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b/setup.py |
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import sys |
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import numpy |
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from setuptools import Extension, setup |
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from setuptools.command.build_ext import build_ext |
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class build_ext_cxx17(build_ext): |
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def build_extensions(self): |
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std_flag = ( |
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"-std:c++17" if self.compiler.compiler_type == "msvc" else "-std=c++17" |
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) |
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for e in self.extensions: |
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e.extra_compile_args.append(std_flag) |
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super().build_extensions() |
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macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")] |
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profiling = False |
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linetrace = False |
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if "--profile" in sys.argv: |
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profiling = True |
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linetrace = True |
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macros += [("CYTHON_TRACE_NOGIL", "1")] |
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sys.argv.remove("--profile") |
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common_cpp = Extension( |
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"inmoose.common_cpp", |
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[ |
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"inmoose/common_cpp/common_cpp.pyx", |
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"inmoose/common_cpp/matrix.cpp", |
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], |
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include_dirs=[numpy.get_include()], |
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define_macros=macros, |
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) |
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stats_cpp = Extension( |
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"inmoose.utils.stats_cpp", |
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[ |
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"inmoose/utils/_stats.pyx", |
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], |
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include_dirs=[numpy.get_include()], |
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define_macros=macros, |
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) |
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edgepy_cpp = Extension( |
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"inmoose.edgepy.edgepy_cpp", |
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[ |
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"inmoose/edgepy/edgepy_cpp/edgepy_cpp.pyx", |
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"inmoose/edgepy/edgepy_cpp/interpolator.cpp", |
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], |
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include_dirs=[numpy.get_include(), "inmoose/common_cpp/"], |
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define_macros=macros, |
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) |
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setup( |
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cmdclass={"build_ext": build_ext_cxx17}, |
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packages=[ |
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"inmoose", |
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"inmoose/consensus_clustering", |
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"inmoose/data", |
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"inmoose/data/airway", |
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"inmoose/data/pasilla", |
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"inmoose/pycombat", |
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"inmoose/limma", |
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"inmoose/common_cpp", |
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"inmoose/edgepy", |
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"inmoose/edgepy/edgepy_cpp", |
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"inmoose/sim", |
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"inmoose/utils", |
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"inmoose/deseq2", |
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"inmoose/diffexp", |
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"inmoose/cohort_qc", |
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], |
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package_data={ |
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"inmoose/edgepy/edgepy_cpp": [ |
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"edgepy_cpp.pyx", |
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"__init__.pxd", |
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"edgepy_cpp.h", |
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"interpolator.h", |
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"maximize_interpolant.cpp", |
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"utils.h", |
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], |
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"inmoose/common_cpp": [ |
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"matrix.h", |
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], |
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"inmoose/data/airway": [ |
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"airway.h5ad", |
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], |
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"inmoose/data/pasilla": [ |
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"Dmel.BDGP5.25.62.DEXSeq.chr.gff", |
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"geneIDsinsubset.txt", |
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"pasilla_gene_counts.tsv", |
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"pasilla_sample_annotation.csv", |
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"treated1fb.txt", |
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"treated2fb.txt", |
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"treated3fb.txt", |
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"untreated1fb.txt", |
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"untreated2fb.txt", |
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"untreated3fb.txt", |
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"untreated4fb.txt", |
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], |
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"inmoose/cohort_qc": ["qc_report.html"], |
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}, |
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ext_modules=[common_cpp, edgepy_cpp, stats_cpp], |
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) |
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