├── .coveragerc ├── .gitattributes ├── .gitignore ├── .gitmodules ├── .mailmap ├── .travis.yml ├── BENTO_BUILD.txt ├── CONTRIBUTING.rst ├── HACKING.rst.txt ├── INSTALL.rst.txt ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── THANKS.txt ├── benchmarks ├── README.rst ├── asv.conf.json ├── benchmarks │ ├── __init__.py │ ├── cluster.py │ ├── common.py │ ├── cython_special.py │ ├── fftpack_basic.py │ ├── fftpack_pseudo_diffs.py │ ├── go_benchmark_functions │ │ ├── __init__.py │ │ ├── go_benchmark.py │ │ ├── go_funcs_A.py │ │ ├── go_funcs_B.py │ │ ├── go_funcs_C.py │ │ ├── go_funcs_D.py │ │ ├── go_funcs_E.py │ │ ├── go_funcs_F.py │ │ ├── go_funcs_G.py │ │ ├── go_funcs_H.py │ │ ├── go_funcs_I.py │ │ ├── go_funcs_J.py │ │ ├── go_funcs_K.py │ │ ├── go_funcs_L.py │ │ ├── go_funcs_M.py │ │ ├── go_funcs_N.py │ │ ├── go_funcs_O.py │ │ ├── go_funcs_P.py │ │ ├── go_funcs_Q.py │ │ ├── go_funcs_R.py │ │ ├── go_funcs_S.py │ │ ├── go_funcs_T.py │ │ ├── go_funcs_U.py │ │ ├── go_funcs_V.py │ │ ├── go_funcs_W.py │ │ ├── go_funcs_X.py │ │ ├── go_funcs_Y.py │ │ ├── go_funcs_Z.py │ │ └── go_funcs_univariate.py │ ├── integrate.py │ ├── interpolate.py │ ├── io_matlab.py │ ├── linalg.py │ ├── linalg_solve_toeplitz.py │ ├── linalg_sqrtm.py │ ├── lsq_problems.py │ ├── optimize.py │ ├── optimize_zeros.py │ ├── signal.py │ ├── signal_filtering.py │ ├── sparse.py │ ├── sparse_csgraph.py │ ├── sparse_linalg_expm.py │ ├── sparse_linalg_lobpcg.py │ ├── sparse_linalg_onenormest.py │ ├── sparse_linalg_solve.py │ ├── spatial.py │ ├── special.py │ ├── stats.py │ ├── test_functions.py │ └── test_go_benchmark_functions.py └── run.py ├── bento.info ├── bscript ├── circle.yml ├── codecov.yml ├── doc ├── API.rst.txt ├── Makefile ├── README.txt ├── ROADMAP.rst.txt ├── postprocess.py ├── release │ ├── 0.10.0-notes.rst │ ├── 0.10.1-notes.rst │ ├── 0.11.0-notes.rst │ ├── 0.12.0-notes.rst │ ├── 0.12.1-notes.rst │ ├── 0.13.0-notes.rst │ ├── 0.13.1-notes.rst │ ├── 0.13.2-notes.rst │ ├── 0.14.0-notes.rst │ ├── 0.14.1-notes.rst │ ├── 0.15.0-notes.rst │ ├── 0.15.1-notes.rst │ ├── 0.16.0-notes.rst │ ├── 0.16.1-notes.rst │ ├── 0.17.0-notes.rst │ ├── 0.17.1-notes.rst │ ├── 0.18.0-notes.rst │ ├── 0.18.1-notes.rst │ ├── 0.19.0-notes.rst │ ├── 0.7.0-notes.rst │ ├── 0.7.1-notes.rst │ ├── 0.7.2-notes.rst │ ├── 0.8.0-notes.rst │ ├── 0.9.0-notes.rst │ └── 1.0.0-notes.rst └── source │ ├── _static │ ├── scipy_fallback.css │ └── scipyshiny_small.png │ ├── _templates │ ├── autosummary │ │ └── class.rst │ ├── indexsidebar.html │ └── layout.html │ ├── api.rst │ ├── ccallback.rst │ ├── cluster.hierarchy.rst │ ├── cluster.rst │ ├── cluster.vq.rst │ ├── conf.py │ ├── constants.rst │ ├── dev │ ├── decisions.rst │ ├── deprecations.rst │ ├── distributing.rst │ ├── github.rst │ ├── index.rst │ ├── licensing.rst │ ├── newfeatures.rst │ ├── releasing.rst │ └── versioning.rst │ ├── doi_role.py │ ├── fftpack.rst │ ├── hacking.rst │ ├── index.rst │ ├── integrate.rst │ ├── interpolate.rst │ ├── io.arff.rst │ ├── io.rst │ ├── linalg.blas.rst │ ├── linalg.cython_blas.rst │ ├── linalg.cython_lapack.rst │ ├── linalg.interpolative.rst │ ├── linalg.lapack.rst │ ├── linalg.rst │ ├── misc.rst │ ├── ndimage.rst │ ├── odr.rst │ ├── optimize.linprog-simplex.rst │ ├── optimize.minimize-bfgs.rst │ ├── optimize.minimize-cg.rst │ ├── optimize.minimize-cobyla.rst │ ├── optimize.minimize-dogleg.rst │ ├── optimize.minimize-lbfgsb.rst │ ├── optimize.minimize-neldermead.rst │ ├── optimize.minimize-newtoncg.rst │ ├── optimize.minimize-powell.rst │ ├── optimize.minimize-slsqp.rst │ ├── optimize.minimize-tnc.rst │ ├── optimize.minimize-trustexact.rst │ ├── optimize.minimize-trustncg.rst │ ├── optimize.minimize_scalar-bounded.rst │ ├── optimize.minimize_scalar-brent.rst │ ├── optimize.minimize_scalar-golden.rst │ ├── optimize.nonlin.rst │ ├── optimize.root-anderson.rst │ ├── optimize.root-broyden1.rst │ ├── optimize.root-broyden2.rst │ ├── optimize.root-dfsane.rst │ ├── optimize.root-diagbroyden.rst │ ├── optimize.root-excitingmixing.rst │ ├── optimize.root-hybr.rst │ ├── optimize.root-krylov.rst │ ├── optimize.root-linearmixing.rst │ ├── optimize.root-lm.rst │ ├── optimize.rst │ ├── release.0.10.0.rst │ ├── release.0.10.1.rst │ ├── release.0.11.0.rst │ ├── release.0.12.0.rst │ ├── release.0.12.1.rst │ ├── release.0.13.0.rst │ ├── release.0.13.1.rst │ ├── release.0.13.2.rst │ ├── release.0.14.0.rst │ ├── release.0.14.1.rst │ ├── release.0.15.0.rst │ ├── release.0.15.1.rst │ ├── release.0.16.0.rst │ ├── release.0.16.1.rst │ ├── release.0.17.0.rst │ ├── release.0.17.1.rst │ ├── release.0.18.0.rst │ ├── release.0.18.1.rst │ ├── release.0.19.0.rst │ ├── release.0.7.0.rst │ ├── release.0.7.1.rst │ ├── release.0.7.2.rst │ ├── release.0.8.0.rst │ ├── release.0.9.0.rst │ ├── release.1.0.0.rst │ ├── release.rst │ ├── roadmap.rst │ ├── scipyoptdoc.py │ ├── signal.rst │ ├── sparse.csgraph.rst │ ├── sparse.linalg.rst │ ├── sparse.rst │ ├── spatial.distance.rst │ ├── spatial.rst │ ├── special.cython_special.rst │ ├── special.rst │ ├── stats.mstats.rst │ ├── stats.rst │ └── tutorial │ ├── arpack.rst │ ├── basic.rst │ ├── csgraph.rst │ ├── examples │ ├── 1-1 │ ├── 4-1 │ ├── 5-1 │ ├── newton_krylov_preconditioning.py │ ├── normdiscr_plot1.py │ └── normdiscr_plot2.py │ ├── fftpack.rst │ ├── general.rst │ ├── index.rst │ ├── integrate.rst │ ├── interpolate.rst │ ├── io.rst │ ├── linalg.rst │ ├── ndimage.rst │ ├── octave_a.mat │ ├── octave_cells.mat │ ├── octave_struct.mat │ ├── optimize.rst │ ├── signal.rst │ ├── spatial.rst │ ├── special.rst │ ├── stats.rst │ └── stats │ ├── continuous.rst │ ├── continuous_alpha.rst │ ├── continuous_anglit.rst │ ├── continuous_arcsine.rst │ ├── continuous_beta.rst │ ├── continuous_betaprime.rst │ ├── continuous_bradford.rst │ ├── continuous_burr.rst │ ├── continuous_cauchy.rst │ ├── continuous_chi.rst │ ├── continuous_chi2.rst │ ├── continuous_cosine.rst │ ├── continuous_dgamma.rst │ ├── continuous_dweibull.rst │ ├── continuous_erlang.rst │ ├── continuous_expon.rst │ ├── continuous_exponpow.rst │ ├── continuous_exponweib.rst │ ├── continuous_f.rst │ ├── continuous_fatiguelife.rst │ ├── continuous_fisk.rst │ ├── continuous_foldcauchy.rst │ ├── continuous_foldnorm.rst │ ├── continuous_frechet_l.rst │ ├── continuous_frechet_r.rst │ ├── continuous_gamma.rst │ ├── continuous_gausshyper.rst │ ├── continuous_genexpon.rst │ ├── continuous_genextreme.rst │ ├── continuous_gengamma.rst │ ├── continuous_genhalflogistic.rst │ ├── continuous_genlogistic.rst │ ├── continuous_gennorm.rst │ ├── continuous_genpareto.rst │ ├── continuous_gilbrat.rst │ ├── continuous_gompertz.rst │ ├── continuous_gumbel_l.rst │ ├── continuous_gumbel_r.rst │ ├── continuous_halfcauchy.rst │ ├── continuous_halflogistic.rst │ ├── continuous_halfnorm.rst │ ├── continuous_hypsecant.rst │ ├── continuous_invgamma.rst │ ├── continuous_invgauss.rst │ ├── continuous_invweibull.rst │ ├── continuous_johnsonsb.rst │ ├── continuous_johnsonsu.rst │ ├── continuous_ksone.rst │ ├── continuous_kstwobign.rst │ ├── continuous_laplace.rst │ ├── continuous_levy.rst │ ├── continuous_levy_l.rst │ ├── continuous_loggamma.rst │ ├── continuous_logistic.rst │ ├── continuous_loglaplace.rst │ ├── continuous_lognorm.rst │ ├── continuous_lomax.rst │ ├── continuous_maxwell.rst │ ├── continuous_mielke.rst │ ├── continuous_nakagami.rst │ ├── continuous_ncf.rst │ ├── continuous_nct.rst │ ├── continuous_ncx2.rst │ ├── continuous_norm.rst │ ├── continuous_pareto.rst │ ├── continuous_powerlaw.rst │ ├── continuous_powerlognorm.rst │ ├── continuous_powernorm.rst │ ├── continuous_rayleigh.rst │ ├── continuous_rdist.rst │ ├── continuous_recipinvgauss.rst │ ├── continuous_reciprocal.rst │ ├── continuous_rice.rst │ ├── continuous_semicircular.rst │ ├── continuous_t.rst │ ├── continuous_trapz.rst │ ├── continuous_triang.rst │ ├── continuous_truncexpon.rst │ ├── continuous_truncnorm.rst │ ├── continuous_tukeylambda.rst │ ├── continuous_uniform.rst │ ├── continuous_vonmises.rst │ ├── continuous_wald.rst │ ├── continuous_wrapcauchy.rst │ ├── discrete.rst │ ├── discrete_bernoulli.rst │ ├── discrete_binom.rst │ ├── discrete_boltzmann.rst │ ├── discrete_dlaplace.rst │ ├── discrete_geom.rst │ ├── discrete_hypergeom.rst │ ├── discrete_logser.rst │ ├── discrete_nbinom.rst │ ├── discrete_planck.rst │ ├── discrete_poisson.rst │ ├── discrete_randint.rst │ ├── discrete_zipf.rst │ └── plots │ ├── kde_plot2.py │ ├── kde_plot3.py │ ├── kde_plot4.py │ └── kde_plot5.py ├── pavement.py ├── runtests.py ├── scipy ├── __init__.py ├── _build_utils │ ├── __init__.py │ ├── _fortran.py │ ├── src │ │ ├── apple_sgemv_fix.c │ │ ├── cblas.h │ │ ├── wrap_accelerate_c.c │ │ ├── wrap_accelerate_f.f │ │ ├── wrap_dummy_accelerate.f │ │ ├── wrap_dummy_g77_abi.f │ │ ├── wrap_g77_abi_c.c │ │ └── wrap_g77_abi_f.f │ └── tests │ │ ├── test_circular_imports.py │ │ └── test_scipy_version.py ├── _lib │ ├── __init__.py │ ├── _ccallback.py │ ├── _ccallback_c.pxd │ ├── _ccallback_c.pyx │ ├── _gcutils.py │ ├── _numpy_compat.py │ ├── _testutils.py │ ├── _threadsafety.py │ ├── _tmpdirs.py │ ├── _util.py │ ├── _version.py │ ├── bento.info │ ├── bscript │ ├── ccallback.pxd │ ├── decorator.py │ ├── setup.py │ ├── six.py │ ├── src │ │ ├── _test_ccallback.c │ │ └── ccallback.h │ └── tests │ │ ├── test__gcutils.py │ │ ├── test__threadsafety.py │ │ ├── test__util.py │ │ ├── test__version.py │ │ ├── test_ccallback.py │ │ └── test_tmpdirs.py ├── bento.info ├── cluster │ ├── __init__.py │ ├── _hierarchy.pyx │ ├── _hierarchy_distance_update.pxi │ ├── _structures.pxi │ ├── _vq.pyx │ ├── bento.info │ ├── bscript │ ├── cluster_blas.h │ ├── cluster_blas.pxd │ ├── hierarchy.py │ ├── setup.py │ ├── tests │ │ ├── hierarchy_test_data.py │ │ ├── test_hierarchy.py │ │ └── test_vq.py │ └── vq.py ├── constants │ ├── __init__.py │ ├── codata.py │ ├── constants.py │ ├── setup.py │ └── tests │ │ ├── test_codata.py │ │ └── test_constants.py ├── fftpack │ ├── MANIFEST.in │ ├── __init__.py │ ├── basic.py │ ├── bento.info │ ├── bscript │ ├── convolve.pyf │ ├── fftpack.pyf │ ├── helper.py │ ├── pseudo_diffs.py │ ├── realtransforms.py │ ├── setup.py │ ├── src │ │ ├── convolve.c │ │ ├── dct.c.src │ │ ├── dfftpack │ │ │ ├── CHANGES │ │ │ ├── README │ │ │ ├── dcosqb.f │ │ │ ├── dcosqf.f │ │ │ ├── dcosqi.f │ │ │ ├── dcost.f │ │ │ ├── dcosti.f │ │ │ ├── dfftb.f │ │ │ ├── dfftb1.f │ │ │ ├── dfftf.f │ │ │ ├── dfftf1.f │ │ │ ├── dffti.f │ │ │ ├── dffti1.f │ │ │ ├── dsinqb.f │ │ │ ├── dsinqf.f │ │ │ ├── dsinqi.f │ │ │ ├── dsint.f │ │ │ ├── dsint1.f │ │ │ ├── dsinti.f │ │ │ ├── zfftb.f │ │ │ ├── zfftb1.f │ │ │ ├── zfftf.f │ │ │ ├── zfftf1.f │ │ │ ├── zffti.f │ │ │ └── zffti1.f │ │ ├── drfft.c │ │ ├── dst.c.src │ │ ├── fftpack.h │ │ ├── fftpack │ │ │ ├── README │ │ │ ├── cfftb.f │ │ │ ├── cfftb1.f │ │ │ ├── cfftf.f │ │ │ ├── cfftf1.f │ │ │ ├── cffti.f │ │ │ ├── cffti1.f │ │ │ ├── cosqb.f │ │ │ ├── cosqf.f │ │ │ ├── cosqi.f │ │ │ ├── cost.f │ │ │ ├── costi.f │ │ │ ├── rfftb.f │ │ │ ├── rfftb1.f │ │ │ ├── rfftf.f │ │ │ ├── rfftf1.f │ │ │ ├── rffti.f │ │ │ ├── rffti1.f │ │ │ ├── sinqb.f │ │ │ ├── sinqf.f │ │ │ ├── sinqi.f │ │ │ ├── sint.f │ │ │ ├── sint1.f │ │ │ └── sinti.f │ │ ├── zfft.c │ │ ├── zfftnd.c │ │ └── zrfft.c │ └── tests │ │ ├── Makefile │ │ ├── fftw_dct.c │ │ ├── fftw_double_ref.npz │ │ ├── fftw_single_ref.npz │ │ ├── gen_fftw_ref.py │ │ ├── gendata.m │ │ ├── gendata.py │ │ ├── test.npz │ │ ├── test_basic.py │ │ ├── test_helper.py │ │ ├── test_import.py │ │ ├── test_pseudo_diffs.py │ │ └── test_real_transforms.py ├── integrate │ ├── __init__.py │ ├── __quadpack.h │ ├── _bvp.py │ ├── _ode.py │ ├── _odepackmodule.c │ ├── _quadpackmodule.c │ ├── bento.info │ ├── bscript │ ├── dop.pyf │ ├── dop │ │ ├── dop853.f │ │ └── dopri5.f │ ├── lsoda.pyf │ ├── mach │ │ ├── d1mach.f │ │ └── xerror.f │ ├── odepack.py │ ├── odepack │ │ ├── blkdta000.f │ │ ├── bnorm.f │ │ ├── cfode.f │ │ ├── ewset.f │ │ ├── fnorm.f │ │ ├── intdy.f │ │ ├── lsoda.f │ │ ├── prja.f │ │ ├── readme │ │ ├── solsy.f │ │ ├── srcma.f │ │ ├── stoda.f │ │ ├── vmnorm.f │ │ ├── vode.f │ │ ├── xerrwv.f │ │ ├── xsetf.f │ │ ├── xsetun.f │ │ └── zvode.f │ ├── quadpack.py │ ├── quadpack │ │ ├── changes │ │ ├── disclaimer │ │ ├── doc │ │ ├── dqag.f │ │ ├── dqage.f │ │ ├── dqagi.f │ │ ├── dqagie.f │ │ ├── dqagp.f │ │ ├── dqagpe.f │ │ ├── dqags.f │ │ ├── dqagse.f │ │ ├── dqawc.f │ │ ├── dqawce.f │ │ ├── dqawf.f │ │ ├── dqawfe.f │ │ ├── dqawo.f │ │ ├── dqawoe.f │ │ ├── dqaws.f │ │ ├── dqawse.f │ │ ├── dqc25c.f │ │ ├── dqc25f.f │ │ ├── dqc25s.f │ │ ├── dqcheb.f │ │ ├── dqelg.f │ │ ├── dqk15.f │ │ ├── dqk15i.f │ │ ├── dqk15w.f │ │ ├── dqk21.f │ │ ├── dqk31.f │ │ ├── dqk41.f │ │ ├── dqk51.f │ │ ├── dqk61.f │ │ ├── dqmomo.f │ │ ├── dqng.f │ │ ├── dqpsrt.f │ │ ├── dqwgtc.f │ │ ├── dqwgtf.f │ │ ├── dqwgts.f │ │ ├── index │ │ ├── permission │ │ └── readme │ ├── quadrature.py │ ├── setup.py │ ├── tests │ │ ├── _test_multivariate.c │ │ ├── banded5x5.f │ │ ├── test_banded_ode_solvers.py │ │ ├── test_bvp.py │ │ ├── test_integrate.py │ │ ├── test_odeint_jac.py │ │ ├── test_quadpack.py │ │ └── test_quadrature.py │ └── vode.pyf ├── interpolate │ ├── README │ ├── __init__.py │ ├── _bspl.pyx │ ├── _bsplines.py │ ├── _cubic.py │ ├── _fitpack_impl.py │ ├── _pade.py │ ├── _ppoly.pyx │ ├── bento.info │ ├── blas_defs.h │ ├── bscript │ ├── fitpack.py │ ├── fitpack │ │ ├── Makefile │ │ ├── README │ │ ├── bispeu.f │ │ ├── bispev.f │ │ ├── clocur.f │ │ ├── cocosp.f │ │ ├── concon.f │ │ ├── concur.f │ │ ├── cualde.f │ │ ├── curev.f │ │ ├── curfit.f │ │ ├── dblint.f │ │ ├── evapol.f │ │ ├── fourco.f │ │ ├── fpader.f │ │ ├── fpadno.f │ │ ├── fpadpo.f │ │ ├── fpback.f │ │ ├── fpbacp.f │ │ ├── fpbfout.f │ │ ├── fpbisp.f │ │ ├── fpbspl.f │ │ ├── fpchec.f │ │ ├── fpched.f │ │ ├── fpchep.f │ │ ├── fpclos.f │ │ ├── fpcoco.f │ │ ├── fpcons.f │ │ ├── fpcosp.f │ │ ├── fpcsin.f │ │ ├── fpcurf.f │ │ ├── fpcuro.f │ │ ├── fpcyt1.f │ │ ├── fpcyt2.f │ │ ├── fpdeno.f │ │ ├── fpdisc.f │ │ ├── fpfrno.f │ │ ├── fpgivs.f │ │ ├── fpgrdi.f │ │ ├── fpgrpa.f │ │ ├── fpgrre.f │ │ ├── fpgrsp.f │ │ ├── fpinst.f │ │ ├── fpintb.f │ │ ├── fpknot.f │ │ ├── fpopdi.f │ │ ├── fpopsp.f │ │ ├── fporde.f │ │ ├── fppara.f │ │ ├── fppasu.f │ │ ├── fpperi.f │ │ ├── fppocu.f │ │ ├── fppogr.f │ │ ├── fppola.f │ │ ├── fprank.f │ │ ├── fprati.f │ │ ├── fpregr.f │ │ ├── fprota.f │ │ ├── fprppo.f │ │ ├── fprpsp.f │ │ ├── fpseno.f │ │ ├── fpspgr.f │ │ ├── fpsphe.f │ │ ├── fpsuev.f │ │ ├── fpsurf.f │ │ ├── fpsysy.f │ │ ├── fptrnp.f │ │ ├── fptrpe.f │ │ ├── insert.f │ │ ├── parcur.f │ │ ├── parder.f │ │ ├── pardeu.f │ │ ├── parsur.f │ │ ├── percur.f │ │ ├── pogrid.f │ │ ├── polar.f │ │ ├── profil.f │ │ ├── regrid.f │ │ ├── spalde.f │ │ ├── spgrid.f │ │ ├── sphere.f │ │ ├── splder.f │ │ ├── splev.f │ │ ├── splint.f │ │ ├── sproot.f │ │ ├── surev.f │ │ └── surfit.f │ ├── fitpack2.py │ ├── interpnd.pyx │ ├── interpnd_info.py │ ├── interpolate.py │ ├── interpolate_wrapper.py │ ├── ndgriddata.py │ ├── polyint.py │ ├── rbf.py │ ├── setup.py │ ├── src │ │ ├── __fitpack.h │ │ ├── _fitpackmodule.c │ │ ├── _interpolate.cpp │ │ ├── fitpack.pyf │ │ ├── interpolate.h │ │ └── multipack.h │ └── tests │ │ ├── data │ │ ├── bug-1310.npz │ │ └── estimate_gradients_hang.npy │ │ ├── test_bsplines.py │ │ ├── test_fitpack.py │ │ ├── test_fitpack2.py │ │ ├── test_gil.py │ │ ├── test_interpnd.py │ │ ├── test_interpolate.py │ │ ├── test_interpolate_wrapper.py │ │ ├── test_ndgriddata.py │ │ ├── test_pade.py │ │ ├── test_polyint.py │ │ ├── test_rbf.py │ │ └── test_regression.py ├── io │ ├── __init__.py │ ├── _fortran.py │ ├── arff │ │ ├── __init__.py │ │ ├── arffread.py │ │ ├── setup.py │ │ └── tests │ │ │ ├── data │ │ │ ├── iris.arff │ │ │ ├── missing.arff │ │ │ ├── nodata.arff │ │ │ ├── test1.arff │ │ │ ├── test2.arff │ │ │ ├── test3.arff │ │ │ ├── test4.arff │ │ │ ├── test5.arff │ │ │ ├── test6.arff │ │ │ ├── test7.arff │ │ │ └── test8.arff │ │ │ └── test_arffread.py │ ├── bento.info │ ├── harwell_boeing │ │ ├── __init__.py │ │ ├── _fortran_format_parser.py │ │ ├── hb.py │ │ ├── setup.py │ │ └── tests │ │ │ ├── test_fortran_format.py │ │ │ └── test_hb.py │ ├── idl.py │ ├── matlab │ │ ├── __init__.py │ │ ├── bento.info │ │ ├── byteordercodes.py │ │ ├── mio.py │ │ ├── mio4.py │ │ ├── mio5.py │ │ ├── mio5_params.py │ │ ├── mio5_utils.pyx │ │ ├── mio_utils.pxd │ │ ├── mio_utils.pyx │ │ ├── miobase.py │ │ ├── numpy_rephrasing.h │ │ ├── py3k.h │ │ ├── pyalloc.pxd │ │ ├── setup.py │ │ ├── streams.pxd │ │ ├── streams.pyx │ │ └── tests │ │ │ ├── afunc.m │ │ │ ├── data │ │ │ ├── bad_miuint32.mat │ │ │ ├── bad_miutf8_array_name.mat │ │ │ ├── big_endian.mat │ │ │ ├── broken_utf8.mat │ │ │ ├── corrupted_zlib_checksum.mat │ │ │ ├── corrupted_zlib_data.mat │ │ │ ├── japanese_utf8.txt │ │ │ ├── little_endian.mat │ │ │ ├── logical_sparse.mat │ │ │ ├── malformed1.mat │ │ │ ├── miuint32_for_miint32.mat │ │ │ ├── miutf8_array_name.mat │ │ │ ├── nasty_duplicate_fieldnames.mat │ │ │ ├── one_by_zero_char.mat │ │ │ ├── parabola.mat │ │ │ ├── single_empty_string.mat │ │ │ ├── some_functions.mat │ │ │ ├── sqr.mat │ │ │ ├── test3dmatrix_6.1_SOL2.mat │ │ │ ├── test3dmatrix_6.5.1_GLNX86.mat │ │ │ ├── test3dmatrix_7.1_GLNX86.mat │ │ │ ├── test3dmatrix_7.4_GLNX86.mat │ │ │ ├── test_empty_struct.mat │ │ │ ├── test_mat4_le_floats.mat │ │ │ ├── test_skip_variable.mat │ │ │ ├── testbool_8_WIN64.mat │ │ │ ├── testcell_6.1_SOL2.mat │ │ │ ├── testcell_6.5.1_GLNX86.mat │ │ │ ├── testcell_7.1_GLNX86.mat │ │ │ ├── testcell_7.4_GLNX86.mat │ │ │ ├── testcellnest_6.1_SOL2.mat │ │ │ ├── testcellnest_6.5.1_GLNX86.mat │ │ │ ├── testcellnest_7.1_GLNX86.mat │ │ │ ├── testcellnest_7.4_GLNX86.mat │ │ │ ├── testcomplex_4.2c_SOL2.mat │ │ │ ├── testcomplex_6.1_SOL2.mat │ │ │ ├── testcomplex_6.5.1_GLNX86.mat │ │ │ ├── testcomplex_7.1_GLNX86.mat │ │ │ ├── testcomplex_7.4_GLNX86.mat │ │ │ ├── testdouble_4.2c_SOL2.mat │ │ │ ├── testdouble_6.1_SOL2.mat │ │ │ ├── testdouble_6.5.1_GLNX86.mat │ │ │ ├── testdouble_7.1_GLNX86.mat │ │ │ ├── testdouble_7.4_GLNX86.mat │ │ │ ├── testemptycell_5.3_SOL2.mat │ │ │ ├── testemptycell_6.5.1_GLNX86.mat │ │ │ ├── testemptycell_7.1_GLNX86.mat │ │ │ ├── testemptycell_7.4_GLNX86.mat │ │ │ ├── testfunc_7.4_GLNX86.mat │ │ │ ├── testhdf5_7.4_GLNX86.mat │ │ │ ├── testmatrix_4.2c_SOL2.mat │ │ │ ├── testmatrix_6.1_SOL2.mat │ │ │ ├── testmatrix_6.5.1_GLNX86.mat │ │ │ ├── testmatrix_7.1_GLNX86.mat │ │ │ ├── testmatrix_7.4_GLNX86.mat │ │ │ ├── testminus_4.2c_SOL2.mat │ │ │ ├── testminus_6.1_SOL2.mat │ │ │ ├── testminus_6.5.1_GLNX86.mat │ │ │ ├── testminus_7.1_GLNX86.mat │ │ │ ├── testminus_7.4_GLNX86.mat │ │ │ ├── testmulti_4.2c_SOL2.mat │ │ │ ├── testmulti_7.1_GLNX86.mat │ │ │ ├── testmulti_7.4_GLNX86.mat │ │ │ ├── testobject_6.1_SOL2.mat │ │ │ ├── testobject_6.5.1_GLNX86.mat │ │ │ ├── testobject_7.1_GLNX86.mat │ │ │ ├── testobject_7.4_GLNX86.mat │ │ │ ├── testonechar_4.2c_SOL2.mat │ │ │ ├── testonechar_6.1_SOL2.mat │ │ │ ├── testonechar_6.5.1_GLNX86.mat │ │ │ ├── testonechar_7.1_GLNX86.mat │ │ │ ├── testonechar_7.4_GLNX86.mat │ │ │ ├── testscalarcell_7.4_GLNX86.mat │ │ │ ├── testsparse_4.2c_SOL2.mat │ │ │ ├── testsparse_6.1_SOL2.mat │ │ │ ├── testsparse_6.5.1_GLNX86.mat │ │ │ ├── testsparse_7.1_GLNX86.mat │ │ │ ├── testsparse_7.4_GLNX86.mat │ │ │ ├── testsparsecomplex_4.2c_SOL2.mat │ │ │ ├── testsparsecomplex_6.1_SOL2.mat │ │ │ ├── testsparsecomplex_6.5.1_GLNX86.mat │ │ │ ├── testsparsecomplex_7.1_GLNX86.mat │ │ │ ├── testsparsecomplex_7.4_GLNX86.mat │ │ │ ├── testsparsefloat_7.4_GLNX86.mat │ │ │ ├── teststring_4.2c_SOL2.mat │ │ │ ├── teststring_6.1_SOL2.mat │ │ │ ├── teststring_6.5.1_GLNX86.mat │ │ │ ├── teststring_7.1_GLNX86.mat │ │ │ ├── teststring_7.4_GLNX86.mat │ │ │ ├── teststringarray_4.2c_SOL2.mat │ │ │ ├── teststringarray_6.1_SOL2.mat │ │ │ ├── teststringarray_6.5.1_GLNX86.mat │ │ │ ├── teststringarray_7.1_GLNX86.mat │ │ │ ├── teststringarray_7.4_GLNX86.mat │ │ │ ├── teststruct_6.1_SOL2.mat │ │ │ ├── teststruct_6.5.1_GLNX86.mat │ │ │ ├── teststruct_7.1_GLNX86.mat │ │ │ ├── teststruct_7.4_GLNX86.mat │ │ │ ├── teststructarr_6.1_SOL2.mat │ │ │ ├── teststructarr_6.5.1_GLNX86.mat │ │ │ ├── teststructarr_7.1_GLNX86.mat │ │ │ ├── teststructarr_7.4_GLNX86.mat │ │ │ ├── teststructnest_6.1_SOL2.mat │ │ │ ├── teststructnest_6.5.1_GLNX86.mat │ │ │ ├── teststructnest_7.1_GLNX86.mat │ │ │ ├── teststructnest_7.4_GLNX86.mat │ │ │ ├── testunicode_7.1_GLNX86.mat │ │ │ ├── testunicode_7.4_GLNX86.mat │ │ │ └── testvec_4_GLNX86.mat │ │ │ ├── gen_mat4files.m │ │ │ ├── gen_mat5files.m │ │ │ ├── save_matfile.m │ │ │ ├── test_byteordercodes.py │ │ │ ├── test_mio.py │ │ │ ├── test_mio5_utils.py │ │ │ ├── test_mio_funcs.py │ │ │ ├── test_mio_utils.py │ │ │ ├── test_miobase.py │ │ │ ├── test_pathological.py │ │ │ └── test_streams.py │ ├── mmio.py │ ├── netcdf.py │ ├── setup.py │ ├── tests │ │ ├── data │ │ │ ├── array_float32_1d.sav │ │ │ ├── array_float32_2d.sav │ │ │ ├── array_float32_3d.sav │ │ │ ├── array_float32_4d.sav │ │ │ ├── array_float32_5d.sav │ │ │ ├── array_float32_6d.sav │ │ │ ├── array_float32_7d.sav │ │ │ ├── array_float32_8d.sav │ │ │ ├── array_float32_pointer_1d.sav │ │ │ ├── array_float32_pointer_2d.sav │ │ │ ├── array_float32_pointer_3d.sav │ │ │ ├── array_float32_pointer_4d.sav │ │ │ ├── array_float32_pointer_5d.sav │ │ │ ├── array_float32_pointer_6d.sav │ │ │ ├── array_float32_pointer_7d.sav │ │ │ ├── array_float32_pointer_8d.sav │ │ │ ├── example_1.nc │ │ │ ├── example_2.nc │ │ │ ├── example_3_maskedvals.nc │ │ │ ├── fortran-mixed.dat │ │ │ ├── fortran-sf8-10x1x11.dat │ │ │ ├── fortran-sf8-1x1x1.dat │ │ │ ├── fortran-sf8-22x10x15.dat │ │ │ ├── fortran-sf8-5x1x1.dat │ │ │ ├── fortran-sf8-5x3x1.dat │ │ │ ├── fortran-sf8-7x1x1.dat │ │ │ ├── fortran-si4-10x1x11.dat │ │ │ ├── fortran-si4-1x1x1.dat │ │ │ ├── fortran-si4-22x10x15.dat │ │ │ ├── fortran-si4-5x1x1.dat │ │ │ ├── fortran-si4-5x3x1.dat │ │ │ ├── fortran-si4-7x1x1.dat │ │ │ ├── invalid_pointer.sav │ │ │ ├── null_pointer.sav │ │ │ ├── scalar_byte.sav │ │ │ ├── scalar_byte_descr.sav │ │ │ ├── scalar_complex32.sav │ │ │ ├── scalar_complex64.sav │ │ │ ├── scalar_float32.sav │ │ │ ├── scalar_float64.sav │ │ │ ├── scalar_heap_pointer.sav │ │ │ ├── scalar_int16.sav │ │ │ ├── scalar_int32.sav │ │ │ ├── scalar_int64.sav │ │ │ ├── scalar_string.sav │ │ │ ├── scalar_uint16.sav │ │ │ ├── scalar_uint32.sav │ │ │ ├── scalar_uint64.sav │ │ │ ├── struct_arrays.sav │ │ │ ├── struct_arrays_byte_idl80.sav │ │ │ ├── struct_arrays_replicated.sav │ │ │ ├── struct_arrays_replicated_3d.sav │ │ │ ├── struct_inherit.sav │ │ │ ├── struct_pointer_arrays.sav │ │ │ ├── struct_pointer_arrays_replicated.sav │ │ │ ├── struct_pointer_arrays_replicated_3d.sav │ │ │ ├── struct_pointers.sav │ │ │ ├── struct_pointers_replicated.sav │ │ │ ├── struct_pointers_replicated_3d.sav │ │ │ ├── struct_scalars.sav │ │ │ ├── struct_scalars_replicated.sav │ │ │ ├── struct_scalars_replicated_3d.sav │ │ │ ├── test-44100Hz-2ch-32bit-float-be.wav │ │ │ ├── test-44100Hz-2ch-32bit-float-le.wav │ │ │ ├── test-44100Hz-le-1ch-4bytes-early-eof.wav │ │ │ ├── test-44100Hz-le-1ch-4bytes-incomplete-chunk.wav │ │ │ ├── test-44100Hz-le-1ch-4bytes.wav │ │ │ ├── test-48000Hz-2ch-64bit-float-le-wavex.wav │ │ │ ├── test-8000Hz-le-2ch-1byteu.wav │ │ │ └── various_compressed.sav │ │ ├── test_fortran.py │ │ ├── test_idl.py │ │ ├── test_mmio.py │ │ ├── test_netcdf.py │ │ └── test_wavfile.py │ └── wavfile.py ├── linalg.pxd ├── linalg │ ├── __init__.py │ ├── _blas_subroutine_wrappers.f │ ├── _blas_subroutines.h │ ├── _cython_signature_generator.py │ ├── _cython_wrapper_generators.py │ ├── _decomp_polar.py │ ├── _decomp_qz.py │ ├── _decomp_update.pyx.in │ ├── _expm_frechet.py │ ├── _interpolative_backend.py │ ├── _lapack_subroutine_wrappers.f │ ├── _lapack_subroutines.h │ ├── _matfuncs_inv_ssq.py │ ├── _matfuncs_sqrtm.py │ ├── _procrustes.py │ ├── _solve_toeplitz.pyx │ ├── _solvers.py │ ├── _testutils.py │ ├── basic.py │ ├── bento.info │ ├── blas.py │ ├── bscript │ ├── calc_lwork.py │ ├── cblas.pyf.src │ ├── cblas_l1.pyf.src │ ├── clapack.pyf.src │ ├── cython_blas.pxd │ ├── cython_blas.pyx │ ├── cython_blas_signatures.txt │ ├── cython_lapack.pxd │ ├── cython_lapack.pyx │ ├── cython_lapack_signatures.txt │ ├── decomp.py │ ├── decomp_cholesky.py │ ├── decomp_lu.py │ ├── decomp_qr.py │ ├── decomp_schur.py │ ├── decomp_svd.py │ ├── fblas.pyf.src │ ├── fblas_l1.pyf.src │ ├── fblas_l2.pyf.src │ ├── fblas_l3.pyf.src │ ├── flapack.pyf.src │ ├── flapack_user.pyf.src │ ├── flinalg.py │ ├── fortran_defs.h │ ├── interpolative.py │ ├── interpolative.pyf │ ├── lapack.py │ ├── linalg_version.py │ ├── matfuncs.py │ ├── misc.py │ ├── setup.py │ ├── special_matrices.py │ ├── src │ │ ├── calc_lwork.f │ │ ├── det.f │ │ ├── id_dist │ │ │ ├── README.txt │ │ │ ├── doc │ │ │ │ ├── doc.bib │ │ │ │ ├── doc.tex │ │ │ │ └── supertabular.sty │ │ │ └── src │ │ │ │ ├── dfft.f │ │ │ │ ├── id_rand.f │ │ │ │ ├── id_rtrans.f │ │ │ │ ├── idd_frm.f │ │ │ │ ├── idd_house.f │ │ │ │ ├── idd_id.f │ │ │ │ ├── idd_id2svd.f │ │ │ │ ├── idd_qrpiv.f │ │ │ │ ├── idd_sfft.f │ │ │ │ ├── idd_snorm.f │ │ │ │ ├── idd_svd.f │ │ │ │ ├── iddp_aid.f │ │ │ │ ├── iddp_asvd.f │ │ │ │ ├── iddp_rid.f │ │ │ │ ├── iddp_rsvd.f │ │ │ │ ├── iddr_aid.f │ │ │ │ ├── iddr_asvd.f │ │ │ │ ├── iddr_rid.f │ │ │ │ ├── iddr_rsvd.f │ │ │ │ ├── idz_frm.f │ │ │ │ ├── idz_house.f │ │ │ │ ├── idz_id.f │ │ │ │ ├── idz_id2svd.f │ │ │ │ ├── idz_qrpiv.f │ │ │ │ ├── idz_sfft.f │ │ │ │ ├── idz_snorm.f │ │ │ │ ├── idz_svd.f │ │ │ │ ├── idzp_aid.f │ │ │ │ ├── idzp_asvd.f │ │ │ │ ├── idzp_rid.f │ │ │ │ ├── idzp_rsvd.f │ │ │ │ ├── idzr_aid.f │ │ │ │ ├── idzr_asvd.f │ │ │ │ ├── idzr_rid.f │ │ │ │ ├── idzr_rsvd.f │ │ │ │ └── prini.f │ │ ├── lapack_deprecations │ │ │ ├── LICENSE │ │ │ ├── cgegv.f │ │ │ ├── dgegv.f │ │ │ ├── sgegv.f │ │ │ └── zgegv.f │ │ └── lu.f │ └── tests │ │ ├── data │ │ ├── carex_15_data.npz │ │ ├── carex_18_data.npz │ │ ├── carex_19_data.npz │ │ ├── carex_20_data.npz │ │ ├── carex_6_data.npz │ │ └── gendare_20170120_data.npz │ │ ├── test_basic.py │ │ ├── test_blas.py │ │ ├── test_build.py │ │ ├── test_cython_blas.py │ │ ├── test_cython_lapack.py │ │ ├── test_decomp.py │ │ ├── test_decomp_cholesky.py │ │ ├── test_decomp_polar.py │ │ ├── test_decomp_update.py │ │ ├── test_fblas.py │ │ ├── test_interpolative.py │ │ ├── test_lapack.py │ │ ├── test_matfuncs.py │ │ ├── test_procrustes.py │ │ ├── test_solve_toeplitz.py │ │ ├── test_solvers.py │ │ └── test_special_matrices.py ├── misc │ ├── __init__.py │ ├── ascent.dat │ ├── common.py │ ├── doccer.py │ ├── face.dat │ ├── pilutil.py │ ├── setup.py │ └── tests │ │ ├── data │ │ ├── 3x3x3.png │ │ ├── 3x3x4.png │ │ ├── 3x4x3.png │ │ ├── 3x4x4.png │ │ ├── 3x5x3.png │ │ ├── 3x5x4.png │ │ ├── 4x3x3.png │ │ ├── 4x3x4.png │ │ ├── 4x4x3.png │ │ ├── 4x4x4.png │ │ ├── 4x5x3.png │ │ ├── 4x5x4.png │ │ ├── 5x3x3.png │ │ ├── 5x3x4.png │ │ ├── 5x4x3.png │ │ ├── 5x4x4.png │ │ ├── 5x5x3.png │ │ ├── 5x5x4.png │ │ ├── blocks2bit.png │ │ ├── box1.png │ │ ├── foo3x5x4indexed.png │ │ ├── icon.png │ │ ├── icon_mono.png │ │ ├── icon_mono_flat.png │ │ └── pattern4bit.png │ │ ├── test_common.py │ │ ├── test_doccer.py │ │ └── test_pilutil.py ├── ndimage │ ├── LICENSE.txt │ ├── __init__.py │ ├── _ni_support.py │ ├── bento.info │ ├── bscript │ ├── filters.py │ ├── fourier.py │ ├── interpolation.py │ ├── io.py │ ├── measurements.py │ ├── morphology.py │ ├── setup.py │ ├── src │ │ ├── _ctest.c │ │ ├── _cytest.pxd │ │ ├── _cytest.pyx │ │ ├── _ni_label.pyx │ │ ├── nd_image.c │ │ ├── nd_image.h │ │ ├── ni_filters.c │ │ ├── ni_filters.h │ │ ├── ni_fourier.c │ │ ├── ni_fourier.h │ │ ├── ni_interpolation.c │ │ ├── ni_interpolation.h │ │ ├── ni_measure.c │ │ ├── ni_measure.h │ │ ├── ni_morphology.c │ │ ├── ni_morphology.h │ │ ├── ni_support.c │ │ └── ni_support.h │ ├── tests │ │ ├── data │ │ │ ├── README.txt │ │ │ ├── label_inputs.txt │ │ │ ├── label_results.txt │ │ │ └── label_strels.txt │ │ ├── dots.png │ │ ├── test_c_api.py │ │ ├── test_datatypes.py │ │ ├── test_filters.py │ │ ├── test_io.py │ │ ├── test_measurements.py │ │ ├── test_ndimage.py │ │ └── test_regression.py │ └── utils │ │ └── generate_label_testvectors.py ├── odr │ ├── __init__.py │ ├── __odrpack.c │ ├── add_newdocs.py │ ├── bento.info │ ├── bscript │ ├── models.py │ ├── odrpack.h │ ├── odrpack.py │ ├── odrpack │ │ ├── Makefile │ │ ├── d_lpk.f │ │ ├── d_lpkbls.f │ │ ├── d_mprec.f │ │ ├── d_odr.f │ │ ├── d_test.f │ │ └── dlunoc.f │ ├── setup.py │ └── tests │ │ └── test_odr.py ├── optimize │ ├── Zeros │ │ ├── bisect.c │ │ ├── brenth.c │ │ ├── brentq.c │ │ ├── ridder.c │ │ └── zeros.h │ ├── __init__.py │ ├── __minpack.h │ ├── _basinhopping.py │ ├── _differentialevolution.py │ ├── _group_columns.pyx │ ├── _hungarian.py │ ├── _linprog.py │ ├── _lsq │ │ ├── __init__.py │ │ ├── bento.info │ │ ├── bvls.py │ │ ├── common.py │ │ ├── dogbox.py │ │ ├── givens_elimination.pyx │ │ ├── least_squares.py │ │ ├── lsq_linear.py │ │ ├── setup.py │ │ ├── trf.py │ │ └── trf_linear.py │ ├── _minimize.py │ ├── _minpackmodule.c │ ├── _numdiff.py │ ├── _root.py │ ├── _spectral.py │ ├── _trustregion.py │ ├── _trustregion_dogleg.py │ ├── _trustregion_exact.py │ ├── _trustregion_ncg.py │ ├── _tstutils.py │ ├── bento.info │ ├── bscript │ ├── cobyla.py │ ├── cobyla │ │ ├── cobyla.pyf │ │ ├── cobyla2.f │ │ └── trstlp.f │ ├── lbfgsb.py │ ├── lbfgsb │ │ ├── README │ │ ├── lbfgsb.f │ │ ├── lbfgsb.pyf │ │ ├── linpack.f │ │ └── timer.f │ ├── linesearch.py │ ├── minpack.h │ ├── minpack.py │ ├── minpack │ │ ├── chkder.f │ │ ├── dogleg.f │ │ ├── dpmpar.f │ │ ├── enorm.f │ │ ├── fdjac1.f │ │ ├── fdjac2.f │ │ ├── hybrd.f │ │ ├── hybrd1.f │ │ ├── hybrj.f │ │ ├── hybrj1.f │ │ ├── lmder.f │ │ ├── lmder1.f │ │ ├── lmdif.f │ │ ├── lmdif1.f │ │ ├── lmpar.f │ │ ├── lmstr.f │ │ ├── lmstr1.f │ │ ├── minpack.txt │ │ ├── qform.f │ │ ├── qrfac.f │ │ ├── qrsolv.f │ │ ├── r1mpyq.f │ │ ├── r1updt.f │ │ └── rwupdt.f │ ├── minpack2 │ │ ├── dcsrch.f │ │ ├── dcstep.f │ │ └── minpack2.pyf │ ├── nnls.py │ ├── nnls │ │ ├── nnls.f │ │ └── nnls.pyf │ ├── nonlin.py │ ├── optimize.py │ ├── setup.py │ ├── slsqp.py │ ├── slsqp │ │ ├── slsqp.pyf │ │ └── slsqp_optmz.f │ ├── tests │ │ ├── test__basinhopping.py │ │ ├── test__differential_evolution.py │ │ ├── test__numdiff.py │ │ ├── test__root.py │ │ ├── test__spectral.py │ │ ├── test_cobyla.py │ │ ├── test_hungarian.py │ │ ├── test_lbfgsb_hessinv.py │ │ ├── test_least_squares.py │ │ ├── test_linesearch.py │ │ ├── test_linprog.py │ │ ├── test_lsq_common.py │ │ ├── test_lsq_linear.py │ │ ├── test_minpack.py │ │ ├── test_nnls.py │ │ ├── test_nonlin.py │ │ ├── test_optimize.py │ │ ├── test_regression.py │ │ ├── test_slsqp.py │ │ ├── test_tnc.py │ │ ├── test_trustregion.py │ │ ├── test_trustregion_exact.py │ │ └── test_zeros.py │ ├── tnc.py │ ├── tnc │ │ ├── HISTORY │ │ ├── LICENSE │ │ ├── README │ │ ├── example.c │ │ ├── example.py │ │ ├── moduleTNC.c │ │ ├── tnc.c │ │ └── tnc.h │ ├── zeros.c │ └── zeros.py ├── setup.py ├── signal │ ├── C_bspline_util.c │ ├── D_bspline_util.c │ ├── S_bspline_util.c │ ├── Z_bspline_util.c │ ├── __init__.py │ ├── _arraytools.py │ ├── _max_len_seq.py │ ├── _max_len_seq_inner.pyx │ ├── _peak_finding.py │ ├── _savitzky_golay.py │ ├── _spectral.pyx │ ├── _upfirdn.py │ ├── _upfirdn_apply.pyx │ ├── bento.info │ ├── bscript │ ├── bspline_util.c │ ├── bsplines.py │ ├── correlate_nd.c.src │ ├── docs │ │ └── signaltools.README │ ├── filter_design.py │ ├── fir_filter_design.py │ ├── firfilter.c │ ├── lfilter.c.src │ ├── lti_conversion.py │ ├── ltisys.py │ ├── medianfilter.c │ ├── setup.py │ ├── signaltools.py │ ├── sigtools.h │ ├── sigtoolsmodule.c │ ├── spectral.py │ ├── splinemodule.c │ ├── tests │ │ ├── mpsig.py │ │ ├── test_array_tools.py │ │ ├── test_cont2discrete.py │ │ ├── test_dltisys.py │ │ ├── test_filter_design.py │ │ ├── test_fir_filter_design.py │ │ ├── test_ltisys.py │ │ ├── test_max_len_seq.py │ │ ├── test_peak_finding.py │ │ ├── test_savitzky_golay.py │ │ ├── test_signaltools.py │ │ ├── test_spectral.py │ │ ├── test_upfirdn.py │ │ ├── test_waveforms.py │ │ ├── test_wavelets.py │ │ └── test_windows.py │ ├── waveforms.py │ ├── wavelets.py │ └── windows.py ├── sparse │ ├── __init__.py │ ├── _csparsetools.pyx.in │ ├── _matrix_io.py │ ├── base.py │ ├── bento.info │ ├── bscript │ ├── bsr.py │ ├── compressed.py │ ├── construct.py │ ├── coo.py │ ├── csc.py │ ├── csgraph │ │ ├── __init__.py │ │ ├── _components.py │ │ ├── _laplacian.py │ │ ├── _min_spanning_tree.pyx │ │ ├── _reordering.pyx │ │ ├── _shortest_path.pyx │ │ ├── _tools.pyx │ │ ├── _traversal.pyx │ │ ├── _validation.py │ │ ├── bento.info │ │ ├── parameters.pxi │ │ ├── setup.py │ │ └── tests │ │ │ ├── test_connected_components.py │ │ │ ├── test_conversions.py │ │ │ ├── test_graph_components.py │ │ │ ├── test_graph_laplacian.py │ │ │ ├── test_reordering.py │ │ │ ├── test_shortest_path.py │ │ │ ├── test_spanning_tree.py │ │ │ └── test_traversal.py │ ├── csr.py │ ├── data.py │ ├── dia.py │ ├── dok.py │ ├── extract.py │ ├── generate_sparsetools.py │ ├── lil.py │ ├── linalg │ │ ├── __init__.py │ │ ├── _expm_multiply.py │ │ ├── _norm.py │ │ ├── _onenormest.py │ │ ├── bento.info │ │ ├── dsolve │ │ │ ├── SuperLU │ │ │ │ ├── README │ │ │ │ ├── SRC │ │ │ │ │ ├── ccolumn_bmod.c │ │ │ │ │ ├── ccolumn_dfs.c │ │ │ │ │ ├── ccopy_to_ucol.c │ │ │ │ │ ├── cdiagonal.c │ │ │ │ │ ├── cgscon.c │ │ │ │ │ ├── cgsequ.c │ │ │ │ │ ├── cgsisx.c │ │ │ │ │ ├── cgsitrf.c │ │ │ │ │ ├── cgsrfs.c │ │ │ │ │ ├── cgssv.c │ │ │ │ │ ├── cgssvx.c │ │ │ │ │ ├── cgstrf.c │ │ │ │ │ ├── cgstrs.c │ │ │ │ │ ├── clacon2.c │ │ │ │ │ ├── clangs.c │ │ │ │ │ ├── claqgs.c │ │ │ │ │ ├── cldperm.c │ │ │ │ │ ├── cmemory.c │ │ │ │ │ ├── cmyblas2.c │ │ │ │ │ ├── colamd.c │ │ │ │ │ ├── colamd.h │ │ │ │ │ ├── cpanel_bmod.c │ │ │ │ │ ├── cpanel_dfs.c │ │ │ │ │ ├── cpivotL.c │ │ │ │ │ ├── cpivotgrowth.c │ │ │ │ │ ├── cpruneL.c │ │ │ │ │ ├── creadhb.c │ │ │ │ │ ├── creadrb.c │ │ │ │ │ ├── creadtriple.c │ │ │ │ │ ├── csnode_bmod.c │ │ │ │ │ ├── csnode_dfs.c │ │ │ │ │ ├── csp_blas2.c │ │ │ │ │ ├── csp_blas3.c │ │ │ │ │ ├── cutil.c │ │ │ │ │ ├── dcolumn_bmod.c │ │ │ │ │ ├── dcolumn_dfs.c │ │ │ │ │ ├── dcomplex.c │ │ │ │ │ ├── dcopy_to_ucol.c │ │ │ │ │ ├── ddiagonal.c │ │ │ │ │ ├── dgscon.c │ │ │ │ │ ├── dgsequ.c │ │ │ │ │ ├── dgsisx.c │ │ │ │ │ ├── dgsitrf.c │ │ │ │ │ ├── dgsrfs.c │ │ │ │ │ ├── dgssv.c │ │ │ │ │ ├── dgssvx.c │ │ │ │ │ ├── dgstrf.c │ │ │ │ │ ├── dgstrs.c │ │ │ │ │ ├── dlacon2.c │ │ │ │ │ ├── dlangs.c │ │ │ │ │ ├── dlaqgs.c │ │ │ │ │ ├── dldperm.c │ │ │ │ │ ├── dmach.c │ │ │ │ │ ├── dmemory.c │ │ │ │ │ ├── dmyblas2.c │ │ │ │ │ ├── dpanel_bmod.c │ │ │ │ │ ├── dpanel_dfs.c │ │ │ │ │ ├── dpivotL.c │ │ │ │ │ ├── dpivotgrowth.c │ │ │ │ │ ├── dpruneL.c │ │ │ │ │ ├── dreadhb.c │ │ │ │ │ ├── dreadrb.c │ │ │ │ │ ├── dreadtriple.c │ │ │ │ │ ├── dsnode_bmod.c │ │ │ │ │ ├── dsnode_dfs.c │ │ │ │ │ ├── dsp_blas2.c │ │ │ │ │ ├── dsp_blas3.c │ │ │ │ │ ├── dutil.c │ │ │ │ │ ├── dzsum1.c │ │ │ │ │ ├── get_perm_c.c │ │ │ │ │ ├── heap_relax_snode.c │ │ │ │ │ ├── html_mainpage.h │ │ │ │ │ ├── icmax1.c │ │ │ │ │ ├── ilu_ccolumn_dfs.c │ │ │ │ │ ├── ilu_ccopy_to_ucol.c │ │ │ │ │ ├── ilu_cdrop_row.c │ │ │ │ │ ├── ilu_cpanel_dfs.c │ │ │ │ │ ├── ilu_cpivotL.c │ │ │ │ │ ├── ilu_csnode_dfs.c │ │ │ │ │ ├── ilu_dcolumn_dfs.c │ │ │ │ │ ├── ilu_dcopy_to_ucol.c │ │ │ │ │ ├── ilu_ddrop_row.c │ │ │ │ │ ├── ilu_dpanel_dfs.c │ │ │ │ │ ├── ilu_dpivotL.c │ │ │ │ │ ├── ilu_dsnode_dfs.c │ │ │ │ │ ├── ilu_heap_relax_snode.c │ │ │ │ │ ├── ilu_relax_snode.c │ │ │ │ │ ├── ilu_scolumn_dfs.c │ │ │ │ │ ├── ilu_scopy_to_ucol.c │ │ │ │ │ ├── ilu_sdrop_row.c │ │ │ │ │ ├── ilu_spanel_dfs.c │ │ │ │ │ ├── ilu_spivotL.c │ │ │ │ │ ├── ilu_ssnode_dfs.c │ │ │ │ │ ├── ilu_zcolumn_dfs.c │ │ │ │ │ ├── ilu_zcopy_to_ucol.c │ │ │ │ │ ├── ilu_zdrop_row.c │ │ │ │ │ ├── ilu_zpanel_dfs.c │ │ │ │ │ ├── ilu_zpivotL.c │ │ │ │ │ ├── ilu_zsnode_dfs.c │ │ │ │ │ ├── izmax1.c │ │ │ │ │ ├── mark_relax.c │ │ │ │ │ ├── memory.c │ │ │ │ │ ├── mmd.c │ │ │ │ │ ├── qselect.c │ │ │ │ │ ├── relax_snode.c │ │ │ │ │ ├── scipy_slu_config.h │ │ │ │ │ ├── scolumn_bmod.c │ │ │ │ │ ├── scolumn_dfs.c │ │ │ │ │ ├── scomplex.c │ │ │ │ │ ├── scopy_to_ucol.c │ │ │ │ │ ├── scsum1.c │ │ │ │ │ ├── sdiagonal.c │ │ │ │ │ ├── sgscon.c │ │ │ │ │ ├── sgsequ.c │ │ │ │ │ ├── sgsisx.c │ │ │ │ │ ├── sgsitrf.c │ │ │ │ │ ├── sgsrfs.c │ │ │ │ │ ├── sgssv.c │ │ │ │ │ ├── sgssvx.c │ │ │ │ │ ├── sgstrf.c │ │ │ │ │ ├── sgstrs.c │ │ │ │ │ ├── slacon2.c │ │ │ │ │ ├── slangs.c │ │ │ │ │ ├── slaqgs.c │ │ │ │ │ ├── sldperm.c │ │ │ │ │ ├── slu_Cnames.h │ │ │ │ │ ├── slu_cdefs.h │ │ │ │ │ ├── slu_dcomplex.h │ │ │ │ │ ├── slu_ddefs.h │ │ │ │ │ ├── slu_scomplex.h │ │ │ │ │ ├── slu_sdefs.h │ │ │ │ │ ├── slu_util.h │ │ │ │ │ ├── slu_zdefs.h │ │ │ │ │ ├── smach.c │ │ │ │ │ ├── smemory.c │ │ │ │ │ ├── smyblas2.c │ │ │ │ │ ├── sp_coletree.c │ │ │ │ │ ├── sp_ienv.c │ │ │ │ │ ├── sp_preorder.c │ │ │ │ │ ├── spanel_bmod.c │ │ │ │ │ ├── spanel_dfs.c │ │ │ │ │ ├── spivotL.c │ │ │ │ │ ├── spivotgrowth.c │ │ │ │ │ ├── spruneL.c │ │ │ │ │ ├── sreadhb.c │ │ │ │ │ ├── sreadrb.c │ │ │ │ │ ├── sreadtriple.c │ │ │ │ │ ├── ssnode_bmod.c │ │ │ │ │ ├── ssnode_dfs.c │ │ │ │ │ ├── ssp_blas2.c │ │ │ │ │ ├── ssp_blas3.c │ │ │ │ │ ├── superlu_enum_consts.h │ │ │ │ │ ├── superlu_timer.c │ │ │ │ │ ├── supermatrix.h │ │ │ │ │ ├── sutil.c │ │ │ │ │ ├── util.c │ │ │ │ │ ├── zcolumn_bmod.c │ │ │ │ │ ├── zcolumn_dfs.c │ │ │ │ │ ├── zcopy_to_ucol.c │ │ │ │ │ ├── zdiagonal.c │ │ │ │ │ ├── zgscon.c │ │ │ │ │ ├── zgsequ.c │ │ │ │ │ ├── zgsisx.c │ │ │ │ │ ├── zgsitrf.c │ │ │ │ │ ├── zgsrfs.c │ │ │ │ │ ├── zgssv.c │ │ │ │ │ ├── zgssvx.c │ │ │ │ │ ├── zgstrf.c │ │ │ │ │ ├── zgstrs.c │ │ │ │ │ ├── zlacon2.c │ │ │ │ │ ├── zlangs.c │ │ │ │ │ ├── zlaqgs.c │ │ │ │ │ ├── zldperm.c │ │ │ │ │ ├── zmemory.c │ │ │ │ │ ├── zmyblas2.c │ │ │ │ │ ├── zpanel_bmod.c │ │ │ │ │ ├── zpanel_dfs.c │ │ │ │ │ ├── zpivotL.c │ │ │ │ │ ├── zpivotgrowth.c │ │ │ │ │ ├── zpruneL.c │ │ │ │ │ ├── zreadhb.c │ │ │ │ │ ├── zreadrb.c │ │ │ │ │ ├── zreadtriple.c │ │ │ │ │ ├── zsnode_bmod.c │ │ │ │ │ ├── zsnode_dfs.c │ │ │ │ │ ├── zsp_blas2.c │ │ │ │ │ ├── zsp_blas3.c │ │ │ │ │ └── zutil.c │ │ │ │ └── scipychanges.patch │ │ │ ├── __init__.py │ │ │ ├── _add_newdocs.py │ │ │ ├── _superlu_utils.c │ │ │ ├── _superlumodule.c │ │ │ ├── _superluobject.c │ │ │ ├── _superluobject.h │ │ │ ├── bento.info │ │ │ ├── bscript │ │ │ ├── linsolve.py │ │ │ ├── setup.py │ │ │ └── tests │ │ │ │ └── test_linsolve.py │ │ ├── eigen │ │ │ ├── __init__.py │ │ │ ├── arpack │ │ │ │ ├── ARPACK │ │ │ │ │ ├── CHANGES │ │ │ │ │ ├── COPYING │ │ │ │ │ ├── README │ │ │ │ │ ├── README.scipy │ │ │ │ │ ├── SRC │ │ │ │ │ │ ├── cgetv0.f │ │ │ │ │ │ ├── cnaitr.f │ │ │ │ │ │ ├── cnapps.f │ │ │ │ │ │ ├── cnaup2.f │ │ │ │ │ │ ├── cnaupd.f │ │ │ │ │ │ ├── cneigh.f │ │ │ │ │ │ ├── cneupd.f │ │ │ │ │ │ ├── cngets.f │ │ │ │ │ │ ├── csortc.f │ │ │ │ │ │ ├── cstatn.f │ │ │ │ │ │ ├── debug.h │ │ │ │ │ │ ├── dgetv0.f │ │ │ │ │ │ ├── dnaitr.f │ │ │ │ │ │ ├── dnapps.f │ │ │ │ │ │ ├── dnaup2.f │ │ │ │ │ │ ├── dnaupd.f │ │ │ │ │ │ ├── dnconv.f │ │ │ │ │ │ ├── dneigh.f │ │ │ │ │ │ ├── dneupd.f │ │ │ │ │ │ ├── dngets.f │ │ │ │ │ │ ├── dsaitr.f │ │ │ │ │ │ ├── dsapps.f │ │ │ │ │ │ ├── dsaup2.f │ │ │ │ │ │ ├── dsaupd.f │ │ │ │ │ │ ├── dsconv.f │ │ │ │ │ │ ├── dseigt.f │ │ │ │ │ │ ├── dsesrt.f │ │ │ │ │ │ ├── dseupd.f │ │ │ │ │ │ ├── dsgets.f │ │ │ │ │ │ ├── dsortc.f │ │ │ │ │ │ ├── dsortr.f │ │ │ │ │ │ ├── dstatn.f │ │ │ │ │ │ ├── dstats.f │ │ │ │ │ │ ├── dstqrb.f │ │ │ │ │ │ ├── sgetv0.f │ │ │ │ │ │ ├── snaitr.f │ │ │ │ │ │ ├── snapps.f │ │ │ │ │ │ ├── snaup2.f │ │ │ │ │ │ ├── snaupd.f │ │ │ │ │ │ ├── snconv.f │ │ │ │ │ │ ├── sneigh.f │ │ │ │ │ │ ├── sneupd.f │ │ │ │ │ │ ├── sngets.f │ │ │ │ │ │ ├── ssaitr.f │ │ │ │ │ │ ├── ssapps.f │ │ │ │ │ │ ├── ssaup2.f │ │ │ │ │ │ ├── ssaupd.f │ │ │ │ │ │ ├── ssconv.f │ │ │ │ │ │ ├── sseigt.f │ │ │ │ │ │ ├── ssesrt.f │ │ │ │ │ │ ├── sseupd.f │ │ │ │ │ │ ├── ssgets.f │ │ │ │ │ │ ├── ssortc.f │ │ │ │ │ │ ├── ssortr.f │ │ │ │ │ │ ├── sstatn.f │ │ │ │ │ │ ├── sstats.f │ │ │ │ │ │ ├── sstqrb.f │ │ │ │ │ │ ├── stat.h │ │ │ │ │ │ ├── version.h │ │ │ │ │ │ ├── zgetv0.f │ │ │ │ │ │ ├── znaitr.f │ │ │ │ │ │ ├── znapps.f │ │ │ │ │ │ ├── znaup2.f │ │ │ │ │ │ ├── znaupd.f │ │ │ │ │ │ ├── zneigh.f │ │ │ │ │ │ ├── zneupd.f │ │ │ │ │ │ ├── zngets.f │ │ │ │ │ │ ├── zsortc.f │ │ │ │ │ │ └── zstatn.f │ │ │ │ │ └── UTIL │ │ │ │ │ │ ├── cmout.f │ │ │ │ │ │ ├── cvout.f │ │ │ │ │ │ ├── dmout.f │ │ │ │ │ │ ├── dvout.f │ │ │ │ │ │ ├── icnteq.f │ │ │ │ │ │ ├── icopy.f │ │ │ │ │ │ ├── iset.f │ │ │ │ │ │ ├── iswap.f │ │ │ │ │ │ ├── ivout.f │ │ │ │ │ │ ├── second_NONE.f │ │ │ │ │ │ ├── smout.f │ │ │ │ │ │ ├── svout.f │ │ │ │ │ │ ├── zmout.f │ │ │ │ │ │ └── zvout.f │ │ │ │ ├── README │ │ │ │ ├── __init__.py │ │ │ │ ├── arpack.py │ │ │ │ ├── arpack.pyf.src │ │ │ │ ├── bento.info │ │ │ │ ├── bscript │ │ │ │ ├── setup.py │ │ │ │ └── tests │ │ │ │ │ └── test_arpack.py │ │ │ ├── bento.info │ │ │ ├── lobpcg │ │ │ │ ├── __init__.py │ │ │ │ ├── lobpcg.py │ │ │ │ ├── setup.py │ │ │ │ └── tests │ │ │ │ │ └── test_lobpcg.py │ │ │ └── setup.py │ │ ├── interface.py │ │ ├── isolve │ │ │ ├── __init__.py │ │ │ ├── bento.info │ │ │ ├── bscript │ │ │ ├── iterative.py │ │ │ ├── iterative │ │ │ │ ├── BiCGREVCOM.f.src │ │ │ │ ├── BiCGSTABREVCOM.f.src │ │ │ │ ├── CGREVCOM.f.src │ │ │ │ ├── CGSREVCOM.f.src │ │ │ │ ├── GMRESREVCOM.f.src │ │ │ │ ├── QMRREVCOM.f.src │ │ │ │ ├── STOPTEST2.f.src │ │ │ │ ├── _iterative.pyf.src │ │ │ │ ├── getbreak.f.src │ │ │ │ └── test.py │ │ │ ├── lgmres.py │ │ │ ├── lsmr.py │ │ │ ├── lsqr.py │ │ │ ├── minres.py │ │ │ ├── setup.py │ │ │ ├── tests │ │ │ │ ├── demo_lgmres.py │ │ │ │ ├── test_iterative.py │ │ │ │ ├── test_lgmres.py │ │ │ │ ├── test_lsmr.py │ │ │ │ ├── test_lsqr.py │ │ │ │ └── test_utils.py │ │ │ └── utils.py │ │ ├── matfuncs.py │ │ ├── setup.py │ │ └── tests │ │ │ ├── test_expm_multiply.py │ │ │ ├── test_interface.py │ │ │ ├── test_matfuncs.py │ │ │ ├── test_norm.py │ │ │ └── test_onenormest.py │ ├── setup.py │ ├── sparsetools.py │ ├── sparsetools │ │ ├── bool_ops.h │ │ ├── bsr.cxx │ │ ├── bsr.h │ │ ├── complex_ops.h │ │ ├── coo.h │ │ ├── csc.cxx │ │ ├── csc.h │ │ ├── csgraph.h │ │ ├── csr.cxx │ │ ├── csr.h │ │ ├── dense.h │ │ ├── dia.h │ │ ├── other.cxx │ │ ├── py3k.h │ │ ├── sparsetools.cxx │ │ ├── sparsetools.h │ │ └── util.h │ ├── spfuncs.py │ ├── sputils.py │ └── tests │ │ ├── test_base.py │ │ ├── test_construct.py │ │ ├── test_csc.py │ │ ├── test_csr.py │ │ ├── test_extract.py │ │ ├── test_matrix_io.py │ │ ├── test_sparsetools.py │ │ ├── test_spfuncs.py │ │ └── test_sputils.py ├── spatial │ ├── __init__.py │ ├── _hausdorff.pyx │ ├── _plotutils.py │ ├── _procrustes.py │ ├── _spherical_voronoi.py │ ├── _voronoi.pyx │ ├── bento.info │ ├── bscript │ ├── ckdtree.pyx │ ├── ckdtree │ │ └── src │ │ │ ├── build.cxx │ │ │ ├── ckdtree_decl.h │ │ │ ├── ckdtree_methods.h │ │ │ ├── coo_entries.h │ │ │ ├── count_neighbors.cxx │ │ │ ├── cpp_exc.cxx │ │ │ ├── cpp_exc.h │ │ │ ├── cpp_utils.h │ │ │ ├── distance.h │ │ │ ├── distance_base.h │ │ │ ├── globals.cxx │ │ │ ├── ordered_pair.h │ │ │ ├── partial_sort.h │ │ │ ├── query.cxx │ │ │ ├── query_ball_point.cxx │ │ │ ├── query_ball_tree.cxx │ │ │ ├── query_pairs.cxx │ │ │ ├── rectangle.h │ │ │ └── sparse_distances.cxx │ ├── distance.py │ ├── kdtree.py │ ├── qhull.pxd │ ├── qhull.pyx │ ├── qhull │ │ ├── Announce.txt │ │ ├── COPYING.txt │ │ ├── README.txt │ │ └── src │ │ │ ├── geom2_r.c │ │ │ ├── geom_r.c │ │ │ ├── geom_r.h │ │ │ ├── global_r.c │ │ │ ├── io_r.c │ │ │ ├── io_r.h │ │ │ ├── libqhull_r.c │ │ │ ├── libqhull_r.h │ │ │ ├── mem_r.c │ │ │ ├── mem_r.h │ │ │ ├── merge_r.c │ │ │ ├── merge_r.h │ │ │ ├── poly2_r.c │ │ │ ├── poly_r.c │ │ │ ├── poly_r.h │ │ │ ├── qhull_ra.h │ │ │ ├── qset_r.c │ │ │ ├── qset_r.h │ │ │ ├── random_r.c │ │ │ ├── random_r.h │ │ │ ├── rboxlib_r.c │ │ │ ├── stat_r.c │ │ │ ├── stat_r.h │ │ │ ├── user_r.c │ │ │ ├── user_r.h │ │ │ ├── usermem_r.c │ │ │ ├── userprintf_r.c │ │ │ └── userprintf_rbox_r.c │ ├── qhull_misc.h │ ├── setlist.pxd │ ├── setup.py │ ├── src │ │ ├── distance_impl.h │ │ └── distance_wrap.c │ └── tests │ │ ├── data │ │ ├── cdist-X1.txt │ │ ├── cdist-X2.txt │ │ ├── degenerate_pointset.npz │ │ ├── iris.txt │ │ ├── pdist-boolean-inp.txt │ │ ├── pdist-chebyshev-ml-iris.txt │ │ ├── pdist-chebyshev-ml.txt │ │ ├── pdist-cityblock-ml-iris.txt │ │ ├── pdist-cityblock-ml.txt │ │ ├── pdist-correlation-ml-iris.txt │ │ ├── pdist-correlation-ml.txt │ │ ├── pdist-cosine-ml-iris.txt │ │ ├── pdist-cosine-ml.txt │ │ ├── pdist-double-inp.txt │ │ ├── pdist-euclidean-ml-iris.txt │ │ ├── pdist-euclidean-ml.txt │ │ ├── pdist-hamming-ml.txt │ │ ├── pdist-jaccard-ml.txt │ │ ├── pdist-minkowski-3.2-ml-iris.txt │ │ ├── pdist-minkowski-3.2-ml.txt │ │ ├── pdist-minkowski-5.8-ml-iris.txt │ │ ├── pdist-seuclidean-ml-iris.txt │ │ ├── pdist-seuclidean-ml.txt │ │ ├── pdist-spearman-ml.txt │ │ ├── random-bool-data.txt │ │ ├── random-double-data.txt │ │ ├── random-int-data.txt │ │ ├── random-uint-data.txt │ │ └── selfdual-4d-polytope.txt │ │ ├── test__plotutils.py │ │ ├── test__procrustes.py │ │ ├── test_distance.py │ │ ├── test_hausdorff.py │ │ ├── test_kdtree.py │ │ ├── test_qhull.py │ │ └── test_spherical_voronoi.py ├── special.pxd ├── special │ ├── Faddeeva.cc │ ├── Faddeeva.hh │ ├── __init__.py │ ├── _boxcox.pxd │ ├── _c99compat.h │ ├── _comb.pyx │ ├── _complexstuff.h │ ├── _complexstuff.pxd │ ├── _convex_analysis.pxd │ ├── _cunity.pxd │ ├── _cython_special.pxi │ ├── _digamma.pxd │ ├── _ellip_harm.pxd │ ├── _ellip_harm.py │ ├── _ellip_harm_2.pxd │ ├── _ellip_harm_2.pyx │ ├── _evalpoly.pxd │ ├── _exprel.pxd │ ├── _faddeeva.cxx │ ├── _faddeeva.h │ ├── _hyp0f1.pxd │ ├── _legacy.pxd │ ├── _loggamma.pxd │ ├── _logit.c.src │ ├── _logit.h │ ├── _logsumexp.py │ ├── _mptestutils.py │ ├── _precompute │ │ ├── __init__.py │ │ ├── expn_asy.py │ │ ├── gammainc_asy.py │ │ ├── gammainc_data.py │ │ ├── loggamma.py │ │ ├── setup.py │ │ └── utils.py │ ├── _round.h │ ├── _sici.pxd │ ├── _spence.pxd │ ├── _spherical_bessel.pxd │ ├── _spherical_bessel.py │ ├── _test_round.pyx │ ├── _testutils.py │ ├── _trig.pxd │ ├── _ufuncs.pyx │ ├── _ufuncs_cxx.pxd │ ├── _ufuncs_cxx.pyx │ ├── _ufuncs_cxx_defs.h │ ├── _ufuncs_defs.h │ ├── _ufuncs_extra_code.pxi │ ├── _ufuncs_extra_code_common.pxi │ ├── _wright.cxx │ ├── _wright.h │ ├── _xlogy.pxd │ ├── add_newdocs.py │ ├── amos │ │ ├── README.md │ │ ├── dgamln.f │ │ ├── zabs.f │ │ ├── zacai.f │ │ ├── zacon.f │ │ ├── zairy.f │ │ ├── zasyi.f │ │ ├── zbesh.f │ │ ├── zbesi.f │ │ ├── zbesj.f │ │ ├── zbesk.f │ │ ├── zbesy.f │ │ ├── zbinu.f │ │ ├── zbiry.f │ │ ├── zbknu.f │ │ ├── zbuni.f │ │ ├── zbunk.f │ │ ├── zdiv.f │ │ ├── zexp.f │ │ ├── zkscl.f │ │ ├── zlog.f │ │ ├── zmlri.f │ │ ├── zmlt.f │ │ ├── zrati.f │ │ ├── zs1s2.f │ │ ├── zseri.f │ │ ├── zshch.f │ │ ├── zsqrt.f │ │ ├── zuchk.f │ │ ├── zunhj.f │ │ ├── zuni1.f │ │ ├── zuni2.f │ │ ├── zunik.f │ │ ├── zunk1.f │ │ ├── zunk2.f │ │ ├── zuoik.f │ │ └── zwrsk.f │ ├── amos_wrappers.c │ ├── amos_wrappers.h │ ├── basic.py │ ├── bento.info │ ├── bscript │ ├── c_misc │ │ ├── besselpoly.c │ │ ├── double2.h │ │ ├── fsolve.c │ │ ├── gammaincinv.c │ │ ├── gammasgn.c │ │ ├── misc.h │ │ ├── poch.c │ │ ├── struve.c │ │ └── struve_convergence.py │ ├── cdf_wrappers.c │ ├── cdf_wrappers.h │ ├── cdflib │ │ ├── algdiv.f │ │ ├── alngam.f │ │ ├── alnrel.f │ │ ├── apser.f │ │ ├── basym.f │ │ ├── bcorr.f │ │ ├── betaln.f │ │ ├── bfrac.f │ │ ├── bgrat.f │ │ ├── bpser.f │ │ ├── bratio.f │ │ ├── brcmp1.f │ │ ├── brcomp.f │ │ ├── bup.f │ │ ├── cdfbet.f │ │ ├── cdfbin.f │ │ ├── cdfchi.f │ │ ├── cdfchn.f │ │ ├── cdff.f │ │ ├── cdffnc.f │ │ ├── cdfgam.f │ │ ├── cdfnbn.f │ │ ├── cdfnor.f │ │ ├── cdfpoi.f │ │ ├── cdft.f │ │ ├── cdftnc.f │ │ ├── cumbet.f │ │ ├── cumbin.f │ │ ├── cumchi.f │ │ ├── cumchn.f │ │ ├── cumf.f │ │ ├── cumfnc.f │ │ ├── cumgam.f │ │ ├── cumnbn.f │ │ ├── cumnor.f │ │ ├── cumpoi.f │ │ ├── cumt.f │ │ ├── cumtnc.f │ │ ├── devlpl.f │ │ ├── dinvnr.f │ │ ├── dinvr.f │ │ ├── dt1.f │ │ ├── dzror.f │ │ ├── erf.f │ │ ├── erfc1.f │ │ ├── esum.f │ │ ├── exparg.f │ │ ├── fpser.f │ │ ├── gam1.f │ │ ├── gaminv.f │ │ ├── gamln.f │ │ ├── gamln1.f │ │ ├── gamma_fort.f │ │ ├── grat1.f │ │ ├── gratio.f │ │ ├── gsumln.f │ │ ├── ipmpar.f │ │ ├── psi_fort.f │ │ ├── rcomp.f │ │ ├── rexp.f │ │ ├── rlog.f │ │ ├── rlog1.f │ │ ├── spmpar.f │ │ └── stvaln.f │ ├── cephes.h │ ├── cephes │ │ ├── airy.c │ │ ├── bdtr.c │ │ ├── beta.c │ │ ├── btdtr.c │ │ ├── cbrt.c │ │ ├── cephes_names.h │ │ ├── chbevl.c │ │ ├── chdtr.c │ │ ├── const.c │ │ ├── dawsn.c │ │ ├── ellie.c │ │ ├── ellik.c │ │ ├── ellpe.c │ │ ├── ellpj.c │ │ ├── ellpk.c │ │ ├── exp10.c │ │ ├── exp2.c │ │ ├── expn.c │ │ ├── expn.h │ │ ├── fdtr.c │ │ ├── fresnl.c │ │ ├── gamma.c │ │ ├── gdtr.c │ │ ├── gels.c │ │ ├── hyp2f1.c │ │ ├── hyperg.c │ │ ├── i0.c │ │ ├── i1.c │ │ ├── igam.c │ │ ├── igam.h │ │ ├── igami.c │ │ ├── incbet.c │ │ ├── incbi.c │ │ ├── j0.c │ │ ├── j1.c │ │ ├── jv.c │ │ ├── k0.c │ │ ├── k1.c │ │ ├── kn.c │ │ ├── kolmogorov.c │ │ ├── lanczos.c │ │ ├── lanczos.h │ │ ├── mconf.h │ │ ├── mtherr.c │ │ ├── nbdtr.c │ │ ├── ndtr.c │ │ ├── ndtri.c │ │ ├── pdtr.c │ │ ├── polevl.h │ │ ├── protos.h │ │ ├── psi.c │ │ ├── rgamma.c │ │ ├── round.c │ │ ├── scipy_iv.c │ │ ├── shichi.c │ │ ├── sici.c │ │ ├── sincos.c │ │ ├── sindg.c │ │ ├── spence.c │ │ ├── stdtr.c │ │ ├── struve.c │ │ ├── tandg.c │ │ ├── tukey.c │ │ ├── unity.c │ │ ├── yn.c │ │ ├── zeta.c │ │ └── zetac.c │ ├── cython_special.pxd │ ├── cython_special.pyx │ ├── generate_ufuncs.py │ ├── lambertw.pxd │ ├── lambertw.py │ ├── lapack_defs.h │ ├── mach │ │ ├── d1mach.f │ │ ├── i1mach.f │ │ └── xerror.f │ ├── orthogonal.py │ ├── orthogonal_eval.pxd │ ├── setup.py │ ├── sf_error.c │ ├── sf_error.h │ ├── sf_error.pxd │ ├── sf_error.py │ ├── specfun.pyf │ ├── specfun │ │ └── specfun.f │ ├── specfun_wrappers.c │ ├── specfun_wrappers.h │ ├── spfun_stats.py │ ├── sph_harm.pxd │ ├── tests │ │ ├── data │ │ │ ├── README │ │ │ ├── boost.npz │ │ │ ├── boost │ │ │ │ ├── acosh_data_ipp │ │ │ │ │ └── acosh_data.txt │ │ │ │ ├── asinh_data_ipp │ │ │ │ │ └── asinh_data.txt │ │ │ │ ├── assoc_legendre_p_ipp │ │ │ │ │ └── assoc_legendre_p.txt │ │ │ │ ├── atanh_data_ipp │ │ │ │ │ └── atanh_data.txt │ │ │ │ ├── bessel_i_data_ipp │ │ │ │ │ └── bessel_i_data.txt │ │ │ │ ├── bessel_i_int_data_ipp │ │ │ │ │ └── bessel_i_int_data.txt │ │ │ │ ├── bessel_j_data_ipp │ │ │ │ │ └── bessel_j_data.txt │ │ │ │ ├── bessel_j_int_data_ipp │ │ │ │ │ └── bessel_j_int_data.txt │ │ │ │ ├── bessel_j_large_data_ipp │ │ │ │ │ └── bessel_j_large_data.txt │ │ │ │ ├── bessel_k_data_ipp │ │ │ │ │ └── bessel_k_data.txt │ │ │ │ ├── bessel_k_int_data_ipp │ │ │ │ │ └── bessel_k_int_data.txt │ │ │ │ ├── bessel_y01_data_ipp │ │ │ │ │ └── bessel_y01_data.txt │ │ │ │ ├── bessel_yn_data_ipp │ │ │ │ │ └── bessel_yn_data.txt │ │ │ │ ├── bessel_yv_data_ipp │ │ │ │ │ └── bessel_yv_data.txt │ │ │ │ ├── beta_exp_data_ipp │ │ │ │ │ └── beta_exp_data.txt │ │ │ │ ├── beta_med_data_ipp │ │ │ │ │ └── beta_med_data.txt │ │ │ │ ├── beta_small_data_ipp │ │ │ │ │ └── beta_small_data.txt │ │ │ │ ├── binomial_data_ipp │ │ │ │ │ └── binomial_data.txt │ │ │ │ ├── binomial_large_data_ipp │ │ │ │ │ └── binomial_large_data.txt │ │ │ │ ├── binomial_quantile_ipp │ │ │ │ │ └── binomial_quantile_data.txt │ │ │ │ ├── cbrt_data_ipp │ │ │ │ │ └── cbrt_data.txt │ │ │ │ ├── digamma_data_ipp │ │ │ │ │ └── digamma_data.txt │ │ │ │ ├── digamma_neg_data_ipp │ │ │ │ │ └── digamma_neg_data.txt │ │ │ │ ├── digamma_root_data_ipp │ │ │ │ │ └── digamma_root_data.txt │ │ │ │ ├── digamma_small_data_ipp │ │ │ │ │ └── digamma_small_data.txt │ │ │ │ ├── ellint_e2_data_ipp │ │ │ │ │ └── ellint_e2_data.txt │ │ │ │ ├── ellint_e_data_ipp │ │ │ │ │ └── ellint_e_data.txt │ │ │ │ ├── ellint_f_data_ipp │ │ │ │ │ └── ellint_f_data.txt │ │ │ │ ├── ellint_k_data_ipp │ │ │ │ │ └── ellint_k_data.txt │ │ │ │ ├── ellint_pi2_data_ipp │ │ │ │ │ └── ellint_pi2_data.txt │ │ │ │ ├── ellint_pi3_data_ipp │ │ │ │ │ └── ellint_pi3_data.txt │ │ │ │ ├── ellint_pi3_large_data_ipp │ │ │ │ │ └── ellint_pi3_large_data.txt │ │ │ │ ├── ellint_rc_data_ipp │ │ │ │ │ └── ellint_rc_data.txt │ │ │ │ ├── ellint_rd_data_ipp │ │ │ │ │ └── ellint_rd_data.txt │ │ │ │ ├── ellint_rf_data_ipp │ │ │ │ │ └── ellint_rf_data.txt │ │ │ │ ├── ellint_rj_data_ipp │ │ │ │ │ └── ellint_rj_data.txt │ │ │ │ ├── erf_data_ipp │ │ │ │ │ └── erf_data.txt │ │ │ │ ├── erf_inv_data_ipp │ │ │ │ │ └── erf_inv_data.txt │ │ │ │ ├── erf_large_data_ipp │ │ │ │ │ └── erf_large_data.txt │ │ │ │ ├── erf_small_data_ipp │ │ │ │ │ └── erf_small_data.txt │ │ │ │ ├── erfc_inv_big_data_ipp │ │ │ │ │ ├── erfc_inv_big_data1.txt │ │ │ │ │ └── erfc_inv_big_data2.txt │ │ │ │ ├── erfc_inv_data_ipp │ │ │ │ │ └── erfc_inv_data.txt │ │ │ │ ├── expint_1_data_ipp │ │ │ │ │ └── expint_1_data.txt │ │ │ │ ├── expint_data_ipp │ │ │ │ │ └── expint_data.txt │ │ │ │ ├── expint_small_data_ipp │ │ │ │ │ └── expint_small_data.txt │ │ │ │ ├── expinti_data_double_ipp │ │ │ │ │ └── expinti_data_double.txt │ │ │ │ ├── expinti_data_ipp │ │ │ │ │ └── expinti_data.txt │ │ │ │ ├── gamma_inv_big_data_ipp │ │ │ │ │ └── gamma_inv_big_data.txt │ │ │ │ ├── gamma_inv_data_ipp │ │ │ │ │ └── gamma_inv_data.txt │ │ │ │ ├── gamma_inv_small_data_ipp │ │ │ │ │ └── gamma_inv_small_data.txt │ │ │ │ ├── hermite_ipp │ │ │ │ │ └── hermite.txt │ │ │ │ ├── ibeta_data_ipp │ │ │ │ │ └── ibeta_data.txt │ │ │ │ ├── ibeta_int_data_ipp │ │ │ │ │ └── ibeta_int_data.txt │ │ │ │ ├── ibeta_inv_data_ipp │ │ │ │ │ └── ibeta_inv_data.txt │ │ │ │ ├── ibeta_inva_data_ipp │ │ │ │ │ └── ibeta_inva_data.txt │ │ │ │ ├── ibeta_large_data_ipp │ │ │ │ │ └── ibeta_large_data.txt │ │ │ │ ├── ibeta_small_data_ipp │ │ │ │ │ └── ibeta_small_data.txt │ │ │ │ ├── igamma_big_data_ipp │ │ │ │ │ └── igamma_big_data.txt │ │ │ │ ├── igamma_int_data_ipp │ │ │ │ │ └── igamma_int_data.txt │ │ │ │ ├── igamma_inva_data_ipp │ │ │ │ │ └── igamma_inva_data.txt │ │ │ │ ├── igamma_med_data_ipp │ │ │ │ │ └── igamma_med_data.txt │ │ │ │ ├── igamma_small_data_ipp │ │ │ │ │ └── igamma_small_data.txt │ │ │ │ ├── laguerre2_ipp │ │ │ │ │ └── laguerre2.txt │ │ │ │ ├── laguerre3_ipp │ │ │ │ │ └── laguerre3.txt │ │ │ │ ├── legendre_p_ipp │ │ │ │ │ └── legendre_p.txt │ │ │ │ ├── legendre_p_large_ipp │ │ │ │ │ └── legendre_p_large.txt │ │ │ │ ├── log1p_expm1_data_ipp │ │ │ │ │ └── log1p_expm1_data.txt │ │ │ │ ├── ncbeta_big_ipp │ │ │ │ │ └── ncbeta_big.txt │ │ │ │ ├── ncbeta_ipp │ │ │ │ │ └── ncbeta.txt │ │ │ │ ├── nccs_big_ipp │ │ │ │ │ └── nccs_big.txt │ │ │ │ ├── nccs_ipp │ │ │ │ │ └── nccs.txt │ │ │ │ ├── negative_binomial_quantile_ipp │ │ │ │ │ └── negative_binomial_quantile_data.txt │ │ │ │ ├── poisson_quantile_ipp │ │ │ │ │ └── poisson_quantile_data.txt │ │ │ │ ├── powm1_sqrtp1m1_test_cpp │ │ │ │ │ ├── powm1_data.txt │ │ │ │ │ └── sqrtp1m1_data.txt │ │ │ │ ├── sph_bessel_data_ipp │ │ │ │ │ └── sph_bessel_data.txt │ │ │ │ ├── sph_neumann_data_ipp │ │ │ │ │ └── sph_neumann_data.txt │ │ │ │ ├── spherical_harmonic_ipp │ │ │ │ │ └── spherical_harmonic.txt │ │ │ │ ├── test_gamma_data_ipp │ │ │ │ │ ├── factorials.txt │ │ │ │ │ ├── gammap1m1_data.txt │ │ │ │ │ ├── near_0.txt │ │ │ │ │ ├── near_1.txt │ │ │ │ │ ├── near_2.txt │ │ │ │ │ ├── near_m10.txt │ │ │ │ │ └── near_m55.txt │ │ │ │ ├── tgamma_delta_ratio_data_ipp │ │ │ │ │ └── tgamma_delta_ratio_data.txt │ │ │ │ ├── tgamma_delta_ratio_int2_ipp │ │ │ │ │ └── tgamma_delta_ratio_int2.txt │ │ │ │ ├── tgamma_delta_ratio_int_ipp │ │ │ │ │ └── tgamma_delta_ratio_int.txt │ │ │ │ ├── tgamma_ratio_data_ipp │ │ │ │ │ └── tgamma_ratio_data.txt │ │ │ │ ├── zeta_1_below_data_ipp │ │ │ │ │ └── zeta_1_below_data.txt │ │ │ │ ├── zeta_1_up_data_ipp │ │ │ │ │ └── zeta_1_up_data.txt │ │ │ │ ├── zeta_data_ipp │ │ │ │ │ └── zeta_data.txt │ │ │ │ └── zeta_neg_data_ipp │ │ │ │ │ └── zeta_neg_data.txt │ │ │ ├── gsl.npz │ │ │ ├── gsl │ │ │ │ ├── mathieu_ab.txt │ │ │ │ ├── mathieu_ce_se.txt │ │ │ │ └── mathieu_mc_ms.txt │ │ │ ├── local.npz │ │ │ └── local │ │ │ │ ├── ellip.txt │ │ │ │ ├── ellipeinc_neg_m.txt │ │ │ │ ├── ellipkinc_neg_m.txt │ │ │ │ ├── ellipkm1.txt │ │ │ │ ├── gammainc.txt │ │ │ │ ├── gammaincc.txt │ │ │ │ └── log1p_expm1_complex.txt │ │ ├── test_basic.py │ │ ├── test_boxcox.py │ │ ├── test_cdflib.py │ │ ├── test_cython_special.py │ │ ├── test_data.py │ │ ├── test_digamma.py │ │ ├── test_ellip_harm.py │ │ ├── test_gammainc.py │ │ ├── test_lambertw.py │ │ ├── test_loggamma.py │ │ ├── test_logit.py │ │ ├── test_logsumexp.py │ │ ├── test_mpmath.py │ │ ├── test_orthogonal.py │ │ ├── test_orthogonal_eval.py │ │ ├── test_pcf.py │ │ ├── test_precompute_expn_asy.py │ │ ├── test_precompute_gammainc.py │ │ ├── test_precompute_utils.py │ │ ├── test_round.py │ │ ├── test_sf_error.py │ │ ├── test_sici.py │ │ ├── test_spence.py │ │ ├── test_spfun_stats.py │ │ ├── test_sph_harm.py │ │ ├── test_spherical_bessel.py │ │ ├── test_trig.py │ │ └── test_wrightomega.py │ ├── utils │ │ ├── README │ │ ├── convert.py │ │ ├── datafunc.py │ │ └── makenpz.py │ ├── wright.cc │ └── wright.hh └── stats │ ├── __init__.py │ ├── _binned_statistic.py │ ├── _constants.py │ ├── _continuous_distns.py │ ├── _discrete_distns.py │ ├── _distn_infrastructure.py │ ├── _distr_params.py │ ├── _multivariate.py │ ├── _stats.pyx │ ├── _stats_mstats_common.py │ ├── _tukeylambda_stats.py │ ├── bento.info │ ├── bscript │ ├── contingency.py │ ├── distributions.py │ ├── kde.py │ ├── morestats.py │ ├── mstats.py │ ├── mstats_basic.py │ ├── mstats_extras.py │ ├── mvn.pyf │ ├── mvndst.f │ ├── setup.py │ ├── statlib.pyf │ ├── statlib │ ├── ansari.f │ ├── spearman.f │ └── swilk.f │ ├── stats.py │ ├── tests │ ├── common_tests.py │ ├── data │ │ ├── nist_anova │ │ │ ├── AtmWtAg.dat │ │ │ ├── SiRstv.dat │ │ │ ├── SmLs01.dat │ │ │ ├── SmLs02.dat │ │ │ ├── SmLs03.dat │ │ │ ├── SmLs04.dat │ │ │ ├── SmLs05.dat │ │ │ ├── SmLs06.dat │ │ │ ├── SmLs07.dat │ │ │ ├── SmLs08.dat │ │ │ └── SmLs09.dat │ │ └── nist_linregress │ │ │ └── Norris.dat │ ├── test_binned_statistic.py │ ├── test_contingency.py │ ├── test_continuous_basic.py │ ├── test_discrete_basic.py │ ├── test_discrete_distns.py │ ├── test_distributions.py │ ├── test_fit.py │ ├── test_kdeoth.py │ ├── test_morestats.py │ ├── test_mstats_basic.py │ ├── test_mstats_extras.py │ ├── test_multivariate.py │ ├── test_rank.py │ ├── test_stats.py │ └── test_tukeylambda_stats.py │ └── vonmises.py ├── setup.py ├── site.cfg.example ├── tools ├── authors.py ├── ci │ ├── README.txt │ ├── devdocs-deploy.key.enc │ └── devdocs-deploy.key.pub ├── cythonize.py ├── gh_lists.py ├── osx │ ├── README.txt │ ├── build.py │ └── install_and_test.py ├── refguide_check.py ├── refguide_summaries.py ├── scipy-macosx-installer │ ├── README.txt │ ├── art │ │ ├── dmgbackground.png │ │ └── dmgbackground.svg │ └── new-create-dmg ├── validate_runtests_log.py └── win32 │ ├── build_scripts │ ├── lib.py │ ├── nsis_scripts │ │ └── scipy-superinstaller.nsi.in │ └── pavement.py │ └── detect_cpu_extensions_wine.py └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | branch = True 3 | include = */scipy/* 4 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "doc/scipy-sphinx-theme"] 2 | path = doc/scipy-sphinx-theme 3 | url = https://github.com/scipy/scipy-sphinx-theme.git 4 | [submodule "doc/sphinxext"] 5 | path = doc/sphinxext 6 | url = https://github.com/numpy/numpydoc.git 7 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include MANIFEST.in 2 | include *.txt 3 | # Top-level build scripts 4 | include setup.py bscript bento.info 5 | # All source files 6 | recursive-include scipy * 7 | # All documentation 8 | recursive-include doc * 9 | # Add build and testing tools 10 | include tox.ini 11 | recursive-include tools * 12 | # Cached Cython signatures 13 | include cythonize.dat 14 | # Exclude what we don't want to include 15 | recursive-exclude scipy/linalg/src/id_dist/src *_subr_*.f 16 | prune benchmarks/env 17 | prune benchmarks/results 18 | prune benchmarks/html 19 | prune benchmarks/scipy 20 | prune scipy/special/tests/data/boost 21 | prune scipy/special/tests/data/gsl 22 | prune doc/build 23 | prune doc/source/generated 24 | prune */__pycache__ 25 | global-exclude *.pyc *~ *.bak *.swp *.pyo 26 | -------------------------------------------------------------------------------- /benchmarks/benchmarks/__init__.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import random 3 | 4 | np.random.seed(1234) 5 | random.seed(1234) 6 | -------------------------------------------------------------------------------- /benchmarks/benchmarks/cluster.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | from .common import Benchmark 4 | 5 | try: 6 | from scipy.cluster.hierarchy import linkage 7 | except ImportError: 8 | pass 9 | 10 | 11 | class HierarchyLinkage(Benchmark): 12 | params = ['single', 'complete', 'average', 'weighted', 'centroid', 13 | 'median', 'ward'] 14 | param_names = ['method'] 15 | 16 | def __init__(self): 17 | rnd = np.random.RandomState(0) 18 | self.X = rnd.randn(2000, 2) 19 | 20 | def time_linkage(self, method): 21 | linkage(self.X, method=method) 22 | -------------------------------------------------------------------------------- /benchmarks/benchmarks/optimize_zeros.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | from math import sqrt 4 | 5 | # Import testing parameters 6 | try: 7 | from scipy.optimize._tstutils import methods, mstrings, functions, fstrings 8 | except ImportError: 9 | pass 10 | 11 | from .common import Benchmark 12 | 13 | 14 | class Zeros(Benchmark): 15 | params = [ 16 | fstrings, 17 | mstrings 18 | ] 19 | param_names = ['test function', 'solver'] 20 | 21 | def setup(self, func, meth): 22 | self.a = .5 23 | self.b = sqrt(3) 24 | 25 | self.func = functions[fstrings.index(func)] 26 | self.meth = methods[mstrings.index(meth)] 27 | 28 | def time_zeros(self, func, meth): 29 | self.meth(self.func, self.a, self.b) 30 | -------------------------------------------------------------------------------- /circle.yml: -------------------------------------------------------------------------------- 1 | dependencies: 2 | override: 3 | - sudo apt-get install libatlas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libfreetype6-dev libpng-dev zlib1g-dev texlive-fonts-recommended 4 | - pip install -q --install-option="--no-cython-compile" Cython==0.23.4 5 | - pip install -q numpy 6 | - pip install -q nose mpmath argparse Pillow codecov matplotlib Sphinx==1.2.3 7 | - git submodule init 8 | - git submodule update 9 | 10 | test: 11 | override: 12 | - python -u runtests.py -g --shell -- -c 'make -C doc html-scipyorg' 13 | 14 | general: 15 | artifacts: 16 | - "doc/build/html-scipyorg" 17 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | coverage: 2 | status: 3 | project: 4 | default: 5 | # Require 1% coverage, i.e., always succeed 6 | target: 1 7 | patch: false 8 | changes: false 9 | comment: off 10 | -------------------------------------------------------------------------------- /doc/README.txt: -------------------------------------------------------------------------------- 1 | SciPy Documentation 2 | =================== 3 | 4 | How to build it 5 | --------------- 6 | The easy way to build the documentation is to run 7 | 8 | python setup.py build_sphinx 9 | 10 | This will first build Scipy in-place, and then generate documentation for it. 11 | 12 | Another way 13 | ----------- 14 | 1. Optionally download an XML dump of the newest docstrings from the doc wiki 15 | at ``/pydocweb/dump`` and save it as ``dump.xml``. 16 | 2. Run ``make html`` or ``make dist`` 17 | 18 | Note that ``make html`` builds the documentation for the currently installed 19 | version of Scipy, not the one corresponding to the source code here. 20 | 21 | -------------------------------------------------------------------------------- /doc/release/0.12.1-notes.rst: -------------------------------------------------------------------------------- 1 | ========================== 2 | SciPy 0.12.1 Release Notes 3 | ========================== 4 | 5 | SciPy 0.12.1 is a bug-fix release with no new features compared to 0.12.0. 6 | The single issue fixed by this release is a security issue in ``scipy.weave``, 7 | which was previously using temporary directories in an insecure manner under 8 | certain circumstances. 9 | -------------------------------------------------------------------------------- /doc/release/0.13.1-notes.rst: -------------------------------------------------------------------------------- 1 | ========================== 2 | SciPy 0.13.1 Release Notes 3 | ========================== 4 | 5 | SciPy 0.13.1 is a bug-fix release with no new features compared to 0.13.0. 6 | The only changes are several fixes in ``ndimage``, one of which was a serious 7 | regression in ``ndimage.label`` (Github issue 3025), which gave 8 | incorrect results in 0.13.0. 9 | 10 | Issues fixed 11 | ------------ 12 | 13 | - 3025: ``ndimage.label`` returns incorrect results in scipy 0.13.0 14 | - 1992: ``ndimage.label`` return type changed from int32 to uint32 15 | - 1992: ``ndimage.find_objects`` doesn't work with int32 input in some cases 16 | -------------------------------------------------------------------------------- /doc/release/0.13.2-notes.rst: -------------------------------------------------------------------------------- 1 | ========================== 2 | SciPy 0.13.2 Release Notes 3 | ========================== 4 | 5 | SciPy 0.13.2 is a bug-fix release with no new features compared to 0.13.1. 6 | 7 | 8 | Issues fixed 9 | ------------ 10 | 11 | - 3096: require Cython 0.19, earlier versions have memory leaks in fused types 12 | - 3079: ``ndimage.label`` fix swapped 64-bitness test 13 | - 3108: ``optimize.fmin_slsqp`` constraint violation 14 | -------------------------------------------------------------------------------- /doc/release/0.15.1-notes.rst: -------------------------------------------------------------------------------- 1 | ========================== 2 | SciPy 0.15.1 Release Notes 3 | ========================== 4 | 5 | SciPy 0.15.1 is a bug-fix release with no new features compared to 0.15.0. 6 | 7 | Issues fixed 8 | ------------ 9 | 10 | * `#4413 `__: BUG: Tests too strict, f2py doesn't have to overwrite this array 11 | * `#4417 `__: BLD: avoid using NPY_API_VERSION to check not using deprecated... 12 | * `#4418 `__: Restore and deprecate scipy.linalg.calc_work 13 | -------------------------------------------------------------------------------- /doc/release/0.7.2-notes.rst: -------------------------------------------------------------------------------- 1 | ========================= 2 | SciPy 0.7.2 Release Notes 3 | ========================= 4 | 5 | .. contents:: 6 | 7 | SciPy 0.7.2 is a bug-fix release with no new features compared to 0.7.1. The 8 | only change is that all C sources from Cython code have been regenerated with 9 | Cython 0.12.1. This fixes the incompatibility between binaries of SciPy 0.7.1 10 | and NumPy 1.4. 11 | -------------------------------------------------------------------------------- /doc/source/_static/scipyshiny_small.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/doc/source/_static/scipyshiny_small.png -------------------------------------------------------------------------------- /doc/source/_templates/indexsidebar.html: -------------------------------------------------------------------------------- 1 |

Resources

2 | 6 | -------------------------------------------------------------------------------- /doc/source/_templates/layout.html: -------------------------------------------------------------------------------- 1 | {% extends "!layout.html" %} 2 | 3 | {% block sidebarsearch %} 4 | {%- if sourcename %} 5 | 12 | {%- endif %} 13 | {{ super() }} 14 | {% endblock %} 15 | -------------------------------------------------------------------------------- /doc/source/api.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../API.rst.txt 2 | -------------------------------------------------------------------------------- /doc/source/cluster.hierarchy.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.cluster.hierarchy 2 | -------------------------------------------------------------------------------- /doc/source/cluster.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.cluster 2 | 3 | .. toctree:: 4 | :hidden: 5 | 6 | cluster.vq 7 | cluster.hierarchy 8 | -------------------------------------------------------------------------------- /doc/source/cluster.vq.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.cluster.vq 2 | -------------------------------------------------------------------------------- /doc/source/constants.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.constants 2 | -------------------------------------------------------------------------------- /doc/source/dev/index.rst: -------------------------------------------------------------------------------- 1 | ********************* 2 | SciPy Developer Guide 3 | ********************* 4 | 5 | .. include:: decisions.rst 6 | 7 | .. include:: newfeatures.rst 8 | 9 | .. include:: github.rst 10 | 11 | .. include:: licensing.rst 12 | 13 | .. include:: versioning.rst 14 | 15 | .. include:: deprecations.rst 16 | 17 | .. include:: distributing.rst 18 | 19 | .. include:: releasing.rst 20 | -------------------------------------------------------------------------------- /doc/source/fftpack.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.fftpack 2 | -------------------------------------------------------------------------------- /doc/source/hacking.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../../HACKING.rst.txt 2 | -------------------------------------------------------------------------------- /doc/source/integrate.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.integrate 2 | -------------------------------------------------------------------------------- /doc/source/interpolate.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.interpolate 2 | -------------------------------------------------------------------------------- /doc/source/io.arff.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.io.arff 2 | -------------------------------------------------------------------------------- /doc/source/io.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.io 2 | 3 | .. toctree:: 4 | :hidden: 5 | 6 | scipy.io.arff 7 | -------------------------------------------------------------------------------- /doc/source/linalg.blas.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg.blas 2 | -------------------------------------------------------------------------------- /doc/source/linalg.cython_blas.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg.cython_blas 2 | -------------------------------------------------------------------------------- /doc/source/linalg.cython_lapack.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg.cython_lapack 2 | -------------------------------------------------------------------------------- /doc/source/linalg.interpolative.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg.interpolative 2 | -------------------------------------------------------------------------------- /doc/source/linalg.lapack.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg.lapack 2 | -------------------------------------------------------------------------------- /doc/source/linalg.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.linalg 2 | 3 | .. toctree:: 4 | :hidden: 5 | 6 | linalg.blas 7 | linalg.lapack 8 | linalg.cython_blas 9 | linalg.cython_lapack 10 | linalg.interpolative 11 | -------------------------------------------------------------------------------- /doc/source/misc.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.misc 2 | -------------------------------------------------------------------------------- /doc/source/ndimage.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.ndimage 2 | -------------------------------------------------------------------------------- /doc/source/odr.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.odr 2 | -------------------------------------------------------------------------------- /doc/source/optimize.linprog-simplex.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.linprog-simplex: 2 | 3 | linprog(method='Simplex') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.linprog 7 | :impl: scipy.optimize._linprog._linprog_simplex 8 | :method: simplex 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-bfgs.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-bfgs: 2 | 3 | minimize(method='BFGS') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.optimize._minimize_bfgs 8 | :method: BFGS 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-cg.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-cg: 2 | 3 | minimize(method='CG') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.optimize._minimize_cg 8 | :method: CG 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-cobyla.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-cobyla: 2 | 3 | minimize(method='COBYLA') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.cobyla._minimize_cobyla 8 | :method: COBYLA 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-dogleg.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-dogleg: 2 | 3 | minimize(method='dogleg') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize._trustregion_dogleg._minimize_dogleg 8 | :method: dogleg 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-lbfgsb.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-lbfgsb: 2 | 3 | minimize(method='L-BFGS-B') 4 | ------------------------------------------ 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.lbfgsb._minimize_lbfgsb 8 | :method: L-BFGS-B 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-neldermead.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-neldermead: 2 | 3 | minimize(method='Nelder-Mead') 4 | --------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.optimize._minimize_neldermead 8 | :method: Nelder-Mead 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-newtoncg.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-newtoncg: 2 | 3 | minimize(method='Newton-CG') 4 | ------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.optimize._minimize_newtoncg 8 | :method: Newton-CG 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-powell.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-powell: 2 | 3 | minimize(method='Powell') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.optimize._minimize_powell 8 | :method: Powell 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-slsqp.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-slsqp: 2 | 3 | minimize(method='SLSQP') 4 | --------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.slsqp._minimize_slsqp 8 | :method: SLSQP 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-tnc.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-tnc: 2 | 3 | minimize(method='TNC') 4 | ---------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize.tnc._minimize_tnc 8 | :method: TNC 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-trustexact.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-trustexact: 2 | 3 | minimize(method='trust-region-exact') 4 | ------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize._trustregion_exact._minimize_trustregion_exact 8 | :method: trust-region-exact 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize-trustncg.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize-trustncg: 2 | 3 | minimize(method='trust-ncg') 4 | ------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize 7 | :impl: scipy.optimize._trustregion_ncg._minimize_trust_ncg 8 | :method: trust-ncg 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize_scalar-bounded.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize_scalar-bounded: 2 | 3 | minimize_scalar(method='bounded') 4 | ------------------------------------------------ 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize_scalar 7 | :impl: scipy.optimize.optimize._minimize_scalar_bounded 8 | :method: bounded 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize_scalar-brent.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize_scalar-brent: 2 | 3 | minimize_scalar(method='brent') 4 | ---------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize_scalar 7 | :impl: scipy.optimize.optimize._minimize_scalar_brent 8 | :method: brent 9 | -------------------------------------------------------------------------------- /doc/source/optimize.minimize_scalar-golden.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.minimize_scalar-golden: 2 | 3 | minimize_scalar(method='golden') 4 | ----------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.minimize_scalar 7 | :impl: scipy.optimize.optimize._minimize_scalar_golden 8 | :method: golden 9 | -------------------------------------------------------------------------------- /doc/source/optimize.nonlin.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.optimize.nonlin 2 | -------------------------------------------------------------------------------- /doc/source/optimize.root-anderson.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-anderson: 2 | 3 | root(method='anderson') 4 | -------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_anderson_doc 8 | :method: anderson 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-broyden1.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-broyden1: 2 | 3 | root(method='broyden1') 4 | -------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_broyden1_doc 8 | :method: broyden1 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-broyden2.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-broyden2: 2 | 3 | root(method='broyden2') 4 | -------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_broyden2_doc 8 | :method: broyden2 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-dfsane.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-dfsane: 2 | 3 | root(method='df-sane') 4 | -------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._spectral._root_df_sane 8 | :method: df-sane 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-diagbroyden.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-diagbroyden: 2 | 3 | root(method='diagbroyden') 4 | -------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_diagbroyden_doc 8 | :method: diagbroyden 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-excitingmixing.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-excitingmixing: 2 | 3 | root(method='excitingmixing') 4 | -------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_excitingmixing_doc 8 | :method: excitingmixing 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-hybr.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-hybr: 2 | 3 | root(method='hybr') 4 | ---------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize.minpack._root_hybr 8 | :method: hybr 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-krylov.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-krylov: 2 | 3 | root(method='krylov') 4 | -------------------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_krylov_doc 8 | :method: krylov 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-linearmixing.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-linearmixing: 2 | 3 | root(method='linearmixing') 4 | ------------------------------------------ 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_linearmixing_doc 8 | :method: linearmixing 9 | -------------------------------------------------------------------------------- /doc/source/optimize.root-lm.rst: -------------------------------------------------------------------------------- 1 | .. _optimize.root-lm: 2 | 3 | root(method='lm') 4 | -------------------------------- 5 | 6 | .. scipy-optimize:function:: scipy.optimize.root 7 | :impl: scipy.optimize._root._root_leastsq 8 | :method: lm 9 | -------------------------------------------------------------------------------- /doc/source/optimize.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.optimize 2 | 3 | .. toctree:: 4 | :hidden: 5 | :maxdepth: 1 6 | 7 | optimize.nonlin 8 | 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-------------------------------------------------------------------------------- /doc/source/release.0.7.1.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../release/0.7.1-notes.rst 2 | -------------------------------------------------------------------------------- /doc/source/release.0.7.2.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../release/0.7.2-notes.rst 2 | -------------------------------------------------------------------------------- /doc/source/release.0.8.0.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../release/0.8.0-notes.rst 2 | -------------------------------------------------------------------------------- /doc/source/release.0.9.0.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../release/0.9.0-notes.rst 2 | -------------------------------------------------------------------------------- /doc/source/release.1.0.0.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../release/1.0.0-notes.rst 2 | -------------------------------------------------------------------------------- /doc/source/release.rst: -------------------------------------------------------------------------------- 1 | ************* 2 | Release Notes 3 | ************* 4 | 5 | .. toctree:: 6 | :maxdepth: 1 7 | 8 | release.1.0.0 9 | release.0.19.0 10 | release.0.18.1 11 | release.0.18.0 12 | release.0.17.1 13 | release.0.17.0 14 | release.0.16.1 15 | release.0.16.0 16 | release.0.15.1 17 | release.0.15.0 18 | release.0.14.1 19 | release.0.14.0 20 | release.0.13.2 21 | release.0.13.1 22 | release.0.13.0 23 | release.0.12.1 24 | release.0.12.0 25 | release.0.11.0 26 | release.0.10.1 27 | release.0.10.0 28 | release.0.9.0 29 | release.0.8.0 30 | release.0.7.2 31 | release.0.7.1 32 | release.0.7.0 33 | -------------------------------------------------------------------------------- /doc/source/roadmap.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../ROADMAP.rst.txt 2 | -------------------------------------------------------------------------------- /doc/source/signal.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.signal 2 | -------------------------------------------------------------------------------- /doc/source/sparse.csgraph.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.sparse.csgraph -------------------------------------------------------------------------------- /doc/source/sparse.linalg.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.sparse.linalg 2 | -------------------------------------------------------------------------------- /doc/source/sparse.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.sparse 2 | -------------------------------------------------------------------------------- /doc/source/spatial.distance.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.spatial.distance 2 | -------------------------------------------------------------------------------- /doc/source/spatial.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.spatial 2 | 3 | .. toctree:: 4 | :hidden: 5 | 6 | spatial.distance 7 | -------------------------------------------------------------------------------- /doc/source/special.cython_special.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.special.cython_special 2 | -------------------------------------------------------------------------------- /doc/source/special.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.special 2 | -------------------------------------------------------------------------------- /doc/source/stats.mstats.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.stats.mstats 2 | -------------------------------------------------------------------------------- /doc/source/stats.rst: -------------------------------------------------------------------------------- 1 | .. automodule:: scipy.stats 2 | 3 | .. toctree:: 4 | :hidden: 5 | 6 | scipy.stats.mstats 7 | -------------------------------------------------------------------------------- /doc/source/tutorial/index.rst: -------------------------------------------------------------------------------- 1 | ************** 2 | SciPy Tutorial 3 | ************** 4 | 5 | .. sectionauthor:: Travis E. Oliphant 6 | 7 | .. toctree:: 8 | :maxdepth: 1 9 | 10 | general 11 | basic 12 | special 13 | integrate 14 | optimize 15 | interpolate 16 | fftpack 17 | signal 18 | linalg 19 | arpack 20 | csgraph 21 | spatial 22 | stats 23 | ndimage 24 | io 25 | -------------------------------------------------------------------------------- /doc/source/tutorial/octave_a.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/doc/source/tutorial/octave_a.mat -------------------------------------------------------------------------------- /doc/source/tutorial/octave_cells.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/doc/source/tutorial/octave_cells.mat -------------------------------------------------------------------------------- /doc/source/tutorial/octave_struct.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/doc/source/tutorial/octave_struct.mat -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_cauchy.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-cauchy: 3 | 4 | Cauchy Distribution 5 | =================== 6 | 7 | .. math:: 8 | :nowrap: 9 | 10 | \begin{eqnarray*} f\left(x\right) & = & \frac{1}{\pi\left(1+x^{2}\right)}\\ F\left(x\right) & = & \frac{1}{2}+\frac{1}{\pi}\tan^{-1}x\\ G\left(\alpha\right) & = & \tan\left(\pi\alpha-\frac{\pi}{2}\right)\\ m_{d} & = & 0\\ m_{n} & = & 0\end{eqnarray*} 11 | 12 | No finite moments. This is the t distribution with one degree of 13 | freedom. 14 | 15 | .. math:: 16 | :nowrap: 17 | 18 | \begin{eqnarray*} h\left[X\right] & = & \log\left(4\pi\right)\\ & \approx & 2.5310242469692907930.\end{eqnarray*} 19 | 20 | Implementation: `scipy.stats.cauchy` 21 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_erlang.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-erlang: 3 | 4 | Erlang Distribution 5 | =================== 6 | 7 | This is just the Gamma distribution with shape parameter :math:`\alpha=n` an integer. 8 | 9 | Implementation: `scipy.stats.erlang` 10 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_exponpow.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-exponpow: 3 | 4 | Exponential Power Distribution 5 | ============================== 6 | 7 | One positive shape parameter :math:`b` . Defined for :math:`x\geq0.` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;b\right) & = & ebx^{b-1}\exp\left[x^{b}-e^{x^{b}}\right]\\ F\left(x;b\right) & = & 1-\exp\left[1-e^{x^{b}}\right]\\ G\left(q;b\right) & = & \log^{1/b}\left[1-\log\left(1-q\right)\right]\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.exponpow` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_exponweib.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-exponweib: 3 | 4 | Exponentiated Weibull Distribution 5 | ================================== 6 | 7 | Two positive shape parameters :math:`a` and :math:`c` and :math:`x\in\left(0,\infty\right)` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;a,c\right) & = & ac\left[1-\exp\left(-x^{c}\right)\right]^{a-1}\exp\left(-x^{c}\right)x^{c-1}\\ F\left(x;a,c\right) & = & \left[1-\exp\left(-x^{c}\right)\right]^{a}\\ G\left(q;a,c\right) & = & \left[-\log\left(1-q^{1/a}\right)\right]^{1/c}\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.exponweib` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_gausshyper.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-gausshyper: 3 | 4 | Gauss Hypergeometric Distribution 5 | ================================= 6 | 7 | :math:`x\in\left[0,1\right]` , :math:`\alpha>0,\,\beta>0` 8 | 9 | .. math:: 10 | 11 | C^{-1}=B\left(\alpha,\beta\right)\,_{2}F_{1}\left(\gamma,\alpha;\alpha+\beta;-z\right) 12 | 13 | .. math:: 14 | :nowrap: 15 | 16 | \begin{eqnarray*} f\left(x;\alpha,\beta,\gamma,z\right) & = & Cx^{\alpha-1}\frac{\left(1-x\right)^{\beta-1}}{\left(1+zx\right)^{\gamma}}\\ \mu_{n}^{\prime} & = & \frac{B\left(n+\alpha,\beta\right)}{B\left(\alpha,\beta\right)}\frac{\,_{2}F_{1}\left(\gamma,\alpha+n;\alpha+\beta+n;-z\right)}{\,_{2}F_{1}\left(\gamma,\alpha;\alpha+\beta;-z\right)}\end{eqnarray*} 17 | 18 | Implementation: `scipy.stats.gausshyper` 19 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_genexpon.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-genexpon: 3 | 4 | Generalized Exponential Distribution 5 | ==================================== 6 | 7 | Three positive shape parameters for :math:`x\geq0.` Note that :math:`a,b,` and :math:`c` are all :math:`>0.` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;a,b,c\right) & = & \left(a+b\left(1-e^{-cx}\right)\right)\exp\left[ax-bx+\frac{b}{c}\left(1-e^{-cx}\right)\right]\\ F\left(x;a,b,c\right) & = & 1-\exp\left[ax-bx+\frac{b}{c}\left(1-e^{-cx}\right)\right]\\ G\left(q;a,b,c\right) & = & F^{-1}\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.genexpon` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_genhalflogistic.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-genhalflogistic: 3 | 4 | Generalized Half-Logistic Distribution 5 | ====================================== 6 | 7 | For :math:`x\in\left[0,1/c\right]` and :math:`c>0` we have 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;c\right) & = & \frac{2\left(1-cx\right)^{\frac{1}{c}-1}}{\left(1+\left(1-cx\right)^{1/c}\right)^{2}}\\ F\left(x;c\right) & = & \frac{1-\left(1-cx\right)^{1/c}}{1+\left(1-cx\right)^{1/c}}\\ G\left(q;c\right) & = & \frac{1}{c}\left[1-\left(\frac{1-q}{1+q}\right)^{c}\right]\end{eqnarray*} 13 | 14 | .. math:: 15 | :nowrap: 16 | 17 | \begin{eqnarray*} h\left[X\right] & = & 2-\left(2c+1\right)\log2.\end{eqnarray*} 18 | 19 | Implementation: `scipy.stats.genhalflogistic` 20 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_gumbel_l.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-gumbel_l: 3 | 4 | Gumbel Left-skewed (for minimum order statistic) Distribution 5 | ============================================================= 6 | 7 | .. math:: 8 | :nowrap: 9 | 10 | \begin{eqnarray*} f\left(x\right) & = & \exp\left(x-e^{x}\right)\\ F\left(x\right) & = & 1-\exp\left(-e^{x}\right)\\ G\left(q\right) & = & \log\left(-\log\left(1-q\right)\right)\end{eqnarray*} 11 | 12 | .. math:: 13 | 14 | M\left(t\right)=\Gamma\left(1+t\right) 15 | 16 | Note, that :math:`\mu` is negative the mean for the right-skewed distribution. Similar for 17 | median and mode. All other moments are the same. 18 | 19 | .. math:: 20 | 21 | h\left[X\right]\approx1.0608407169541684911. 22 | 23 | Implementation: `scipy.stats.gumbel_l` 24 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_invweibull.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-invweibull: 3 | 4 | Inverted Weibull Distribution 5 | ============================= 6 | 7 | Shape parameter :math:`c>0` and :math:`x>0` . Then 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;c\right) & = & cx^{-c-1}\exp\left(-x^{-c}\right)\\ F\left(x;c\right) & = & \exp\left(-x^{-c}\right)\\ G\left(q;c\right) & = & \left(-\log q\right)^{-1/c}\end{eqnarray*} 13 | 14 | .. math:: 15 | 16 | h\left[X\right]=1+\gamma+\frac{\gamma}{c}-\log\left(c\right) 17 | 18 | where :math:`\gamma` is Euler's constant. 19 | 20 | Implementation: `scipy.stats.invweibull` 21 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_johnsonsb.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-johnsonsb: 3 | 4 | Johnson SB Distribution 5 | ======================= 6 | 7 | Defined for :math:`x\in\left(0,1\right)` with two shape parameters :math:`a` and :math:`b>0.` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;a,b\right) & = & \frac{b}{x\left(1-x\right)}\phi\left(a+b\log\frac{x}{1-x}\right)\\ F\left(x;a,b\right) & = & \Phi\left(a+b\log\frac{x}{1-x}\right)\\ G\left(q;a,b\right) & = & \frac{1}{1+\exp\left[-\frac{1}{b}\left(\Phi^{-1}\left(q\right)-a\right)\right]}\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.johnsonsb` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_johnsonsu.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-johnsonsu: 3 | 4 | Johnson SU Distribution 5 | ======================= 6 | 7 | Defined for all :math:`x` with two shape parameters :math:`a` and :math:`b>0` . 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;a,b\right) & = & \frac{b}{\sqrt{x^{2}+1}}\phi\left(a+b\log\left(x+\sqrt{x^{2}+1}\right)\right)\\ F\left(x;a,b\right) & = & \Phi\left(a+b\log\left(x+\sqrt{x^{2}+1}\right)\right)\\ G\left(q;a,b\right) & = & \sinh\left[\frac{\Phi^{-1}\left(q\right)-a}{b}\right]\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.johnsonsu` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_ksone.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-ksone: 3 | 4 | KSone Distribution 5 | ================== 6 | 7 | Implementation: `scipy.stats.ksone` 8 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_kstwobign.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-kstwobign: 3 | 4 | KStwo Distribution 5 | ================== 6 | 7 | Implementation: `scipy.stats.kstwobign` 8 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_levy.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-levy: 3 | 4 | Lévy Distribution 5 | ================== 6 | 7 | A special case of Lévy-stable distributions with :math:`\alpha=\frac{1}{2}` and :math:`\beta=1` . In standard form it is defined for :math:`x>0` as 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x\right) & = & \frac{1}{x\sqrt{2\pi x}}\exp\left(-\frac{1}{2x}\right)\\ F\left(x\right) & = & 2\left[1-\Phi\left(\frac{1}{\sqrt{x}}\right)\right]\\ G\left(q\right) & = & \left[\Phi^{-1}\left(1-\frac{q}{2}\right)\right]^{-2}.\end{eqnarray*} 13 | 14 | It has no finite moments. 15 | 16 | Implementation: `scipy.stats.levy` 17 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_levy_l.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-levy_l: 3 | 4 | Left-skewed Lévy Distribution 5 | ============================== 6 | 7 | Special case of Lévy-stable distribution with :math:`\alpha=\frac{1}{2}` and :math:`\beta=-1` the support is :math:`x<0` . In standard form 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x\right) & = & \frac{1}{\left|x\right|\sqrt{2\pi\left|x\right|}}\exp\left(-\frac{1}{2\left|x\right|}\right)\\ F\left(x\right) & = & 2\Phi\left(\frac{1}{\sqrt{\left|x\right|}}\right)-1\\ G\left(q\right) & = & -\left[\Phi^{-1}\left(\frac{q+1}{2}\right)\right]^{-2}.\end{eqnarray*} 13 | 14 | No moments. 15 | 16 | Implementation: `scipy.stats.levy_l` 17 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_lomax.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-lomax: 3 | 4 | Pareto Second Kind (Lomax) Distribution 5 | ======================================= 6 | 7 | :math:`c>0.` This is Pareto of the first kind with :math:`L=-1.0` so :math:`x\geq0` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;c\right) & = & \frac{c}{\left(1+x\right)^{c+1}}\\ F\left(x;c\right) & = & 1-\frac{1}{\left(1+x\right)^{c}}\\ G\left(q;c\right) & = & \left(1-q\right)^{-1/c}-1\end{eqnarray*} 13 | 14 | .. math:: 15 | 16 | h\left[X\right]=\frac{1}{c}+1-\log\left(c\right). 17 | 18 | Implementation: `scipy.stats.lomax` 19 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_mielke.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-mielke: 3 | 4 | Mielke's Beta-Kappa Distribution 5 | ================================ 6 | 7 | A generalized F distribution. Two shape parameters :math:`\kappa` and :math:`\theta` , and :math:`x>0` . The :math:`\beta` in the DATAPLOT reference is a scale parameter. 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;\kappa,\theta\right) & = & \frac{\kappa x^{\kappa-1}}{\left(1+x^{\theta}\right)^{1+\frac{\kappa}{\theta}}}\\ F\left(x;\kappa,\theta\right) & = & \frac{x^{\kappa}}{\left(1+x^{\theta}\right)^{\kappa/\theta}}\\ G\left(q;\kappa,\theta\right) & = & \left(\frac{q^{\theta/\kappa}}{1-q^{\theta/\kappa}}\right)^{1/\theta}\end{eqnarray*} 13 | 14 | Implementation: `scipy.stats.mielke` 15 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_norm.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-norm: 3 | 4 | Normal Distribution 5 | =================== 6 | 7 | .. math:: 8 | :nowrap: 9 | 10 | \begin{eqnarray*} f\left(x\right) & = & \frac{e^{-x^{2}/2}}{\sqrt{2\pi}}\\ F\left(x\right) & = & \Phi\left(x\right)=\frac{1}{2}+\frac{1}{2}\mathrm{erf}\left(\frac{\mathrm{x}}{\sqrt{2}}\right)\\ G\left(q\right) & = & \Phi^{-1}\left(q\right)\end{eqnarray*} 11 | 12 | .. math:: 13 | :nowrap: 14 | 15 | \begin{eqnarray*} m_{d}=m_{n}=\mu & = & 0\\ \mu_{2} & = & 1\\ \gamma_{1} & = & 0\\ \gamma_{2} & = & 0\end{eqnarray*} 16 | 17 | .. math:: 18 | :nowrap: 19 | 20 | \begin{eqnarray*} h\left[X\right] & = & \log\left(\sqrt{2\pi e}\right)\\ & \approx & 1.4189385332046727418\end{eqnarray*} 21 | 22 | Implementation: `scipy.stats.norm` 23 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_rice.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-rice: 3 | 4 | Rice Distribution 5 | ================= 6 | 7 | Defined for :math:`x>0` and :math:`b>0` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x;b\right) & = & x\exp\left(-\frac{x^{2}+b^{2}}{2}\right)I_{0}\left(xb\right)\\ F\left(x;b\right) & = & \int_{0}^{x}\alpha\exp\left(-\frac{\alpha^{2}+b^{2}}{2}\right)I_{0}\left(\alpha b\right)d\alpha\end{eqnarray*} 13 | 14 | .. math:: 15 | 16 | \mu_{n}^{\prime}=\sqrt{2^{n}}\Gamma\left(1+\frac{n}{2}\right)\,_{1}F_{1}\left(-\frac{n}{2};1;-\frac{b^{2}}{2}\right) 17 | 18 | Implementation: `scipy.stats.rice` 19 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_semicircular.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-semicircular: 3 | 4 | Semicircular Distribution 5 | ========================= 6 | 7 | Defined on :math:`x\in\left[-1,1\right]` 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x\right) & = & \frac{2}{\pi}\sqrt{1-x^{2}}\\ F\left(x\right) & = & \frac{1}{2}+\frac{1}{\pi}\left[x\sqrt{1-x^{2}}+\arcsin x\right]\\ G\left(q\right) & = & F^{-1}\left(q\right)\end{eqnarray*} 13 | 14 | .. math:: 15 | :nowrap: 16 | 17 | \begin{eqnarray*} m_{d}=m_{n}=\mu & = & 0\\ \mu_{2} & = & \frac{1}{4}\\ \gamma_{1} & = & 0\\ \gamma_{2} & = & -1\end{eqnarray*} 18 | 19 | .. math:: 20 | 21 | h\left[X\right]=0.64472988584940017414. 22 | 23 | Implementation: `scipy.stats.semicircular` 24 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/continuous_truncexpon.rst: -------------------------------------------------------------------------------- 1 | 2 | .. _continuous-truncexpon: 3 | 4 | Truncated Exponential Distribution 5 | ================================== 6 | 7 | This is an exponential distribution defined only over a certain region :math:`00` . 8 | 9 | .. math:: 10 | :nowrap: 11 | 12 | \begin{eqnarray*} f\left(x\right) & = & \frac{1}{\sqrt{2\pi x^{3}}}\exp\left(-\frac{\left(x-1\right)^{2}}{2x}\right).\\ F\left(x\right) & = & \Phi\left(\frac{x-1}{\sqrt{x}}\right)+\exp\left(2\right)\Phi\left(-\frac{x+1}{\sqrt{x}}\right)\\ G\left(q;\mu\right) & = & F^{-1}\left(q;\mu\right)\end{eqnarray*} 13 | 14 | .. math:: 15 | :nowrap: 16 | 17 | \begin{eqnarray*} \mu & = & 1\\ \mu_{2} & = & 1\\ \gamma_{1} & = & 3\\ \gamma_{2} & = & 15\\ m_{d} & = & \frac{1}{2}\left(\sqrt{13}-3\right)\end{eqnarray*} 18 | 19 | Implementation: `scipy.stats.wald` 20 | -------------------------------------------------------------------------------- /doc/source/tutorial/stats/plots/kde_plot2.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import matplotlib.pyplot as plt 3 | from scipy import stats 4 | 5 | x1 = np.array([-7, -5, 1, 4, 5], dtype=float) 6 | x_eval = np.linspace(-10, 10, num=200) 7 | kde1 = stats.gaussian_kde(x1) 8 | kde2 = stats.gaussian_kde(x1, bw_method='silverman') 9 | 10 | def my_kde_bandwidth(obj, fac=1./5): 11 | """We use Scott's Rule, multiplied by a constant factor.""" 12 | return np.power(obj.n, -1./(obj.d+4)) * fac 13 | 14 | fig = plt.figure() 15 | ax = fig.add_subplot(111) 16 | 17 | ax.plot(x1, np.zeros(x1.shape), 'b+', ms=20) # rug plot 18 | kde3 = stats.gaussian_kde(x1, bw_method=my_kde_bandwidth) 19 | ax.plot(x_eval, kde3(x_eval), 'g-', label="With smaller BW") 20 | 21 | plt.show() 22 | -------------------------------------------------------------------------------- /scipy/_build_utils/__init__.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from ._fortran import * 3 | from scipy._lib._version import NumpyVersion 4 | 5 | 6 | # Don't use deprecated Numpy C API. Define this to a fixed version instead of 7 | # NPY_API_VERSION in order not to break compilation for released Scipy versions 8 | # when Numpy introduces a new deprecation. Use in setup.py:: 9 | # 10 | # config.add_extension('_name', sources=['source_fname'], **numpy_nodepr_api) 11 | # 12 | if NumpyVersion(np.__version__) >= '1.10.0.dev': 13 | numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API", 14 | "NPY_1_9_API_VERSION")]) 15 | else: 16 | numpy_nodepr_api = dict() 17 | 18 | 19 | from numpy.testing import Tester 20 | test = Tester().test 21 | -------------------------------------------------------------------------------- /scipy/_lib/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Module containing private utility functions 3 | =========================================== 4 | 5 | The ``scipy._lib`` namespace is empty (for now). Tests for all 6 | utilities in submodules of ``_lib`` can be run with:: 7 | 8 | from scipy import _lib 9 | _lib.test() 10 | 11 | """ 12 | from __future__ import division, print_function, absolute_import 13 | 14 | from numpy.testing import Tester 15 | test = Tester().test 16 | -------------------------------------------------------------------------------- /scipy/_lib/_ccallback_c.pxd: -------------------------------------------------------------------------------- 1 | # 2 | # Test function exports 3 | # 4 | 5 | cdef double plus1_cython(double a, int *error_flag, void *user_data) nogil except * 6 | cdef double plus1b_cython(double a, double b, int *error_flag, void *user_data) nogil except * 7 | cdef double plus1bc_cython(double a, double b, double c, int *error_flag, void *user_data) nogil except * 8 | 9 | cdef double sine(double a, void *user_data) nogil except * 10 | -------------------------------------------------------------------------------- /scipy/_lib/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | Extension: _ccallback_c 5 | Sources: 6 | _ccallback_c.c 7 | Extension: _test_ccallback 8 | Sources: 9 | src/_test_ccallback.c 10 | -------------------------------------------------------------------------------- /scipy/_lib/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | context.tweak_extension("_ccallback_c", includes='src') 6 | -------------------------------------------------------------------------------- /scipy/bento.info: -------------------------------------------------------------------------------- 1 | Recurse: 2 | _lib, 3 | cluster, 4 | fftpack, 5 | integrate, 6 | interpolate, 7 | io, 8 | linalg, 9 | ndimage, 10 | odr, 11 | optimize, 12 | signal, 13 | sparse, 14 | spatial, 15 | special, 16 | stats 17 | 18 | Library: 19 | Packages: 20 | cluster, 21 | constants, 22 | fftpack, 23 | integrate, 24 | interpolate, 25 | io, 26 | _lib, 27 | linalg, 28 | misc, 29 | ndimage, 30 | odr, 31 | optimize, 32 | signal, 33 | sparse, 34 | spatial, 35 | special, 36 | stats, 37 | ndimage 38 | -------------------------------------------------------------------------------- /scipy/cluster/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | Extension: _hierarchy 5 | Sources: 6 | _hierarchy.c 7 | Extension: _vq 8 | Sources: 9 | _vq.c 10 | -------------------------------------------------------------------------------- /scipy/cluster/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | context.tweak_extension("_vq", 6 | use="LAPACK CLIB") 7 | -------------------------------------------------------------------------------- /scipy/cluster/cluster_blas.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Handle different Fortran conventions. 3 | */ 4 | 5 | #if defined(NO_APPEND_FORTRAN) 6 | #if defined(UPPERCASE_FORTRAN) 7 | #define F_FUNC(f,F) F 8 | #else 9 | #define F_FUNC(f,F) f 10 | #endif 11 | #else 12 | #if defined(UPPERCASE_FORTRAN) 13 | #define F_FUNC(f,F) F##_ 14 | #else 15 | #define F_FUNC(f,F) f##_ 16 | #endif 17 | #endif 18 | 19 | #define f_sgemm F_FUNC(sgemm,SGEMM) 20 | #define f_dgemm F_FUNC(dgemm,DGEMM) 21 | -------------------------------------------------------------------------------- /scipy/cluster/cluster_blas.pxd: -------------------------------------------------------------------------------- 1 | cdef extern from "cluster_blas.h": 2 | 3 | void f_sgemm(char *transA, char *transB, int *m, int *n, int *k, 4 | float *alpha, float *A, int *lda, float *B, int *ldb, 5 | float *beta, float *C, int *ldc) nogil 6 | 7 | void f_dgemm(char *transA, char *transB, int *m, int *n, int *k, 8 | double *alpha, double *A, int *lda, double *B, int *ldb, 9 | double *beta, double *C, int *ldc) nogil 10 | 11 | -------------------------------------------------------------------------------- /scipy/constants/setup.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | 4 | def configuration(parent_package='', top_path=None): 5 | from numpy.distutils.misc_util import Configuration 6 | config = Configuration('constants', parent_package, top_path) 7 | config.add_data_dir('tests') 8 | return config 9 | 10 | 11 | if __name__ == '__main__': 12 | from numpy.distutils.core import setup 13 | setup(**configuration(top_path='').todict()) 14 | -------------------------------------------------------------------------------- /scipy/fftpack/MANIFEST.in: -------------------------------------------------------------------------------- 1 | recursive-include src *.c 2 | recursive-include tests test_*.py 3 | recursive-include dfftpack *.f doc doc.double 4 | include NOTES.txt 5 | include *.pyf 6 | recursive-include djbfft-0.76 * 7 | -------------------------------------------------------------------------------- /scipy/fftpack/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: fftpack 5 | Sources: 6 | src/fftpack/*.f 7 | CompiledLibrary: dfftpack 8 | Sources: 9 | src/dfftpack/*.f 10 | Extension: _fftpack 11 | Sources: 12 | src/zfft.c, 13 | src/drfft.c, 14 | src/zrfft.c, 15 | src/zfftnd.c, 16 | fftpack.pyf, 17 | src/dct.c.src, 18 | src/dst.c.src 19 | Extension: convolve 20 | Sources: 21 | src/convolve.c, 22 | convolve.pyf 23 | -------------------------------------------------------------------------------- /scipy/fftpack/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pbuild(context): 5 | context.tweak_extension("_fftpack", features="c cshlib bento f2py pyext", 6 | includes="src", use="dfftpack fftpack CLIB") 7 | context.tweak_extension("convolve", features="c cshlib bento f2py pyext", 8 | includes="src", use="dfftpack fftpack CLIB") 9 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dcosqi.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DCOSQI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | DATA PIH /1.57079632679489661923D0/ 5 | DT = PIH/FLOAT(N) 6 | FK = 0.0D0 7 | DO 101 K=1,N 8 | FK = FK+1.0D0 9 | WSAVE(K) = COS(FK*DT) 10 | 101 CONTINUE 11 | CALL DFFTI (N,WSAVE(N+1)) 12 | RETURN 13 | END 14 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dcosti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DCOSTI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | DATA PI /3.14159265358979323846D0/ 5 | IF (N .LE. 3) RETURN 6 | NM1 = N-1 7 | NP1 = N+1 8 | NS2 = N/2 9 | DT = PI/FLOAT(NM1) 10 | FK = 0.0D0 11 | DO 101 K=2,NS2 12 | KC = NP1-K 13 | FK = FK+1.0D0 14 | WSAVE(K) = 2.0D0*SIN(FK*DT) 15 | WSAVE(KC) = 2.0D0*COS(FK*DT) 16 | 101 CONTINUE 17 | CALL DFFTI (NM1,WSAVE(N+1)) 18 | RETURN 19 | END 20 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dfftb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DFFTB (N,R,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION R(1) ,WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | CALL DFFTB1 (N,R,WSAVE,WSAVE(N+1),WSAVE(2*N+1)) 6 | RETURN 7 | END 8 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dfftf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DFFTF (N,R,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION R(1) ,WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | CALL DFFTF1 (N,R,WSAVE,WSAVE(N+1),WSAVE(2*N+1)) 6 | RETURN 7 | END 8 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dffti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DFFTI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | CALL DFFTI1 (N,WSAVE(N+1),WSAVE(2*N+1)) 6 | RETURN 7 | END 8 | 9 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dsinqb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DSINQB (N,X,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION X(1) ,WSAVE(1) 4 | IF (N .GT. 1) GO TO 101 5 | X(1) = 4.0D0*X(1) 6 | RETURN 7 | 101 NS2 = N/2 8 | DO 102 K=2,N,2 9 | X(K) = -X(K) 10 | 102 CONTINUE 11 | CALL DCOSQB (N,X,WSAVE) 12 | DO 103 K=1,NS2 13 | KC = N-K 14 | XHOLD = X(K) 15 | X(K) = X(KC+1) 16 | X(KC+1) = XHOLD 17 | 103 CONTINUE 18 | RETURN 19 | END 20 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dsinqf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DSINQF (N,X,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION X(1) ,WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | NS2 = N/2 6 | DO 101 K=1,NS2 7 | KC = N-K 8 | XHOLD = X(K) 9 | X(K) = X(KC+1) 10 | X(KC+1) = XHOLD 11 | 101 CONTINUE 12 | CALL DCOSQF (N,X,WSAVE) 13 | DO 102 K=2,N,2 14 | X(K) = -X(K) 15 | 102 CONTINUE 16 | RETURN 17 | END 18 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dsinqi.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DSINQI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | CALL DCOSQI (N,WSAVE) 5 | RETURN 6 | END 7 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dsint.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DSINT (N,X,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION X(1) ,WSAVE(1) 4 | NP1 = N+1 5 | IW1 = N/2+1 6 | IW2 = IW1+NP1 7 | IW3 = IW2+NP1 8 | CALL DSINT1(N,X,WSAVE,WSAVE(IW1),WSAVE(IW2),WSAVE(IW3)) 9 | RETURN 10 | END 11 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/dsinti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DSINTI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | DATA PI /3.14159265358979323846D0/ 5 | IF (N .LE. 1) RETURN 6 | NS2 = N/2 7 | NP1 = N+1 8 | DT = PI/FLOAT(NP1) 9 | DO 101 K=1,NS2 10 | WSAVE(K) = 2.0D0*SIN(K*DT) 11 | 101 CONTINUE 12 | CALL DFFTI (NP1,WSAVE(NS2+1)) 13 | RETURN 14 | END 15 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/zfftb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZFFTB (N,C,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION C(1) ,WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | IW1 = N+N+1 6 | IW2 = IW1+N+N 7 | CALL ZFFTB1 (N,C,WSAVE,WSAVE(IW1),WSAVE(IW2)) 8 | RETURN 9 | END 10 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/zfftf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZFFTF (N,C,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION C(1) ,WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | IW1 = N+N+1 6 | IW2 = IW1+N+N 7 | CALL ZFFTF1 (N,C,WSAVE,WSAVE(IW1),WSAVE(IW2)) 8 | RETURN 9 | END 10 | -------------------------------------------------------------------------------- /scipy/fftpack/src/dfftpack/zffti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZFFTI (N,WSAVE) 2 | IMPLICIT DOUBLE PRECISION (A-H,O-Z) 3 | DIMENSION WSAVE(1) 4 | IF (N .EQ. 1) RETURN 5 | IW1 = N+N+1 6 | IW2 = IW1+N+N 7 | CALL ZFFTI1 (N,WSAVE(IW1),WSAVE(IW2)) 8 | RETURN 9 | END 10 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/cfftb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE CFFTB (N,C,WSAVE) 2 | DIMENSION C(*) ,WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | IW1 = N+N+1 5 | IW2 = IW1+N+N 6 | CALL CFFTB1 (N,C,WSAVE,WSAVE(IW1),WSAVE(IW2)) 7 | RETURN 8 | END 9 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/cfftf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE CFFTF (N,C,WSAVE) 2 | DIMENSION C(*) ,WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | IW1 = N+N+1 5 | IW2 = IW1+N+N 6 | CALL CFFTF1 (N,C,WSAVE,WSAVE(IW1),WSAVE(IW2)) 7 | RETURN 8 | END 9 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/cffti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE CFFTI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | IW1 = N+N+1 5 | IW2 = IW1+N+N 6 | CALL CFFTI1 (N,WSAVE(IW1),WSAVE(IW2)) 7 | RETURN 8 | END 9 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/cosqi.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE COSQI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | DATA PIH /1.57079632679491/ 4 | DT = PIH/FLOAT(N) 5 | FK = 0. 6 | DO 101 K=1,N 7 | FK = FK+1. 8 | WSAVE(K) = COS(FK*DT) 9 | 101 CONTINUE 10 | CALL RFFTI (N,WSAVE(N+1)) 11 | RETURN 12 | END 13 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/costi.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE COSTI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | DATA PI /3.14159265358979/ 4 | IF (N .LE. 3) RETURN 5 | NM1 = N-1 6 | NP1 = N+1 7 | NS2 = N/2 8 | DT = PI/FLOAT(NM1) 9 | FK = 0. 10 | DO 101 K=2,NS2 11 | KC = NP1-K 12 | FK = FK+1. 13 | WSAVE(K) = 2.*SIN(FK*DT) 14 | WSAVE(KC) = 2.*COS(FK*DT) 15 | 101 CONTINUE 16 | CALL RFFTI (NM1,WSAVE(N+1)) 17 | RETURN 18 | END 19 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/rfftb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE RFFTB (N,R,WSAVE) 2 | DIMENSION R(*) ,WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | CALL RFFTB1 (N,R,WSAVE,WSAVE(N+1),WSAVE(2*N+1)) 5 | RETURN 6 | END 7 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/rfftf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE RFFTF (N,R,WSAVE) 2 | DIMENSION R(*) ,WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | CALL RFFTF1 (N,R,WSAVE,WSAVE(N+1),WSAVE(2*N+1)) 5 | RETURN 6 | END 7 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/rffti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE RFFTI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | CALL RFFTI1 (N,WSAVE(N+1),WSAVE(2*N+1)) 5 | RETURN 6 | END 7 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/sinqb.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SINQB (N,X,WSAVE) 2 | DIMENSION X(*) ,WSAVE(*) 3 | IF (N .GT. 1) GO TO 101 4 | X(1) = 4.*X(1) 5 | RETURN 6 | 101 NS2 = N/2 7 | DO 102 K=2,N,2 8 | X(K) = -X(K) 9 | 102 CONTINUE 10 | CALL COSQB (N,X,WSAVE) 11 | DO 103 K=1,NS2 12 | KC = N-K 13 | XHOLD = X(K) 14 | X(K) = X(KC+1) 15 | X(KC+1) = XHOLD 16 | 103 CONTINUE 17 | RETURN 18 | END 19 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/sinqf.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SINQF (N,X,WSAVE) 2 | DIMENSION X(*) ,WSAVE(*) 3 | IF (N .EQ. 1) RETURN 4 | NS2 = N/2 5 | DO 101 K=1,NS2 6 | KC = N-K 7 | XHOLD = X(K) 8 | X(K) = X(KC+1) 9 | X(KC+1) = XHOLD 10 | 101 CONTINUE 11 | CALL COSQF (N,X,WSAVE) 12 | DO 102 K=2,N,2 13 | X(K) = -X(K) 14 | 102 CONTINUE 15 | RETURN 16 | END 17 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/sinqi.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SINQI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | CALL COSQI (N,WSAVE) 4 | RETURN 5 | END 6 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/sint.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SINT (N,X,WSAVE) 2 | DIMENSION X(*) ,WSAVE(*) 3 | NP1 = N+1 4 | IW1 = N/2+1 5 | IW2 = IW1+NP1 6 | IW3 = IW2+NP1 7 | CALL SINT1(N,X,WSAVE,WSAVE(IW1),WSAVE(IW2),WSAVE(IW3)) 8 | RETURN 9 | END 10 | -------------------------------------------------------------------------------- /scipy/fftpack/src/fftpack/sinti.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SINTI (N,WSAVE) 2 | DIMENSION WSAVE(*) 3 | DATA PI /3.14159265358979/ 4 | IF (N .LE. 1) RETURN 5 | NS2 = N/2 6 | NP1 = N+1 7 | DT = PI/FLOAT(NP1) 8 | DO 101 K=1,NS2 9 | WSAVE(K) = 2.*SIN(K*DT) 10 | 101 CONTINUE 11 | CALL RFFTI (NP1,WSAVE(NS2+1)) 12 | RETURN 13 | END 14 | -------------------------------------------------------------------------------- /scipy/fftpack/tests/Makefile: -------------------------------------------------------------------------------- 1 | CC = gcc 2 | LD = gcc 3 | 4 | fftw_single: fftw_dct.c 5 | $(CC) -W -Wall -DDCT_TEST_USE_SINGLE $< -o $@ -lfftw3f 6 | 7 | fftw_double: fftw_dct.c 8 | $(CC) -W -Wall $< -o $@ -lfftw3 9 | 10 | clean: 11 | rm -f fftw_single 12 | rm -f fftw_double 13 | rm -f *.o 14 | -------------------------------------------------------------------------------- /scipy/fftpack/tests/fftw_double_ref.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/fftpack/tests/fftw_double_ref.npz -------------------------------------------------------------------------------- /scipy/fftpack/tests/fftw_single_ref.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/fftpack/tests/fftw_single_ref.npz -------------------------------------------------------------------------------- /scipy/fftpack/tests/gendata.m: -------------------------------------------------------------------------------- 1 | x0 = linspace(0, 10, 11); 2 | x1 = linspace(0, 10, 15); 3 | x2 = linspace(0, 10, 16); 4 | x3 = linspace(0, 10, 17); 5 | 6 | x4 = randn(32, 1); 7 | x5 = randn(64, 1); 8 | x6 = randn(128, 1); 9 | x7 = randn(256, 1); 10 | 11 | y0 = dct(x0); 12 | y1 = dct(x1); 13 | y2 = dct(x2); 14 | y3 = dct(x3); 15 | y4 = dct(x4); 16 | y5 = dct(x5); 17 | y6 = dct(x6); 18 | y7 = dct(x7); 19 | 20 | save('test.mat', 'x0', 'x1', 'x2', 'x3', 'x4', 'x5', 'x6', 'x7', ... 21 | 'y0', 'y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7'); 22 | -------------------------------------------------------------------------------- /scipy/fftpack/tests/gendata.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | import numpy as np 4 | from scipy.io import loadmat 5 | 6 | m = loadmat('test.mat', squeeze_me=True, struct_as_record=True, 7 | mat_dtype=True) 8 | np.savez('test.npz', **m) 9 | -------------------------------------------------------------------------------- /scipy/fftpack/tests/test.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/fftpack/tests/test.npz -------------------------------------------------------------------------------- /scipy/integrate/mach/xerror.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE XERROR(MESS,NMESS,L1,L2) 2 | C 3 | C THIS IS A DUMMY XERROR ROUTINE TO PRINT ERROR MESSAGES WITH NMESS 4 | C CHARACTERS. L1 AND L2 ARE DUMMY PARAMETERS TO MAKE THIS CALL 5 | C COMPATIBLE WITH THE SLATEC XERROR ROUTINE. THIS IS A FORTRAN 77 6 | C ROUTINE. 7 | C 8 | CHARACTER*(*) MESS 9 | NN=NMESS/70 10 | NR=NMESS-70*NN 11 | IF(NR.NE.0) NN=NN+1 12 | K=1 13 | PRINT 900 14 | 900 FORMAT(/) 15 | DO 10 I=1,NN 16 | KMIN=MIN0(K+69,NMESS) 17 | PRINT *, MESS(K:KMIN) 18 | K=K+70 19 | 10 CONTINUE 20 | PRINT 900 21 | RETURN 22 | END 23 | -------------------------------------------------------------------------------- /scipy/integrate/odepack/vmnorm.f: -------------------------------------------------------------------------------- 1 | double precision function vmnorm (n, v, w) 2 | clll. optimize 3 | c----------------------------------------------------------------------- 4 | c this function routine computes the weighted max-norm 5 | c of the vector of length n contained in the array v, with weights 6 | c contained in the array w of length n.. 7 | c vmnorm = max(i=1,...,n) abs(v(i))*w(i) 8 | c----------------------------------------------------------------------- 9 | integer n, i 10 | double precision v, w, vm 11 | dimension v(n), w(n) 12 | vm = 0.0d0 13 | do 10 i = 1,n 14 | 10 vm = dmax1(vm,dabs(v(i))*w(i)) 15 | vmnorm = vm 16 | return 17 | c----------------------- end of function vmnorm ------------------------ 18 | end 19 | -------------------------------------------------------------------------------- /scipy/integrate/odepack/xsetf.f: -------------------------------------------------------------------------------- 1 | subroutine xsetf (mflag) 2 | c 3 | c this routine resets the print control flag mflag. 4 | c 5 | integer mflag, mesflg, lunit 6 | common /eh0001/ mesflg, lunit 7 | c 8 | if (mflag .eq. 0 .or. mflag .eq. 1) mesflg = mflag 9 | return 10 | c----------------------- end of subroutine xsetf ----------------------- 11 | end 12 | -------------------------------------------------------------------------------- /scipy/integrate/odepack/xsetun.f: -------------------------------------------------------------------------------- 1 | subroutine xsetun (lun) 2 | c 3 | c this routine resets the logical unit number for messages. 4 | c 5 | integer lun, mesflg, lunit 6 | common /eh0001/ mesflg, lunit 7 | c 8 | if (lun .gt. 0) lunit = lun 9 | return 10 | c----------------------- end of subroutine xsetun ---------------------- 11 | end 12 | -------------------------------------------------------------------------------- /scipy/integrate/quadpack/changes: -------------------------------------------------------------------------------- 1 | 1 Aug 86 ehg 2 | qwgt*.f were declared double precision, but should have been single 3 | 4 | 21 May 87 ehg, reported by dongarra 5 | dqc25c.f was missing data x(11). copied from dqc25s.f 6 | -------------------------------------------------------------------------------- /scipy/integrate/quadpack/disclaimer: -------------------------------------------------------------------------------- 1 | This version obtained on 1 Jun 84 from (kahaner@nbs-sdc) 2 | David K. Kahaner 3 | Scientific Computing Division 4 | National Bureau of Standards 5 | Washington DC 20234 6 | 7 | WARNING: the calling sequences here differ from those in the book: 8 | R. Piessens, E. deDoncker-Kapenga, C. Uberhuber, D. Kahaner 9 | Quadpack: a Subroutine Package for Automatic Integration 10 | Springer Verlag, 1983. Series in Computational Mathematics v.1 11 | -------------------------------------------------------------------------------- /scipy/integrate/quadpack/dqwgtc.f: -------------------------------------------------------------------------------- 1 | double precision function dqwgtc(x,c,p2,p3,p4,kp) 2 | c***begin prologue dqwgtc 3 | c***refer to dqk15w 4 | c***routines called (none) 5 | c***revision date 810101 (yymmdd) 6 | c***keywords weight function, cauchy principal value 7 | c***author piessens,robert,appl. math. & progr. div. - k.u.leuven 8 | c de doncker,elise,appl. math. & progr. div. - k.u.leuven 9 | c***purpose this function subprogram is used together with the 10 | c routine qawc and defines the weight function. 11 | c***end prologue dqwgtc 12 | c 13 | double precision c,p2,p3,p4,x 14 | integer kp 15 | c***first executable statement dqwgtc 16 | dqwgtc = 0.1d+01/(x-c) 17 | return 18 | end 19 | -------------------------------------------------------------------------------- /scipy/integrate/quadpack/dqwgtf.f: -------------------------------------------------------------------------------- 1 | double precision function dqwgtf(x,omega,p2,p3,p4,integr) 2 | c***begin prologue dqwgtf 3 | c***refer to dqk15w 4 | c***routines called (none) 5 | c***revision date 810101 (yymmdd) 6 | c***keywords cos or sin in weight function 7 | c***author piessens,robert, appl. math. & progr. div. - k.u.leuven 8 | c de doncker,elise,appl. math. * progr. div. - k.u.leuven 9 | c***end prologue dqwgtf 10 | c 11 | double precision dcos,dsin,omega,omx,p2,p3,p4,x 12 | integer integr 13 | c***first executable statement dqwgtf 14 | omx = omega*x 15 | go to(10,20),integr 16 | 10 dqwgtf = dcos(omx) 17 | go to 30 18 | 20 dqwgtf = dsin(omx) 19 | 30 return 20 | end 21 | -------------------------------------------------------------------------------- /scipy/integrate/quadpack/permission: -------------------------------------------------------------------------------- 1 | prehistoric 2 | -------------------------------------------------------------------------------- /scipy/interpolate/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: fitpack 5 | Sources: 6 | fitpack/*.f 7 | Extension: _fitpack 8 | Sources: src/_fitpackmodule.c 9 | Extension: _bspl 10 | Sources: _bspl.c 11 | Extension: dfitpack 12 | Sources: src/fitpack.pyf 13 | Extension: _interpolate 14 | Sources: src/_interpolate.cpp 15 | Extension: interpnd 16 | Sources: interpnd.c 17 | Extension: _ppoly 18 | Sources: _ppoly.c 19 | -------------------------------------------------------------------------------- /scipy/interpolate/blas_defs.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Handle different Fortran conventions. 3 | */ 4 | 5 | #if defined(NO_APPEND_FORTRAN) 6 | #if defined(UPPERCASE_FORTRAN) 7 | #define F_FUNC(f,F) F 8 | #else 9 | #define F_FUNC(f,F) f 10 | #endif 11 | #else 12 | #if defined(UPPERCASE_FORTRAN) 13 | #define F_FUNC(f,F) F##_ 14 | #else 15 | #define F_FUNC(f,F) f##_ 16 | #endif 17 | #endif 18 | 19 | #define c_dgeev F_FUNC(dgeev,DGEEV) 20 | -------------------------------------------------------------------------------- /scipy/interpolate/fitpack/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile that builts a library lib$(LIB).a from all 2 | # of the Fortran files found in the current directory. 3 | # Usage: make LIB= 4 | # Pearu 5 | 6 | OBJ=$(patsubst %.f,%.o,$(shell ls *.f)) 7 | all: lib$(LIB).a 8 | $(OBJ): 9 | $(FC) -c $(FFLAGS) $(FSHARED) $(patsubst %.o,%.f,$(@F)) -o $@ 10 | lib$(LIB).a: $(OBJ) 11 | $(AR) rus lib$(LIB).a $? 12 | clean: 13 | rm *.o 14 | 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /scipy/interpolate/fitpack/README: -------------------------------------------------------------------------------- 1 | - ddierckx is a 'real*8' version of dierckx 2 | generated by Pearu Peterson . 3 | - dierckx (in netlib) is fitpack by P. Dierckx 4 | -------------------------------------------------------------------------------- /scipy/interpolate/fitpack/fpgivs.f: -------------------------------------------------------------------------------- 1 | subroutine fpgivs(piv,ww,cos,sin) 2 | c subroutine fpgivs calculates the parameters of a givens 3 | c transformation . 4 | c .. 5 | c ..scalar arguments.. 6 | real*8 piv,ww,cos,sin 7 | c ..local scalars.. 8 | real*8 dd,one,store 9 | c ..function references.. 10 | real*8 abs,sqrt 11 | c .. 12 | one = 0.1e+01 13 | store = abs(piv) 14 | if(store.ge.ww) dd = store*sqrt(one+(ww/piv)**2) 15 | if(store.lt.ww) dd = ww*sqrt(one+(piv/ww)**2) 16 | cos = ww/dd 17 | sin = piv/dd 18 | ww = dd 19 | return 20 | end 21 | -------------------------------------------------------------------------------- /scipy/interpolate/fitpack/fprota.f: -------------------------------------------------------------------------------- 1 | subroutine fprota(cos,sin,a,b) 2 | c subroutine fprota applies a givens rotation to a and b. 3 | c .. 4 | c ..scalar arguments.. 5 | real*8 cos,sin,a,b 6 | c ..local scalars.. 7 | real*8 stor1,stor2 8 | c .. 9 | stor1 = a 10 | stor2 = b 11 | b = cos*stor2+sin*stor1 12 | a = cos*stor1-sin*stor2 13 | return 14 | end 15 | -------------------------------------------------------------------------------- /scipy/interpolate/tests/data/bug-1310.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/interpolate/tests/data/bug-1310.npz -------------------------------------------------------------------------------- /scipy/interpolate/tests/data/estimate_gradients_hang.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/interpolate/tests/data/estimate_gradients_hang.npy -------------------------------------------------------------------------------- /scipy/interpolate/tests/test_regression.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | import numpy as np 4 | import scipy.interpolate as interp 5 | from numpy.testing import assert_almost_equal, TestCase 6 | 7 | 8 | class TestRegression(TestCase): 9 | def test_spalde_scalar_input(self): 10 | """Ticket #629""" 11 | x = np.linspace(0,10) 12 | y = x**3 13 | tck = interp.splrep(x, y, k=3, t=[5]) 14 | res = interp.spalde(np.float64(1), tck) 15 | des = np.array([1., 3., 6., 6.]) 16 | assert_almost_equal(res, des) 17 | -------------------------------------------------------------------------------- /scipy/io/arff/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Module to read ARFF files, which are the standard data format for WEKA. 3 | 4 | ARFF is a text file format which support numerical, string and data values. 5 | The format can also represent missing data and sparse data. 6 | 7 | Notes 8 | ----- 9 | The ARFF support in ``scipy.io`` provides file reading functionality only. 10 | For more extensive ARFF functionality, see `liac-arff 11 | `_. 12 | 13 | See the `WEKA website `_ 14 | for more details about the ARFF format and available datasets. 15 | 16 | """ 17 | from __future__ import division, print_function, absolute_import 18 | 19 | from .arffread import * 20 | from . import arffread 21 | 22 | __all__ = arffread.__all__ 23 | 24 | from numpy.testing import Tester 25 | test = Tester().test 26 | -------------------------------------------------------------------------------- /scipy/io/arff/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='io',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | config = Configuration('arff', parent_package, top_path) 8 | config.add_data_dir('tests') 9 | return config 10 | 11 | if __name__ == '__main__': 12 | from numpy.distutils.core import setup 13 | setup(**configuration(top_path='').todict()) 14 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/missing.arff: -------------------------------------------------------------------------------- 1 | % This arff file contains some missing data 2 | @relation missing 3 | @attribute yop real 4 | @attribute yap real 5 | @data 6 | 1,5 7 | 2,4 8 | ?,? 9 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/nodata.arff: -------------------------------------------------------------------------------- 1 | @RELATION iris 2 | 3 | @ATTRIBUTE sepallength REAL 4 | @ATTRIBUTE sepalwidth REAL 5 | @ATTRIBUTE petallength REAL 6 | @ATTRIBUTE petalwidth REAL 7 | @ATTRIBUTE class {Iris-setosa,Iris-versicolor,Iris-virginica} 8 | 9 | @DATA 10 | 11 | % This file has no data 12 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test1.arff: -------------------------------------------------------------------------------- 1 | @RELATION test1 2 | 3 | @ATTRIBUTE attr0 REAL 4 | @ATTRIBUTE attr1 REAL 5 | @ATTRIBUTE attr2 REAL 6 | @ATTRIBUTE attr3 REAL 7 | @ATTRIBUTE class {class0, class1, class2, class3} 8 | 9 | @DATA 10 | 0.1, 0.2, 0.3, 0.4,class1 11 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test2.arff: -------------------------------------------------------------------------------- 1 | @RELATION test2 2 | 3 | @ATTRIBUTE attr0 REAL 4 | @ATTRIBUTE attr1 real 5 | @ATTRIBUTE attr2 integer 6 | @ATTRIBUTE attr3 Integer 7 | @ATTRIBUTE attr4 Numeric 8 | @ATTRIBUTE attr5 numeric 9 | @ATTRIBUTE attr6 string 10 | @ATTRIBUTE attr7 STRING 11 | @ATTRIBUTE attr8 {bla} 12 | @ATTRIBUTE attr9 {bla, bla} 13 | 14 | @DATA 15 | 0.1, 0.2, 0.3, 0.4,class1 16 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test3.arff: -------------------------------------------------------------------------------- 1 | @RELATION test3 2 | 3 | @ATTRIBUTE attr0 crap 4 | 5 | @DATA 6 | 0.1, 0.2, 0.3, 0.4,class1 7 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test4.arff: -------------------------------------------------------------------------------- 1 | @RELATION test5 2 | 3 | @ATTRIBUTE attr0 REAL 4 | @ATTRIBUTE attr1 REAL 5 | @ATTRIBUTE attr2 REAL 6 | @ATTRIBUTE attr3 REAL 7 | @ATTRIBUTE class {class0, class1, class2, class3} 8 | @DATA 9 | 0.1, 0.2, 0.3, 0.4,class1 10 | -0.1, -0.2, -0.3, -0.4,class2 11 | 1, 2, 3, 4,class3 12 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test5.arff: -------------------------------------------------------------------------------- 1 | @RELATION test4 2 | 3 | @ATTRIBUTE attr0 REAL 4 | @ATTRIBUTE attr1 REAL 5 | @ATTRIBUTE attr2 REAL 6 | @ATTRIBUTE attr3 REAL 7 | @ATTRIBUTE class {class0, class1, class2, class3} 8 | 9 | @DATA 10 | 11 | % lsdflkjhaksjdhf 12 | 13 | % lsdflkjhaksjdhf 14 | 15 | 0.1, 0.2, 0.3, 0.4,class1 16 | % laksjdhf 17 | 18 | % lsdflkjhaksjdhf 19 | -0.1, -0.2, -0.3, -0.4,class2 20 | 21 | % lsdflkjhaksjdhf 22 | % lsdflkjhaksjdhf 23 | 24 | % lsdflkjhaksjdhf 25 | 26 | 1, 2, 3, 4,class3 27 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test6.arff: -------------------------------------------------------------------------------- 1 | @RELATION test6 2 | 3 | @ATTRIBUTE attr0 REAL 4 | @ATTRIBUTE attr1 REAL 5 | @ATTRIBUTE attr2 REAL 6 | @ATTRIBUTE attr3 REAL 7 | @ATTRIBUTE class {C} 8 | 9 | @DATA 10 | 0.1, 0.2, 0.3, 0.4,C 11 | -0.1, -0.2, -0.3, -0.4,C 12 | 1, 2, 3, 4,C 13 | -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test7.arff: -------------------------------------------------------------------------------- 1 | @RELATION test7 2 | 3 | @ATTRIBUTE attr_year DATE yyyy 4 | @ATTRIBUTE attr_month DATE yyyy-MM 5 | @ATTRIBUTE attr_date DATE yyyy-MM-dd 6 | @ATTRIBUTE attr_datetime_local DATE "yyyy-MM-dd HH:mm" 7 | @ATTRIBUTE attr_datetime_missing DATE "yyyy-MM-dd HH:mm" 8 | 9 | @DATA 10 | 1999,1999-01,1999-01-31,"1999-01-31 00:01",? 11 | 2004,2004-12,2004-12-01,"2004-12-01 23:59","2004-12-01 23:59" 12 | 1817,1817-04,1817-04-28,"1817-04-28 13:00",? 13 | 2100,2100-09,2100-09-10,"2100-09-10 12:00",? 14 | 2013,2013-11,2013-11-30,"2013-11-30 04:55","2013-11-30 04:55" 15 | 1631,1631-10,1631-10-15,"1631-10-15 20:04","1631-10-15 20:04" -------------------------------------------------------------------------------- /scipy/io/arff/tests/data/test8.arff: -------------------------------------------------------------------------------- 1 | @RELATION test8 2 | 3 | @ATTRIBUTE attr_datetime_utc DATE "yyyy-MM-dd HH:mm Z" 4 | @ATTRIBUTE attr_datetime_full DATE "yy-MM-dd HH:mm:ss z" 5 | 6 | @DATA 7 | "1999-01-31 00:01 UTC","99-01-31 00:01:08 +0430" 8 | "2004-12-01 23:59 UTC","04-12-01 23:59:59 -0800" 9 | "1817-04-28 13:00 UTC","17-04-28 13:00:33 +1000" 10 | "2100-09-10 12:00 UTC","21-09-10 12:00:21 -0300" 11 | "2013-11-30 04:55 UTC","13-11-30 04:55:48 -1100" 12 | "1631-10-15 20:04 UTC","31-10-15 20:04:10 +0000" -------------------------------------------------------------------------------- /scipy/io/bento.info: -------------------------------------------------------------------------------- 1 | Recurse: matlab 2 | 3 | Library: 4 | Packages: arff, matlab, harwell_boeing 5 | -------------------------------------------------------------------------------- /scipy/io/harwell_boeing/__init__.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | from scipy.io.harwell_boeing.hb import MalformedHeader, HBInfo, HBFile, \ 4 | HBMatrixType, hb_read, hb_write 5 | -------------------------------------------------------------------------------- /scipy/io/harwell_boeing/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | config = Configuration('harwell_boeing',parent_package,top_path) 8 | config.add_data_dir('tests') 9 | 10 | return config 11 | 12 | if __name__ == '__main__': 13 | from numpy.distutils.core import setup 14 | setup(**configuration(top_path='').todict()) 15 | -------------------------------------------------------------------------------- /scipy/io/matlab/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Utilities for dealing with MATLAB(R) files 3 | 4 | Notes 5 | ----- 6 | MATLAB(R) is a registered trademark of The MathWorks, Inc., 3 Apple Hill 7 | Drive, Natick, MA 01760-2098, USA. 8 | 9 | """ 10 | from __future__ import division, print_function, absolute_import 11 | 12 | # Matlab file read and write utilities 13 | from .mio import loadmat, savemat, whosmat 14 | from . import byteordercodes 15 | 16 | __all__ = ['loadmat', 'savemat', 'whosmat', 'byteordercodes'] 17 | 18 | from numpy.testing import Tester 19 | test = Tester().test 20 | -------------------------------------------------------------------------------- /scipy/io/matlab/bento.info: -------------------------------------------------------------------------------- 1 | Library: 2 | Extension: streams 3 | Sources: streams.c 4 | Extension: mio_utils 5 | Sources: mio_utils.c 6 | Extension: mio5_utils 7 | Sources: mio5_utils.c 8 | -------------------------------------------------------------------------------- /scipy/io/matlab/mio_utils.pxd: -------------------------------------------------------------------------------- 1 | cimport numpy as np 2 | 3 | cpdef object squeeze_element(np.ndarray) 4 | cpdef np.ndarray chars_to_strings(object) 5 | -------------------------------------------------------------------------------- /scipy/io/matlab/numpy_rephrasing.h: -------------------------------------------------------------------------------- 1 | #include 2 | #define PyArray_Set_BASE(arr, obj) PyArray_BASE(arr) = obj 3 | #define PyArray_PyANewFromDescr(descr, nd, dims, data, parent) \ 4 | PyArray_NewFromDescr(&PyArray_Type, descr, nd, dims, \ 5 | NULL, data, 0, parent) 6 | -------------------------------------------------------------------------------- /scipy/io/matlab/pyalloc.pxd: -------------------------------------------------------------------------------- 1 | # -*- python -*- or rather like 2 | 3 | from cpython cimport PyBytes_FromStringAndSize, \ 4 | PyBytes_AS_STRING, PyBytes_Size 5 | 6 | 7 | # Function to allocate, wrap memory via Python string creation 8 | cdef inline object pyalloc_v(Py_ssize_t n, void **pp): 9 | cdef object ob = PyBytes_FromStringAndSize(NULL, n) 10 | pp[0] = PyBytes_AS_STRING(ob) 11 | return ob 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /scipy/io/matlab/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='io',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | config = Configuration('matlab', parent_package, top_path) 8 | config.add_extension('streams', sources=['streams.c']) 9 | config.add_extension('mio_utils', sources=['mio_utils.c']) 10 | config.add_extension('mio5_utils', sources=['mio5_utils.c']) 11 | config.add_data_dir('tests') 12 | return config 13 | 14 | if __name__ == '__main__': 15 | from numpy.distutils.core import setup 16 | setup(**configuration(top_path='').todict()) 17 | -------------------------------------------------------------------------------- /scipy/io/matlab/streams.pxd: -------------------------------------------------------------------------------- 1 | # -*- python -*- or rather like 2 | 3 | cdef class GenericStream: 4 | cdef object fobj 5 | 6 | cpdef int seek(self, long int offset, int whence=*) except -1 7 | cpdef long int tell(self) except -1 8 | cdef int read_into(self, void *buf, size_t n) except -1 9 | cdef object read_string(self, size_t n, void **pp, int copy=*) 10 | 11 | cpdef GenericStream make_stream(object fobj) 12 | -------------------------------------------------------------------------------- /scipy/io/matlab/tests/afunc.m: -------------------------------------------------------------------------------- 1 | function [a, b] = afunc(c, d) 2 | % A function 3 | a = c + 1; 4 | b = d + 10; 5 | -------------------------------------------------------------------------------- /scipy/io/matlab/tests/data/bad_miuint32.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/io/matlab/tests/data/bad_miuint32.mat -------------------------------------------------------------------------------- /scipy/io/matlab/tests/data/bad_miutf8_array_name.mat: -------------------------------------------------------------------------------- 1 | MATLAB 5.0 MAT-file Platform: posix, Created on: Sat Jan 31 14:27:42 2015IMH 2 | äray_name  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-------------------------------------------------------------------------------- /scipy/linalg/calc_lwork.py: -------------------------------------------------------------------------------- 1 | """ 2 | calc_lwork was an internal module in Scipy and has been removed. 3 | 4 | Several functions in scipy.linalg.lapack have *_lwork variants 5 | that perform the lwork calculation (from Scipy >= 0.15.0), or 6 | allow passing in LWORK=-1 argument to perform the computation. 7 | 8 | """ 9 | 10 | from __future__ import division, print_function, absolute_import 11 | 12 | from numpy import deprecate 13 | 14 | from ._calc_lwork import * 15 | 16 | @deprecate(old_name="scipy.linalg.calc_lwork", message=__doc__) 17 | def _deprecated(): 18 | pass 19 | try: 20 | _deprecated() 21 | except DeprecationWarning as e: 22 | # don't fail import if DeprecationWarnings raise error -- works around 23 | # the situation with Numpy's test framework 24 | pass 25 | -------------------------------------------------------------------------------- /scipy/linalg/cblas.pyf.src: -------------------------------------------------------------------------------- 1 | !%f90 -*- f90 -*- 2 | ! Signatures for f2py-wrappers of ATLAS C BLAS functions. 3 | ! 4 | ! Author: Pearu Peterson 5 | ! Created: Jan-Feb 2002 6 | ! $Revision$ $Date$ 7 | ! 8 | 9 | python module _cblas 10 | interface 11 | 12 | include "cblas_l1.pyf.src" 13 | 14 | end interface 15 | end python module _cblas 16 | -------------------------------------------------------------------------------- /scipy/linalg/fblas.pyf.src: -------------------------------------------------------------------------------- 1 | !%f90 -*- f90 -*- 2 | ! Signatures for f2py-wrappers of FORTRAN BLAS functions. 3 | ! 4 | ! Author: Pearu Peterson 5 | ! Created: Jan-Feb 2002 6 | ! $Revision$ $Date$ 7 | ! 8 | 9 | 10 | python module _fblas 11 | interface 12 | 13 | include 'fblas_l1.pyf.src' 14 | include 'fblas_l2.pyf.src' 15 | include 'fblas_l3.pyf.src' 16 | 17 | end interface 18 | end python module _fblas 19 | -------------------------------------------------------------------------------- /scipy/linalg/flapack_user.pyf.src: -------------------------------------------------------------------------------- 1 | python module gees__user__routines 2 | interface 3 | function select(<_arg=arg1\,arg2,\0,arg,\2>) 4 | :: <_arg> 5 | logical :: select 6 | end function select 7 | end interface 8 | end python module gees__user__routines 9 | 10 | python module gges__user__routines 11 | interface 12 | function select(alpha, beta) 13 | :: alpha, beta 14 | logical :: select 15 | end function select 16 | function select(alphar, alphai, beta) 17 | :: alphar, alphai, beta 18 | logical :: select 19 | end function select 20 | end interface 21 | end python module gges__user__routines 22 | -------------------------------------------------------------------------------- /scipy/linalg/fortran_defs.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Handle different Fortran conventions. 3 | */ 4 | 5 | #if defined(NO_APPEND_FORTRAN) 6 | #if defined(UPPERCASE_FORTRAN) 7 | #define F_FUNC(f,F) F 8 | #else 9 | #define F_FUNC(f,F) f 10 | #endif 11 | #else 12 | #if defined(UPPERCASE_FORTRAN) 13 | #define F_FUNC(f,F) F##_ 14 | #else 15 | #define F_FUNC(f,F) f##_ 16 | #endif 17 | #endif 18 | -------------------------------------------------------------------------------- /scipy/linalg/linalg_version.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | major = 0 4 | minor = 4 5 | micro = 9 6 | 7 | linalg_version = '%(major)d.%(minor)d.%(micro)d' % (locals()) 8 | -------------------------------------------------------------------------------- /scipy/linalg/src/id_dist/README.txt: -------------------------------------------------------------------------------- 1 | Please see the documentation in subdirectory doc of this id_dist directory. 2 | 3 | At the minimum, please read Subsection 2.1 and Section 3 in the documentation, 4 | and beware that the _N.B._'s in the source code comments highlight important 5 | information about the routines -- _N.B._ stands for _nota_bene_ (Latin for 6 | "note well"). 7 | -------------------------------------------------------------------------------- /scipy/linalg/src/id_dist/doc/doc.bib: -------------------------------------------------------------------------------- 1 | @book{golub-van_loan, 2 | author = {Gene Golub and Charles {Van L}oan}, 3 | title = {Matrix Computations}, 4 | edition = {Third}, 5 | publisher = {Johns Hopkins University Press}, 6 | year = {1996}, 7 | address = {Baltimore, Maryland} 8 | } 9 | 10 | @article{halko-martinsson-tropp, 11 | author = {Nathan Halko and {P.-G.} Martinsson and Joel A. Tropp}, 12 | title = {Finding structure with randomness: probabilistic algorithms 13 | for constructing approximate matrix decompositions}, 14 | journal = {SIAM Review}, 15 | volume = {53}, 16 | number = {2}, 17 | pages = {217--288}, 18 | year = {2011} 19 | } 20 | -------------------------------------------------------------------------------- /scipy/linalg/tests/data/carex_15_data.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/linalg/tests/data/carex_15_data.npz -------------------------------------------------------------------------------- /scipy/linalg/tests/data/carex_18_data.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/linalg/tests/data/carex_18_data.npz 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https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/linalg/tests/data/carex_6_data.npz -------------------------------------------------------------------------------- /scipy/linalg/tests/data/gendare_20170120_data.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/linalg/tests/data/gendare_20170120_data.npz -------------------------------------------------------------------------------- /scipy/linalg/tests/test_cython_lapack.py: -------------------------------------------------------------------------------- 1 | from numpy.testing import TestCase, run_module_suite, assert_allclose 2 | from scipy.linalg import cython_lapack as cython_lapack 3 | from scipy.linalg import lapack 4 | 5 | 6 | class test_lamch(TestCase): 7 | 8 | def test_slamch(self): 9 | for c in [b'e', b's', b'b', b'p', b'n', b'r', b'm', b'u', b'l', b'o']: 10 | assert_allclose(cython_lapack._test_slamch(c), 11 | lapack.slamch(c)) 12 | 13 | def test_dlamch(self): 14 | for c in [b'e', b's', b'b', b'p', b'n', b'r', b'm', b'u', b'l', b'o']: 15 | assert_allclose(cython_lapack._test_dlamch(c), 16 | lapack.dlamch(c)) 17 | 18 | 19 | if __name__ == "__main__": 20 | run_module_suite() 21 | -------------------------------------------------------------------------------- /scipy/misc/ascent.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/misc/ascent.dat -------------------------------------------------------------------------------- /scipy/misc/face.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/misc/face.dat 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-------------------------------------------------------------------------------- /scipy/ndimage/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | Extension: _nd_image 5 | Sources: src/nd_image.c, 6 | src/ni_filters.c, 7 | src/ni_fourier.c, 8 | src/ni_interpolation.c, 9 | src/ni_measure.c, 10 | src/ni_morphology.c, 11 | src/ni_support.c 12 | Extension: _ni_label 13 | Sources: src/_ni_label.c 14 | Extension: _ctest 15 | Sources: src/_ctest.c 16 | Extension: _ctest_oldapi 17 | Sources: src/_ctest.c 18 | Extension: _cytest 19 | Sources: src/_cytest.c 20 | -------------------------------------------------------------------------------- /scipy/ndimage/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | context.tweak_extension("_ctest_oldapi", features="c cshlib pyext bento", 6 | defines=('OLDAPI', )) 7 | 8 | context.tweak_extension("_nd_image", includes='../_lib/src') 9 | -------------------------------------------------------------------------------- /scipy/ndimage/src/_cytest.pxd: -------------------------------------------------------------------------------- 1 | from numpy cimport npy_intp as intp 2 | 3 | cdef int _filter1d(double *input_line, intp input_length, double *output_line, 4 | intp output_length, void *callback_data) 5 | cdef int _filter2d(double *buffer, intp filter_size, double *res, 6 | void *callback_data) 7 | cdef int _transform(intp *output_coordinates, double *input_coordinates, 8 | int output_rank, int input_rank, void *callback_data) 9 | -------------------------------------------------------------------------------- /scipy/ndimage/tests/data/README.txt: -------------------------------------------------------------------------------- 1 | label_inputs.txt, label_strels.txt, and label_results.txt are test 2 | vectors generated using ndimage.label from scipy version 0.10.0, and 3 | are used to verify that the cython version behaves as expected. The 4 | script to generate them is in ../../utils/generate_label_testvectors.py 5 | -------------------------------------------------------------------------------- /scipy/ndimage/tests/data/label_inputs.txt: -------------------------------------------------------------------------------- 1 | 1 1 1 1 1 1 1 2 | 1 1 1 1 1 1 1 3 | 1 1 1 1 1 1 1 4 | 1 1 1 1 1 1 1 5 | 1 1 1 1 1 1 1 6 | 1 1 1 1 1 1 1 7 | 1 1 1 1 1 1 1 8 | 1 1 1 0 1 1 1 9 | 1 1 0 0 0 1 1 10 | 1 0 1 0 1 0 1 11 | 0 0 0 1 0 0 0 12 | 1 0 1 0 1 0 1 13 | 1 1 0 0 0 1 1 14 | 1 1 1 0 1 1 1 15 | 1 0 1 1 1 0 1 16 | 0 0 0 1 0 0 0 17 | 1 0 0 1 0 0 1 18 | 1 1 1 1 1 1 1 19 | 1 0 0 1 0 0 1 20 | 0 0 0 1 0 0 0 21 | 1 0 1 1 1 0 1 22 | -------------------------------------------------------------------------------- /scipy/ndimage/tests/data/label_strels.txt: -------------------------------------------------------------------------------- 1 | 0 0 1 2 | 1 1 1 3 | 1 0 0 4 | 1 0 0 5 | 1 1 1 6 | 0 0 1 7 | 0 0 0 8 | 1 1 1 9 | 0 0 0 10 | 0 1 1 11 | 0 1 0 12 | 1 1 0 13 | 0 0 0 14 | 0 0 0 15 | 0 0 0 16 | 0 1 1 17 | 1 1 1 18 | 1 1 0 19 | 0 1 0 20 | 1 1 1 21 | 0 1 0 22 | 1 0 0 23 | 0 1 0 24 | 0 0 1 25 | 0 1 0 26 | 0 1 0 27 | 0 1 0 28 | 1 1 1 29 | 1 1 1 30 | 1 1 1 31 | 1 1 0 32 | 0 1 0 33 | 0 1 1 34 | 1 0 1 35 | 0 1 0 36 | 1 0 1 37 | 0 0 1 38 | 0 1 0 39 | 1 0 0 40 | 1 1 0 41 | 1 1 1 42 | 0 1 1 43 | -------------------------------------------------------------------------------- /scipy/ndimage/tests/dots.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/ndimage/tests/dots.png -------------------------------------------------------------------------------- /scipy/odr/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: odrpack 5 | Sources: odrpack/d_odr.f, odrpack/d_mprec.f, odrpack/dlunoc.f, odrpack/d_lpk.f 6 | Extension: __odrpack 7 | Sources: __odrpack.c 8 | -------------------------------------------------------------------------------- /scipy/odr/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | context.tweak_extension("__odrpack", 6 | features="c fc pyext bento cshlib", 7 | use="odrpack BLAS CLIB") 8 | -------------------------------------------------------------------------------- /scipy/odr/odrpack/Makefile: -------------------------------------------------------------------------------- 1 | # Make the ODRPACK library 2 | 3 | FC = g77 4 | FOPT = -O 5 | LIB = libodrpack.a 6 | OBJS = d_odr.o d_mprec.o d_lpkbls.o dlunoc.o 7 | 8 | .f.o: 9 | $(FC) $(FOPT) -c $< 10 | 11 | $(LIB): $(OBJS) 12 | ar cru $(LIB) $(OBJS) 13 | 14 | all: $(LIB) 15 | 16 | clean: 17 | rm -f $(LIB) $(OBJS) 18 | 19 | -------------------------------------------------------------------------------- /scipy/odr/odrpack/dlunoc.f: -------------------------------------------------------------------------------- 1 | subroutine dluno 2 | + (lun, fn) 3 | 4 | integer lun 5 | character*(*) fn 6 | 7 | open(unit=lun, file=fn, status='new') 8 | 9 | return 10 | 11 | end 12 | 13 | subroutine dlunc 14 | + (lun) 15 | 16 | integer lun 17 | 18 | close(unit=lun) 19 | 20 | return 21 | 22 | end 23 | -------------------------------------------------------------------------------- /scipy/optimize/_lsq/__init__.py: -------------------------------------------------------------------------------- 1 | """This module contains least-squares algorithms.""" 2 | from __future__ import division, print_function, absolute_import 3 | 4 | from .least_squares import least_squares 5 | from .lsq_linear import lsq_linear 6 | 7 | __all__ = ['least_squares', 'lsq_linear'] 8 | -------------------------------------------------------------------------------- /scipy/optimize/_lsq/bento.info: -------------------------------------------------------------------------------- 1 | Library: 2 | Extension: givens_elimination 3 | Sources: givens_elimination.c 4 | -------------------------------------------------------------------------------- /scipy/optimize/_lsq/setup.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | 4 | def configuration(parent_package='', top_path=None): 5 | from numpy.distutils.misc_util import Configuration 6 | config = Configuration('_lsq', parent_package, top_path) 7 | config.add_extension('givens_elimination', 8 | sources=['givens_elimination.c']) 9 | return config 10 | 11 | 12 | if __name__ == '__main__': 13 | from numpy.distutils.core import setup 14 | setup(**configuration(top_path='').todict()) 15 | -------------------------------------------------------------------------------- /scipy/optimize/tests/test_nnls.py: -------------------------------------------------------------------------------- 1 | """ Unit tests for nonnegative least squares 2 | Author: Uwe Schmitt 3 | Sep 2008 4 | """ 5 | from __future__ import division, print_function, absolute_import 6 | 7 | from numpy.testing import assert_, TestCase, run_module_suite 8 | 9 | from scipy.optimize import nnls 10 | from numpy import arange, dot 11 | from numpy.linalg import norm 12 | 13 | 14 | class TestNNLS(TestCase): 15 | 16 | def test_nnls(self): 17 | a = arange(25.0).reshape(-1,5) 18 | x = arange(5.0) 19 | y = dot(a,x) 20 | x, res = nnls(a,y) 21 | assert_(res < 1e-7) 22 | assert_(norm(dot(a,x)-y) < 1e-7) 23 | 24 | if __name__ == "__main__": 25 | run_module_suite() 26 | -------------------------------------------------------------------------------- /scipy/signal/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | Extension: sigtools 5 | Sources: 6 | lfilter.c.src, 7 | correlate_nd.c.src, 8 | sigtoolsmodule.c, 9 | firfilter.c, 10 | medianfilter.c 11 | Extension: _spectral 12 | Sources: _spectral.c 13 | Extension: _max_len_seq_inner 14 | Sources: _max_len_seq_inner.c 15 | Extension: _upfirdn_apply 16 | Sources: _upfirdn_apply.c 17 | Extension: spline 18 | Sources: 19 | splinemodule.c, 20 | S_bspline_util.c, 21 | D_bspline_util.c, 22 | C_bspline_util.c, 23 | Z_bspline_util.c, 24 | bspline_util.c 25 | -------------------------------------------------------------------------------- /scipy/signal/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | context.tweak_extension("sigtools", includes=".") 6 | -------------------------------------------------------------------------------- /scipy/signal/bspline_util.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include 6 | 7 | void compute_root_from_lambda(double, double *, double *); 8 | 9 | 10 | void 11 | compute_root_from_lambda(lambda, r, omega) 12 | double lambda; 13 | double *r; 14 | double *omega; 15 | { 16 | double xi; 17 | double tmp, tmp2; 18 | 19 | tmp = sqrt(3 + 144*lambda); 20 | xi = 1 - 96*lambda + 24*lambda * tmp; 21 | *omega = atan(sqrt((144*lambda - 1.0)/xi)); 22 | tmp2 = sqrt(xi); 23 | *r = (24*lambda - 1 - tmp2)/(24*lambda) \ 24 | * sqrt((48*lambda + 24*lambda*tmp))/tmp2; 25 | return; 26 | } 27 | -------------------------------------------------------------------------------- /scipy/sparse/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Recurse: 4 | linalg, 5 | csgraph 6 | 7 | Library: 8 | Packages: 9 | linalg, 10 | csgraph 11 | Extension: _csparsetools 12 | Sources: _csparsetools.c 13 | Extension: _sparsetools 14 | Sources: 15 | sparsetools/sparsetools.cxx, 16 | sparsetools/bsr.cxx, 17 | sparsetools/csc.cxx, 18 | sparsetools/csr.cxx, 19 | sparsetools/other.cxx 20 | -------------------------------------------------------------------------------- /scipy/sparse/bscript: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | import subprocess 4 | 5 | from bento.commands import hooks 6 | 7 | 8 | @hooks.pre_build 9 | def pre_build(context): 10 | subprocess.check_call([sys.executable, 11 | os.path.join(os.path.dirname(__file__), 12 | 'generate_sparsetools.py'), 13 | '--no-force']) 14 | context.tweak_extension("_sparsetools", features="cxx cxxshlib pyext bento", 15 | defines=('__STDC_FORMAT_MACROS',)) 16 | -------------------------------------------------------------------------------- /scipy/sparse/csgraph/bento.info: -------------------------------------------------------------------------------- 1 | Library: 2 | Extension: _shortest_path 3 | Sources: _shortest_path.c 4 | Extension: _traversal 5 | Sources: _traversal.c 6 | Extension: _min_spanning_tree 7 | Sources: _min_spanning_tree.c 8 | Extension: _reordering 9 | Sources: _reordering.c 10 | Extension: _tools 11 | Sources: _tools.c 12 | -------------------------------------------------------------------------------- /scipy/sparse/csgraph/parameters.pxi: -------------------------------------------------------------------------------- 1 | 2 | DTYPE = np.float64 3 | ctypedef np.float64_t DTYPE_t 4 | 5 | ITYPE = np.int32 6 | ctypedef np.int32_t ITYPE_t 7 | 8 | # Fused type for int32 and int64 9 | ctypedef fused int32_or_int64: 10 | np.int32_t 11 | np.int64_t 12 | 13 | # EPS is the precision of DTYPE 14 | DEF DTYPE_EPS = 1E-15 15 | 16 | # NULL_IDX is the index used in predecessor matrices to store a non-path 17 | DEF NULL_IDX = -9999 18 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/bento.info: -------------------------------------------------------------------------------- 1 | Recurse: dsolve, eigen, isolve 2 | 3 | Library: 4 | Packages: 5 | dsolve, 6 | eigen, 7 | isolve 8 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/dsolve/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: superlu_src 5 | Sources: 6 | SuperLU/SRC/*.c 7 | Extension: _superlu 8 | Sources: 9 | _superlu_utils.c, 10 | _superluobject.c, 11 | _superlumodule.c 12 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Sparse Eigenvalue Solvers 3 | ------------------------- 4 | 5 | The submodules of sparse.linalg.eigen: 6 | 1. lobpcg: Locally Optimal Block Preconditioned Conjugate Gradient Method 7 | 8 | """ 9 | from __future__ import division, print_function, absolute_import 10 | 11 | from .arpack import * 12 | from .lobpcg import * 13 | 14 | __all__ = [s for s in dir() if not s.startswith('_')] 15 | from numpy.testing import Tester 16 | test = Tester().test 17 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icnteq.f: -------------------------------------------------------------------------------- 1 | c 2 | c----------------------------------------------------------------------- 3 | c 4 | c Count the number of elements equal to a specified integer value. 5 | c 6 | integer function icnteq (n, array, value) 7 | c 8 | integer n, value 9 | integer array(*) 10 | c 11 | k = 0 12 | do 10 i = 1, n 13 | if (array(i) .eq. value) k = k + 1 14 | 10 continue 15 | icnteq = k 16 | c 17 | return 18 | end 19 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/iset.f: -------------------------------------------------------------------------------- 1 | c 2 | c----------------------------------------------------------------------- 3 | c 4 | c Only work with increment equal to 1 right now. 5 | c 6 | subroutine iset (n, value, array, inc) 7 | c 8 | integer n, value, inc 9 | integer array(*) 10 | c 11 | do 10 i = 1, n 12 | array(i) = value 13 | 10 continue 14 | c 15 | return 16 | end 17 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/arpack/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Eigenvalue solver using iterative methods. 3 | 4 | Find k eigenvectors and eigenvalues of a matrix A using the 5 | Arnoldi/Lanczos iterative methods from ARPACK [1]_,[2]_. 6 | 7 | These methods are most useful for large sparse matrices. 8 | 9 | - eigs(A,k) 10 | - eigsh(A,k) 11 | 12 | References 13 | ---------- 14 | .. [1] ARPACK Software, http://www.caam.rice.edu/software/ARPACK/ 15 | .. [2] R. B. Lehoucq, D. C. Sorensen, and C. Yang, ARPACK USERS GUIDE: 16 | Solution of Large Scale Eigenvalue Problems by Implicitly Restarted 17 | Arnoldi Methods. SIAM, Philadelphia, PA, 1998. 18 | 19 | """ 20 | from __future__ import division, print_function, absolute_import 21 | 22 | from .arpack import * 23 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/arpack/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: arpack_scipy 5 | Sources: 6 | ARPACK/SRC/*.f, 7 | ARPACK/UTIL/*.f 8 | Extension: _arpack 9 | Sources: arpack.pyf.src 10 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/bento.info: -------------------------------------------------------------------------------- 1 | Recurse: arpack 2 | 3 | Library: 4 | Packages: arpack, lobpcg 5 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/lobpcg/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Locally Optimal Block Preconditioned Conjugate Gradient Method (LOBPCG) 3 | 4 | LOBPCG is a preconditioned eigensolver for large symmetric positive definite 5 | (SPD) generalized eigenproblems. 6 | 7 | Call the function lobpcg - see help for lobpcg.lobpcg. 8 | 9 | """ 10 | from __future__ import division, print_function, absolute_import 11 | 12 | from .lobpcg import * 13 | 14 | __all__ = [s for s in dir() if not s.startswith('_')] 15 | from numpy.testing import Tester 16 | test = Tester().test 17 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/lobpcg/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | 8 | config = Configuration('lobpcg',parent_package,top_path) 9 | config.add_data_dir('tests') 10 | 11 | return config 12 | 13 | if __name__ == '__main__': 14 | from numpy.distutils.core import setup 15 | setup(**configuration(top_path='').todict()) 16 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/eigen/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | 8 | config = Configuration('eigen',parent_package,top_path) 9 | 10 | config.add_subpackage(('arpack')) 11 | config.add_subpackage(('lobpcg')) 12 | 13 | return config 14 | 15 | if __name__ == '__main__': 16 | from numpy.distutils.core import setup 17 | setup(**configuration(top_path='').todict()) 18 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/isolve/__init__.py: -------------------------------------------------------------------------------- 1 | "Iterative Solvers for Sparse Linear Systems" 2 | 3 | from __future__ import division, print_function, absolute_import 4 | 5 | #from info import __doc__ 6 | from .iterative import * 7 | from .minres import minres 8 | from .lgmres import lgmres 9 | from .lsqr import lsqr 10 | from .lsmr import lsmr 11 | 12 | __all__ = [s for s in dir() if not s.startswith('_')] 13 | from numpy.testing import Tester 14 | test = Tester().test 15 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/isolve/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | Extension: _iterative 5 | Sources: 6 | iterative/BiCGREVCOM.f.src, 7 | iterative/BiCGSTABREVCOM.f.src, 8 | iterative/CGREVCOM.f.src, 9 | iterative/CGSREVCOM.f.src, 10 | iterative/GMRESREVCOM.f.src, 11 | iterative/QMRREVCOM.f.src, 12 | iterative/STOPTEST2.f.src, 13 | iterative/getbreak.f.src, 14 | iterative/_iterative.pyf.src 15 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/isolve/iterative/getbreak.f.src: -------------------------------------------------------------------------------- 1 | * -*- fortran -*- 2 | * GetBreak 3 | 4 | $ FUNCTION <_c>GETBREAK() 5 | * 6 | * Get breakdown parameter tolerance; for the test routine, 7 | * set to machine precision. 8 | * 9 | EPS, LAMCH 10 | * 11 | EPS = LAMCH('EPS') 12 | <_c>GETBREAK = EPS**2 13 | * 14 | RETURN 15 | * 16 | END 17 | * END FUNCTION <_c>GETBREAK 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/isolve/tests/test_utils.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | import numpy as np 4 | from numpy.testing import assert_raises 5 | 6 | from scipy.sparse.linalg import utils 7 | 8 | 9 | def test_make_system_bad_shape(): 10 | assert_raises(ValueError, utils.make_system, np.zeros((5,3)), None, np.zeros(4), np.zeros(4)) 11 | -------------------------------------------------------------------------------- /scipy/sparse/linalg/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_package='',top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | 8 | config = Configuration('linalg',parent_package,top_path) 9 | 10 | config.add_subpackage(('isolve')) 11 | config.add_subpackage(('dsolve')) 12 | config.add_subpackage(('eigen')) 13 | 14 | config.add_data_dir('tests') 15 | 16 | return config 17 | 18 | if __name__ == '__main__': 19 | from numpy.distutils.core import setup 20 | setup(**configuration(top_path='').todict()) 21 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools.py: -------------------------------------------------------------------------------- 1 | """ 2 | sparsetools is not a public module in scipy.sparse, but this file is 3 | for backward compatibility if someone happens to use it. 4 | """ 5 | from numpy import deprecate 6 | 7 | # This file shouldn't be imported by scipy --- Scipy code should use 8 | # internally scipy.sparse._sparsetools 9 | 10 | 11 | @deprecate(old_name="scipy.sparse.sparsetools", 12 | message=("scipy.sparse.sparsetools is a private module for scipy.sparse, " 13 | "and should not be used.")) 14 | def _deprecated(): 15 | pass 16 | 17 | del deprecate 18 | 19 | try: 20 | _deprecated() 21 | except DeprecationWarning as e: 22 | # don't fail import if DeprecationWarnings raise error -- works around 23 | # the situation with Numpy's test framework 24 | pass 25 | 26 | from ._sparsetools import * 27 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/bsr.cxx: -------------------------------------------------------------------------------- 1 | #define NO_IMPORT_ARRAY 2 | #define PY_ARRAY_UNIQUE_SYMBOL _scipy_sparse_sparsetools_ARRAY_API 3 | 4 | #include "sparsetools.h" 5 | #include "bsr.h" 6 | 7 | extern "C" { 8 | #include "bsr_impl.h" 9 | } 10 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/csc.cxx: -------------------------------------------------------------------------------- 1 | #define NO_IMPORT_ARRAY 2 | #define PY_ARRAY_UNIQUE_SYMBOL _scipy_sparse_sparsetools_ARRAY_API 3 | 4 | #include "sparsetools.h" 5 | #include "csc.h" 6 | 7 | extern "C" { 8 | #include "csc_impl.h" 9 | } 10 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/csr.cxx: -------------------------------------------------------------------------------- 1 | #define NO_IMPORT_ARRAY 2 | #define PY_ARRAY_UNIQUE_SYMBOL _scipy_sparse_sparsetools_ARRAY_API 3 | 4 | #include "sparsetools.h" 5 | #include "csr.h" 6 | 7 | extern "C" { 8 | #include "csr_impl.h" 9 | } 10 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/other.cxx: -------------------------------------------------------------------------------- 1 | #define NO_IMPORT_ARRAY 2 | #define PY_ARRAY_UNIQUE_SYMBOL _scipy_sparse_sparsetools_ARRAY_API 3 | 4 | #include "sparsetools.h" 5 | #include "dia.h" 6 | #include "csgraph.h" 7 | #include "coo.h" 8 | 9 | extern "C" { 10 | #include "other_impl.h" 11 | } 12 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/py3k.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Undefine macros defined by SWIG 3 | */ 4 | #if PY_VERSION_HEX >= 0x03000000 5 | 6 | #ifdef PyInt_Check 7 | #undef PyInt_Check 8 | #endif 9 | 10 | static int __pyfile_check_guard(PyObject *x) 11 | { 12 | return 0; 13 | } 14 | #define PyFile_Check(x) __pyfile_check_guard((x)) 15 | static int __pyinstance_check_guard(PyObject *x) 16 | { 17 | return 0; 18 | } 19 | #define PyInstance_Check(x) __pyinstance_check_guard((x)) 20 | 21 | #endif 22 | 23 | #include "numpy/npy_3kcompat.h" 24 | -------------------------------------------------------------------------------- /scipy/sparse/sparsetools/sparsetools.h: -------------------------------------------------------------------------------- 1 | #ifndef SPARSETOOLS_H 2 | #define SPARSETOOLS_H 3 | 4 | #include 5 | #include "numpy/ndarrayobject.h" 6 | 7 | #include 8 | 9 | #include "bool_ops.h" 10 | #include "complex_ops.h" 11 | 12 | typedef Py_ssize_t thunk_t(int I_typenum, int T_typenum, void **args); 13 | 14 | NPY_VISIBILITY_HIDDEN PyObject * 15 | call_thunk(char ret_spec, const char *spec, thunk_t *thunk, PyObject *args); 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /scipy/spatial/bscript: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | from bento.commands import hooks 4 | 5 | 6 | @hooks.pre_build 7 | def pre_build(context): 8 | conf = context.waf_context 9 | conf.check_cc(function_name='open_memstream', header_name="stdio.h") 10 | conf.write_config_header('qhull_misc_config.h') 11 | 12 | context.tweak_extension("qhull", use="LAPACK CLIB") 13 | 14 | context.tweak_extension("ckdtree", features="c cxxshlib pyext bento", 15 | includes="ckdtree/src") 16 | 17 | context.tweak_extension("_distance_wrap", use="NPYMATH") 18 | -------------------------------------------------------------------------------- /scipy/spatial/ckdtree/src/coo_entries.h: -------------------------------------------------------------------------------- 1 | #ifndef CKDTREE_COO_ENTRIES 2 | #define CKDTREE_COO_ENTRIES 3 | 4 | #include 5 | #include "numpy/arrayobject.h" 6 | 7 | struct coo_entry { 8 | npy_intp i; 9 | npy_intp j; 10 | npy_float64 v; 11 | }; 12 | 13 | #endif 14 | 15 | -------------------------------------------------------------------------------- /scipy/spatial/ckdtree/src/cpp_exc.h: -------------------------------------------------------------------------------- 1 | /* 2 | * Catch C++ standard exceptions and raise corresponding 3 | * Python exceptions. Use simplified GIL API to ensure 4 | * we have the GIL. 5 | */ 6 | 7 | 8 | #ifndef CKDTREE_CPP_EXC_H 9 | #define CKDTREE_CPP_EXC_H 10 | 11 | extern "C" void 12 | translate_cpp_exception(); 13 | 14 | extern "C" void 15 | translate_cpp_exception_with_gil(); 16 | 17 | #endif 18 | 19 | -------------------------------------------------------------------------------- /scipy/spatial/ckdtree/src/globals.cxx: -------------------------------------------------------------------------------- 1 | int number_of_processors; 2 | -------------------------------------------------------------------------------- /scipy/spatial/ckdtree/src/ordered_pair.h: -------------------------------------------------------------------------------- 1 | 2 | #ifndef CKDTREE_ORDERED_PAIR 3 | #define CKDTREE_ORDERED_PAIR 4 | 5 | struct ordered_pair { 6 | npy_intp i; 7 | npy_intp j; 8 | }; 9 | 10 | inline void 11 | add_ordered_pair(std::vector *results, 12 | const npy_intp i, const npy_intp j) 13 | { 14 | if (i > j) { 15 | ordered_pair p = {j,i}; 16 | results->push_back(p); 17 | } 18 | else { 19 | ordered_pair p = {i,j}; 20 | results->push_back(p);; 21 | } 22 | } 23 | 24 | #endif 25 | 26 | 27 | -------------------------------------------------------------------------------- /scipy/spatial/tests/data/degenerate_pointset.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/spatial/tests/data/degenerate_pointset.npz -------------------------------------------------------------------------------- /scipy/spatial/tests/data/selfdual-4d-polytope.txt: -------------------------------------------------------------------------------- 1 | # The facets of a self-dual 4-dim regular polytope 2 | # with 24 octahedron facets. Taken from cddlib. 3 | # Format b + Ax >= 0 4 | 1 1 1 1 1 5 | 1 1 1 1 -1 6 | 1 1 1 -1 1 7 | 1 1 1 -1 -1 8 | 1 1 -1 1 1 9 | 1 1 -1 1 -1 10 | 1 1 -1 -1 1 11 | 1 1 -1 -1 -1 12 | 1 -1 1 1 1 13 | 1 -1 1 1 -1 14 | 1 -1 1 -1 1 15 | 1 -1 1 -1 -1 16 | 1 -1 -1 1 1 17 | 1 -1 -1 1 -1 18 | 1 -1 -1 -1 1 19 | 1 -1 -1 -1 -1 20 | 1 2 0 0 0 21 | 1 0 2 0 0 22 | 1 0 0 2 0 23 | 1 0 0 0 2 24 | 1 -2 0 0 0 25 | 1 0 -2 0 0 26 | 1 0 0 -2 0 27 | 1 0 0 0 -2 28 | -------------------------------------------------------------------------------- /scipy/special.pxd: -------------------------------------------------------------------------------- 1 | from .special cimport cython_special 2 | -------------------------------------------------------------------------------- /scipy/special/_complexstuff.h: -------------------------------------------------------------------------------- 1 | #ifdef __cplusplus 2 | extern "C" { 3 | #endif 4 | 5 | #include 6 | 7 | #ifdef __cplusplus 8 | } 9 | #endif 10 | -------------------------------------------------------------------------------- /scipy/special/_ellip_harm_2.pxd: -------------------------------------------------------------------------------- 1 | cdef double _F_integrand(double t, void *data) nogil 2 | cdef double _F_integrand1(double t, void *data) nogil 3 | cdef double _F_integrand2(double t, void *data) nogil 4 | cdef double _F_integrand3(double t, void *data) nogil 5 | cdef double _F_integrand4(double t, void *data) nogil 6 | -------------------------------------------------------------------------------- /scipy/special/_exprel.pxd: -------------------------------------------------------------------------------- 1 | #cython: cdivison=True 2 | cdef extern from "numpy/npy_math.h": 3 | double NPY_INFINITY 4 | 5 | from libc.math cimport expm1, fabs, log 6 | 7 | cdef inline double exprel(double x) nogil: 8 | if fabs(x) < 1e-16: 9 | return 1.0 10 | elif x > 717: # near log(DBL_MAX) 11 | return NPY_INFINITY 12 | else: 13 | return expm1(x) / x 14 | 15 | -------------------------------------------------------------------------------- /scipy/special/_logit.c.src: -------------------------------------------------------------------------------- 1 | /*-*-c-*-*/ 2 | 3 | /* 4 | * ufuncs to compute logit(p) = log(p/(1-p)) and 5 | * expit(x) = 1/(1+exp(-x)) 6 | */ 7 | 8 | #include 9 | #include 10 | 11 | #include "numpy/npy_math.h" 12 | #include "_logit.h" 13 | 14 | /* 15 | * Inner loops for logit and expit 16 | */ 17 | 18 | /**begin repeat 19 | * #type = npy_float, npy_double, npy_longdouble# 20 | * #c = f,,l# 21 | */ 22 | 23 | @type@ logit@c@(@type@ x) 24 | { 25 | x /= 1 - x; 26 | return npy_log@c@(x); 27 | } 28 | 29 | @type@ expit@c@(@type@ x) 30 | { 31 | return 1 / (1 + npy_exp@c@(-x)); 32 | } 33 | 34 | /**end repeat**/ 35 | -------------------------------------------------------------------------------- /scipy/special/_logit.h: -------------------------------------------------------------------------------- 1 | #ifndef _LOGIT_H_ 2 | #define _LOGIT_H_ 3 | 4 | #include "numpy/npy_math.h" 5 | 6 | npy_float logitf(npy_float x); 7 | npy_double logit(npy_double x); 8 | npy_longdouble logitl(npy_longdouble x); 9 | 10 | npy_float expitf(npy_float x); 11 | npy_double expit(npy_double x); 12 | npy_longdouble expitl(npy_longdouble x); 13 | 14 | #endif 15 | -------------------------------------------------------------------------------- /scipy/special/_precompute/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/special/_precompute/__init__.py -------------------------------------------------------------------------------- /scipy/special/_precompute/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | from __future__ import division, print_function, absolute_import 3 | 4 | 5 | def configuration(parent_name='special', top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | config = Configuration('_precompute', parent_name, top_path) 8 | return config 9 | 10 | 11 | if __name__ == '__main__': 12 | from numpy.distutils.core import setup 13 | setup(**configuration().todict()) 14 | 15 | -------------------------------------------------------------------------------- /scipy/special/_ufuncs_cxx.pxd: -------------------------------------------------------------------------------- 1 | cimport sf_error 2 | cdef void _set_action(sf_error.sf_error_t, sf_error.sf_action_t) nogil 3 | cdef void *_export_faddeeva_dawsn 4 | cdef void *_export_faddeeva_dawsn_complex 5 | cdef void *_export_faddeeva_erf 6 | cdef void *_export_faddeeva_erfc 7 | cdef void *_export_faddeeva_erfcx 8 | cdef void *_export_faddeeva_erfcx_complex 9 | cdef void *_export_faddeeva_erfi 10 | cdef void *_export_faddeeva_erfi_complex 11 | cdef void *_export_faddeeva_log_ndtr 12 | cdef void *_export_faddeeva_ndtr 13 | cdef void *_export_faddeeva_w 14 | cdef void *_export_wrightomega -------------------------------------------------------------------------------- /scipy/special/_ufuncs_cxx_defs.h: -------------------------------------------------------------------------------- 1 | #ifndef UFUNCS_PROTO_H 2 | #define UFUNCS_PROTO_H 1 3 | #include "_faddeeva.h" 4 | npy_double faddeeva_dawsn(npy_double); 5 | npy_cdouble faddeeva_dawsn_complex(npy_cdouble); 6 | npy_cdouble faddeeva_erf(npy_cdouble); 7 | npy_cdouble faddeeva_erfc(npy_cdouble); 8 | npy_double faddeeva_erfcx(npy_double); 9 | npy_cdouble faddeeva_erfcx_complex(npy_cdouble); 10 | npy_double faddeeva_erfi(npy_double); 11 | npy_cdouble faddeeva_erfi_complex(npy_cdouble); 12 | npy_cdouble faddeeva_log_ndtr(npy_cdouble); 13 | npy_cdouble faddeeva_ndtr(npy_cdouble); 14 | npy_cdouble faddeeva_w(npy_cdouble); 15 | #include "_wright.h" 16 | npy_cdouble wrightomega(npy_cdouble); 17 | #endif 18 | -------------------------------------------------------------------------------- /scipy/special/_wright.cxx: -------------------------------------------------------------------------------- 1 | #include 2 | 3 | #include "_wright.h" 4 | 5 | using namespace std; 6 | 7 | EXTERN_C_START 8 | 9 | npy_cdouble wrightomega(npy_cdouble zp) 10 | { 11 | complex z(zp.real, zp.imag); 12 | complex w = wright::wrightomega(z); 13 | return npy_cpack(real(w), imag(w)); 14 | } 15 | 16 | EXTERN_C_END 17 | -------------------------------------------------------------------------------- /scipy/special/_wright.h: -------------------------------------------------------------------------------- 1 | #ifndef WRIGHT_H 2 | #define WRIGHT_H 3 | 4 | #ifdef __cplusplus 5 | #define EXTERN_C_START extern "C" { 6 | #define EXTERN_C_END } 7 | #else 8 | #define EXTERN_C_START 9 | #define EXTERN_C_END 10 | #endif 11 | 12 | #include 13 | #include 14 | 15 | #include "wright.hh" 16 | 17 | EXTERN_C_START 18 | 19 | #include 20 | 21 | npy_cdouble wrightomega(npy_cdouble zp); 22 | 23 | EXTERN_C_END 24 | 25 | #endif 26 | -------------------------------------------------------------------------------- /scipy/special/_xlogy.pxd: -------------------------------------------------------------------------------- 1 | # -*-cython-*- 2 | 3 | from _complexstuff cimport zlog, npy_log1p, zisnan, number_t 4 | from _cunity cimport clog1p 5 | 6 | cdef inline number_t xlogy(number_t x, number_t y) nogil: 7 | if x == 0 and not zisnan(y): 8 | return 0 9 | else: 10 | return x * zlog(y) 11 | 12 | cdef inline number_t xlog1py(number_t x, number_t y) nogil: 13 | if x == 0 and not zisnan(y): 14 | return 0 15 | else: 16 | if number_t is double: 17 | return x * npy_log1p(y) 18 | else: 19 | return x * clog1p(y) 20 | -------------------------------------------------------------------------------- /scipy/special/amos/zdiv.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZDIV(AR, AI, BR, BI, CR, CI) 2 | C***BEGIN PROLOGUE ZDIV 3 | C***REFER TO ZBESH,ZBESI,ZBESJ,ZBESK,ZBESY,ZAIRY,ZBIRY 4 | C 5 | C DOUBLE PRECISION COMPLEX DIVIDE C=A/B. 6 | C 7 | C***ROUTINES CALLED AZABS 8 | C***END PROLOGUE ZDIV 9 | DOUBLE PRECISION AR, AI, BR, BI, CR, CI, BM, CA, CB, CC, CD 10 | DOUBLE PRECISION AZABS 11 | BM = 1.0D0/AZABS(BR,BI) 12 | CC = BR*BM 13 | CD = BI*BM 14 | CA = (AR*CC+AI*CD)*BM 15 | CB = (AI*CC-AR*CD)*BM 16 | CR = CA 17 | CI = CB 18 | RETURN 19 | END 20 | -------------------------------------------------------------------------------- /scipy/special/amos/zexp.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE AZEXP(AR, AI, BR, BI) 2 | C***BEGIN PROLOGUE AZEXP 3 | C***REFER TO ZBESH,ZBESI,ZBESJ,ZBESK,ZBESY,ZAIRY,ZBIRY 4 | C 5 | C DOUBLE PRECISION COMPLEX EXPONENTIAL FUNCTION B=EXP(A) 6 | C 7 | C***ROUTINES CALLED (NONE) 8 | C***END PROLOGUE AZEXP 9 | DOUBLE PRECISION AR, AI, BR, BI, ZM, CA, CB 10 | ZM = DEXP(AR) 11 | CA = ZM*DCOS(AI) 12 | CB = ZM*DSIN(AI) 13 | BR = CA 14 | BI = CB 15 | RETURN 16 | END 17 | -------------------------------------------------------------------------------- /scipy/special/amos/zmlt.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZMLT(AR, AI, BR, BI, CR, CI) 2 | C***BEGIN PROLOGUE ZMLT 3 | C***REFER TO ZBESH,ZBESI,ZBESJ,ZBESK,ZBESY,ZAIRY,ZBIRY 4 | C 5 | C DOUBLE PRECISION COMPLEX MULTIPLY, C=A*B. 6 | C 7 | C***ROUTINES CALLED (NONE) 8 | C***END PROLOGUE ZMLT 9 | DOUBLE PRECISION AR, AI, BR, BI, CR, CI, CA, CB 10 | CA = AR*BR - AI*BI 11 | CB = AR*BI + AI*BR 12 | CR = CA 13 | CI = CB 14 | RETURN 15 | END 16 | -------------------------------------------------------------------------------- /scipy/special/amos/zshch.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE ZSHCH(ZR, ZI, CSHR, CSHI, CCHR, CCHI) 2 | C***BEGIN PROLOGUE ZSHCH 3 | C***REFER TO ZBESK,ZBESH 4 | C 5 | C ZSHCH COMPUTES THE COMPLEX HYPERBOLIC FUNCTIONS CSH=SINH(X+I*Y) 6 | C AND CCH=COSH(X+I*Y), WHERE I**2=-1. 7 | C 8 | C***ROUTINES CALLED (NONE) 9 | C***END PROLOGUE ZSHCH 10 | C 11 | DOUBLE PRECISION CCHI, CCHR, CH, CN, CSHI, CSHR, SH, SN, ZI, ZR, 12 | * DCOSH, DSINH 13 | SH = DSINH(ZR) 14 | CH = DCOSH(ZR) 15 | SN = DSIN(ZI) 16 | CN = DCOS(ZI) 17 | CSHR = SH*CN 18 | CSHI = CH*SN 19 | CCHR = CH*CN 20 | CCHI = SH*SN 21 | RETURN 22 | END 23 | -------------------------------------------------------------------------------- /scipy/special/c_misc/gammasgn.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include "misc.h" 3 | 4 | double gammasgn(double x) 5 | { 6 | double fx; 7 | 8 | if (x > 0) { 9 | return 1.0; 10 | } 11 | else { 12 | fx = floor(x); 13 | if (x - fx == 0.0) { 14 | return 0.0; 15 | } 16 | else if ((int)fx % 2) { 17 | return -1.0; 18 | } 19 | else { 20 | return 1.0; 21 | } 22 | } 23 | } 24 | 25 | -------------------------------------------------------------------------------- /scipy/special/mach/xerror.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE XERROR(MESS,NMESS,L1,L2) 2 | C 3 | C THIS IS A DUMMY XERROR ROUTINE TO PRINT ERROR MESSAGES WITH NMESS 4 | C CHARACTERS. L1 AND L2 ARE DUMMY PARAMETERS TO MAKE THIS CALL 5 | C COMPATIBLE WITH THE SLATEC XERROR ROUTINE. THIS IS A FORTRAN 77 6 | C ROUTINE. 7 | C 8 | CHARACTER*(*) MESS 9 | NN=NMESS/70 10 | NR=NMESS-70*NN 11 | IF(NR.NE.0) NN=NN+1 12 | K=1 13 | PRINT 900 14 | 900 FORMAT(/) 15 | DO 10 I=1,NN 16 | KMIN=MIN0(K+69,NMESS) 17 | PRINT *, MESS(K:KMIN) 18 | K=K+70 19 | 10 CONTINUE 20 | PRINT 900 21 | RETURN 22 | END 23 | -------------------------------------------------------------------------------- /scipy/special/sf_error.py: -------------------------------------------------------------------------------- 1 | """Warnings and Exceptions that can be raised by special functions.""" 2 | import warnings 3 | 4 | 5 | class SpecialFunctionWarning(Warning): 6 | """Warning that can be emitted by special functions.""" 7 | pass 8 | warnings.simplefilter("always", category=SpecialFunctionWarning) 9 | 10 | 11 | class SpecialFunctionError(Exception): 12 | """Exception that can be raised by special functions.""" 13 | pass 14 | -------------------------------------------------------------------------------- /scipy/special/tests/data/boost.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/special/tests/data/boost.npz -------------------------------------------------------------------------------- /scipy/special/tests/data/gsl.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/special/tests/data/gsl.npz -------------------------------------------------------------------------------- /scipy/special/tests/data/local.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/scipy/special/tests/data/local.npz -------------------------------------------------------------------------------- /scipy/special/tests/test_pcf.py: -------------------------------------------------------------------------------- 1 | """Tests for parabolic cylinder functions. 2 | 3 | """ 4 | import numpy as np 5 | from numpy.testing import assert_allclose, assert_equal 6 | import scipy.special as sc 7 | 8 | 9 | def test_pbwa_segfault(): 10 | # Regression test for https://github.com/scipy/scipy/issues/6208. 11 | # 12 | # Data generated by mpmath. 13 | # 14 | w = 1.02276567211316867161 15 | wp = -0.48887053372346189882 16 | assert_allclose(sc.pbwa(0, 0), (w, wp), rtol=1e-13, atol=0) 17 | 18 | 19 | def test_pbwa_nan(): 20 | # Check that NaN's are returned outside of the range in which the 21 | # implementation is accurate. 22 | pts = [(-6, -6), (-6, 6), (6, -6), (6, 6)] 23 | for p in pts: 24 | assert_equal(sc.pbwa(*p), (np.nan, np.nan)) 25 | -------------------------------------------------------------------------------- /scipy/special/tests/test_precompute_expn_asy.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | from numpy.testing import assert_equal 4 | 5 | from scipy.special._testutils import check_version, MissingModule 6 | from scipy.special._precompute.expn_asy import generate_A 7 | 8 | try: 9 | import sympy 10 | from sympy import Poly 11 | except ImportError: 12 | sympy = MissingModule("sympy") 13 | 14 | 15 | @check_version(sympy, "1.0") 16 | def test_generate_A(): 17 | # Data from DLMF 8.20.5 18 | x = sympy.symbols('x') 19 | Astd = [Poly(1, x), 20 | Poly(1, x), 21 | Poly(1 - 2*x), 22 | Poly(1 - 8*x + 6*x**2)] 23 | Ares = generate_A(len(Astd)) 24 | 25 | for p, q in zip(Astd, Ares): 26 | assert_equal(p, q) 27 | -------------------------------------------------------------------------------- /scipy/special/tests/test_round.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function, absolute_import 2 | 3 | import numpy as np 4 | from numpy.testing import dec 5 | 6 | from scipy.special import _test_round 7 | 8 | 9 | @dec.skipif(not _test_round.have_fenv()) 10 | def test_add_round_up(): 11 | np.random.seed(1234) 12 | _test_round.test_add_round(10**5, 'up') 13 | 14 | 15 | @dec.skipif(not _test_round.have_fenv()) 16 | def test_add_round_down(): 17 | np.random.seed(1234) 18 | _test_round.test_add_round(10**5, 'down') 19 | -------------------------------------------------------------------------------- /scipy/special/utils/README: -------------------------------------------------------------------------------- 1 | This contains a few hacks to re-use BOOST C++ library special function tests 2 | data for scipy.special 3 | 4 | convert.py 5 | ---------- 6 | 7 | This script parse the BOOST data and write the data into a CVS text file. For 8 | each data file, a subdirectory is created, as one boost data file (.ipp) can 9 | have several test sets. 10 | -------------------------------------------------------------------------------- /scipy/special/wright.hh: -------------------------------------------------------------------------------- 1 | #ifndef WRIGHT_HH 2 | #define WRIGHT_HH 3 | 4 | #include 5 | 6 | namespace wright { 7 | 8 | int wrightomega_ext(std::complex z, std::complex *w, 9 | std::complex *cond); 10 | std::complex wrightomega(std::complex z); 11 | 12 | }; 13 | 14 | #endif /* wright.hh */ 15 | -------------------------------------------------------------------------------- /scipy/stats/_constants.py: -------------------------------------------------------------------------------- 1 | """ 2 | Statistics-related constants. 3 | 4 | """ 5 | from __future__ import division, print_function, absolute_import 6 | 7 | import numpy as np 8 | 9 | 10 | # The smallest representable positive number such that 1.0 + _EPS != 1.0. 11 | _EPS = np.finfo(float).eps 12 | 13 | # The largest [in magnitude] usable floating value. 14 | _XMAX = np.finfo(float).max 15 | 16 | # The log of the largest usable floating value; useful for knowing 17 | # when exp(something) will overflow 18 | _LOGXMAX = np.log(_XMAX) 19 | 20 | # The smallest [in magnitude] usable floating value. 21 | _XMIN = np.finfo(float).tiny 22 | 23 | # -special.psi(1) 24 | _EULER = 0.577215664901532860606512090082402431042 25 | 26 | # special.zeta(3, 1) Apery's constant 27 | _ZETA3 = 1.202056903159594285399738161511449990765 28 | -------------------------------------------------------------------------------- /scipy/stats/bento.info: -------------------------------------------------------------------------------- 1 | HookFile: bscript 2 | 3 | Library: 4 | CompiledLibrary: statlibimp 5 | Sources: 6 | statlib/ansari.f, 7 | statlib/spearman.f, 8 | statlib/swilk.f 9 | Extension: statlib 10 | Sources: statlib.pyf 11 | Extension: mvn 12 | Sources: mvn.pyf, mvndst.f 13 | Extension: _stats 14 | Sources: _stats.c 15 | -------------------------------------------------------------------------------- /scipy/stats/bscript: -------------------------------------------------------------------------------- 1 | from bento.commands import hooks 2 | 3 | @hooks.pre_build 4 | def pre_build(context): 5 | default_builder = context.default_builder 6 | 7 | def builder(extension): 8 | return default_builder(extension, features="c cstlib pyext bento") 9 | context.register_compiled_library_builder("statlibimp", builder) 10 | 11 | context.tweak_extension("statlib", features="c fc cshlib pyext bento f2py", 12 | use="statlibimp CLIB") 13 | context.tweak_extension("mvn", features="c fc cshlib pyext bento f2py", 14 | use="CLIB") 15 | -------------------------------------------------------------------------------- /tools/ci/README.txt: -------------------------------------------------------------------------------- 1 | Continuous integration support files 2 | ------------------------------------ 3 | 4 | - devdocs-deploy.key.enc 5 | 6 | Encrypted upload key for developer docs, built on travis-ci 7 | -------------------------------------------------------------------------------- /tools/ci/devdocs-deploy.key.enc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/tools/ci/devdocs-deploy.key.enc -------------------------------------------------------------------------------- /tools/ci/devdocs-deploy.key.pub: -------------------------------------------------------------------------------- 1 | ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC26iO18v6sItplYLAjWT/27EJF+HVMvJQr4P4g/3jZFbKsmKwSzW+Li9sVUoI/mqoN6EVCE1wuj/Ytbf6As9kXMDRHeuyHOA0GAygvq4bDb//xzs10DslmgIqcvKoA/NvebqF2FR3lVBFEKgGY7dlrhaARVE06SmoRrCOr5D9lww3YCUYHSWs7hS5Ci/McUAfw61Eqh+bBDJ2ym2REYN45PxvhtzaVwmqo4a1OrX7HAvkdW+K4l5LHAilHjoeZRZXqm7AlJXuf1rT2YxrRnW2h9hxD6/GkdoF7NpAqxP3scVHBwrsXjket9PuD+d/Ci0DHTxqOoFPaIhbwximiaEyP scipy-travis-bot@nomail 2 | -------------------------------------------------------------------------------- /tools/scipy-macosx-installer/README.txt: -------------------------------------------------------------------------------- 1 | This is a set of scripts used to build a scipy .dmg installer with 2 | documentation. 3 | 4 | The actual content of the dmg is to be put in content: documentation go into 5 | the Documentation subdir, and the .mpkg installer for numpuy itself in the 6 | content directory. The name of the installer should match exactly the one in 7 | the scipy script (otherwise, the background will not appear correctly). 8 | 9 | The artwork is done in inkscape. 10 | 11 | The main script (new-create-dmg) was taken from stackoverflow. 12 | -------------------------------------------------------------------------------- /tools/scipy-macosx-installer/art/dmgbackground.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jakevdp/scipy/d3c5c88a51fe29b9c5e7f6187b35c14917a68de0/tools/scipy-macosx-installer/art/dmgbackground.png --------------------------------------------------------------------------------