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
|
import os
from cffi import FFI
if 'MANYLINUX' in os.environ:
src_dir = os.path.join('/io', 'src')
# build-wheels.sh determines these
libraries=['openblas']
library_dirs=['/usr/local/lib/']
else:
if os.path.isfile(os.path.join('..', 'src','decode.h')):
# assume the git repo
src_dir = os.path.join('..', 'src')
elif os.path.isfile(os.path.join('src','decode.h')):
# else we're from an sdist
src_dir = 'src'
else:
raise IOError('Cannot find scrappie C sources.')
# this might want to be cblas on some systems
libraries=['blas']
library_dirs=[]
ffibuilder = FFI()
ffibuilder.set_source("libscrappy",
r"""
#include "decode.h"
#include "networks.h"
#include "scrappie_common.h"
#include "util.h"
#include "scrappie_seq_helpers.h"
#include "scrappie_matrix.h"
int get_raw_model_stride_from_string(const char * modelstr){
// Obtain the model stride from its str name
// avoid the intermediate errx from C signalling bad model
// name with a return of -1.
const enum raw_model_type modeltype = get_raw_model(modelstr);
if(modeltype == SCRAPPIE_MODEL_INVALID){
return -1;
} else {
return get_raw_model_stride(modeltype);
}
}
""",
libraries=libraries,
library_dirs=library_dirs,
include_dirs=[src_dir],
sources=[
os.path.join(src_dir, '{}.c'.format(x)) for x in
r'''decode
event_detection
layers
networks
nnfeatures
scrappie_common
scrappie_matrix
scrappie_seq_helpers
util'''.split()
],
extra_compile_args=['-std=c99', '-O3']
)
with open('pyscrap.h', 'r') as fh:
pyscrap_function_prototypes = fh.read()
ffibuilder.cdef("""
typedef struct {
char * uuid;
size_t n;
size_t start;
size_t end;
float *raw;
} raw_table;
typedef struct {
size_t nr, nrq, nc, stride;
union {
//__m128 *v; // we don't need this
float *f;
} data;
} _Mat;
typedef _Mat *scrappie_matrix;
typedef _Mat const *const_scrappie_matrix;
""" pyscrap_function_prototypes)
if __name__ == "__main__":
ffibuilder.compile(verbose=True)
|
