Commit f899b3bd authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.7.3

parent ad9ebe70

.gitignore

+6 −0
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@@ -87,3 +87,9 @@ unit_tests 
stuff

.dirstamp

configure.lineno



# test coverage

*.gcda

*.gcno

libbash_test.info

testCoverage/

.travis.yml

+4 −3
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@@ -13,14 +13,14 @@ matrix: 
    - os: osx

      env: CXXFLAGS="-m32 -Werror"

sudo: required

dist: trusty

dist: xenial

before_install: .travis/setup.sh "$TRAVIS_OS_NAME" "$CXX" "$CXXFLAGS"

before_script:

  - ./bootstrap

script:

  - make unittests

  - make scrm scrm_dbg && ./tests/test_binaries.sh

  - make algorithmtest

  - ./tests/test_binaries.sh "$TRAVIS_OS_NAME"

before_deploy:

  - ./.travis/build_src_pkg.sh

  - ./.travis/build_static_binaries.sh
@@ -40,3 +40,4 @@ deploy: 
    condition: "$CC = gcc"

    condition: "$CXXFLAGS == -Werror"

    condition: "$TRAVIS_OS_NAME == linux"

.travis/test_coverage.sh

0 → 100755
+20 −0
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#!/bin/bash



os=$1

cxx=$2

cxxflags=$3



echo "os: $os; cxx: $cxx; cxxflags: $cxxflags"



if [ "$os" == "linux" ]; then

  if [[ "$cxxflags" == *"-m32"* ]]; then

    echo "On 32bit. Skipping coverage test."

  else

    coveralls --exclude lib --exclude tests --gcov-options '\-lp'

  fi

fi



if [ "$os" == "osx" ]; then

    echo "On OS X. Skipping coverage test."

fi

Makefile.am

+4 −2
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@@ -3,7 +3,7 @@ bin_PROGRAMS = scrm 
man_MANS = doc/scrm.1



TESTS = unit_tests algorithm_tests

check_PROGRAMS = unit_tests algorithm_tests scrm_dbg scrm_prof

check_PROGRAMS = unit_tests algorithm_tests scrm_dbg scrm_asan scrm_prof

PROG = SCRM



dist-hook:
@@ -59,13 +59,15 @@ alg_test_src = tests/cppunit/test_runner.cc tests/algorithmtest/test_algorithm.c 
scrm_SOURCES = $(scrm_src) src/scrm.cc

scrm_dbg_SOURCES = $(scrm_src) $(debug_src) src/scrm.cc

scrm_prof_SOURCES = $(scrm_src) src/scrm.cc

scrm_asan_SOURCES = $(scrm_src) src/scrm.cc

unit_tests_SOURCES = $(scrm_src) $(debug_src) $(unit_test_src)

algorithm_tests_SOURCES = $(scrm_src) $(alg_test_src)



scrm_CXXFLAGS= -DNDEBUG @OPT_CXXFLAGS@

scrm_dbg_CXXFLAGS= -g

scrm_prof_CXXFLAGS= -pg -DNDEBUG

unit_tests_CXXFLAGS = -g -DUNITTEST -DNDEBUG

scrm_asan_CXXFLAGS= -g -DNDEBUG -fsanitize=undefined,address -fno-sanitize-recover

unit_tests_CXXFLAGS = -g -DUNITTEST -DNDEBUG @TEST_CXXFLAGS@ 

algorithm_tests_CXXFLAGS = -g -DNDEBUG

unit_tests_LDADD= -L/opt/local/lib -lcppunit -ldl #link the cppunit unittest library in mac, cppunit was installed via macports

algorithm_tests_LDADD= -L/opt/local/lib -lcppunit -ldl  #link the cppunit unittest library in mac, cppunit was installed via macports

NEWS.md

+22 −0
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scrm Version History

========================



scrm 1.7.3

------------------------

Released: 2018-11-18



### Improvements

+ The labeling of internal nodes in the oriented forest output

  no longer changes within the same tree topology. That makes

  it easier to identify different topologies.



### Bug Fixes

+ Now requires that subpopulation are defined via the `-I` argument

  before any demographic options for all population (`-M`, `-G` or `-N`)

  are given (#108).

  Thanks to Jonathan Terhorst (@terhorst) for reporting this bug.

+ When the multiple of the merge/admixure arguemtns (`-ep`, `-eps` and `-ej`)

  are used at the time, they are now executed in order in which

  they are provided on the command line (#121). This behavior now

  follows ms' implementation. 

  Thanks to Scott T Small (@stsmall) for reporting this.







scrm 1.7.2

------------------------

Released: 2016-04-10