New upstream version 2.00~a2-191022

###########################################################################

# Note: This Makefile is intended for development.  For production

# builds, use build_dynamic/Makefile.

###########################################################################

# Does not currently support -DCPU_CHECK_...

BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mlzcnt -DZSTD_MULTITHREAD

# BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD

# BASEFLAGS=-g -DZSTD_MULTITHREAD

include Makefile.src

# Respect the environment:

# Use defaults below only if not set in env or make arguments

CC		?= gcc

CXX		?= g++

CFLAGS		?= -O3

CXXFLAGS	?= -O2

ZLIB		?= ../zlib-1.2.11/libz-64.a

BLASFLAGS64	?= -llapack -lf77blas -latlas

ARCH32		?=

# Mandatory flags added to defaults or env settings

CFLAGS		+= -std=gnu99 $(BASEFLAGS) $(CWARN) $(CINCLUDE)

CXXFLAGS	+= -std=c++14 $(BASEFLAGS) $(CXXWARN)

LDFLAGS		+= -lm -lpthread -L. $(ZLIB) -lzstd

# Installation defaults

MKDIR		?= mkdir

INSTALL		?= install

STRIP_CMD	?= strip

PREFIX		?= /usr/local

DESTDIR		?= .

UNAME := $(shell uname)

ifeq ($(UNAME), Darwin)

  BLASFLAGS=-framework Accelerate

  BLASFLAGS64=-framework Accelerate

  LDFLAGS=-ldl -lpthread -lz -lzstd

endif

%.o: %.c

	$(CC) -c $(CFLAGS) $(ARCH32) -o $@ $<

%.o: %.cc

	$(CXX) -c $(CXXFLAGS) $(ARCH32) -o $@ $<

all: plink2 pgen_compress

# for clean build, "make clean" first

# Run mkdir for both plink2 and pgen_compress as we don't know which

# target will run first

plink2: $(OBJ_NO_ZSTD)

	$(MKDIR) -p bin

	$(CXX) $(ARCH32) $(OBJ_NO_ZSTD) -o bin/plink2 $(BLASFLAGS64) $(LDFLAGS)

# basic pgenlib_internal.h usage example; also needed for tests

pgen_compress: plink2_base.o pgenlib_internal.o pgen_compress.o

	$(MKDIR) -p bin

	$(CXX) plink2_base.o pgenlib_internal.o pgen_compress.o \

		-o bin/pgen_compress

.PHONY: install-strip install clean

install-strip: install

	$(STRIP_CMD) $(DESTDIR)$(PREFIX)/bin/*

install: all

	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin

	$(INSTALL) -c bin/* $(DESTDIR)$(PREFIX)/bin

clean:

	rm -f $(CLEAN)

CWARN = -Wall -Wextra -Wshadow -Wformat-security -Wdouble-promotion -Wfloat-conversion

CXXWARN = ${CWARN} -Wold-style-cast

# Necessary for older gcc versions.

CWARN2 = -Wall -Wextra -Wshadow -Wformat-security

CXXWARN2 = ${CWARN2} -Wold-style-cast

CSRC = SFMT.c libdeflate/lib/adler32.c libdeflate/lib/aligned_malloc.c libdeflate/lib/crc32.c libdeflate/lib/deflate_compress.c libdeflate/lib/deflate_decompress.c libdeflate/lib/gzip_compress.c libdeflate/lib/gzip_decompress.c libdeflate/lib/zlib_compress.c libdeflate/lib/zlib_decompress.c libdeflate/lib/x86/cpu_features.c

ZCSRC = zstd/lib/common/debug.c zstd/lib/common/entropy_common.c zstd/lib/common/zstd_common.c zstd/lib/common/error_private.c zstd/lib/common/xxhash.c zstd/lib/common/fse_decompress.c zstd/lib/common/pool.c zstd/lib/common/threading.c zstd/lib/compress/fse_compress.c zstd/lib/compress/hist.c zstd/lib/compress/huf_compress.c zstd/lib/compress/zstd_double_fast.c zstd/lib/compress/zstd_fast.c zstd/lib/compress/zstd_lazy.c zstd/lib/compress/zstd_ldm.c zstd/lib/compress/zstd_opt.c zstd/lib/compress/zstd_compress.c zstd/lib/compress/zstdmt_compress.c zstd/lib/decompress/huf_decompress.c zstd/lib/decompress/zstd_decompress.c zstd/lib/decompress/zstd_ddict.c zstd/lib/decompress/zstd_decompress_block.c

CCSRC = plink2_base.cc pgenlib_internal.cc plink2.cc plink2_adjust.cc plink2_bgzf.cc plink2_cmdline.cc plink2_common.cc plink2_compress_stream.cc plink2_data.cc plink2_decompress.cc plink2_export.cc plink2_fasta.cc plink2_filter.cc plink2_glm.cc plink2_help.cc plink2_import.cc plink2_ld.cc plink2_matrix.cc plink2_matrix_calc.cc plink2_misc.cc plink2_psam.cc plink2_pvar.cc plink2_random.cc plink2_set.cc plink2_stats.cc plink2_string.cc plink2_text.cc plink2_thread.cc plink2_zstfile.cc

OBJ_NO_ZSTD = $(CSRC:.c=.o) $(CCSRC:.cc=.o)

OBJ = $(CSRC:.c=.o) $(ZCSRC:.c=.o) $(CCSRC:.cc=.o)

CSRC2 = $(foreach fname,$(CSRC),../$(fname))

ZCSRC2 = $(foreach fname,$(ZCSRC),../$(fname))

CCSRC2 = $(foreach fname,$(CCSRC),../$(fname))

OBJ2 = $(notdir $(OBJ))

OBJ3 = $(CSRC2:.c=.o) $(ZCSRC2:.c=.o) $(CCSRC2:.cc=.o)

CINCLUDE = -Ilibdeflate -Ilibdeflate/common

CINCLUDE2 = -I../libdeflate -I../libdeflate/common

ZSTD_INCLUDE = -Izstd/lib -Izstd/lib/common

ZSTD_INCLUDE2 = -I../zstd/lib -I../zstd/lib/common

CLEAN = *.o libdeflate/lib/*.o libdeflate/lib/x86/*.o zstd/lib/common/*.o zstd/lib/compress/*.o zstd/lib/decompress/*.o bin/plink2 bin/pgen_compress

CLEAN3 = $(foreach expr,$(CLEAN),../$(expr))

Cython and NumPy must be installed.

Build this with e.g.

  python setup.py build_ext

  [sudo] python setup.py install

  python3 setup.py build_ext

  [sudo] python3 setup.py install

#!/usr/bin/python

#!/usr/bin/env python3

from distutils.core import setup

from distutils.extension import Extension

from setuptools import setup

from setuptools.extension import Extension

from Cython.Build import cythonize

import numpy as np

ext_modules = [

    Extension('pgenlib',

              sources = ['pgenlib.pyx', '../pgenlib_python_support.cpp', '../pgenlib_internal.cpp'],

              sources = ['pgenlib.pyx', '../pgenlib_ffi_support.cc', '../pgenlib_internal.cc', '../plink2_base.cc'],

              language = "c++",

              # do not compile as c++11, since cython doesn't yet support

              # overload of uint32_t operator

              # extra_compile_args = ["-std=c++11", "-Wno-unused-function"],

              # extra_link_args = ["-std=c++11"],

              extra_compile_args = ["-std=c++98", "-Wno-unused-function"],

              extra_compile_args = ["-std=c++98", "-Wno-unused-function", "-Wno-macro-redefined"],

              extra_link_args = ["-std=c++98"],

              include_dirs = [np.get_include()]

              )