[med-svn] [Git][med-team/hyphy][upstream] New upstream version 2.5.57+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / hyphy


Commits:
39b2a0ec by Étienne Mollier at 2023-11-24T12:26:19+01:00
New upstream version 2.5.57+dfsg
- - - - -


3 changed files:

- CMakeLists.txt
- res/TemplateBatchFiles/MSS-selector.bf
- src/core/global_things.cpp


Changes:

=====================================
CMakeLists.txt
=====================================
@@ -183,9 +183,9 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     endif()
 
     if(${GCC_VERSION} VERSION_LESS 6.0)
-      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2   -Wall -std=gnu++14 -g ")
+      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2   -Wall -std=gnu++14")
     else(${GCC_VERSION} VERSION_LESS 6.0)
-      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2   -Wall -std=c++14 -g")
+      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2   -Wall -std=c++14")
     endif(${GCC_VERSION} VERSION_LESS 6.0)
 
     #set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}  -fopt-info")
@@ -492,11 +492,11 @@ if(${MPI_FOUND})
         HYPHYMPI
         PROPERTIES
         if(${OPENMP_FOUND})
-            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g"
-            LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g"
+            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
+            LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
         else(${OPENMP_FOUND})
-            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} -g"
-            LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} -g"
+            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS}"
+            LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS}"
         endif(${OPENMP_FOUND})
     )
 endif(${MPI_FOUND})
@@ -631,11 +631,11 @@ set_target_properties(
     hyphy
     PROPERTIES
     if(${OPENMP_FOUND})
-        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g "
-        LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g "
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
+        LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
     else(${OPENMP_FOUND})
-        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} -g "
-        LINK_FLAGS "${DEFAULT_LINK_FLAGS} -g "
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS}"
+        LINK_FLAGS "${DEFAULT_LINK_FLAGS}"
     endif(${OPENMP_FOUND})
 )
 


=====================================
res/TemplateBatchFiles/MSS-selector.bf
=====================================
@@ -69,7 +69,7 @@ mss.ic_score = io.SelectAnOption  ({"AIC-c" : "Small Sample AIC score",
 mss.is_bic = mss.ic_score == "BIC";
 
 KeywordArgument ("classes",        "How many rate classes should be considered", "2");  
-mss.rate_classes = io.PromptUser ("How many rate classes should be considered?", 2, 2, 5, TRUE);
+mss.rate_classes = io.PromptUser ("How many rate classes should be considered?", 2, 2, 6, TRUE);
 
 
 mss.file_records = {};


=====================================
src/core/global_things.cpp
=====================================
@@ -122,7 +122,7 @@ namespace hy_global {
                      kErrorStringMatrixExportError    ("Export matrix called with a non-polynomial matrix argument"),
                      kErrorStringNullOperand          ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
                      kErrorNumerical                   ("To treat numerical errors as warnings, please specify \"ENV=TOLERATE_NUMERICAL_ERRORS=1;\" as the command line argument. This often resolves the issue, which is indicative of numerical instability."),
-                     kHyPhyVersion  = _String ("2.5.56"),
+                     kHyPhyVersion  = _String ("2.5.57"),
     
                     kNoneToken = "None",
                     kNullToken = "null",



View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/39b2a0ecbed9e57d460f94e22dee214d46300852

-- 
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/commit/39b2a0ecbed9e57d460f94e22dee214d46300852
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