setup.py

from setuptools import setup, find_packages, Extension
import sys


class SetupOptions():
    fully_install = False
    options = {
        "name": 'exceRNApipeline',
        "version": '0.1.0',
        "author": 'Chenghao Zhu',
        "author_email": 'zhuchcn@gmail.com',
        "install_requires": [
            'snakemake'
        ],
        "packages": find_packages(exclude=[
            "exceRNApipeline.tasks*",
            "exceRNApipeline.includes*",
            "exceRNApipeline.tests*"
        ]),
        "package_data": {
            "exceRNApipeline.pipeline": ["smk/*", "smk/reports/*"]
        },
        "entry_points": {
            'console_scripts': [
                'pipeline=exceRNApipeline.pipeline.__main__:main',
            ]
        }
    }

    def __init__(self):
        i = 0
        while i < len(sys.argv):
            if sys.argv[i] == '--fully-install':
                self.fully_install = True
                sys.argv.pop(i)
                break
            i += 1
        if self.fully_install:
            self.fullySetup()

    def fullySetup(self):
        extra_link_args = ['-lz']

        if sys.platform == 'darwin':
            os.environ["MACOSX_DEPLOYMENT_TARGET"] = "10.9"
            extra_link_args += ['-bundle', '-flat_namespace', '-undefined', 'suppress']

        self.options['entry_points']['console_scripts'] += [
            'task_preprocess.py=exceRNApipeline.tasks.task_preprocess:main',
            'task_preprocess_stats.py=exceRNApipeline.tasks.task_preprocess_stats:main',
            'task_star_index.py=exceRNApipeline.tasks.task_star_index:main',
            'task_star_align.py=exceRNApipeline.tasks.task_star_align:main',
            'task_anno_to_fasta.py=exceRNApipeline.tasks.task_anno_to_fasta:main',
            'task_solve_silva_taxa.py=exceRNApipeline.tasks.task_solve_silva_taxa:main',
            'task_extract_fastx.py=exceRNApipeline.tasks.task_extract_fastx:main',
            'task_summarize_counts.py=exceRNApipeline.tasks.task_summarize_counts:main',
            'task_endogenous_count_barplot.py=exceRNApipeline.tasks.task_endogenous_count_barplot:main',
            'task_silva_extract_unmapped.py=exceRNApipeline.tasks.task_silva_extract_unmapped:main',
            'task_split_fasta.py=exceRNApipeline.tasks.task_split_fasta:main',
            'task_bacteria_download_genome.py=exceRNApipeline.tasks.task_bacteria_download_genome:main',
            'task_star_align_silva.py=exceRNApipeline.tasks.task_star_align_silva:main',
            'task_star_align_bacteria.py=exceRNApipeline.tasks.task_star_align_bacteria:main',
            'task_count_exogenous_taxa.py=exceRNApipeline.tasks.task_count_exogenous_taxa:main'
        ]

        self.options['ext_modules'] = [
            Extension(
                name="_exceRNApipeline_taxaCounter",
                sources=[
                    'exceRNApipeline/includes/taxonomy/taxonomy.i',
                    'exceRNApipeline/includes/taxonomy/NCBITaxonomy.cpp',
                    'exceRNApipeline/includes/taxonomy/TaxaCounter.cpp',
                    'exceRNApipeline/includes/gzstream/gzstream.C'
                ],
                swig_opts=['-c++'],
                extra_compile_args=['-IexceRNApipeline/includes/gzstream', '-lz', '-g', '-fPIC'],
                extra_link_args=extra_link_args
            )
        ]

        self.options["install_requires"] += [
            "pandas",
            "numpy",
            "matplotlib",
            "seaborn",
            'pathos',
            'python-magic',
            'biopython'
        ]
        self.options["packages"] = find_packages(exclude=["exceRNApipeline.tests*"])

setup(
    **SetupOptions().options
)