From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch | 154 +++++++++++++++++++++ 1 file changed, 154 insertions(+) create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch (limited to 'sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch') diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch new file mode 100644 index 000000000000..96cb21531bbf --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch @@ -0,0 +1,154 @@ + .../scitbx/math/boost_python/distributions.cpp | 60 +++++++++++++------ + cctbx_sources/scitbx/rigid_body/spatial_lib.h | 1 + + cctbx_sources/scitbx/rigid_body/tardy.h | 4 +- + .../refinement/boost_python/weighting_schemes.cpp | 4 +- + .../smtbx/structure_factors/direct/standard_xray.h | 4 +- + 5 files changed, 48 insertions(+), 25 deletions(-) + +diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +index a676798..68818e7 100644 +--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp ++++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +@@ -59,29 +59,51 @@ namespace { + { + typedef Distribution wt; + ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self) { \ ++ return boost::math::name(self); \ ++ } ++ ++ NEW_MEMBER(mean); ++ NEW_MEMBER(median); ++ NEW_MEMBER(mode); ++ NEW_MEMBER(variance); ++ NEW_MEMBER(standard_deviation); ++ NEW_MEMBER(skewness); ++ NEW_MEMBER(kurtosis); ++ ++ #undef NEW_MEMBER ++ ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self, FloatType arg) { \ ++ return boost::math::name(self, arg); \ ++ } ++ ++ NEW_MEMBER(pdf); ++ NEW_MEMBER(cdf); ++ NEW_MEMBER(quantile); ++ ++ #undef NEW_MEMBER ++ ++ static scitbx::af::shared quantiles(wt const &self, std::size_t n) { ++ return scitbx::math::quantiles(self, n); ++ } ++ + static void + wrap() + { + using namespace boost::python; +- def("mean", (FloatType(*)(wt const&)) boost::math::mean); +- def("median", (FloatType(*)(wt const&)) boost::math::median); +- def("mode", (FloatType(*)(wt const&)) boost::math::mode); +- def("variance", (FloatType(*)(wt const&)) boost::math::variance); +- def("standard_deviation", +- (FloatType(*)(wt const&)) boost::math::standard_deviation); +- def("skewness", (FloatType(*)(wt const&)) boost::math::skewness); +- def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis); +- def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf); +- def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf); +- def("quantile", (FloatType(*)(wt const&, FloatType const&)) +- boost::math::quantile); +- def("quantiles", +-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306)) +- (scitbx::af::shared(*)(wt const&, std::size_t)) quantiles +-#else +- quantiles +-#endif +- ); ++ def("mean" , mean); ++ def("median" , median); ++ def("mode" , mode); ++ def("variance" , variance); ++ def("standard_deviation", standard_deviation); ++ def("skewness" , skewness); ++ def("kurtosis" , kurtosis); ++ def("pdf" , pdf); ++ def("cdf" , cdf); ++ def("quantile" , quantile); ++ def("quantiles" , quantiles); + } + }; + +diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +index a084f0f..e377292 100755 +--- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h ++++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +@@ -2,6 +2,7 @@ + #define SCITBX_RIGID_BODY_SPATIAL_LIB_H + + #include ++#include + #include + + namespace scitbx { namespace rigid_body { +diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h +index 104f16b..a8f76cc 100755 +--- a/cctbx_sources/scitbx/rigid_body/tardy.h ++++ b/cctbx_sources/scitbx/rigid_body/tardy.h +@@ -346,7 +346,7 @@ namespace tardy { + unsigned nb = this->bodies_size(); + af::shared > result((af::reserve(nb))); + af::shared > +- tau_array = f_ext_as_tau(f_ext_array().const_ref()); ++ tau_array = this->f_ext_as_tau(f_ext_array().const_ref()); + for(unsigned ib=0;ibbodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib])); +@@ -379,7 +379,7 @@ namespace tardy { + qdd_array() + { + if (!qdd_array_) { +- qdd_array_ = forward_dynamics_ab( ++ qdd_array_ = this->forward_dynamics_ab( + /*tau_array*/ af::const_ref >(0, 0), + f_ext_array().const_ref(), + /*grav_accn*/ af::const_ref(0, 0)); +diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +index ce0c27b..904e8d7 100644 +--- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp ++++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares { + : base_t(name, boost::python::no_init) + { + using namespace boost::python; +- def("__call__", &wt::operator(), ++ this->def("__call__", &wt::operator(), + (arg("fo_sq"), arg("sigma"), arg("fc_sq"))); +- def("__call__", weights, ++ this->def("__call__", weights, + (arg("fo_sq"), arg("sigmas"), arg("fc_sq"))); + } + }; +diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +index 5e2df76..911bfde 100644 +--- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h ++++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); + f *= dw; +@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + float_type fa = f.real(), fb = f.imag(); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); -- cgit v1.2.3