Commit 524e0f2c authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 3.3.20190909

parent a5c562ff

.travis.yml

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sudo: required

cache: apt

language: c



os:

  - linux

  - osx

  

compiler:

  - gcc



script:

# build and install software into $HOME/local

  - ./autogen.sh

  - ./configure

  - make

  - sudo make install

  - ./configure --enable-phyrex

  - make clean

  - make

  - ./configure --enable-phytime

  - make clean

  - make

  

# put the installed binary into the $PATH

  - export PATH=$HOME/local/bin:$PATH



# install testiphy

  - cd

  - git clone https://gitlab.com/testiphy/testiphy.git



# run testiphy

  - cd testiphy

  - ./testiphy phyml
 
 No newline at end of file

README.md

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[![Build Status](https://travis-ci.org/stephaneguindon/phyml.svg?branch=master)](https://travis-ci.org/stephaneguindon/phyml)

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/phyml/README.html) 



### 1. You downloaded a stable release  of PhyML from [here](https://github.com/stephaneguindon/phyml/releases)

configure.ac

+16 −12
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#                                               -*- Autoconf -*-

# Process this file with autoconf to produce a configure script.



AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20190321" | tr -d '\n'"]),[guindon@lirmm.fr])

AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20190909" | tr -d '\n'"]),[guindon@lirmm.fr])

AM_INIT_AUTOMAKE([foreign])



AC_CONFIG_SRCDIR([src/simu.c],[doc/phyml-manual.tex])
@@ -46,9 +46,11 @@ AC_FUNC_VPRINTF 
AC_CHECK_FUNCS([floor pow rint sqrt strchr strstr])



dnl DEFAULT_VECTOR_FLAG=

dnl DEFAULT_VECTOR_FLAG=-mavx

dnl DEFAULT_VECTOR_FLAG="-mavx -mfma"

dnl DEFAULT_VECTOR_FLAG=-msse3

DEFAULT_VECTOR_FLAG=-march=native

DEFAULT_VECTOR_FLAG="-march=native"





AC_ARG_ENABLE([native],

              [AS_HELP_STRING([--disable-native],

                              [Remove AVX or SSE compilation options.])])
@@ -64,15 +66,17 @@ dnl LT_INIT 
dnl AC_PROG_LIBTOOL





DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline ${VECTOR_FLAG}"

dnl default_C_FLAG="-O2 ${VECTOR_FLAG}"

dnl DEFAULT_C_FLAG="-O3 -fPIC"

dnl DEFAULT_C_FLAG="-fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls -O2 -fno-omit-frame-pointer -g ${VECTOR_FLAG}"

DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG}"

dnl DEFAULT_C_FLAG="-O2 ${VECTOR_FLAG}"

dnl DEFAULT_C_FLAG="${VECTOR_FLAG}"

dnl DEFAULT_C_FLAG="-pthread  -O3 -g -ffunction-sections -fdata-sections"



AC_ARG_ENABLE([debug],

              [AS_HELP_STRING([--enable-debug],

                              [Remove optimization options and add debug informations.])])

AS_IF([test "x$enable_debug" = "xyes"],

      [CFLAGS="-ansi ${VECTOR_FLAG} -pedantic -Wall -std=c99 -O0 -g -Wuninitialized"],

      [CFLAGS="-ansi ${VECTOR_FLAG} -pedantic -Wall -std=c99 -O0 -g -Wuninitialized -Wunused -Wunreachable-code"],

      [CFLAGS="${DEFAULT_C_FLAG}"])



AC_ARG_ENABLE([safemode],
@@ -104,11 +108,11 @@ AS_IF([test "x$enable_win" = "xyes"],AC_DEFINE([WIN32],[1],[WIN32 tag on])) 
AM_CONDITIONAL([WANT_WIN], [test "$enable_win" = yes])





AC_ARG_ENABLE([beagle], [AS_HELP_STRING([--enable-beagle], [Compute likelihoods using BEAGLE library.])], [beagle=yes],[beagle=no])

AS_IF([test "x$enable_beagle" = "xyes"],[PKG_CHECK_MODULES(BEAGLE, hmsbeagle-1)])

AS_IF([test "x$enable_beagle" = "xyes"],

      [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} -lstdc++"],

      [CFLAGS=${CFLAGS}])

dnl AC_ARG_ENABLE([beagle], [AS_HELP_STRING([--enable-beagle], [Compute likelihoods using BEAGLE library.])], [beagle=yes],[beagle=no])

dnl AS_IF([test "x$enable_beagle" = "xyes"],[PKG_CHECK_MODULES([BEAGLE],[hmsbeagle-1])])

dnl AS_IF([test "x$enable_beagle" = "xyes"],

dnl       [CFLAGS="${CFLAGS} ${BEAGLE_CFLAGS} ${BEAGLE_LIBS} -lstdc++"],

dnl       [CFLAGS=${CFLAGS}])

AS_IF([test "x$enable_beagle" = "xyes"], AC_DEFINE([BEAGLE],[1],[BEAGLE tag on]))

AM_CONDITIONAL([WANT_BEAGLE], [test "$enable_beagle" = yes])

doc/Makefile.in

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@@ -160,8 +160,6 @@ AUTOCONF = @AUTOCONF@ 
AUTOHEADER = @AUTOHEADER@

AUTOMAKE = @AUTOMAKE@

AWK = @AWK@

BEAGLE_CFLAGS = @BEAGLE_CFLAGS@

BEAGLE_LIBS = @BEAGLE_LIBS@

CC = @CC@

CCDEPMODE = @CCDEPMODE@

CFLAGS = @CFLAGS@
@@ -198,9 +196,6 @@ PACKAGE_URL = @PACKAGE_URL@ 
PACKAGE_VERSION = @PACKAGE_VERSION@

PATH_SEPARATOR = @PATH_SEPARATOR@

PDFLATEX = @PDFLATEX@

PKG_CONFIG = @PKG_CONFIG@

PKG_CONFIG_LIBDIR = @PKG_CONFIG_LIBDIR@

PKG_CONFIG_PATH = @PKG_CONFIG_PATH@

SET_MAKE = @SET_MAKE@

SHELL = @SHELL@

STRIP = @STRIP@

doc/phyml-manual.pdf

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