fix pyabpoa installation on macos

.gitignore

@@ -60,6 +60,7 @@ cscope.*
 
 # python
 dist/*
+.eggs/*
 pyabpoa.egg-info/*
 python/build/*
 python/dist/*

Makefile

@@ -113,10 +113,10 @@ $(SRC_DIR)/simd_check.o:$(SRC_DIR)/simd_check.c $(SRC_DIR)/simd_instruction.h
 $(SRC_DIR)/simd_abpoa_align.o:$(SRC_DIR)/simd_abpoa_align.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
 	$(CC) -c $(CFLAGS) $(SIMD_FLAG) -I$(INC_DIR) $< -o $@
 
-install_py: python/cabpoa.pxd python/pyabpoa.pyx python/README.md
+install_py: setup.py python/cabpoa.pxd python/pyabpoa.pyx python/README.md
 	${py_SIMD_FLAG} python setup.py install
 
-sdist: install_py
+sdist: setup.py python/cabpoa.pxd python/pyabpoa.pyx python/README.md
 	${py_SIMD_FLAG} python setup.py sdist #bdist_wheel
 
 publish_pypi: clean_py sdist

README.md

@@ -8,15 +8,15 @@
 [![Build Status](https://img.shields.io/travis/yangao07/abPOA/master.svg?label=Master)](https://travis-ci.org/yangao07/abPOA)
 [![License](https://img.shields.io/badge/License-MIT-black.svg)](https://github.com/yangao07/abPOA/blob/master/LICENSE)
 <!-- [![PyPI](https://img.shields.io/pypi/v/pyabpoa.svg?style=flat)](https://pypi.python.org/pypi/pyabpoa) -->
-## Updates (v1.4.2)
+## Updates (v1.4.3)
 
-- Remove cython installation dependency
+- Fix pyabpoa installation on macos (pip also works now)
 
 ## Getting started
 Download the [latest release](https://github.com/yangao07/abPOA/releases):
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2.tar.gz
-tar -zxvf abPOA-v1.4.2.tar.gz && cd abPOA-v1.4.2
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.3/abPOA-v1.4.3.tar.gz
+tar -zxvf abPOA-v1.4.3.tar.gz && cd abPOA-v1.4.3
 ```
 Make from source and run with test data:
 ```
@@ -84,9 +84,9 @@ You can also build abPOA from source files.
 Make sure you have gcc (>=6.4.0) and zlib installed before compiling.
 It is recommended to download the [latest release](https://github.com/yangao07/abPOA/releases).
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2.tar.gz
-tar -zxvf abPOA-v1.4.2.tar.gz
-cd abPOA-v1.4.2; make
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.3/abPOA-v1.4.3.tar.gz
+tar -zxvf abPOA-v1.4.3.tar.gz
+cd abPOA-v1.4.3; make
 ```
 Or, you can use `git clone` command to download the source code.
 This gives you the latest version of abPOA, which might be still under development.
@@ -98,8 +98,8 @@ cd abPOA; make
 ### <a name="binary"></a>Pre-built binary executable file for Linux/Unix 
 If you meet any compiling issue, please try the pre-built binary file:
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.4.2/abPOA-v1.4.2_x64-linux.tar.gz
-tar -zxvf abPOA-v1.4.2_x64-linux.tar.gz
+wget https://github.com/yangao07/abPOA/releases/download/v1.4.3/abPOA-v1.4.3_x64-linux.tar.gz
+tar -zxvf abPOA-v1.4.3_x64-linux.tar.gz
 ```
 
 ## <a name="usage"></a>General usage

python/README.md

@@ -31,8 +31,7 @@ seqs=[
 'CCCGGAAGA',
 'CCGAAGA'
 ]
-res=a.msa(seqs, out_cons=True, out_msa=True, out_pog='pog.png', incr_fn='') # perform multiple sequence alignment 
-                                                                # generate a figure of alignment graph to pog.png
+res=a.msa(seqs, out_cons=True, out_msa=True) # perform multiple sequence alignment 
 
 for seq in res.cons_seq:
     print(seq)  # print consensus sequence

python/example.py

@@ -37,11 +37,11 @@
 #seqs: multiple sequences
 out_cons=True # generate consensus sequence, set as False to disable
 out_msa=True # generate row-column multiple sequence alignment, set as False to disable
-out_pog="example1.png" # generate plot of alignment graph, set None to disable
+#out_pog="example1.png" # generate plot of alignment graph, set None to disable, require `dot` to be installed
 max_n_cons = 2
 
 # multiple sequence alignment for 'seqs'
-res=a.msa(seqs, out_cons=out_cons, out_msa=out_msa, max_n_cons=max_n_cons, out_pog=out_pog)
+res=a.msa(seqs, out_cons=out_cons, out_msa=out_msa, max_n_cons=max_n_cons) #, out_pog=out_pog)
 
 # output result
 if out_cons:
@@ -70,11 +70,11 @@
 #seqs: multiple sequences
 out_cons=True # generate consensus sequence, set as False to disable
 out_msa=True # generate row-column multiple sequence alignment, set as False to disable
-out_pog="example2.png" # generate plot of alignment graph, set None to disable
+# out_pog="example2.png" # generate plot of alignment graph, set None to disable
 max_n_cons = 1
 
 # multiple sequence alignment for 'seqs'
-res=a.msa(seqs, out_cons=out_cons, out_msa=out_msa, max_n_cons=max_n_cons, out_pog=out_pog)
+res=a.msa(seqs, out_cons=out_cons, out_msa=out_msa, max_n_cons=max_n_cons) #, out_pog=out_pog)
 
 # output result
 if out_cons:

src/abpoa.c

@@ -16,7 +16,7 @@ char PROG[20] = "abpoa";
 #define _bO BOLD UNDERLINE "O" NONE
 #define _bA BOLD UNDERLINE "A" NONE
 char DESCRIPTION[100] = _ba "daptive " _bb "anded " _bP "artial " _bO "rder " _bA "lignment";
-char VERSION[20] = "1.4.2";
+char VERSION[20] = "1.4.3";
 char CONTACT[30] = "[email protected]";
 
 const struct option abpoa_long_opt [] = {