changes related to MacOS update to 14.1

ssandrews · Oct 31, 2023 · 95bd2f1 · 95bd2f1
1 parent a1a77a5
commit 95bd2f1
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Showing 14 changed files with 1,106 additions and 1,413 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -254,7 +254,7 @@ elseif (APPLE)
     message(STATUS "Compiling on an Apple computer")
     message(STATUS "Host system version is ${CMAKE_HOST_SYSTEM_VERSION}")
     if(CMAKE_HOST_SYSTEM_VERSION VERSION_GREATER_EQUAL 21)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-deprecated -mmacosx-version-min=13")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-deprecated -mmacosx-version-min=14")
     elseif()
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-deprecated -mmacosx-version-min=10.9")
     endif()
@@ -412,6 +412,11 @@ if (OPTION_USE_LIBTIFF)
         find_library(TIFF_LIBRARY libtiff.a ${CMAKE_SOURCE_DIR}/Mac/libtiff/lib NO_DEFAULT_PATH)
     else ()
         find_package(TIFF)
+        if(TIFF_LIBRARY)
+            cmake_path(GET TIFF_LIBRARY PARENT_PATH TIFF_RPATH)
+            message(STATUS "Libtiff run path: '${TIFF_RPATH}'")
+            list(APPEND RUN_LIBS ${TIFF_RPATH})
+        endif()
     endif()
 
     if(TIFF_INCLUDE_DIR AND TIFF_LIBRARY)
@@ -505,6 +510,9 @@ if (OPTION_TARGET_SMOLDYN)
     add_executable(smoldyn ${MAIN_FILES})
     target_link_libraries(smoldyn PUBLIC smoldyn_static)
     target_link_libraries(smoldyn PUBLIC ${DEP_LIBS})
+    if(RUN_LIBS)
+        set_target_properties(smoldyn PROPERTIES INSTALL_RPATH ${RUN_LIBS})
+		endif()
 endif ()
 
 

diff --git a/Mac/libtiff/lib/libtiff.5.7.0.dylib b/Mac/libtiff/lib/libtiff.5.7.0.dylib
diff --git a/Mac/libtiff/lib/libtiff.5.dylib b/Mac/libtiff/lib/libtiff.5.dylib
diff --git a/Mac/libtiff/lib/libtiff.dylib b/Mac/libtiff/lib/libtiff.dylib
diff --git a/Mac/libtiff/lib/libtiffxx.5.7.0.dylib b/Mac/libtiff/lib/libtiffxx.5.7.0.dylib
diff --git a/Mac/libtiff/lib/libtiffxx.5.dylib b/Mac/libtiff/lib/libtiffxx.5.dylib
diff --git a/Mac/libtiff/lib/libtiffxx.dylib b/Mac/libtiff/lib/libtiffxx.dylib
diff --git a/docs/Smoldyn/SmoldynCodeDoc.pdf b/docs/Smoldyn/SmoldynCodeDoc.pdf
diff --git a/docs/Smoldyn/SmoldynCodeDoc.tex b/docs/Smoldyn/SmoldynCodeDoc.tex
diff --git a/docs/libSteve/SurfaceParam.pdf b/docs/libSteve/SurfaceParam.pdf
diff --git a/docs/libSteve/SurfaceParam.tex b/docs/libSteve/SurfaceParam.tex
@@ -200,7 +200,7 @@ \section{Functions for external use}
 
 
 \item[\ttt{int}]
-\ttt{surfacetransmit(double *kap1ptr,double *kap2ptr,double *p1ptr,double *p2ptr,double difc1,double difc2,double dt);}
+\ttt{surfacetransmit(double *kap1ptr, double *kap2ptr, double *p1ptr, double *p2ptr, double difc1, double difc2, double dt);}
 
 This expands upon \ttt{surfaceprob} and \ttt{surfacerate} for partial transmission, offering additional functionality. This function allows for, but doesn't require, different diffusion coefficients on the two sides of the surface, entered in \ttt{difc1} and \ttt{difc2}. Also, \ttt{dt} is the simulation time step. The four transmission parameters are $\kappa_1$, $\kappa_2$, $P_1$, and $P_2$, of which one side 1 value and one side 2 value should be entered as inputs, and the other two values will be returned as outputs; the side number represents the side that a molecule diffuses \textit{from}. All of these values are entered as pointers due to the fact that two of them will be outputs. Enter the output parameters with the value $-2$ to show that they are unknowns. The input parameters are not changed by this function.
 

diff --git a/examples/S94_archive/Andrews_Arkin_2010/ellipse_12_12.txt b/examples/S94_archive/Andrews_Arkin_2010/ellipse_12_12.txt