diff --git a/SigProfilerSimulator/SigProfilerSimulator.py b/SigProfilerSimulator/SigProfilerSimulator.py index 9c682ad..0b4510d 100644 --- a/SigProfilerSimulator/SigProfilerSimulator.py +++ b/SigProfilerSimulator/SigProfilerSimulator.py @@ -336,7 +336,7 @@ def SigProfilerSimulator (project, project_path, genome, contexts, exome=None, s if context == "288": nucleotide_context_file = nucleotide_context_file.split("_") - nucleotide_context_file[4] = "384" + nucleotide_context_file[5] = "384" nucleotide_context_file = "_".join([x for x in nucleotide_context_file]) elif context == '4608': nucleotide_context_file = nucleotide_context_file.split("_") diff --git a/setup.py b/setup.py index fb231b7..e564430 100644 --- a/setup.py +++ b/setup.py @@ -3,45 +3,57 @@ import shutil -#remove the dist folder first if exists +# remove the dist folder first if exists if os.path.exists("dist"): - shutil.rmtree("dist") + shutil.rmtree("dist") + def readme(): - this_directory = os.path.abspath(os.path.dirname(__file__)) - with open(os.path.join(this_directory, 'README.md'), encoding='latin-1') as f: - long_description = f.read() - return(long_description) - -VERSION = '1.1.5' - -def write_version_py(filename='SigProfilerSimulator/version.py'): - # Copied from numpy setup.py - cnt = """ + this_directory = os.path.abspath(os.path.dirname(__file__)) + with open(os.path.join(this_directory, "README.md"), encoding="latin-1") as f: + long_description = f.read() + return long_description + + +VERSION = "1.1.6" + + +def write_version_py(filename="SigProfilerSimulator/version.py"): + # Copied from numpy setup.py + cnt = """ # THIS FILE IS GENERATED FROM SIGPROFILERSIMULATOR SETUP.PY short_version = '%(version)s' version = '%(version)s' """ - fh = open(filename, 'w') - fh.write(cnt % {'version': VERSION,}) - fh.close() + fh = open(filename, "w") + fh.write( + cnt + % { + "version": VERSION, + } + ) + fh.close() + write_version_py() -setup(name='SigProfilerSimulator', - version=VERSION, - description='SigProfiler simulator tool', - long_description= readme(), - long_description_content_type='text/markdown', - url='', - author='Erik Bergstrom', - author_email='ebergstr@eng.ucsd.edu', - license='UCSD', - packages=find_packages(), - install_requires =[ - "SigProfilerMatrixGenerator>=1.2.18", - "sigProfilerPlotting>=1.3.16", - "fastrand>=1.2"], - include_package_data=True, - zip_safe=False) +setup( + name="SigProfilerSimulator", + version=VERSION, + description="SigProfiler simulator tool", + long_description=readme(), + long_description_content_type="text/markdown", + url="", + author="Erik Bergstrom", + author_email="ebergstr@eng.ucsd.edu", + license="UCSD", + packages=find_packages(), + install_requires=[ + "SigProfilerMatrixGenerator>=1.2.25", + "sigProfilerPlotting>=1.3.21", + "fastrand>=1.2", + ], + include_package_data=True, + zip_safe=False, +)