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[WIP] build pysam on Windows #964

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[WIP] build pysam on Windows #964

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5 changes: 5 additions & 0 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,8 @@ addopts = -s -v
testpaths = pysam tests
pep8maxlinelength = 120
pep8ignore = E402

[build]
compiler=mingw32
[build_ext]
compiler=mingw32
39 changes: 25 additions & 14 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
import subprocess
import sys
import sysconfig
import distutils
from contextlib import contextmanager
from setuptools import setup
from cy_build import CyExtension as Extension, cy_build_ext as build_ext
Expand All @@ -54,7 +55,7 @@ def run_configure(option):
sys.stdout.flush()
try:
retcode = subprocess.call(
" ".join(("./configure", option)),
" ".join(("sh ./configure", option)),
shell=True)
if retcode != 0:
return False
Expand Down Expand Up @@ -242,7 +243,7 @@ def get_pysam_version():
for key, value in htslib_make_options.items():
print ("# pysam: htslib_config {}={}".format(key, value))

external_htslib_libraries = ['z']
external_htslib_libraries = ['z', 'regex', 'tre', 'intl', 'iconv']
if "LIBS" in htslib_make_options:
external_htslib_libraries.extend(
[re.sub("^-l", "", x) for x in htslib_make_options["LIBS"].split(" ") if x.strip()])
Expand Down Expand Up @@ -319,7 +320,7 @@ def get_pysam_version():

#######################################################
# Windows compatibility - untested
if platform.system() == 'Windows':
if False:
include_os = ['win32']
os_c_files = ['win32/getopt.c']
extra_compile_args = []
Expand All @@ -338,20 +339,27 @@ def get_pysam_version():

define_macros = []

suffix = sysconfig.get_config_var('EXT_SUFFIX')
suffix = distutils.sysconfig.get_config_var('EXT_SUFFIX')
if not suffix:
suffix = sysconfig.get_config_var('SO')
suffix = distutils.sysconfig.get_config_var('SO')

internal_htslib_libraries = [
os.path.splitext("chtslib{}".format(suffix))[0]]
":libchtslib{}".format(suffix)]
internal_samtools_libraries = [
os.path.splitext("csamtools{}".format(suffix))[0],
os.path.splitext("cbcftools{}".format(suffix))[0],
":libcsamtools{}".format(suffix),
":libcbcftools{}".format(suffix),
]
internal_pysamutil_libraries = [
os.path.splitext("cutils{}".format(suffix))[0]]
":libcutils{}".format(suffix)]

libraries_for_pysam_module = external_htslib_libraries + internal_htslib_libraries + internal_pysamutil_libraries
external_htslib_objects = []
for lib in external_htslib_libraries:
if lib != "ws2_32":
external_htslib_objects.append("C:/msys64/mingw64/lib/lib{}.a".format(lib))

internal_htslib_libraries.append("ws2_32")

libraries_for_pysam_module = internal_htslib_libraries + internal_pysamutil_libraries

# Order of modules matters in order to make sure that dependencies are resolved.
# The structures of dependencies is as follows:
Expand All @@ -367,17 +375,19 @@ def get_pysam_version():
modules = [
dict(name="pysam.libchtslib",
sources=[source_pattern % "htslib", "pysam/htslib_util.c"] + shared_htslib_sources + os_c_files,
libraries=external_htslib_libraries),
extra_link_args=["-Wl,--export-all-symbols"]),
dict(name="pysam.libcsamtools",
sources=[source_pattern % "samtools"] + glob.glob(os.path.join("samtools", "*.pysam.c")) +
[os.path.join("samtools", "lz4", "lz4.c")] + htslib_sources + os_c_files,
libraries=external_htslib_libraries + internal_htslib_libraries),
libraries=internal_htslib_libraries,
extra_link_args=["-Wl,--export-all-symbols"]),
dict(name="pysam.libcbcftools",
sources=[source_pattern % "bcftools"] + glob.glob(os.path.join("bcftools", "*.pysam.c")) + htslib_sources + os_c_files,
libraries=external_htslib_libraries + internal_htslib_libraries),
libraries=internal_htslib_libraries,
extra_link_args=["-Wl,--export-all-symbols"]),
dict(name="pysam.libcutils",
sources=[source_pattern % "utils", "pysam/pysam_util.c"] + htslib_sources + os_c_files,
libraries=external_htslib_libraries + internal_htslib_libraries + internal_samtools_libraries),
libraries=internal_htslib_libraries + internal_samtools_libraries),
dict(name="pysam.libcalignmentfile",
sources=[source_pattern % "alignmentfile"] + htslib_sources + os_c_files,
libraries=libraries_for_pysam_module),
Expand Down Expand Up @@ -413,6 +423,7 @@ def get_pysam_version():
define_macros=define_macros,
# for out-of-tree compilation, use absolute paths
library_dirs=[os.path.abspath(x) for x in ["pysam"] + htslib_library_dirs],
extra_objects=external_htslib_objects,
include_dirs=[os.path.abspath(x) for x in htslib_include_dirs + \
["samtools", "samtools/lz4", "bcftools", "pysam", "."] + include_os])

Expand Down