New upstream version 2.5.0+dfsg

# OpenMP projects should set the environment variable OMP_NUM_THREADS to a reasonably small value (say, 4). 

dist: trusty

sudo : false

notifications:

    slack: veg-igem:rqQd95zjTuZoRNElekQx2CLf

    email:

        recipients:

            - spond@temple.edu

            - steven@stevenweaver.org

            - spond@temple.edu

            - tuj86312@temple.edu

        on_success: change

        on_failure: always

branches:

  only:

    - master

    - beta

env:

  - METHOD_TEST=tests/hbltests/libv3/SLAC.wbf

  - METHOD_TEST=tests/hbltests/libv3/SLAC-partitioned.wbf

  - METHOD_TEST=tests/hbltests/libv3/FEL.wbf

  - METHOD_TEST=tests/hbltests/libv3/MEME.wbf

  - METHOD_TEST=tests/hbltests/libv3/MEME-partitioned.wbf

  - METHOD_TEST=tests/hbltests/libv3/FUBAR.wbf

  - METHOD_TEST=tests/hbltests/libv3/RELAX.wbf

  - METHOD_TEST=tests/hbltests/libv3/aBSREL.wbf

  - METHOD_TEST=tests/hbltests/libv3/BUSTED.wbf

  - METHOD_TEST=tests/hbltests/libv3/LEISR.wbf

  - METHOD_TEST=tests/hbltests/libv3/BGM.wbf

    - develop

dist: xenial

sudo : false

language: c++

compiler: 

  - gcc

  - clang

script: 

  - export OMP_NUM_THREADS=4

  - travis_wait 60 eval $envSpecificTest

matrix:

  include:

    # ---- Run all the tests with gcc-7 ----

    - os: linux

      env:

        - envSpecificTest="bash ./test_kwargs.sh"

      addons:

        apt:

          sources:

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="bash ./run_unit_tests.sh"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

  - make HYPHYMP

  - make HYPHYGTEST

        - make

script: 

  - export OMP_NUM_THREADS=8

  - export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH

  - ./HYPHYGTEST

  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/math.bf

  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/iofunctions.bf

  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/utilityfunctions.bf

  - ./HYPHYMP LIBPATH=`pwd`/res/ $METHOD_TEST

    - os: linux

      env:

        - envSpecificTest="export PATH=$PATH:$(pwd); cd; git clone https://gitlab.com/rdvelazquez/testiphy.git; cd testiphy; ./testiphy HYPHYMP"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/SLAC.wbf"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP SLAC --alignment ./tests/hbltests/libv3/data/partitioned.nex --branches Internal"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP FEL --alignment ./tests/hbltests/libv3/data/CD2.nex"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP MEME --alignment ./tests/hbltests/data/CD2.nex"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP MEME --alignment ./tests/hbltests/libv3/data/CD2.nex --branches GROUP1"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP FUBAR --alignment ./tests/hbltests/libv3/data/CD2.nex"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/RELAX.wbf"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/aBSREL.wbf"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP BUSTED --alignment ./tests/hbltests/data/CD2.nex --srv No --branches Internal"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./HYPHYMP BGM --alignment ./tests/hbltests/data/CD2.nex"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./hyphy fade --alignment ./tests/hbltests/data/CD2_AA.fna"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    - os: linux

      env:

        - envSpecificTest="./hyphy gard --alignment ./tests/hbltests/data/CD2.nex"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-7

              - gcc-7

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi

        - cmake . 

        - make

    # ---- Just run the hbl unit tests with gcc-4, 5 and 6 ----

    # gcc-4

    - os: linux

      env:

        - envSpecificTest="bash ./run_unit_tests.sh"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-4.9

              - gcc-4.9

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-4.9" CC="gcc-4.9"; fi

        - cmake . 

        - make

    # gcc-5

    - os: linux

      env:

        - envSpecificTest="bash ./run_unit_tests.sh"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-5

              - gcc-5

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi

        - cmake . 

        - make

    # gcc-6

    - os: linux

      env:

        - envSpecificTest="bash ./run_unit_tests.sh"

      addons:

        apt:

          sources:

              - llvm-toolchain-precise

              - ubuntu-toolchain-r-test

              - george-edison55-precise-backports

          packages:

              - g++-6

              - gcc-6

      install:

        - if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi

        - cmake . 

        - make

### Functions, classes  

Capital case, as in `ComputeExpression()` or `VariableContainer` (class). 

Capital case, as in `ComputeExpression()` or `VariableContainer` (class). Prefix the names of *auxiliary* classes and types with an `_`.

### Simple types

Types such as enums, structs, and typedefs should prefixed with `hy` and followed by capital case identifiers, e.g. `hyFloat`

#### Cheap functions

Capital case prefixed with a lower case `k`, as in `kHarvestFrequenciesResolveAmbiguities`

### Bit-flags 

Capital case prefixed with `f`, as in `fSearchCaseSensitive`

### Environment variables (HBL only)

All capitals with underscore-separated words, as in `LIKELIHOOD_FUNCTION_EXPORT_FORMAT`

HyPhy - Hypothesis testing using Phylogenies

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

# HyPhy - Hypothesis testing using Phylogenies

Introduction

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

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. 

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. HyPhy is the computational backbone powering datamonkey.org. Additional information is available at hyphy.org.

Requirements

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

* cmake >= 3.0

* gcc >= 4.9

* libcurl

## Quick Start

#### Install  

`conda install hyphy`

#### Run with Command Line Arguments

`hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>`  

+ _`<method_name>` is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)_

+ _`<path_to_alignment_file>` is the relative or absolute path to a fasta, nexus or phylib file containing an alignment and tree_

+ _A list of the available `<additional_method_specific_arguments>` can be seen by running `hyphy <method_name> --help`_

Installation

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

or  

Hyphy depends on CMake for its build system.

#### Run in Interactive Mode

`hyphy -i`  

To install, make sure you have CMake >3.0 installed. Hyphy is dependent on other development libraries like

libcurl and libpthread. Libcurl requires development libraries such as crypto++ and openssl ( or gnutls depending on your configuration)

On Ubuntu these are libcurl-dev, libcrypto++-dev and libssl-dev.

## Building from Source

You can download a specific release from this repository or if you prefer the master branch simply 

clone the repo with

#### Requirements

* cmake >= 3.12

* gcc >= 4.9

* libcurl

* libpthread

* openmp (can be installed on mac via `brew install libomp`)

#### Download

You can download a specific release [here](https://github.com/veg/hyphy/releases) or clone this repo with

`git clone https://github.com/veg/hyphy.git`

Change your directory to the newly cloned directory

Change your directory to the downloaded/cloned directory

`cd hyphy`

Configure the project from the source directory using CMake.

#### Build

`cmake .`

If you prefer to use other build systems, such as Xcode,

configure using the -G switch

`make install`

`cmake -G Xcode .`

## Additional Options for Building from Source

CMake supports a number of build system generators,

feel free to peruse these and use them if you wish.

#### Build Systems

If you prefer to use other build systems, such as Xcode, configure using the -G switch

By default, HyPhy installs into `/usr/local`

but it can be installed on any location of your system 

by providing an installation prefix

`cmake -G Xcode .`

`cmake -DINSTALL_PREFIX=/location/of/choice`

CMake supports a number of build system generators, feel free to peruse these and use them if you wish.

For example, this configuration will install hyphy at /opt/hyphy

If you are on an OS X platform, you can specify which OS X SDK to use

`mkdir -p /opt/hyphy`

`cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .`

`cmake -DINSTALL_PREFIX=/opt/hyphy .`

If building on a heterogeneous cluster with some nodes that do not support auto-vectorization  

If building on a hetereogenous cluster with some nodes that do not support auto-vectorization

`cmake -DNOAVX=ON .`.

If you're on a UNIX-compatible system,

and you're comfortable with GNU make,

then run `make` with one of the following build targets:

If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run `make` with one of the following build targets:

+   MAC - build a Mac Carbon application

+   HYPHYGTK - HYPHY with GTK

+   SP - build a HyPhy executable (HYPHYSP) without multiprocessing

+   MP - build a HyPhy executable (HYPHYMP) using pthreads to do multiprocessing

+   MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") using pthreads to do multiprocessing

+   MPI - build a HyPhy executable (HYPHYMPI) using MPI to do multiprocessing

+   HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI 

+   LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing

-   GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)

For example to create a MPI build of HYPHY using openMPI ensure that you 

have openmpi installed and available on your  path. You can check if this

is the case after running 

`cmake .` you should see something similar to this in your output

#### Example (MPI build of hyphy using openMPI)

Ensure that you have openmpi installed and available on your  path. You can check if this is the case after running `cmake .` you should see something similar to this in your output

`-- Found MPI_C: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so `

`make install`

+   HYPHYMP(I) will be installed at  `/location/of/choice/bin`

+   hyphy will be installed at  `/location/of/choice/bin`

+   libhyphy_mp.(so/dylib/dll) will be installed at `/location/of/choice/lib`

+   HyPhy's standard library of batchfiles will go into `/location/of/choice/lib/hyphy`

HYPHYGTEST isn't installed normally,

because it serves no utility outside of testing.

#### Building for Testing

HYPHYGTEST isn't installed normally, because it serves no utility outside of testing.

To test HyPhy, build with the  GTEST target and run ./HYPHYGTEST from the source directory.  

`make GTEST`  

`./HYPHYGTEST`

#### Executable Location

By default, HyPhy installs into `/usr/local` but it can be installed on any location of your system by providing an installation prefix

`cmake -DINSTALL_PREFIX=/location/of/choice`

For example, this configuration will install hyphy at /opt/hyphy

`mkdir -p /opt/hyphy`

`cmake -DINSTALL_PREFIX=/opt/hyphy .`

#### Building Documentation

```

make docs

cd docs

python3 -m http.server

```

#!/bin/sh

# This configuration file was taken originally from the mpi4py project

# <http://mpi4py.scipy.org/>, and then modified for Julia

set -e

set -x

MPI_IMPL="$1"

os=`uname`

case "$os" in

    Darwin)

        brew update

        brew upgrade cmake

      brew upgrade gcc

        case "$MPI_IMPL" in

            mpich|mpich3)

                brew install mpich

                ;;

            openmpi)

                brew install openmpi

                ;;

            *)

                echo "Unknown MPI implementation: $MPI_IMPL"

                exit 1

                ;;

        esac

    ;;

    Linux)

        sudo apt-get update -q

        case "$MPI_IMPL" in

            mpich1)

                sudo apt-get install -y gfortran mpich-shmem-bin libmpich-shmem1.0-dev

                ;;

            mpich2)

                sudo apt-get install -y gfortran mpich2 libmpich2-3 libmpich2-dev

                ;;

            mpich|mpich3)

                sudo apt-get install -y gfortran libcr0 default-jdk hwloc libmpich10 libmpich-dev

                wget -q http://de.archive.ubuntu.com/ubuntu/pool/universe/m/mpich/mpich_3.0.4-6ubuntu1_amd64.deb

                sudo dpkg -i ./mpich_3.0.4-6ubuntu1_amd64.deb

                # rm -f ./mpich_3.1-1ubuntu_amd64.deb

                ;;

            openmpi)

                sudo apt-get install -y gfortran

                wget --no-check-certificate https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz

                tar -zxf openmpi-1.10.2.tar.gz

                cd openmpi-1.10.2

                sh ./configure --prefix=$HOME/OpenMPI > /dev/null

                make -j > /dev/null

                sudo make install > /dev/null

                ;;

            *)

                echo "Unknown MPI implementation: $MPI_IMPL"

                exit 1

                ;;

        esac

        ;;

    *)

        echo "Unknown operating system: $os"

        exit 1

        ;;

esac