Fix: update documents and version

ChangeLog

@@ -1,3 +1,41 @@
+2020-04-10  Tao Liu  <[email protected]>
+	MACS version 2.2.7
+
+	* Bugs fixed
+
+	1) MACS2 has been tested on multiple architectures to make sure it
+	can successfully generate consistent results. Currently the
+	supported architectures are: AMD64, ARM64, i386, PPC64LE, and
+	S390X. Thanks to @mr-c, @junaruga, and @tillea! Related to issue
+	#340, #349, #351, and #359; to PR #348, #350, #360, #361, #367,
+	and #370. The lesson is that if the project is built on Cython and
+	is aimed at memory efficiency, we should specifically define all
+	int/float types in pyx files such as int8_t or uint32_t using
+	either libc or numpy (c version) instead of relying on Cython
+	types such as short, long, double.
+
+	2) MACS2 setup script will check numpy and install numpy if
+	necessary. PR #378, issue #364
+
+	3) `bdgbroadcall` command will correctly add the score column (5th
+	column). The score (5th) column contains 10 times of the average
+	score in the broad region. PR #373, issue #362
+
+	4) The missing test on `bdgopt` subcommand has been added. PR #363
+
+	5) The obsolete option `--ratio` from `callpeak` subcommand has
+	been removed. PR #369, issue #366
+
+	6) Fixed the incorrect description in README on the 'maximum
+	length of broad region is 4 times of d' to 'maximum gap for
+	merging broad regions is 4 times of tag size by default'. PR #380,
+	issue #365.
+
+	* Other
+
+	1) CODE OF CONDUCT document has been added to MACS2 github
+	repository. PR #358
+
 2019-12-12  Tao Liu  <[email protected]>
 	MACS version 2.2.6
 

DOCKER/Dockerfile-slim

@@ -1,16 +1,16 @@
 # Use an official Python runtime as a parent image
-FROM python:3.7 AS build
+FROM python:3.8 AS build
 
 # install numpy and MACS2
 RUN git clone https://github.com/taoliu/MACS.git /MACS
 RUN pip install --trusted-host pypi.python.org --upgrade pip && pip install --trusted-host pypi.python.org -r /MACS/requirements.txt
 RUN cd /MACS && python setup.py install
 
-FROM python:3.7-slim
+FROM python:3.8-slim
 
 # copy compiled files over to python-slim
 COPY --from=build /usr/local/bin/macs2 /usr/local/bin/
-COPY --from=build /usr/local/lib/python3.7/site-packages/ /usr/local/lib/python3.7/site-packages/
+COPY --from=build /usr/local/lib/python3.8/site-packages/ /usr/local/lib/python3.8/site-packages/
 
 # Define environment variable
 ENTRYPOINT ["macs2"]

DOCKER/README.md

@@ -1,18 +1,18 @@
-# Official MACS2 v2.2.6 docker
+# Official MACS2 v2.2.7 docker
 
 MACS2 is a bioinformatics algorithm to analyze ChIP-seq datasets. 
 
 # Get Started
 
 ## Pull the image
 
-Currently, there are two types of MACS2 images, one based on official Python3.7 docker image, and the other based on official Python3.7-slim docker image. Only if space is a concern, and you keep using Python3.7-slim docker for all the Python 3.7 applications, pull the slim one.
+Currently, there are two types of MACS2 images, one based on official Python3.8 docker image, and the other based on official Python3.8-slim docker image. Only if space is a concern, and you keep using Python3.8-slim docker for all the Python 3.8 applications, pull the slim one.
 
 To pull the regular MACS2 image:
 
 ```docker pull fooliu/macs2```
 
-To pull the MACS2 image based on Python3.7-slim
+To pull the MACS2 image based on Python3.8-slim
 
 ```docker pull fooliu/macs2:py37-slim```
 
@@ -28,7 +28,7 @@ The first part ```-v $PWD:/data/``` will mount the CURRENT directory ```$PWD```
 
 # Built with
 
-* Python3.7 docker image 3.7
+* Python3.8 docker image 3.8
 * pip install numpy version 1.17, cython 0.29, and pytest 4.6 
 * git clone MACS codes from github master branch then run ```setup.py```
 

MACS2/Constants.py

@@ -1,4 +1,4 @@
-MACS_VERSION = "2.2.6"
+MACS_VERSION = "2.2.7"
 FILTERDUP_VERSION = "1.0.0 20140616"
 RANDSAMPLE_VERSION = "1.0.0 20120703"
 MAX_PAIRNUM = 1000