New upstream version 0.2.4 (9c16f116) · Commits · Debian Med / mptp

.travis.yml

+112 −4

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		language: c

		compiler:
		- gcc
		- clang
		matrix:
		include:
		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-4.6']
		env:
		- COMPILER=gcc-4.6

		script: ./autogen.sh && ./configure && make && make check
		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-4.7']
		env:
		- COMPILER=gcc-4.7

		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-4.8']
		env:
		- COMPILER=gcc-4.8

		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-4.9']
		env:
		- COMPILER=gcc-4.9

		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-5']
		env:
		- COMPILER=gcc-5

		- os: linux
		compiler: gcc
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test']
		packages: ['gcc-6']
		env:
		- COMPILER=gcc-6

		- os: linux
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-precise-3.5']
		packages: ['clang-3.5']
		env:
		- COMPILER=clang-3.5

		- os: linux
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-precise-3.6']
		packages: ['clang-3.6']
		env:
		- COMPILER=clang-3.6

		- os: linux
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-precise-3.7']
		packages: ['clang-3.7']
		env:
		- COMPILER=clang-3.7

		- os: linux
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-precise-3.8']
		packages: ['clang-3.8']
		env:
		- COMPILER=clang-3.8

		- os: linux
		dist: trusty
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-trusty-3.9']
		packages: ['clang-3.9']
		env:
		- COMPILER=clang-3.9

		- os: linux
		dist: trusty
		compiler: clang
		addons:
		apt:
		sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-trusty-4.0']
		packages: ['clang-4.0']
		env:
		- COMPILER=clang-4.0

		script: ./autogen.sh && CC=$COMPILER ./configure && make && make check

ChangeLog.md

+6 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,12 @@
		All notable changes to `mptp` will be documented in this file.
		This project adheres to [Semantic Versioning](http://semver.org/).

		## [0.2.4] - 2018-05-14
		### Fixed
		- If we do not manage to generate a random starting delimitation with the
		wanted number of species (randomly chosen), we use the currently generated
		delimitation instead.

		## [0.2.3] - 2017-07-25
		### Fixed
		- Replaced hsearch which was causing problems on APPLE with custom hashtable

README.md

+6 −6

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		@@ -78,9 +78,9 @@ where `DIR` is the directory where bash autocompletion is stored. You can use
		and the documentation, use the following commands:

		```bash
		wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.2/mptp-src-0.2.2.tar.gz
		tar zxvf mptp-src-0.2.2.tar.gz
		cd mptp-src-0.2.2
		wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.4/mptp-src-0.2.4.tar.gz
		tar zxvf mptp-src-0.2.4.tar.gz
		cd mptp-src-0.2.4
		./configure
		make
		make install # as root, or run sudo make install
		@@ -110,12 +110,12 @@ To use the pre-compiled binary, download the appropriate executable for your
		system using the following commands if you are using a Linux system:

		```bash
		wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.2/mptp-0.2.2-linux-x86_64.tar.gz
		tar zxvf mptp-0.2.2-linux-x86_64.tar.gz
		wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.4/mptp-0.2.4-linux-x86_64.tar.gz
		tar zxvf mptp-0.2.4-linux-x86_64.tar.gz
		```

		You will now have the binary distribution in a folder called
		`mptp-0.2.2-linux-x86_64` in which you will find three subfolders `bin`, `man`
		`mptp-0.2.4-linux-x86_64` in which you will find three subfolders `bin`, `man`
		and `doc`. We recommend making a copy or a symbolic link to the mptp binary
		`bin/mptp` in a folder included in your `$PATH`, and a copy or a symbolic link
		to the mptp man page `man/mptp.1` in a folder included in your `$MANPATH`. The

configure.ac

+15 −1

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		@@ -2,13 +2,15 @@
		# Process this file with autoconf to produce a configure script.

		AC_PREREQ([2.63])
		AC_INIT([mptp], [0.2.3], [Tomas.Flouri@h-its.org])
		AC_INIT([mptp], [0.2.4], [t.flouris@ucl.ac.uk])
		AM_INIT_AUTOMAKE([subdir-objects])
		AC_LANG([C])
		AC_CONFIG_SRCDIR([src/mptp.c])
		AC_CONFIG_HEADERS([config.h])
		AC_CANONICAL_HOST

		${CFLAGS=""}

		# Checks for programs.
		AC_PROG_CC
		AC_PROG_RANLIB
		@@ -72,6 +74,18 @@ AS_IF([test "x$enable_pdfman" != "xno"], [
		fi
		])

		# Various OS-related dependencies
		case "${host_os}" in
		linux*)
		;;
		cygwin\|mingw)
		AC_CHECK_LIB([psapi],[GetProcessMemoryInfo])
		;;
		darwin*)
		;;
		esac


		AM_CONDITIONAL(HAVE_PS2PDF, test "x${have_ps2pdf}" = "xyes")
		AM_PROG_CC_C_O

man/mptp.1

+6 −1

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		.\" -- coding: utf-8 --
		.\" ============================================================================
		.TH mptp 1 "January 31, 2017" "mptp 0.2.2" "USER COMMANDS"
		.TH mptp 1 "May 14, 2018" "mptp 0.2.4" "USER COMMANDS"
		.\" ============================================================================
		.SH NAME
		mptp \(em single-locus species delimitation
		@@ -354,5 +354,10 @@ incorrectly formatted trees.
		.TP
		.BR v0.2.3\~ "released July 25th, 2017"
		Replaced hsearch() with custom hashtable. Fixed minor output error messages.
		.TP
		.BR v0.2.4\~ "released May 14th, 2018"
		If we do not manage to generate a random starting delimitation with the wanted
		number of species (randomly chosen), we use the currently generated
		delimitation instead.
		.RE
		.LP