New upstream version 2.2.4

2019-10-01  Tao Liu  <vladimir.liu@gmail.com>

	MACS version 2.2.4 (Python3)

	* Features added

	1) First Python3 version MACS2 released.

	2) Version number 2.2.X will be used for MACS2 in Python3, in

	parallel to 2.1.X.

	3) More comprehensive test.sh script to check the consistency of

	results from Python2 version and Python3 version.

	4) Simplify setup.py script since the newest version transparently

	supports cython. And when cython is not installed by the user,

	setup.py can still compile using only C codes.

	5) Fix Signal.pyx to use np.array instead of np.mat.

2019-09-30  Tao Liu  <vladimir.liu@gmail.com>

	MACS version 2.1.4

# INSTALL Guide For MACS

Time-stamp: <2019-09-30 14:47:45 taoliu>

Time-stamp: <2019-10-03 11:56:03 taoliu>

Please check the following instructions to complete your installation.

## Prerequisites

Python version must be equal to *2.7* to run MACS.

MACS v2.2.x requires Python3. We have tested MACS in Python3.5, 3.6

and 3.7. MACS runs slower under Python3.5, so Python3.6 or Python3.7

is recommended.

[Numpy](http://www.scipy.org/Download) (>=1.16) are required to run MACS v2. 

MACS also requires [Numpy](http://www.scipy.org/Download) (>=1.17).

GCC is required to compile `.c` codes in MACS v2 package, and python

header files are needed. If you are using Mac OSX, I recommend you

install Xcode; if you are using Linux, you need to make sure

`python-dev` is installed.

`python-dev` package is installed -- the actual package name depends

on the Linux OS distribution, you are using.

[Cython](http://cython.org/) (>=0.29) is required to generate `.c`

files from `.pyx` files using `setup.py` script.

[Cython](http://cython.org/) is **NOT** required although most of MACS

codes are written in Cython. But if you plan to generate `.c` files

from `.pyx` by yourself, you can install Cython (>=0.29), then use

`setup.py` script.

## Easy installation through PyPI

## Prepare a virtual Python environment 

The easiest way to install MACS2 is through PyPI system. Get pip_ if

it's not available in your system. *Note* if you have already

installed numpy and scipy system-wide, you can use `virtualenv

--system-site-packages` to let your virtual Python environment have

access to system-wide numpy and scipy libraries so that you don't need

to install them again.

I strongly recommend installing your MACS program in a virtual

environment, so that you have full control of your installation and

won't mess up with your system libraries. To learn about virtual

environment, read [this

article](https://docs.python.org/3/library/venv.html). A simple way to

create a virtual environment of Python3 is

Then under command line, type `pip install MACS2`. PyPI will

install Numpy and Cython automatically if they are absent. 

`$ python3 -m venv MyPythonEnv/`

To upgrade MACS2, type `pip install --upgrade MACS2`. It will check

Then active it by

`$ source MyPythonEnv/bin/active`

## Install through PyPI

The easiest way to install MACS is through PyPI system. Get `pip` if

it's not available in your system. If you create a virtual environment

as described before, your `pip` command will install everything under

the folder you specified previously through `python3 -m env` command.

Then under the command line, type `pip install macs2`. PyPI will

install Numpy automatically if it is absent.

To upgrade MACS2, type `pip install --upgrade macs2`. It will check

currently installed MACS2, compare the version with the one on PyPI

repository, download and install newer version while necessary.

repository, download and install a newer version while necessary.

## Install through Conda

Please check [MACS2 page on

bioconda](https://anaconda.org/bioconda/macs2) for instructions.

## Install through Debian APT

MACS is included in Debian Stretch/Buster/Unstable blessed by some

kind of Supper Cow Powers.

## Install from source

MACS uses Python's distutils tools for source installations. To

install a source distribution of MACS, unpack the distribution tarball

and open up a command terminal. Go to the directory where you unpacked

MACS, and simply run the install script:

MACS uses Python's [setuptools](https://setuptools.readthedocs.io) for

source code installations. To install a source distribution of MACS,

unpack the distribution tarball, or clone Git repository with `git

clone git@github.com:taoliu/MACS.git`. Go to the directory where you

unpacked MACS, and simply run the install script:

 `$ python setup.py install`

By default, the script will install python library and executable

codes globally, which means you need to be root or administrator of

the machine so as to complete the installation. Please contact the

administrator of that machine if you want their help. If you need to

provide a nonstandard install prefix, or any other nonstandard

options, you can provide many command line options to the install

script. Use the –help option to see a brief list of available options:

codes according to the environment. When you run the command under

virtualenv, the script will install to the virtual environment

instead. When you run it without virtual environment, you may need to

be root or administrator of the machine so as to complete the

installation. Please contact the system administrator if you want

their help. If you need to provide a nonstandard install prefix, or

any other nonstandard options, you can provide many command line

options to the install script. Use the `--help` option to see a brief

list of available options:

 `$ python setup.py --help`

 `$ python setup.py install --prefix /home/taoliu/`

As mentioned in *Prerequisites*, you don't need to install Cython in

order to install MACS. When Cython is available, this setup script

will regenerate C codes from Pyx codes when necessary. When Cython is

not available, this setup script will just use the C codes included in

the release package (or your Github clone) for installation.

## Configure enviroment variables

## Configure environment variables

*Note*, if you are using a virtual environment, you should skip this

section since all the corresponding environment variables have been

correctly set while you `activate` the environment.

After running the setup script, you might need to add the install

location to your `PYTHONPATH` and `PATH` environment variables. The

### PYTHONPATH

To set up your `PYTHONPATH` environment variable, you'll need to add the

value `PREFIX/lib/pythonX.Y/site-packages` to your existing

To set up your `PYTHONPATH` environment variable, you'll need to add

the value `PREFIX/lib/pythonX.Y/site-packages` to your existing

`PYTHONPATH`. In this value, X.Y stands for the major–minor version of

Python you are using (such as 2.7 ; you can find this with

Python you are using (such as 3.7; you can find this with

`sys.version[:3]` from a Python command line). `PREFIX` is the install

prefix where you installed MACS. If you did not specify a prefix on

the command line, MACS will be installed using Python's sys.prefix

On Linux, using bash, I include the new value in my `PYTHONPATH` by

adding this line to my `~/.bashrc`::

 `$ export PYTHONPATH=/home/taoliu/lib/python2.7/site-packages:$PYTHONPATH`

 `$ export

 PYTHONPATH=/home/taoliu/lib/python3.7/site-packages:$PYTHONPATH`

Using Windows, you need to open up the system properties dialog, and

Using Windows, you need to open up the system properties dialog and

locate the tab labeled Environment. Add your value to the `PYTHONPATH`

variable, or create a new `PYTHONPATH` variable if there isn't one

already.

### PATH

Just like your `PYTHONPATH`, you'll also need to add a new value to your

PATH environment variable so that you can use the MACS command line

directly. Unlike the `PYTHONPATH` value, however, this time you'll need

to add `PREFIX/bin` to your PATH environment variable. The process for

updating this is the same as described above for the `PYTHONPATH`

variable::

Just like your `PYTHONPATH`, you'll also need to add a new value to

your PATH environment variable so that you can use the MACS command

line directly. Unlike the `PYTHONPATH` value, however, this time

you'll need to add `PREFIX/bin` to your PATH environment variable. The

process for updating this is the same as described above for the

`PYTHONPATH` variable::

 `$ export PATH=/home/taoliu/bin:$PATH`

--

Tao Liu <vladimir.liu@gmail.com>

-- Tao Liu <vladimir.liu@gmail.com>

MACS2/IO/BedGraphIO.pyx

MACS2/IO/CallPeakUnit.c

MACS2/IO/CallPeakUnit.pyx

MACS2/IO/CallPeakUnitPrecompiled.c

MACS2/IO/FixWidthTrack.c

MACS2/IO/FixWidthTrack.pyx

MACS2/IO/PairedEndTrack.c

MACS2/IO/ScoreTrack.c

MACS2/IO/ScoreTrack.pyx

MACS2/IO/__init__.py

MACS2/data/__init__.py

bin/macs2

 No newline at end of file

numpy>=1.16

numpy>=1.17