configure.ac | 2 1 + 1 - 0 !
src/Makefile.am | 16 8 + 8 - 0 !
src/util.c | 4 2 + 2 - 0 !
3 files changed, 11 insertions(+), 11 deletions(-)

 use debian packaged libsprng

tests/build-puzzle | 2 1 + 1 - 0 !
tests/build-remark | 2 1 + 1 - 0 !
tests/cons-pure-prot.test | 2 1 + 1 - 0 !
tests/generate-scripts.sh | 2 1 + 1 - 0 !
tests/lm-pure-prot.test | 2 1 + 1 - 0 !
tests/qp-clock.test | 2 1 + 1 - 0 !
tests/qp-hky-clock-nucl.test | 2 1 + 1 - 0 !
tests/qp-hky-rhet-clock-nucl.test | 2 1 + 1 - 0 !
tests/qp-hky-rhet-nucl.test | 2 1 + 1 - 0 !
tests/qp-jtt-prot.test | 2 1 + 1 - 0 !
tests/qp-jtt-rhet-clock-prot.test | 2 1 + 1 - 0 !
tests/qp-jtt-rhet-prot.test | 2 1 + 1 - 0 !
tests/qp-mtrev-prot.test | 2 1 + 1 - 0 !
tests/qp-pure-bin.test | 2 1 + 1 - 0 !
tests/qp-pure-nucl.test | 2 1 + 1 - 0 !
tests/qp-pure-prot.test | 2 1 + 1 - 0 !
tests/qp-tn-nucl.test | 2 1 + 1 - 0 !
tests/qp-vt-prot.test | 2 1 + 1 - 0 !
tests/qp-wag-prot.test | 2 1 + 1 - 0 !
tests/template-test | 2 1 + 1 - 0 !
tests/ut-pure-prot.test | 2 1 + 1 - 0 !
21 files changed, 21 insertions(+), 21 deletions(-)

 tests are using bash syntax so declare this on top

src/ml2.c | 2 1 + 1 - 0 !
src/puzzle1.c | 4 2 + 2 - 0 !
src/puzzle2.c | 2 1 + 1 - 0 !
src/treesort.c | 6 3 + 3 - 0 !
4 files changed, 7 insertions(+), 7 deletions(-)

 fix some spelling issues

src/ppuzzle.c | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 replace obsolete mpi-2.0 api with their mpi-3.0 equivalents
Bug-Debian: https://bugs.debian.org/951984

tests/check-cons-pure-prot | 91 59 + 32 - 0 !
tests/check-lm-pure-prot | 188 129 + 59 - 0 !
tests/check-qp-clock | 188 108 + 80 - 0 !
tests/check-qp-hky-clock-nucl | 188 108 + 80 - 0 !
tests/check-qp-hky-rhet-clock-nucl | 376 201 + 175 - 0 !
tests/check-qp-hky-rhet-nucl | 311 168 + 143 - 0 !
tests/check-qp-jtt-prot | 175 101 + 74 - 0 !
tests/check-qp-jtt-rhet-clock-prot | 271 147 + 124 - 0 !
tests/check-qp-jtt-rhet-prot | 221 122 + 99 - 0 !
tests/check-qp-mtrev-prot | 127 77 + 50 - 0 !
tests/check-qp-pure-bin | 83 54 + 29 - 0 !
tests/check-qp-pure-nucl | 182 105 + 77 - 0 !
tests/check-qp-pure-prot | 123 75 + 48 - 0 !
tests/check-qp-tn-nucl | 279 154 + 125 - 0 !
tests/check-qp-vt-prot | 167 97 + 70 - 0 !
tests/check-qp-wag-prot | 163 95 + 68 - 0 !
tests/check-ut-pure-prot | 89 58 + 31 - 0 !
17 files changed, 1858 insertions(+), 1364 deletions(-)

 test results to compare with are just wrong as discussed
 with upstream
 See https://lists.debian.org/debian-med/2020/05/msg00118.html

src/puzzle1.c | 58 33 + 25 - 0 !
1 file changed, 33 insertions(+), 25 deletions(-)

 make the build reproducible

tests/check-cons-pure-prot | 54 27 + 27 - 0 !
tests/check-lm-pure-prot | 20 10 + 10 - 0 !
tests/check-qp-clock | 158 79 + 79 - 0 !
tests/check-qp-hky-clock-nucl | 158 79 + 79 - 0 !
tests/check-qp-hky-rhet-clock-nucl | 164 82 + 82 - 0 !
tests/check-qp-hky-rhet-nucl | 132 66 + 66 - 0 !
tests/check-qp-jtt-prot | 54 27 + 27 - 0 !
tests/check-qp-jtt-rhet-clock-prot | 92 46 + 46 - 0 !
tests/check-qp-jtt-rhet-prot | 62 31 + 31 - 0 !
tests/check-qp-mtrev-prot | 60 30 + 30 - 0 !
tests/check-qp-pure-bin | 36 18 + 18 - 0 !
tests/check-qp-pure-nucl | 124 62 + 62 - 0 !
tests/check-qp-pure-prot | 54 27 + 27 - 0 !
tests/check-qp-tn-nucl | 124 62 + 62 - 0 !
tests/check-qp-vt-prot | 54 27 + 27 - 0 !
tests/check-qp-wag-prot | 54 27 + 27 - 0 !
tests/check-ut-pure-prot | 108 54 + 54 - 0 !
tests/cons-pure-prot.test | 2 2 + 0 - 0 !
tests/lm-pure-prot.test | 2 2 + 0 - 0 !
tests/qp-clock.test | 2 2 + 0 - 0 !
tests/qp-hky-clock-nucl.test | 2 2 + 0 - 0 !
tests/qp-hky-rhet-clock-nucl.test | 2 2 + 0 - 0 !
tests/qp-hky-rhet-nucl.test | 2 2 + 0 - 0 !
tests/qp-jtt-prot.test | 2 2 + 0 - 0 !
tests/qp-jtt-rhet-clock-prot.test | 2 2 + 0 - 0 !
tests/qp-jtt-rhet-prot.test | 2 2 + 0 - 0 !
tests/qp-mtrev-prot.test | 2 2 + 0 - 0 !
tests/qp-pure-bin.test | 2 2 + 0 - 0 !
tests/qp-pure-nucl.test | 2 2 + 0 - 0 !
tests/qp-pure-prot.test | 2 2 + 0 - 0 !
tests/qp-tn-nucl.test | 2 2 + 0 - 0 !
tests/qp-vt-prot.test | 2 2 + 0 - 0 !
tests/qp-wag-prot.test | 2 2 + 0 - 0 !
tests/template-test | 2 2 + 0 - 0 !
tests/ut-pure-prot.test | 2 2 + 0 - 0 !
35 files changed, 790 insertions(+), 754 deletions(-)

 reduce decimals for testing
 Tests often fail because the last few decimals of the output
 depend on the compiler. This patch circumvents that.

tests/ut-pure-prot.test | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 add failsafe for ut-prottest

configure.ac | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix failure to detect mpicc with gcc-14.
 Starting with gcc-14, when specifying mpicc, the configuration test
 considers it unusable:
 .
         checking for mpicc... /usr/bin/mpicc
         []
         checking whether /usr/bin/mpicc works as MPI compiler... no
 .
 This turns out to be caused by a warning gone fatal in the conftest.c:
 .
         $ mpicc conftest.c 
         conftest.c: In function main:
         conftest.c:6:1: error: implicit declaration of function exit [-Wimplicit-function-declaration]
             6 | exit(0);
               | ^~~~
         conftest.c:2:1: note: include <stdlib.h> or provide a declaration of exit

tests/Makefile.am | 2 0 + 2 - 0 !
1 file changed, 2 deletions(-)

 preserve some of the test artifacts.
 These artifacts are necessary to be able to run the test suite outside
 the context of tree-puzzle source code, i.e. in autopkgtest context.
 These test started to fail when running the clean target of the tests
 directory, so this patch is an attempt to keep useful files while
 keeping at bay unnecessary bloat, potentially introducing
 non-deterministic data in resulting binary packages.
 .
 This change fixes a Debian specificity and would probably not be
 welcome upstream, hence forwarding not needed.