extra/boost to 1.75.0-5

extra/boost/5bd5bfb9.patch

@@ -0,0 +1,216 @@
+From 5bd5bfb978df5f345518d2444d8f2ddba849d8d6 Mon Sep 17 00:00:00 2001
+From: Hans Dembinski <HDembinski@users.noreply.github.com>
+Date: Mon, 7 Dec 2020 15:12:20 +0100
+Subject: [PATCH] Bug-fix for one-sided cropping and clarify how cropping works
+ (#302)
+
+---
+ boost/histogram/algorithm/reduce.hpp | 28 +++++++--
+ libs/histogram/test/algorithm_reduce_test.cpp               | 63 ++++++++++++++++----
+ 2 files changed, 77 insertions(+), 14 deletions(-)
+
+diff --git a/include/boost/histogram/algorithm/reduce.hpp b/include/boost/histogram/algorithm/reduce.hpp
+index a5d2fffa6..0646db34e 100644
+--- a/boost/histogram/algorithm/reduce.hpp
++++ b/boost/histogram/algorithm/reduce.hpp
+@@ -111,7 +111,14 @@ inline reduce_command crop(unsigned iaxis, double lower, double upper) {
+   Command is applied to corresponding axis in order of reduce arguments.
+ 
+   Works like `shrink` (see shrink documentation for details), but counts in removed bins
+-  are discarded, whether underflow and overflow bins are present or not.
++  are discarded, whether underflow and overflow bins are present or not. If the cropped
++  range goes beyond the axis range, then the content of the underflow
++  or overflow bin which overlaps with the range is kept.
++
++  If the counts in an existing underflow or overflow bin are discared by the crop, the
++  corresponding memory cells are not physically removed. Only their contents are set to
++  zero. This technical limitation may be lifted in the future, then crop may completely
++  remove the cropped memory cells.
+ 
+   @param lower bin which contains lower is first to be kept.
+   @param upper bin which contains upper is last to be kept, except if upper is equal to
+@@ -323,6 +330,8 @@ inline reduce_command slice_and_rebin(axis::index_type begin, axis::index_type e
+   exception. Histograms with  non-reducible axes can still be reduced along the
+   other axes that are reducible.
+ 
++  An overload allows one to pass reduce_command as positional arguments.
++
+   @param hist original histogram.
+   @param options iterable sequence of reduce commands: `shrink`, `slice`, `rebin`,
+   `shrink_and_rebin`, or `slice_and_rebin`. The element type of the iterable should be
+@@ -343,14 +352,16 @@ Histogram reduce(const Histogram& hist, const Iterable& options) {
+         auto& o = opts[iaxis];
+         o.is_ordered = axis::traits::ordered(a_in);
+         if (o.merge > 0) { // option is set?
+-          o.use_underflow_bin = !o.crop && AO::test(axis::option::underflow);
+-          o.use_overflow_bin = !o.crop && AO::test(axis::option::overflow);
++          o.use_underflow_bin = AO::test(axis::option::underflow);
++          o.use_overflow_bin = AO::test(axis::option::overflow);
+           return detail::static_if_c<axis::traits::is_reducible<A>::value>(
+               [&o](const auto& a_in) {
+                 if (o.range == reduce_command::range_t::none) {
++                  // no range restriction, pure rebin
+                   o.begin.index = 0;
+                   o.end.index = a_in.size();
+                 } else {
++                  // range striction, convert values to indices as needed
+                   if (o.range == reduce_command::range_t::values) {
+                     const auto end_value = o.end.value;
+                     o.begin.index = axis::traits::index(a_in, o.begin.value);
+@@ -359,7 +370,14 @@ Histogram reduce(const Histogram& hist, const Iterable& options) {
+                     if (axis::traits::value_as<double>(a_in, o.end.index) != end_value)
+                       ++o.end.index;
+                   }
+-                  // limit [begin, end] to [0, size()]
++
++                  // crop flow bins if index range does not include them
++                  if (o.crop) {
++                    o.use_underflow_bin &= o.begin.index < 0;
++                    o.use_overflow_bin &= o.end.index > a_in.size();
++                  }
++
++                  // now limit [begin, end] to [0, size()]
+                   if (o.begin.index < 0) o.begin.index = 0;
+                   if (o.end.index > a_in.size()) o.end.index = a_in.size();
+                 }
+@@ -435,6 +453,8 @@ Histogram reduce(const Histogram& hist, const Iterable& options) {
+   the other axes. Trying to reducing a non-reducible axis triggers an invalid_argument
+   exception.
+ 
++  An overload allows one to pass an iterable of reduce_command.
++
+   @param hist original histogram.
+   @param opt first reduce command; one of `shrink`, `slice`, `rebin`,
+   `shrink_and_rebin`, or `slice_or_rebin`.
+diff --git a/test/algorithm_reduce_test.cpp b/test/algorithm_reduce_test.cpp
+index 6ea42fadf..c6b4df4a4 100644
+--- a/libs/histogram/test/algorithm_reduce_test.cpp
++++ b/libs/histogram/test/algorithm_reduce_test.cpp
+@@ -105,15 +105,16 @@ void run_tests() {
+     BOOST_TEST_EQ(reduce(h, crop(0, 1.999)).axis(), ID(0, 2));
+   }
+ 
++  // shrink and rebin
+   {
+     auto h = make_s(Tag(), std::vector<int>(), R(4, 1, 5, "1"), R(3, -1, 2, "2"));
+ 
+     /*
+       matrix layout:
+-      x
++      x ->
+     y 1 0 1 0
+-      1 1 0 0
+-      0 2 1 3
++    | 1 1 0 0
++    v 0 2 1 3
+     */
+     h.at(0, 0) = 1;
+     h.at(0, 1) = 1;
+@@ -122,11 +123,13 @@ void run_tests() {
+     h.at(2, 0) = 1;
+     h.at(2, 2) = 1;
+     h.at(3, 2) = 3;
++    h.at(-1, -1) = 1; // underflow
++    h.at(4, 3) = 1; // overflow
+ 
+     // should do nothing, index order does not matter
+     auto hr = reduce(h, shrink(1, -1, 2), rebin(0, 1));
+     BOOST_TEST_EQ(hr.rank(), 2);
+-    BOOST_TEST_EQ(sum(hr), 10);
++    BOOST_TEST_EQ(sum(hr), 12);
+     BOOST_TEST_EQ(hr.axis(0), R(4, 1, 5, "1"));
+     BOOST_TEST_EQ(hr.axis(1), R(3, -1, 2, "2"));
+     BOOST_TEST_EQ(hr, h);
+@@ -138,7 +141,7 @@ void run_tests() {
+     // shrinking along first axis
+     hr = reduce(h, shrink(0, 2, 4));
+     BOOST_TEST_EQ(hr.rank(), 2);
+-    BOOST_TEST_EQ(sum(hr), 10);
++    BOOST_TEST_EQ(sum(hr), 12);
+     BOOST_TEST_EQ(hr.axis(0), R(2, 2, 4, "1"));
+     BOOST_TEST_EQ(hr.axis(1), R(3, -1, 2, "2"));
+     BOOST_TEST_EQ(hr.at(-1, 0), 1); // underflow
+@@ -164,7 +167,7 @@ void run_tests() {
+ 
+     hr = reduce(h, shrink_and_rebin(0, 2, 5, 2), rebin(1, 3));
+     BOOST_TEST_EQ(hr.rank(), 2);
+-    BOOST_TEST_EQ(sum(hr), 10);
++    BOOST_TEST_EQ(sum(hr), 12);
+     BOOST_TEST_EQ(hr.axis(0), R(1, 2, 4, "1"));
+     BOOST_TEST_EQ(hr.axis(1), R(1, -1, 2, "2"));
+     BOOST_TEST_EQ(hr.at(-1, 0), 2); // underflow
+@@ -184,16 +187,16 @@ void run_tests() {
+     BOOST_TEST_EQ(hr4, hr);
+   }
+ 
+-  // crop
++  // crop and rebin
+   {
+     auto h = make_s(Tag(), std::vector<int>(), R(4, 1, 5), R(3, 1, 4));
+ 
+     /*
+       matrix layout:
+-      x
++      x ->
+     y 1 0 1 0
+-      1 1 0 0
+-      0 2 1 3
++    | 1 1 0 0
++    v 0 2 1 3
+     */
+     h.at(0, 0) = 1;
+     h.at(0, 1) = 1;
+@@ -202,6 +205,9 @@ void run_tests() {
+     h.at(2, 0) = 1;
+     h.at(2, 2) = 1;
+     h.at(3, 2) = 3;
++    h.at(-1, -1) = 1; // underflow
++    h.at(4, 3) = 1; // overflow
++
+ 
+     /*
+       crop first and last column in x and y
+@@ -231,6 +237,43 @@ void run_tests() {
+     BOOST_TEST_EQ(hr, hr4);
+   }
+ 
++  // one-sided crop
++  {
++    auto h = make_s(Tag(), std::vector<int>(), ID(1, 4));
++    std::fill(h.begin(), h.end(), 1);
++    // underflow: 1
++    // index 0, x 1: 1
++    // index 1, x 2: 1
++    // index 2, x 3: 1
++    // overflow: 1
++    BOOST_TEST_EQ(sum(h), 5);
++    BOOST_TEST_EQ(h.size(), 5);
++
++    // keep underflow
++    auto hr1 = reduce(h, crop(0, 3));
++    BOOST_TEST_EQ(hr1, reduce(h, slice(-1, 2, slice_mode::crop)));
++    BOOST_TEST_EQ(sum(hr1), 3);
++    BOOST_TEST_EQ(hr1.size(), 4); // flow bins are not physically removed, only zeroed
++
++    // remove underflow
++    auto hr2 = reduce(h, crop(1, 3));
++    BOOST_TEST_EQ(hr2, reduce(h, slice(0, 2, slice_mode::crop)));
++    BOOST_TEST_EQ(sum(hr2), 2);
++    BOOST_TEST_EQ(hr2.size(), 4); // flow bins are not physically removed, only zeroed
++
++    // keep overflow
++    auto hr3 = reduce(h, crop(2, 5));
++    BOOST_TEST_EQ(hr3, reduce(h, slice(1, 4, slice_mode::crop)));
++    BOOST_TEST_EQ(sum(hr3), 3);
++    BOOST_TEST_EQ(hr3.size(), 4); // flow bins are not physically removed, only zeroed
++
++    // remove overflow
++    auto hr4 = reduce(h, crop(2, 4));
++    BOOST_TEST_EQ(hr4, reduce(h, slice(1, 3, slice_mode::crop)));
++    BOOST_TEST_EQ(sum(hr4), 2);
++    BOOST_TEST_EQ(hr4.size(), 4); // flow bins are not physically removed, only zeroed
++  }
++
+   // mixed axis types
+   {
+     R r(5, 0.0, 5.0);

extra/boost/PKGBUILD

@@ -16,24 +16,33 @@ pkgbase=boost
 pkgname=('boost-libs' 'boost')
 pkgver=1.75.0
 _boostver=${pkgver//./_}
-pkgrel=3
+pkgrel=5
 pkgdesc='Free peer-reviewed portable C++ source libraries'
 url='https://www.boost.org/'
 arch=('x86_64')
 license=('custom')
 makedepends=('icu' 'python' 'python-numpy' 'bzip2' 'zlib' 'openmpi' 'zstd' 'findutils')
-source=(https://dl.bintray.com/boostorg/release/${pkgver}/source/boost_${_boostver}.tar.bz2
+source=(https://boostorg.jfrog.io/artifactory/main/release/$pkgver/source/boost_$_boostver.tar.gz
-        ${pkgbase}-ublas-c++20-iterator.patch::https://github.com/boostorg/ublas/commit/a31e5cffa85f.patch)
+        ${pkgbase}-ublas-c++20-iterator.patch::https://github.com/boostorg/ublas/commit/a31e5cffa85f.patch
-sha256sums=('953db31e016db7bb207f11432bef7df100516eeb746843fa0486a222e3fd49cb'
+        5bd5bfb9.patch
-            'aa38addb40d5f44b4a8472029b475e7e6aef1c460509eb7d8edf03491dc1b5ee')
+        b29603fa.patch)
-b2sums=('ce7ecd8bcee518ce54f7e5302f202acbea60cedd6ae9248708c0bb5bbc2713607b2e1967a9e6f77cc20a4c008c1ee4db651def55937efc80407487a7a44fa8d6'
+sha256sums=('aeb26f80e80945e82ee93e5939baebdca47b9dee80a07d3144be1e1a6a66dd6a'
-        'e5f6d4884eaa557d5547e7e079c2edb4ed9f2f4cd8579aa32a2150f824a5d04413f2a91e79b3139d5b915da6a46f7835f1438ad53f33096973f1a99f378ec1d3')
+            'aa38addb40d5f44b4a8472029b475e7e6aef1c460509eb7d8edf03491dc1b5ee'
+            'fbb27a583a6c61c4fe50621d08a8b4fd5b4a0563a48f47185fc462cb29a38540'
+            '3e431e5f7f023feb8e7c4d64e8d9989315dfcd4e36cdb965043ac5221497746c')
+b2sums=('98f8bb2d3198a74044e7db1549f6f2e68a9f381febac36aa976f7ed4d1cc7be47e79f86cde0b13e3b5d1109fc1792408c9dc78b01198b53690449d5842f1fe2d'
+        'e5f6d4884eaa557d5547e7e079c2edb4ed9f2f4cd8579aa32a2150f824a5d04413f2a91e79b3139d5b915da6a46f7835f1438ad53f33096973f1a99f378ec1d3'
+        'e54c2939c8f965294c4d3726c97965725890cabd09d25cfc177c316c8a072bbc1e272ce127f1352be83c668116d70992e52ab24b41d19aaccd89fb1701235c48'
+        '9b336d8726e2636112724f19510cf1fe02c8306854d386308b77dd2c318f78e0c6cb4412a916e2e69544b218e9e455d50550c086c88c49736c5f551bda777132')
 
 prepare() {
    cd ${pkgbase}_${_boostver}
 
    # https://github.com/boostorg/ublas/pull/97
    patch -Np2 -i ../${pkgbase}-ublas-c++20-iterator.patch
+
+   patch -p1 < ../5bd5bfb9.patch # https://github.com/boostorg/histogram/pull/302
+   patch -d tools/build -p1 < ../b29603fa.patch # https://github.com/boostorg/build/issues/650
 }
 
 build() {
@@ -41,6 +50,11 @@ build() {
    export _stagedir="${srcdir}/stagedir"
    local JOBS="$(sed -e 's/.*\(-j *[0-9]\+\).*/\1/' <<< ${MAKEFLAGS})"
 
+   pushd ${pkgbase}_${_boostver}/tools/build
+   ./bootstrap.sh
+   ./b2 install --prefix="${_stagedir}"
+   popd
+
    cd ${pkgbase}_${_boostver}
 
    ./bootstrap.sh \
@@ -48,8 +62,6 @@ build() {
      --with-icu \
      --with-python=/usr/bin/python3 \
 
-   install -Dm755 tools/build/src/engine/b2 "${_stagedir}"/bin/b2
-
    # Support for OpenMPI
    echo "using mpi ;" >> project-config.jam
 

extra/boost/b29603fa.patch

@@ -0,0 +1,17 @@
+From b29603fa88a614835359168e70b5a44eae8e642c Mon Sep 17 00:00:00 2001
+From: Rene Rivera <grafikrobot@gmail.com>
+Date: Sat, 26 Sep 2020 18:02:59 -0500
+Subject: [PATCH] Fix path to bootstrap for back compat.
+
+fixes #650
+--- a/src/engine/startup.cpp
++++ b/src/engine/startup.cpp
+@@ -195,7 +195,7 @@ bool b2::startup::bootstrap(FRAME *frame)
+     {
+         const std::string path{
+             b2::paths::normalize(
+-                b2_exe_path + "/../../share/boost-build/" + boost_build_jam)};
++                b2_exe_path + "/../../share/boost-build/src/kernel/" + boost_build_jam)};
+         if (b2::filesys::is_file(path))
+             b2_file_path = path;
+     }