-
Notifications
You must be signed in to change notification settings - Fork 14
/
Copy pathextensions.toml
125 lines (119 loc) · 4.07 KB
/
extensions.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
# FIXME: these live outside pyproject.toml for the moment because
# setuptools >=75 which supports them is not available on Python <=3.7.
# once we drop support for older Pythons we can merge back into
# pyproject.toml
[[tool.setuptools.ext-modules]]
name = "PyPop._EWSlatkinExact"
sources = ["src/slatkin-exact/monte-carlo_wrap.i", "src/slatkin-exact/monte-carlo.c"]
swig-opts = ["-Isrc/SWIG", "-Isrc"]
[[tool.setuptools.ext-modules]]
name = "PyPop._Emhaplofreq"
sources = ["src/emhaplofreq/emhaplofreq_wrap.i", "src/emhaplofreq/emhaplofreq.c"]
swig-opts = ["-Isrc/SWIG", "-Isrc"]
include-dirs = ["src/emhaplofreq"]
extra-compile-args = ["-D__SWIG__=1",
"-DDEBUG=0",
"-DEXTERNAL_MODE=1",
"-DXML_OUTPUT=1"]
depends = ["src/SWIG/typemap.i",
"src/emhaplofreq/emhaplofreq.h",
"src/emhaplofreq/drand48.c"]
[[tool.setuptools.ext-modules]]
name = "PyPop._Gthwe"
sources = [
"src/gthwe/gthwe_wrap.i",
"src/gthwe/hwe.c",
"src/gthwe/cal_const.c",
"src/gthwe/cal_n.c",
"src/gthwe/cal_prob.c",
"src/gthwe/check_file.c",
"src/gthwe/do_switch.c",
"src/gthwe/new_rand.c",
"src/gthwe/ln_p_value.c",
"src/gthwe/to_calculate_log.c",
"src/gthwe/print_data.c",
"src/gthwe/random_choose.c",
"src/gthwe/read_data.c",
"src/gthwe/select_index.c",
"src/gthwe/stamp_time.c",
"src/gthwe/test_switch.c",
"src/gthwe/statistics.c"]
swig-opts = ["-Isrc/SWIG", "-Isrc"]
include-dirs = ["src/gthwe"]
library-dirs = []
libraries=["gsl", "gslcblas"]
extra-compile-args=["-D__SWIG__=1",
"-DDEBUG=0",
"-DXML_OUTPUT=1",
"-DSUPPRESS_ALLELE_TABLE=1",
"-DINDIVID_GENOTYPES=1",
]
depends = ["src/SWIG/typemap.i", "src/gthwe/func.h", "src/gthwe/hwe.h"]
[[tool.setuptools.ext-modules]]
name = "PyPop._Pvalue"
sources = [
"src/pval/pval_wrap.i",
"src/pval/pval.c",
"src/pval/pchisq.c",
"src/pval/chebyshev.c",
"src/pval/ftrunc.c",
"src/pval/lgamma.c",
"src/pval/mlutils.c",
"src/pval/pgamma.c",
"src/pval/fmin2.c",
"src/pval/fmax2.c",
"src/pval/dnorm.c",
"src/pval/dpois.c",
"src/pval/gamma.c",
"src/pval/bd0.c",
"src/pval/stirlerr.c",
"src/pval/lgammacor.c",
"src/pval/pnorm.c"]
swig-opts = ["-Isrc/SWIG", "-Isrc"]
include-dirs = ["src/pval"]
extra-compile-args = ["-DMATHLIB_STANDALONE=1"]
depends = ["src/SWIG/typemap.i", "src/pval/Rconfig.h", "src/pval/Rmath.h", "src/pval/dpq.h", "src/pval/nmath.h"]
[[tool.setuptools.ext-modules]]
name = "PyPop._Haplostats"
sources = ["src/haplo-stats/haplostats_wrap.i", "src/haplo-stats/haplo_em_pin.c"]
swig-opts = ["-Isrc/SWIG", "-Isrc"]
include-dirs = ["src/haplo-stats", "src/pval"]
extra-compile-args = [
"-DMATHLIB_STANDALONE=1",
"-D__SWIG__=1",
"-DDEBUG=0",
"-DR_NO_REMAP=1"
]
depends = ["src/SWIG/typemap.i", "src/haplo-stats/haplo_em_pin.h"]
# FIXME: currently disabled, needs to be converted
# ext_HweEnum = Extension(
# "PyPop._HweEnum",
# [
# "src/hwe-enumeration/src/hwe_enum_wrap.i",
# "src/hwe-enumeration/src/hwe_enum.c",
# "src/hwe-enumeration/src/factorial.c",
# "src/hwe-enumeration/src/main.c",
# "src/hwe-enumeration/src/common.c",
# "src/hwe-enumeration/src/statistics.c",
# "src/hwe-enumeration/src/external.c",
# ],
# swig_opts=["-Isrc/SWIG", "-Isrc"],
# include_dirs=[
# ["src/hwe-enumeration/src/include"],
# "/usr/include/glib-2.0",
# "/usr/include/glib-2.0/include",
# "/usr/lib/glib-2.0/include",
# "/usr/lib64/glib-2.0/include/",
# "/usr/include/libxml2",
# "/usr/include/gsl",
# ],
# libraries=["glib-2.0", "xml2", "popt", "m", "gsl", "gslcblas"],
# define_macros=[
# ("__SORT_TABLE__", "1"),
# ("g_fprintf", "pyfprintf"),
# ("VERSION", '"internal"'),
# ("PACKAGE_NAME", '"hwe-enumeration"'),
# ("INDIVID_GENOTYPES", "1"),
# ("HAVE_LIBGSL", "1"),
# ],
# )