forked from BoPeng/simuPOP
-
Notifications
You must be signed in to change notification settings - Fork 0
/
MANIFEST.in
332 lines (321 loc) · 8.82 KB
/
MANIFEST.in
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
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
# use explicit file list to avoid inclusion of unnecessary files in the source distribution
#
# general files
include README
include INSTALL
include ChangeLog
include COPYING
include TODO
include AUTHORS
include MANIFEST.in
include setup.py
# source header files
include config.h
include src/simuPOP_cfg.h
include src/boost_pch.hpp
include src/mutant_vector.h
include src/utility.h
include src/genoStru.h
include src/individual.h
include src/population.h
include src/simulator.h
include src/mating.h
include src/operator.h
include src/initializer.h
include src/migrator.h
include src/outputer.h
include src/selector.h
include src/penetrance.h
include src/qtrait.h
include src/stator.h
include src/mutator.h
include src/transmitter.h
include src/tagger.h
include src/pedigree.h
include src/virtualSubPop.h
# source files
include src/customizedTypes.c
include src/customizedTemplates.cpp
include src/utility.cpp
include src/genoStru.cpp
include src/individual.cpp
include src/population.cpp
include src/simulator.cpp
include src/mating.cpp
include src/operator.cpp
include src/initializer.cpp
include src/migrator.cpp
include src/outputer.cpp
include src/selector.cpp
include src/penetrance.cpp
include src/qtrait.cpp
include src/stator.cpp
include src/mutator.cpp
include src/transmitter.cpp
include src/tagger.cpp
include src/pedigree.cpp
include src/virtualSubPop.cpp
# source generated files
include src/swigpyrun.h
include src/simuPOP_std_wrap.cpp
include src/simuPOP_op_wrap.cpp
include src/simuPOP_la_wrap.cpp
include src/simuPOP_laop_wrap.cpp
include src/simuPOP_ba_wrap.cpp
include src/simuPOP_baop_wrap.cpp
include src/simuPOP_mu_wrap.cpp
include src/simuPOP_muop_wrap.cpp
include src/simuPOP_lin_wrap.cpp
include src/simuPOP_linop_wrap.cpp
include src/_version.py
include src/simuPOP_std.py
include src/simuPOP_op.py
include src/simuPOP_la.py
include src/simuPOP_laop.py
include src/simuPOP_ba.py
include src/simuPOP_baop.py
include src/simuPOP_lin.py
include src/simuPOP_linop.py
include src/gsl_wrap.c
# source wrap files
include src/simuPOP_common.i
include src/simuPOP_doc.i
include src/simuPOP_std.i
include src/simuPOP_op.i
include src/simuPOP_la.i
include src/simuPOP_laop.i
include src/simuPOP_ba.i
include src/simuPOP_baop.i
include src/simuPOP_lin.i
include src/simuPOP_linop.i
include src/simuPOP_mu.i
include src/simuPOP_muop.i
include src/gsl.i
# source python files (modules)
include simuOpt.py
include src/__init__.py
include src/utils.py
include src/demography.py
include src/plotter.py
include src/sampling.py
# gsl files
include gsl/build.h
include gsl/gsl_machine.h
include gsl/gsl_minmax.h
include gsl/gsl_inline.h
include gsl/gsl_sf_exp.h
include gsl/gsl_sf_expint.h
include gsl/gsl_sf_erf.h
include gsl/gsl_sf_pow_int.h
include gsl/gsl_sf_trig.h
include gsl/gsl_sf_psi.h
include gsl/gsl_message.h
include gsl/gsl_rng.h
include gsl/gsl_math.h
include gsl/gsl_complex.h
include gsl/gsl_complex_math.h
include gsl/gsl_sf_result.h
include gsl/gsl_types.h
include gsl/gsl_cdf.h
include gsl/gsl_version.h
include gsl/gsl_nan.h
include gsl/gsl_precision.h
include gsl/gsl_randist.h
include gsl/gsl_pow_int.h
include gsl/gsl_sf_elementary.h
include gsl/gsl_errno.h
include gsl/gsl_sf_zeta.h
include gsl/gsl_sf_gamma.h
include gsl/gsl_sf_log.h
include gsl/gsl_sys.h
include gsl/specfunc/chebyshev.h
include gsl/specfunc/eval.h
include gsl/specfunc/error.h
include gsl/specfunc/check.h
include gsl/complex/math.c
include gsl/randist/poisson.c
include gsl/randist/chisq.c
include gsl/randist/exponential.c
include gsl/randist/binomial.c
include gsl/randist/binomial_tpe.c
include gsl/randist/geometric.c
include gsl/randist/nbinomial.c
include gsl/randist/multinomial.c
include gsl/randist/gauss.c
include gsl/randist/gausszig.c
include gsl/randist/gamma.c
include gsl/randist/beta.c
include gsl/specfunc/beta.c
include gsl/specfunc/zeta.c
include gsl/specfunc/gamma.c
include gsl/specfunc/log.c
include gsl/specfunc/cheb_eval.c
include gsl/specfunc/trig.c
include gsl/specfunc/exp.c
include gsl/specfunc/expint.c
include gsl/specfunc/erfc.c
include gsl/specfunc/psi.c
include gsl/specfunc/elementary.c
include gsl/specfunc/gamma_inc.c
include gsl/error.h
include gsl/error.c
include gsl/sys/pow_int.c
include gsl/sys/fdiv.c
include gsl/sys/fcmp.c
include gsl/sys/coerce.c
include gsl/sys/infnan.c
include gsl/sys/log1p.c
include gsl/sys/expm1.c
include gsl/sys/invhyp.c
include gsl/rng/ranf.c
include gsl/rng/rand.c
include gsl/rng/ran0.c
include gsl/rng/rand48.c
include gsl/rng/coveyou.c
include gsl/rng/borosh13.c
include gsl/rng/ranlxd.c
include gsl/rng/ran1.c
include gsl/rng/ran3.c
include gsl/rng/taus.c
include gsl/rng/fishman20.c
include gsl/rng/uni32.c
include gsl/rng/minstd.c
include gsl/rng/file.c
include gsl/rng/lecuyer21.c
include gsl/rng/fishman18.c
include gsl/rng/vax.c
include gsl/rng/uni.c
include gsl/rng/ran2.c
include gsl/rng/randu.c
include gsl/rng/cmrg.c
include gsl/rng/transputer.c
include gsl/rng/mrg.c
include gsl/rng/rng.c
include gsl/rng/taus113.c
include gsl/rng/gfsr4.c
include gsl/rng/knuthran.c
include gsl/rng/default.c
include gsl/rng/zuf.c
include gsl/rng/mt.c
include gsl/rng/random.c
include gsl/rng/r250.c
include gsl/rng/types.c
include gsl/rng/fishman2x.c
include gsl/rng/waterman14.c
include gsl/rng/slatec.c
include gsl/rng/ranlxs.c
include gsl/rng/tt.c
include gsl/rng/schrage.c
include gsl/rng/knuthran2.c
include gsl/rng/ranmar.c
include gsl/rng/ranlux.c
include gsl/rng/knuthran2002.c
include gsl/cdf/beta.c
include gsl/cdf/betainv.c
include gsl/cdf/beta_inc.c
include gsl/cdf/binomial.c
include gsl/cdf/gauss.c
include gsl/cdf/gaussinv.c
include gsl/cdf/exponential.c
include gsl/cdf/exponentialinv.c
include gsl/cdf/chisq.c
include gsl/cdf/chisqinv.c
include gsl/cdf/gamma.c
include gsl/cdf/gammainv.c
include gsl/cdf/rat_eval.h
include gsl/cdf/poisson.c
# tests
include test/run_tests.py
include test/test_00_genoStru.py
include test/test_01_individual.py
include test/test_02_population.py
include test/test_03_operator.py
include test/test_04_simulator.py
include test/test_05_matings.py
include test/test_06_initialization.py
include test/test_07_tagging.py
include test/test_08_stat.py
include test/test_09_selection.py
include test/test_10_qtrait.py
include test/test_11_terminator.py
include test/test_12_migration.py
include test/test_13_mutation.py
include test/test_14_transmitter.py
include test/test_15_penetrance.py
include test/test_16_sampling.py
include test/test_17_utils.py
include test/test_18_plotter.py
include test/test_19_demography.py
include test/sample_32_ba.pop
include test/sample_32_la.pop
include test/sample_32_std.pop
include test/sample_32_ba_v1.pop
include test/sample_32_la_v1.pop
include test/sample_32_lin_v1.pop
include test/sample_32_mu_v1.pop
include test/sample_32_std_v1.pop
include test/sample_32_ba_v2.pop
include test/sample_32_la_v2.pop
include test/sample_32_lin_v2.pop
include test/sample_32_mu_v2.pop
include test/sample_32_std_v2.pop
include test/sample_64_ba.pop
include test/sample_64_la.pop
include test/sample_64_std.pop
include test/sample_64_ba_v1.pop
include test/sample_64_la_v1.pop
include test/sample_64_lin_v1.pop
include test/sample_64_mu_v1.pop
include test/sample_64_std_v1.pop
include test/sample_64_ba_v2.pop
include test/sample_64_la_v2.pop
include test/sample_64_lin_v2.pop
include test/sample_64_mu_v2.pop
include test/sample_64_std_v2.pop
# documentations
include doc/userGuide.pdf
include doc/userGuide.py
include doc/refManual.pdf
# win32 files
include development/win32/stdint.h
recursive-include development/win32/zlib-1.2.3 *.h *.c
# bundle boost 1.70.0
recursive-include boost_1_70_0/boost *.hpp *.ipp *.h
recursive-include boost_1_70_0/libs/iostreams/src *.cpp
recursive-include boost_1_70_0/libs/serialization/src *.cpp *.ipp
recursive-include boost_1_70_0/libs/regex/src *.cpp *.hpp
recursive-include boost_1_70_0/libs/detail *.cpp
prune boost_1_70_0/boost/accumulators
prune boost_1_70_0/boost/algorithm
prune boost_1_70_0/boost/asio
prune boost_1_70_0/boost/assign
prune boost_1_70_0/boost/bimap
prune boost_1_70_0/boost/chrono
prune boost_1_70_0/boost/circular_buffer
prune boost_1_70_0/boost/date_time
prune boost_1_70_0/boost/flyweight
prune boost_1_70_0/boost/function_types
prune boost_1_70_0/boost/fusion
prune boost_1_70_0/boost/geometry
prune boost_1_70_0/boost/gil
prune boost_1_70_0/boost/graph
prune boost_1_70_0/boost/icl
prune boost_1_70_0/boost/interprocess
prune boost_1_70_0/boost/intrusive
prune boost_1_70_0/boost/mpi
prune boost_1_70_0/boost/msm
prune boost_1_70_0/boost/phoenix
prune boost_1_70_0/boost/polygon
prune boost_1_70_0/boost/property_tree
prune boost_1_70_0/boost/proto
prune boost_1_70_0/boost/ptr_container
prune boost_1_70_0/boost/python
prune boost_1_70_0/boost/random
prune boost_1_70_0/boost/signals2
prune boost_1_70_0/boost/spirit
prune boost_1_70_0/boost/test
prune boost_1_70_0/boost/thread
prune boost_1_70_0/boost/units
prune boost_1_70_0/boost/variant
prune boost_1_70_0/boost/wave
prune boost_1_70_0/boost/xpressive