biology/hyphy: Update to 2.5.38

Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38

Sponsored by:	The FreeBSD Foundation

5 files changed, 11 insertions, 231 deletions

diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 9f1d25f3fd12..80ae747bc589 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.36
+DISTVERSION=	2.5.38
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index db30c7c8c9e3..0e642ff3cb29 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1643865503
-SHA256 (veg-hyphy-2.5.36_GH0.tar.gz) = c48a077deff3e06cadffa94cd5e91ab659b0ebc6cb60a0d090747bfeff69aae1
-SIZE (veg-hyphy-2.5.36_GH0.tar.gz) = 5362425
+TIMESTAMP = 1650376110
+SHA256 (veg-hyphy-2.5.38_GH0.tar.gz) = 1b66af17f9f7dd0e9951a9bd3b106b95bf5915a78523973ba79af64f970770d6
+SIZE (veg-hyphy-2.5.38_GH0.tar.gz) = 5365153
diff --git a/biology/hyphy/files/patch-src_core_include_function__templates.h b/biology/hyphy/files/patch-src_core_include_function__templates.h
deleted file mode 100644
index 7ca06b1cc56a..000000000000
--- a/biology/hyphy/files/patch-src_core_include_function__templates.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/core/include/function_templates.h.orig	2022-02-21 19:44:45 UTC
-+++ src/core/include/function_templates.h
-@@ -156,7 +156,6 @@ void ArrayForEach(ARG_TYPE *array, unsigned long dimen
- template <typename ARG_TYPE>
- void InitializeArray(ARG_TYPE *array, unsigned long dimension,
-                      ARG_TYPE &&value) {
--  #pragma clang loop unroll_count(8)
-   #pragma GCC unroll 4
-   for (unsigned long i = 0UL; i < dimension; i++) {
-     array[i] = value;
diff --git a/biology/hyphy/files/patch-src_core_matrix.cpp b/biology/hyphy/files/patch-src_core_matrix.cpp
index 0d5720b2751b..a4a280d2d94c 100644
--- a/biology/hyphy/files/patch-src_core_matrix.cpp
+++ b/biology/hyphy/files/patch-src_core_matrix.cpp
@@ -1,6 +1,6 @@
---- src/core/matrix.cpp.orig	2022-02-21 19:46:34 UTC
+--- src/core/matrix.cpp.orig	2022-04-24 18:04:11 UTC
 +++ src/core/matrix.cpp
-@@ -3391,7 +3391,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
+@@ -3405,7 +3405,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
          #pragma GCC unroll 4
          #pragma clang loop vectorize(enable)
          #pragma clang loop interleave(enable)
@@ -8,31 +8,7 @@
          #pragma GCC ivdep
          #pragma ivdep
                 for (long idx = 0; idx < upto; idx+=16) {
-@@ -3410,7 +3409,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
-         #pragma GCC unroll 4
-         #pragma clang loop vectorize(enable)
-         #pragma clang loop interleave(enable)
--        #pragma clang loop unroll(enable)
-         #pragma GCC ivdep
-         #pragma ivdep
-                for (long idx = 0; idx < upto; idx+=8) {
-@@ -3440,7 +3438,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
-             #pragma GCC unroll 4
-             #pragma clang loop vectorize(enable)
-             #pragma clang loop interleave(enable)
--            #pragma clang loop unroll(enable)
-                  for (long idx = 0; idx < upto; idx+=16) {
-                      CELL_OP (idx);
-                      CELL_OP (idx+4);
-@@ -3454,7 +3451,6 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix
-         #pragma GCC unroll 4
-         #pragma clang loop vectorize(enable)
-         #pragma clang loop interleave(enable)
--        #pragma clang loop unroll(enable)
-         #pragma GCC ivdep
-         #pragma ivdep
-                for (long idx = 0; idx < upto; idx+=8) {
-@@ -3895,7 +3891,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
+@@ -3909,7 +3908,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
                                   #pragma GCC unroll 4
                                   #pragma clang loop vectorize(enable)
                                   #pragma clang loop interleave(enable)
@@ -40,7 +16,7 @@
                                   for (long k = 0; k < vDim; k+=4) {
                                        __m256d D4, B4;
                                        DO_GROUP_OP (D4, B4, k);
-@@ -3946,7 +3941,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
+@@ -3960,7 +3958,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
                                    #pragma GCC unroll 4
                                    #pragma clang loop vectorize(enable)
                                    #pragma clang loop interleave(enable)
@@ -48,15 +24,7 @@
                                    for (long k = 0; k < vDim; k+=2) {
                                        __m128d D4, B4;
                                        DO_GROUP_OP1 (D4, B4, k);
-@@ -3998,7 +3992,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                             #pragma GCC unroll 4
-                             #pragma clang loop vectorize(enable)
-                             #pragma clang loop interleave(enable)
--                            #pragma clang loop unroll(enable)
-                             for (long k = 0; k < vDim; k+=2) {
-                                 float64x2_t D4, B4;
-                                 DO_GROUP_OP1 (D4, B4, k);
-@@ -4163,7 +4156,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
+@@ -4177,7 +4174,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
                              #pragma GCC unroll 4
                              #pragma clang loop vectorize(enable)
                              #pragma clang loop interleave(enable)
@@ -64,7 +32,7 @@
                                for (long k = 0; k < dimm4; k+=4) {
                                    __m256d D4, B4;
                                    DO_GROUP_OP (D4, B4, k);
-@@ -4271,7 +4263,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
+@@ -4285,7 +4281,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
                                          #pragma GCC unroll 4
                                          #pragma clang loop vectorize(enable)
                                          #pragma clang loop interleave(enable)
@@ -72,15 +40,7 @@
                                          for (long k = 0; k < dimm4; k+=2) {
                                              __m128d D4, B4;
                                              DO_GROUP_OP1 (D4, B4, k);
-@@ -4380,7 +4371,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
-                                   #pragma GCC unroll 4
-                                   #pragma clang loop vectorize(enable)
-                                   #pragma clang loop interleave(enable)
--                                  #pragma clang loop unroll(enable)
-                                   for (long k = 0; k < dimm4; k+=2) {
-                                       float64x2_t D4, B4;
-                                       DO_GROUP_OP1 (D4, B4, k);
-@@ -4441,7 +4431,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
+@@ -4455,7 +4450,6 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix 
                          #pragma GCC unroll 8
                          #pragma clang loop vectorize(enable)
                          #pragma clang loop interleave(enable)
@@ -88,19 +48,3 @@
                          for (long k = 0, column = j*hDim; k < vDim; k++, column ++) {
                              resCell += row[k] * secondArg.theData [column];
                          }
-@@ -5822,7 +5811,6 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, b
-                     #pragma GCC unroll 4
-                     #pragma clang loop vectorize(enable)
-                     #pragma clang loop interleave(enable)
--                    #pragma clang loop unroll(enable)
-                     for (long c = from; c < compressedIndex[r]; c++, i++) {
-                         theIndex[i] = compressedIndex[c+hDim] * vDim + r;
-                     }
-@@ -6988,7 +6976,6 @@ hyFloat        _Matrix::Sqr (hyFloat* _hprestrict_ sta
-                         #pragma GCC unroll 4
-                         #pragma clang loop vectorize(enable)
-                         #pragma clang loop interleave(enable)
--                        #pragma clang loop unroll(enable)
-                         #pragma GCC ivdep
-                         #pragma ivdep
-                         for (long k = 0; k < loopBound; k+=4) {
diff --git a/biology/hyphy/files/patch-src_core_tree__evaluator.cpp b/biology/hyphy/files/patch-src_core_tree__evaluator.cpp
deleted file mode 100644
index 3adcafaf5866..000000000000
--- a/biology/hyphy/files/patch-src_core_tree__evaluator.cpp
+++ /dev/null
@@ -1,154 +0,0 @@
---- src/core/tree_evaluator.cpp.orig	2022-02-21 19:48:41 UTC
-+++ src/core/tree_evaluator.cpp
-@@ -127,7 +127,6 @@ inline double _sse_sum_2 (__m128d const & x) {
- template<long D> inline void __ll_handle_matrix_transpose (hyFloat const * __restrict transitionMatrix, hyFloat * __restrict tMatrixT) {
-     long i = 0L;
-     for (long r = 0L; r < D; r++) {
--        #pragma unroll(4)
-         #pragma GCC unroll 4
-         for (long c = 0L; c < D; c++, i++) {
-             tMatrixT[c*D+r] = transitionMatrix[i];
-@@ -154,7 +153,6 @@ template<long D> inline bool __ll_handle_conditional_a
-                 }
-             }*/
-             
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long k = 0L; k < D; k++) {
-                 parentConditionals[k] *= tMatrix[siteState+D*k];
-@@ -172,7 +170,6 @@ template<long D> inline bool __ll_handle_conditional_a
-     } else {
-         if (tcc) {
-             if (__builtin_expect((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom,0)) {
--                #pragma unroll(4)
-                 #pragma GCC unroll 4
-                 for (long k = 0L; k < D; k++) {
-                     childVector[k] = lastUpdatedSite[k];
-@@ -200,7 +197,6 @@ inline bool __ll_handle_conditional_array_initializati
-         }
-         if (__builtin_expect(siteState >= 0L,1)) {
-             // a single character state; sweep down the appropriate column
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long k = 0L; k < D; k++) {
-                 parentConditionals[k] *= tMatrix[siteState+D*k];
-@@ -212,7 +208,6 @@ inline bool __ll_handle_conditional_array_initializati
-     } else {
-         if (tcc) {
-             if (__builtin_expect((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom,0)) {
--                #pragma unroll(4)
-                 #pragma GCC unroll 4
-                 for (long k = 0L; k < D; k++) {
-                     childVector[k] = lastUpdatedSite[k];
-@@ -542,7 +537,6 @@ template<long D> inline void __ll_product_sum_loop (hy
-         #pragma GCC unroll 8
-         #pragma clang loop vectorize(enable)
-         #pragma clang loop interleave(enable)
--        #pragma clang loop unroll(enable)
-         for (long c = 0; c < D; c++)
-             accumulator +=  tMatrix[c]   * childVector[c];
-         
-@@ -558,7 +552,6 @@ inline void __ll_product_sum_loop_generic (hyFloat con
-         #pragma GCC unroll 8
-         #pragma clang loop vectorize(enable)
-         #pragma clang loop interleave(enable)
--        #pragma clang loop unroll(enable)
-         for (long c = 0; c < D; c++)
-             accumulator +=  tMatrix[c]   * childVector[c];
-         
-@@ -595,7 +588,6 @@ template<long D, bool ADJUST> inline void __ll_loop_ha
-             fprintf (stderr, "UP %ld (%ld) %lg\n", didScale, parentCode, scaler);
-         }*/
-         if (didScale) {
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long c = 0; c < D; c++) {
-                 parentConditionals [c] *= scaler;
-@@ -626,7 +618,6 @@ template<long D, bool ADJUST> inline void __ll_loop_ha
-                 }*/
-                 
-                 if (didScale) {
--                    #pragma unroll(4)
-                     #pragma GCC unroll 4
-                     for (long c = 0; c < D; c++) {
-                         parentConditionals [c] *= scaler;
-@@ -657,7 +648,6 @@ template<bool ADJUST> inline void __ll_loop_handle_sca
-         hyFloat scaler = _computeBoostScaler(scalingAdjustments [parentCode*siteCount + siteID] * _lfScalerUpwards, sum, didScale);
-         
-         if (didScale) {
--            #pragma unroll(8)
-             #pragma GCC unroll 8
-             for (long c = 0; c < D; c++) {
-                 parentConditionals [c] *= scaler;
-@@ -679,7 +669,6 @@ template<bool ADJUST> inline void __ll_loop_handle_sca
-                 hyFloat scaler = _computeReductionScaler (scalingAdjustments [parentCode*siteCount + siteID] * _lfScalingFactorThreshold, sum, didScale);
-                 
-                 if (didScale) {
--                    #pragma unroll(8)
-                     #pragma GCC unroll 8
-                     for (long c = 0; c < D; c++) {
-                          parentConditionals [c] *= scaler;
-@@ -707,7 +696,6 @@ template<long D> inline void __ll_loop_handle_leaf_cas
-     } else {
-         for (long k = siteFrom; k < siteTo; k++, pp += D) {
-             hyFloat lsf = localScalingFactor[k];
--#pragma unroll(4)
- #pragma GCC unroll 4
-             for (long s = 0; s < D; s++) {
-                 pp[s] = lsf;
-@@ -1585,7 +1573,6 @@ hyFloat      _TheTree::ComputeTreeBlockByBranch  (    
-             accumulator         = rootConditionals[rootIndex + rootState] * theProbs[rootState];
-             rootIndex           += alphabetDimension;
-         } else {
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long p = 0; p < alphabetDimension; p++,rootIndex++) {
-                 accumulator += rootConditionals[rootIndex] * theProbs[p];
-@@ -1644,7 +1631,6 @@ template<long D> inline bool __lcache_loop_preface (bo
-         long siteState = lNodeFlags[nodeCode*siteCount + siteOrdering.list_data[siteID]] ;
-         if (siteState >= 0L) {
-             unsigned long target_index = siteState;
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long k = 0L; k < D; k++, target_index+=D) {
-                 parentConditionals[k]   *= tMatrix[target_index];
-@@ -1659,7 +1645,6 @@ template<long D> inline bool __lcache_loop_preface (bo
-             if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom)
-                 // the value of this conditional vector needs to be copied from a previously stored site
-                 // subtree duplication
--                #pragma unroll(4)
-                 #pragma GCC unroll 4
-                 for (long k = 0UL; k < D; k++) {
-                     childVector[k] = lastUpdatedSite[k];
-@@ -1688,7 +1673,6 @@ inline bool __lcache_loop_preface_generic (bool isLeaf
-         long siteState = lNodeFlags[nodeCode*siteCount + siteOrdering.list_data[siteID]] ;
-         if (siteState >= 0L) {
-             unsigned long target_index = siteState;
--            #pragma unroll(4)
-             #pragma GCC unroll 4
-             for (long k = 0L; k < D; k++, target_index+=D) {
-                 parentConditionals[k]   *= tMatrix[target_index];
-@@ -1704,7 +1688,6 @@ inline bool __lcache_loop_preface_generic (bool isLeaf
-             if ((tcc->list_data[currentTCCIndex] & bitMaskArray.masks[currentTCCBit]) > 0 && siteID > siteFrom)
-                 // the value of this conditional vector needs to be copied from a previously stored site
-                 // subtree duplication
--                #pragma unroll(4)
-                 #pragma GCC unroll 4
-                 for (long k = 0UL; k < D; k++) {
-                     childVector[k] = lastUpdatedSite[k];
-@@ -1966,7 +1949,6 @@ void            _TheTree::ComputeBranchCache    (
-                 unsigned long k3     = 0UL;
-                 for (unsigned long k = siteFrom; k < siteTo; k++) {
-                     hyFloat scaler = localScalingFactor[k];
--                    #pragma unroll(4)
-                     #pragma GCC unroll 4
-                     for (unsigned long k2 = 0UL; k2 < alphabetDimension; k2++, k3++) {
-                         parentConditionals [k3] = scaler;
-@@ -2474,7 +2456,6 @@ void            _TheTree::ComputeBranchCache    (
-                     #pragma GCC unroll 8
-                     #pragma clang loop vectorize(enable)
-                     #pragma clang loop interleave(enable)
--                    #pragma clang loop unroll(enable)
-                     for (long k = 0; k < alphabetDimension; k++) {
-                         sum += parentConditionals[k];
-                     }