MALOC=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DBUILD_SUPERLU=OFF \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DBUILD_SHARED_LIBS=ON \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DFETCHCONTENT_SOURCE_DIR_FETK=${worksrcpath}/FETK-${FETK_version} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DSUPERLU_INCLUDES=${prefix}/include -DSUPERLU_LIBRARIES=${prefix}/lib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles cmake-maloc.patch disable_python_cmake_check.patch patch-testfiles.patch open-U-obsolete.patch python3.patch wrong-path-for-interpreter.patch
</span> test.run yes
test {
ln ${worksrcpath}/tools/manip/inputgen.py ${worksrcpath}/tests/
ln ${worksrcpath}/tools/manip/psize.py ${worksrcpath}/tests/
<span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[mpi_variant_isset]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace "s|mpiexec|\"${mpi.exec}\", \"-n\", \"${build.jobs}\"|" ${worksrcpath}/tests/apbs_tester.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ platform darwin {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ system -W ${worksrcpath}/tests "PATH=${destroot}${prefix}/bin:/usr/bin:/bin:${prefix}/bin ${python} apbs_tester.py -c test_cases.cfg || exit 0"
</span> }
<span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- system -W ${worksrcpath}/tests "python apbs_tester.py"
</span> system -W ${worksrcpath}/tests "cat test.log"
system -W ${worksrcpath}/tests "if grep FAILED test.log; then echo \"FAIL\"; exit 1; fi"
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Some cmake tests will fail with "error: unrecognized option '-arch'" from gcc 4.6 and earlier. Same with dragonegg based on it.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# llvm-gcc-4.2 will fail to build with: error: unrecognized command line option "-std=c++0x"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# It comes with clang for OSX 10.6 so we need to blacklist clang to prevent it being used.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-compiler.blacklist macports-gcc-4.4 macports-gcc-4.5 macports-gcc-4.6 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- macports-dragonegg-3.4 gcc-4.2 llvm-gcc-4.2 apple-gcc-4.2 macports-llvm-gcc-4.2 {clang < 425} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- macports-clang-3.4
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# g++ will just fail to link apbs_geoflow. probably about -lstdc++ stuff. So, just use Fortran.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-compilers.choose fc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-mpi.setup
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-extract {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ move ${worksrcdir}/../FETK-${FETK_version} ${worksrcdir}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.args-append -DENABLE_MPI:BOOL=OFF
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-patch {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|EXACT REQUIRED|REQUIRED|" ${worksrcpath}/CMakeLists.txt ${worksrcpath}/tests/CMakeLists.txt ${worksrcpath}/tools/python/CMakeLists.txt
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ platform darwin {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {${os.major} < 19} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|env python3|env ${prefix}/bin/python3.12|" ${worksrcpath}/tools/manip/psize.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace "s|/usr/bin/python3|${prefix}/bin/python3.12|" ${worksrcpath}/tools/python/vgrid/mergedx.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span>
post-destroot {
set tools ${destroot}${prefix}/share/${subport}/tools
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -93,38 +117,4 @@ post-destroot {
</span> }
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-pre-configure {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {[mpi_variant_isset]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-delete -DENABLE_MPI:BOOL=OFF
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-append -DENABLE_MPI:BOOL=ON \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- -DMPI_C_COMPILER=${mpi.cc} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- -DMPI_CXX_COMPILER=${mpi.cxx}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-variant bem description {Build with support for Boundary Element Method} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-delete -DENABLE_BEM=OFF
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- configure.args-append -DENABLE_BEM=ON
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if {![fortran_variant_isset]} {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ui_error "+bem requires a Fortran variant, e.g. +gccX or +g95."
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return -code error "+bem requires a Fortran variant."
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # BEM looks for 'gfortran', hard-coded, and configure fails without it if BEM is enabled, with a syntax error
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #CMake Error at CMakeLists.txt:217 (get_filename_component):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # get_filename_component called with incorrect number of arguments
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- post-patch {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # -lstdc++ does not seem necessary and may cause trouble; specifying full paths avoid possible use of -ltabip from an earlier installation in ${prefix}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace "s|-L\${LIBGFORTRAN_PATH} -lgfortran -ltabipb -lstdc\+\+|${compilers.libfortran} ${worksrcpath}/lib/libtabipb.a|" ${worksrcpath}/CMakeLists.txt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # provide this information to subsidiary cmake command run in tabipb directory during build phase
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace "s|CMAKE_ARGS|CMAKE_ARGS -DCMAKE_Fortran_COMPILER:STRING=${configure.fc}|" ${worksrcpath}/CMakeLists.txt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace "s|FCFLAGS|${configure.fcflags}|g" ${worksrcpath}/contrib/tabipb/CMakeLists.txt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# check for real releases, not github commits
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.type regex
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.version ${version}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.url https://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-livecheck.regex APBS (\[0-9.\]+)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.livecheck.regex {([0-9.]+)}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/cmake-maloc.patch b/science/apbs/files/cmake-maloc.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..789abe61740
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/cmake-maloc.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,62 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- FETK-1.9.3/punc/CMakeLists.txt.orig 2024-04-16 14:10:11
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ FETK-1.9.3/punc/CMakeLists.txt 2024-04-16 14:11:00
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -122,9 +122,10 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # maloc library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(NOT TARGET maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- message(FATAL_ERROR "Maloc target not found")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND PUNC_EXT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND PUNC_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-list(APPEND PUNC_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ################################################################################
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- FETK-1.9.3/mc/CMakeLists.txt.orig 2024-04-16 14:08:40
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ FETK-1.9.3/mc/CMakeLists.txt 2024-04-16 14:09:41
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -65,9 +65,10 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # maloc library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(NOT TARGET maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- message(FATAL_ERROR "Maloc target not found")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND MC_EXT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND MC_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-list(APPEND MC_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # punc library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(NOT TARGET punc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- FETK-1.9.3/gamer/CMakeLists.txt.orig 2024-04-16 14:11:32
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ FETK-1.9.3/gamer/CMakeLists.txt 2024-04-16 14:12:59
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -51,7 +51,9 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # maloc library
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(NOT TARGET maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- message(FATAL_ERROR "Maloc target not found")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND GAMER_EXT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ list(APPEND GAMER_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include_directories(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # ${CMAKE_CURRENT_SOURCE_DIR}/../maloc/src/base
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -59,7 +61,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # ${CMAKE_CURRENT_SOURCE_DIR}/../maloc/src/vsh
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # ${CMAKE_CURRENT_SOURCE_DIR}/../maloc/src/vsys
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-list(APPEND GAMER_INT_LIBS maloc)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ################################################################################
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- FETK-1.9.3/CMakeLists.txt.orig 2024-04-16 14:30:41
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ FETK-1.9.3/CMakeLists.txt 2024-04-16 14:28:59
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -67,7 +67,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(BUILD_PUNC OR BUILD_GAMER) # SG would be included in this if statement
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- set(BUILD_MALOC TRUE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ set(BUILD_MALOC FALSE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/disable_python_cmake_check.patch b/science/apbs/files/disable_python_cmake_check.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..306fdb202b3
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/disable_python_cmake_check.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,31 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- CMakeLists.txt.orig 2024-04-19 08:18:12
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ CMakeLists.txt 2024-04-19 08:18:30
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -92,7 +92,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set(APBS_LIBS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set(APBS_LIB_DIRS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-set(PYTHON_VERSION 3.6 CACHE STRING "Python version to be used (or compatible)") # Python 3.6 is the lowest version tested so far
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#set(PYTHON_VERSION 3.6 CACHE STRING "Python version to be used (or compatible)") # Python 3.6 is the lowest version tested so far
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ find_file(CONTRIB_PATH "contrib"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ PATHS "${APBS_ROOT}"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- CMakeLists.txt.orig 2024-04-19 07:57:02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ CMakeLists.txt 2024-04-19 07:58:45
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -126,7 +126,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .a)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- set(Python3_USE_STATIC_LIBS TRUE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# set(Python3_USE_STATIC_LIBS TRUE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set(FETK_STATIC_BUILD OFF)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set(BLA_STATIC OFF)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -143,7 +143,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .so)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- set(Python3_USE_STATIC_LIBS FALSE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++# set(Python3_USE_STATIC_LIBS FALSE)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif()
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ message(STATUS "")
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/open-U-obsolete.patch b/science/apbs/files/open-U-obsolete.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..c9e780f2138
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/open-U-obsolete.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,11 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tools/manip/inputgen.py.orig 2024-04-16 07:39:21
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tools/manip/inputgen.py 2024-04-16 07:39:41
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -311,7 +311,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ file (string)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ nproc = 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- file = open(filename, "rU")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ file = open(filename, "r")
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ text = ""
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ while 1:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ line = file.readline()
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-CMakeLists.txt.diff b/science/apbs/files/patch-CMakeLists.txt.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index e0852762a27..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/files/patch-CMakeLists.txt.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,27 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- CMakeLists.txt.orig 2016-06-07 15:34:23.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ CMakeLists.txt 2016-06-07 15:31:19.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -214,8 +214,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if(HAVE_GFORTRAN GREATER 0)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- message(FATAL_ERROR gfortran is currently required for using BEM/TABIPB in APBS)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- endif()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ #get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ #find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb -lstdc++" )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- endif() # ENABLE_BEM
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -277,7 +277,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set(MALOC_LIBRARY ${LIBRARY_OUTPUT_PATH}/${MALOC_LIBRARY_BASENAME})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- endif()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--list(APPEND APBS_LIBS -lmaloc)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+list(APPEND APBS_LIBS -lmaloc -lreadline)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ##############################################################################
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -676,3 +676,4 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- DESTINATION ${EXECUTABLE_INSTALL_PATH})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- endif()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- endif()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+include_directories(${APBS_ROOT}/include)
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-Eigen-include-path.diff b/science/apbs/files/patch-Eigen-include-path.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index fb6e2bbbc6f..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/files/patch-Eigen-include-path.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,22 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/geoflow/Mat.h.orig 2015-11-10 18:03:45.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/geoflow/Mat.h 2015-11-10 18:04:15.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -57,7 +57,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <cmath>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <vector>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#include <Eigen/Core>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include "Eigen/Core"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // The following is from modules.h, which includes this file, Mat.h. We need
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // the declaration here because we use it below in the deriv method. If we
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/geoflow/pbsolvercz.cpp.orig 2015-11-10 18:03:52.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/geoflow/pbsolvercz.cpp 2015-11-10 18:04:31.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -56,7 +56,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <valarray>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include <vector>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#include <Eigen/Sparse>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#include "Eigen/Sparse"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include "Mat.h"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #include "modules.h"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-contrib-tabipb-CMakeLists.txt.diff b/science/apbs/files/patch-contrib-tabipb-CMakeLists.txt.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index cc4d0fd8e20..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/files/patch-contrib-tabipb-CMakeLists.txt.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,31 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- contrib/tabipb/CMakeLists.txt.orig 2016-06-09 20:42:21.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ contrib/tabipb/CMakeLists.txt 2016-06-09 20:44:22.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -19,26 +19,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # FFLAGS depend on the compiler
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--if (Fortran_COMPILER_NAME MATCHES "gfortran.*")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- # gfortran
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_DEBUG "-fno-f2c -O0 -g")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--elseif (Fortran_COMPILER_NAME MATCHES "ifort.*")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- # ifort (untested)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_RELEASE "-f77rtl -O3")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_DEBUG "-f77rtl -O0 -g")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--elseif (Fortran_COMPILER_NAME MATCHES "g77")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- # g77
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_RELEASE "-funroll-all-loops -fno-f2c -O3 -m32")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_DEBUG "-fno-f2c -O0 -g -m32")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--else (Fortran_COMPILER_NAME MATCHES "gfortran.*")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- message ("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- message ("Fortran compiler: " ${Fortran_COMPILER_NAME})
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- message ("No optimized Fortran compiler flags are known, we just try -O2...")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_RELEASE "-O2")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- set (CMAKE_Fortran_FLAGS_DEBUG "-O0 -g")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--endif (Fortran_COMPILER_NAME MATCHES "gfortran.*")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+set (CMAKE_Fortran_FLAGS_RELEASE "FCFLAGS")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+set (CMAKE_Fortran_FLAGS_DEBUG "FCFLAGS")
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- set (LIBFILES src/tabipb.f90 src/var_modules.f90 src/treecode3d_pb.f
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- src/readin.f90 src/dgmres_dep.f)
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-pbsolvercz.cpp.diff b/science/apbs/files/patch-pbsolvercz.cpp.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 4b794ce6c25..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/files/patch-pbsolvercz.cpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/geoflow/pbsolvercz.cpp.orig 2018-03-27 20:30:36.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/geoflow/pbsolvercz.cpp 2018-03-27 20:31:13.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -77,7 +77,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- std::vector <Eigen::Triplet<double>> tripletList;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ std::vector <Eigen::Triplet<double> > tripletList;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- tripletList.reserve(nx*ny*nz);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Eigen::VectorXd phi_flat(nx*ny*nz);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-testfiles.patch b/science/apbs/files/patch-testfiles.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..b2944f93c13
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/patch-testfiles.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,62 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/test_cases.cfg.orig 2024-04-16 10:18:48
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/test_cases.cfg 2024-04-16 10:21:19
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -76,36 +76,36 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ apbs-smol : 1.847860440020E+03 1.885436377745E+03 2.734040568569E+03 3.125279428954E+03 -3.757593797629E+01 -3.912388198513E+02 -3.536628818750E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[geoflow]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/geoflow
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-imidazole : -1.030222099963E+01 5.417419E-01
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[geoflow]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/geoflow
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#imidazole : -1.030222099963E+01 5.417419E-01
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[bem]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/bem
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-451c_order1 : -4.678324477794E+03
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-451c_order5 : -4.678190000000e+03
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[bem]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/bem
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#451c_order1 : -4.678324477794E+03
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#451c_order5 : -4.678190000000e+03
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[bem-pKa]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/bem-pKa
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ASH66 : -4.005763343995E+00
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-2LZT-ASH66 : -3.636994149197E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-2LZT-noASH66 : -3.625121468362E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[bem-pKa]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/bem-pKa
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#ASH66 : -4.005763343995E+00
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#2LZT-ASH66 : -3.636994149197E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#2LZT-noASH66 : -3.625121468362E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[bem-binding-energy]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/bem-binding-energy
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-1d30 : -2.197264516397E+04
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-1d30_monomer1 : -2.608072100934E+04
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-1d30_monomer2 : -7.676311645066E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[bem-binding-energy]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/bem-binding-energy
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#1d30 : -2.197264516397E+04
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#1d30_monomer1 : -2.608072100934E+04
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#1d30_monomer2 : -7.676311645066E+02
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[pbam]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/pbam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-toy_energyforce : -4.965018552290E+01 -4.965018552290E+01
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[pbam]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/pbam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#toy_energyforce : -4.965018552290E+01 -4.965018552290E+01
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-[pbsam]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-input_dir : ../examples/pbsam-gly
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-gly_energyforce : 6.176608555569E-05 6.210593742215E-05
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#[pbsam]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#input_dir : ../examples/pbsam-gly
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#gly_energyforce : 6.176608555569E-05 6.210593742215E-05
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # Very slow test
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #[protein-rna]
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/patch-tests-apbs_tester.py.diff b/science/apbs/files/patch-tests-apbs_tester.py.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 73de945ed97..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/apbs/files/patch-tests-apbs_tester.py.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- tests/apbs_tester.py.orig 2016-06-08 13:55:06.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ tests/apbs_tester.py 2016-06-08 13:55:32.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -59,7 +59,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- output_file = open( output_name, 'w' )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # Construct the system command and make the call
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- command = [ binary, input_file ]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ command = [ mpiexec, binary, input_file ]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- subprocess.call( command, stdout = output_file )
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # Look for the results in the output file
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/python3.patch b/science/apbs/files/python3.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..722a5950dd8
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/python3.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,16 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- examples/protein-rna/postprocess.sh.orig 2024-04-17 06:58:34
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ examples/protein-rna/postprocess.sh 2024-04-17 06:59:31
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -13,11 +13,11 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ echo ${ionstr} ${energy_kJ} | awk '{ printf("%1.12E %1.12E\n", log($1)/2.303, $2/4.184) }' >> log10conc-energykcal.dat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ done
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-cat lnconc-energyRT.dat | python fit.py > lnconc-energyRT.fit
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++cat lnconc-energyRT.dat | python3 fit.py > lnconc-energyRT.fit
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ n=`grep "slope:" lnconc-energyRT.fit | awk '{print $2}'`
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ dn=`grep "slope error:" lnconc-energyRT.fit | awk '{print $3}'`
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ echo "n = -(${n} +/- ${dn})"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-cat log10conc-energykcal.dat | python fit.py > log10conc-energykcal.fit
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++cat log10conc-energykcal.dat | python3 fit.py > log10conc-energykcal.fit
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ dGdl=`grep "slope:" log10conc-energykcal.fit | awk '{print $2}'`
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ddGdl=`grep "slope error:" log10conc-energykcal.fit | awk '{print $3}'`
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ echo "dG/d(log10 [KCl]) = ${dGdl} +/- (${ddGdl})"
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/apbs/files/wrong-path-for-interpreter.patch b/science/apbs/files/wrong-path-for-interpreter.patch
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..dd61b3f3ac6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/apbs/files/wrong-path-for-interpreter.patch
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,64 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/apbs_tester.py.orig 2024-04-17 07:15:37
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/apbs_tester.py 2024-04-17 07:15:59
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#! /usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#! /usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Provides utility for testing apbs against examples and known results
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/apbs_logger.py.orig 2024-04-17 07:17:38
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/apbs_logger.py 2024-04-17 07:17:45
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#! /usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#! /usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Provides a logger that prints regular messages and logger messages.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/apbs_check_forces.py.orig 2024-04-17 07:18:31
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/apbs_check_forces.py 2024-04-17 07:18:40
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#! /usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#! /usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Checks computed forces from an apbs run
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tools/python/noinput.py.orig 2024-04-17 07:19:08
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tools/python/noinput.py 2024-04-17 07:19:19
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#!/usr/bin/python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#!/usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """ Python APBS No Input Driver File
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ This module allows a user to run APBS through Python. Use this module if
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- examples/protein-rna/fit.py.orig 2024-04-17 07:20:08
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ examples/protein-rna/fit.py 2024-04-17 07:20:16
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#!/usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#!/usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """Performs unweighted linear regression. Can be invoked from command line by
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ providing data pairs through stdin.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/apbs_check_results.py.orig 2024-04-17 07:20:51
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/apbs_check_results.py 2024-04-17 07:20:58
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#! /usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#! /usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Provides functions for verifying results from a test run
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- examples/protein-rna/apbs_dx.py.orig 2024-04-17 07:21:38
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ examples/protein-rna/apbs_dx.py 2024-04-17 07:22:03
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#!/bin/python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#!/usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Create files for the protein-rna tests
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- tests/apbs_check_intermediate_energies.py.orig 2024-04-17 07:23:23
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ tests/apbs_check_intermediate_energies.py 2024-04-17 07:23:28
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,4 +1,4 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#!/usr/bin/env python
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#!/usr/bin/env python3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ """
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Check intermediate computed energies form an APBS run
</span></pre><pre style='margin:0'>
</pre>