https://github.com/tskit-dev/msprime
Tip revision: becc7b948123f8683c49ed41480ca2682d979a7f authored by Yan Wong on 09 December 2022, 18:50:12 UTC
Update docs/mutations.md
Update docs/mutations.md
Tip revision: becc7b9
setup.py
import os.path
import platform
import subprocess
from warnings import warn
import numpy
from setuptools import Extension
from setuptools import setup
CONDA_PREFIX = os.getenv("MSP_CONDA_PREFIX", None)
IS_WINDOWS = platform.system() == "Windows"
class PathConfigurator:
"""
A class to attempt configuration of the compile search paths
on various platforms.
"""
def __init__(self):
self.include_dirs = []
self.library_dirs = []
try:
self._configure_gsl()
except OSError as e:
warn(f"Error occured getting GSL path config: {e}")
# If the conda prefix is defined, then we are compiling in a conda
# context. All include and lib paths should come from within this prefix.
if CONDA_PREFIX is not None:
prefix = CONDA_PREFIX
if IS_WINDOWS:
prefix = os.path.join(prefix, "Library")
self.library_dirs.append(os.path.join(prefix, "lib"))
self.include_dirs.append(os.path.join(prefix, "include"))
def _run_command(self, args):
return subprocess.check_output(args, text=True)
def _configure_gsl(self):
output = self._run_command(["gsl-config", "--cflags"]).split()
if len(output) > 0:
token = output[0]
self.include_dirs.append(token[2:])
output = self._run_command(["gsl-config", "--libs"]).split()
for token in output:
if token.startswith("-L"):
self.library_dirs.append(token[2:])
libdir = "lib"
tskroot = os.path.join("git-submodules", "tskit", "c")
tskdir = os.path.join(tskroot, "tskit")
kasdir = os.path.join(tskroot, "subprojects", "kastore")
includes = ["lwt_interface", libdir, tskroot, tskdir, kasdir]
configurator = PathConfigurator()
msp_source_files = [
"msprime.c",
"fenwick.c",
"avl.c",
"util.c",
"object_heap.c",
"rate_map.c",
"mutgen.c",
"likelihood.c",
]
tsk_source_files = ["core.c", "tables.c", "trees.c"]
kas_source_files = ["kastore.c"]
sources = (
["msprime/_msprimemodule.c"]
+ [os.path.join(libdir, f) for f in msp_source_files]
+ [os.path.join(tskdir, f) for f in tsk_source_files]
+ [os.path.join(kasdir, f) for f in kas_source_files]
)
libraries = ["gsl", "gslcblas"]
defines = []
if IS_WINDOWS:
# Needed for generating UUIDs
libraries.append("Advapi32")
defines += [
# These two are required for GSL to compile and link against the
# conda-forge version.
("GSL_DLL", None),
("WIN32", None),
]
_msprime_module = Extension(
"msprime._msprime",
sources=sources,
extra_compile_args=["-std=c99"],
libraries=libraries,
define_macros=defines,
include_dirs=includes + configurator.include_dirs + [numpy.get_include()],
library_dirs=configurator.library_dirs,
)
setup(
# The package name along with all the other metadata is specified in setup.cfg
# However, GitHub's dependency graph can't see the package unless we put this here.
name="msprime",
ext_modules=[_msprime_module],
)