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34fa2b1
first working module
May 24, 2018
65568e3
throws exception for non existent files
May 24, 2018
9975947
added keywords to the main "starcode" method
May 24, 2018
b3fd558
added "verbose" kwarg
May 24, 2018
14d1a18
added "threads" kwarg
May 24, 2018
b033f9a
finalized kwargs
May 24, 2018
67e0b08
transferred output to separate function in starcode
May 24, 2018
8ff847b
read files now in main
May 24, 2018
a140542
"starcode" function takes gstack_t as argument
Jun 1, 2018
33cb2a1
put flag check in separate function
Jun 12, 2018
af37304
fixed all compiler warnings
Jun 12, 2018
35f7096
new function "starcode" takes list as input
Jun 12, 2018
bbca4ab
new layout of output, doesn't work yet
Jun 12, 2018
aef6764
added test.py to test
Jun 13, 2018
a777810
fixed check_input function, takes flags not chars
Jun 13, 2018
cbdf794
pystarcode.starcode returns a dictionary with starcoded barcodes
Jun 13, 2018
c68dabd
pystarcode.starcode outputs all the information that starcode does
Jun 14, 2018
8efbd0c
main starcode is now mostly a sequence of encapsulated functions
Jun 14, 2018
8010479
removed starcode_c function from python module
Jun 14, 2018
c41f351
cleaned input keywords passed to pystarcode.starcode
Jun 14, 2018
3083df8
updated test.py
Jun 14, 2018
2859e4c
draft output for different algorithms
Jun 15, 2018
8047b13
moved source files of pystarcode
Jun 18, 2018
e6542ad
updated test.py with example sequence file
Jun 18, 2018
52a9fa9
updated sources and setup.py
Jun 18, 2018
d808312
set input_flag = 1 in the case where input file is not specified with -i
Jun 25, 2018
1872a3e
fixed output type setting
Jun 28, 2018
609c3b1
fixed 'read_file' calls in test_starcode
Jun 28, 2018
31eb8a3
Moves new files to their folders. Adds pystarcode tests to main test …
ezorita Jun 29, 2018
47dbe16
test: installs pystarcode before running travis tests.
ezorita Jun 29, 2018
9b20038
travis.yml: installs pystarcode in main routine to avoid clang failure.
ezorita Jun 29, 2018
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -12,3 +12,4 @@ test/.inspect.gdb
test/runtests
doc/*.log
*\#*
*.txt
2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ branches:
before_install:
- sudo pip install cpp-coveralls

script: make && cd test && make test
script: sudo python setup.py install && make && cd test && make test

after_success:
- coveralls --verbose --gcov-options '\-lp' -r .. -E '.*test*'
4 changes: 2 additions & 2 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ SOURCES= $(addprefix $(SRC_DIR)/,$(SOURCE_FILES))
INCLUDES= $(addprefix -I, $(INC_DIR))

# Development and debug flags.
#CFLAGS= -std=c99 -g -O0 -Wunused-parameter -Wredundant-decls \
CFLAGS= -std=c99 -g -O0 -Wunused-parameter -Wredundant-decls \
-Wreturn-type -Wswitch-default -Wunused-value -Wimplicit \
-Wimplicit-function-declaration -Wimplicit-int -Wimport \
-Wunused -Wunused-function -Wunused-label -Wbad-function-cast \
Expand All @@ -19,7 +19,7 @@ INCLUDES= $(addprefix -I, $(INC_DIR))
-Wunused-variable -Wformat-nonliteral -Wparentheses -Wundef \
-Wsequence-point -Wuninitialized -Wbad-function-cast
# Release flags.
CFLAGS= -std=c99 -O3 -Wall
#CFLAGS= -std=c99 -O3 -Wall

LDLIBS= -lpthread -lm
CC= gcc
Expand Down
12 changes: 12 additions & 0 deletions setup.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
from distutils.core import setup, Extension

module1 = Extension('pystarcode',
define_macros = [('MAJOR_VERSION', '1'), ('MINOR_VERSION', '0')],
include_dirs = ['src/'],
sources = ['src/pystarcode.c', 'src/starcode.c', 'src/trie.c'],
extra_compile_args = ['-std=c99'])

setup(name = 'pystarcode',
version = '1.0',
description = 'Starcode library for Python',
ext_modules = [module1])
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