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Nonchombo build #31

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merged 74 commits into from
May 25, 2024
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91bdb32
fix implicit C declaration, no longer allowed
jcschaff Oct 27, 2023
bc70c85
add imports for std::numeric_limits and sqrt
jcschaff Oct 27, 2023
e7c2423
fix bug in SundialsPdeSolver, incorrect masks for Dirichlet boundaries
jcschaff Oct 27, 2023
83aa4f3
fix warnings due to unsafe sprintf
jcschaff Oct 27, 2023
b6a7de5
changed cd.yml to re-enable all platforms
CodeByDrescher Jan 16, 2024
3c95294
Added quick fix to allow Gibson solver on linux (needs proper CMake fix)
CodeByDrescher Jan 16, 2024
4691fca
updated to ubuntu latest; started fixing problems
CodeByDrescher Jan 16, 2024
c3e302b
removed superfluous relocatable object path stuff
CodeByDrescher Jan 16, 2024
71c4667
temporary comment out of Docker code
CodeByDrescher Jan 16, 2024
43e7104
fixing tar pathing
CodeByDrescher Jan 16, 2024
8612a09
Converted almost all dangerous char buffers to std::string
CodeByDrescher Jan 18, 2024
13403d1
Update cd.yml to try and perform build on windows
CodeByDrescher Jan 18, 2024
de30d2a
Attempting to fix pthreads issue in GH action
CodeByDrescher Jan 18, 2024
db05bac
Update cd.yml to try and use working windows-desktop config
CodeByDrescher Jan 19, 2024
f0aad87
attempt to fix syntax errors
CodeByDrescher Jan 19, 2024
01249c6
forgot backslash
CodeByDrescher Jan 19, 2024
f79b913
invesitgating
CodeByDrescher Jan 19, 2024
25d4448
More investigation
CodeByDrescher Jan 19, 2024
13e2cbc
attempting manual call to pacman to install dependencies
CodeByDrescher Jan 19, 2024
8bffb84
Restoring old style of build
CodeByDrescher Jan 23, 2024
9f59ac2
Update cd.yml to fix bad comment
CodeByDrescher Jan 23, 2024
14ff251
investigating fix for compiler complaint
CodeByDrescher Jan 23, 2024
677fc3c
Merge branch 'nonchombo-build' of https://github.com/virtualcell/vcel…
CodeByDrescher Jan 23, 2024
cb9bfe0
Attempting to add missing libs
CodeByDrescher Jan 23, 2024
7d04945
fixed curl install
CodeByDrescher Jan 23, 2024
6b376c9
attempting to add libaec to fix linking issue
CodeByDrescher Jan 23, 2024
d66c8ef
Attempting to insert linker flag.
CodeByDrescher Jan 24, 2024
952d780
Attempting a different link method
CodeByDrescher Jan 25, 2024
a8c46eb
attempting to force MINGW build
CodeByDrescher Jan 25, 2024
87d84e0
Attempting to remove static link flags
CodeByDrescher Jan 25, 2024
afff0cc
more static deactivation
CodeByDrescher Jan 25, 2024
38416f7
Attempting to grab dlls
CodeByDrescher Jan 25, 2024
b47cd11
Adding Mac and Docker back to gh action
CodeByDrescher Jan 25, 2024
2bc7cdd
updating hard link to Cellar package
CodeByDrescher Jan 25, 2024
8f0446f
added checkpoints
CodeByDrescher Jan 25, 2024
cdcab4c
Struggling to get gtest to work
CodeByDrescher Jan 26, 2024
98f8008
added to git ingore
CodeByDrescher Jan 26, 2024
f243f86
Explicitly gave `_mode` to fstream in order to work
CodeByDrescher Jan 26, 2024
7be1b2d
Cleaned up debug messages
CodeByDrescher Jan 26, 2024
495b57f
added `this` prefixes and cleaned up appearence
CodeByDrescher Jan 26, 2024
cca40a8
Removed bad-practice using call.
CodeByDrescher Jan 26, 2024
0a55ca6
Clarified SimulationMessage Constructor
CodeByDrescher Jan 26, 2024
c7b7847
Used delegating constructor and added SimulationMessage::create() call
CodeByDrescher Jan 26, 2024
c4b18cf
Post-Development Cleanup
CodeByDrescher Jan 26, 2024
2a61976
Brought back include and using statements
CodeByDrescher Jan 26, 2024
d85c617
Fixed windows compression to zip
CodeByDrescher Jan 29, 2024
d835841
Add zip package through pacman
CodeByDrescher Jan 29, 2024
1da104e
Forgot to change file suffix
CodeByDrescher Jan 29, 2024
b4a2855
Forgot to change file suffix (x2)
CodeByDrescher Jan 29, 2024
9ee57dc
Merge branch 'nonchombo-build' of https://github.com/virtualcell/vcel…
CodeByDrescher Jan 29, 2024
6d3cf54
One last syntax change
CodeByDrescher Jan 29, 2024
c4bfc0d
fix sprintf overflows, missing return values and type warnings in NFSim
jcschaff Feb 9, 2024
d3a8cda
fix build issue with empty dummy.c in sundials (to allow a parent lib)
jcschaff Feb 9, 2024
c83ccc2
upgrade deprecated github actions - artifacts aren't uploaded
jcschaff Feb 9, 2024
fd47480
replace all SVN versions with git, build MovingBoundary solver on MacOS
jcschaff Feb 9, 2024
1694a12
build moving boundary solver for native linux and windows.
jcschaff Feb 11, 2024
e317436
added missing includes / defines for MovingBoundary on Linux and Windows
jcschaff Feb 11, 2024
0b4fc33
try to run on arm64 running for Mac M1,M2,M3
jcschaff Apr 18, 2024
c1a9507
separate builds for macos-13 Intel and macos-14 ARM
jcschaff May 23, 2024
4ae3c05
WIP: build for macOS AMD
jcschaff May 24, 2024
89a5810
in vcell/smoldyn bridge smoldyn queue class conflused with c++ queue
jcschaff May 24, 2024
06d3c07
rename smoldyn queue to queue_c to avoid conflict
jcschaff May 25, 2024
d0e965c
ARM has only 64bit long double, fixed a moving boundary test
jcschaff May 25, 2024
be0a2d1
fix logic for macOS Intel in Stochastic solver CMakeLists.txt
jcschaff May 25, 2024
fcd8c4b
fix thrown exception syntax in MB solver
jcschaff May 25, 2024
e08a450
include <stdexcept> to resolve domain_error
jcschaff May 25, 2024
b62140f
include <limits> to define numeric_limits in Polygon
jcschaff May 25, 2024
07d3fd0
import <limits> everywhere numeric_limits are used
jcschaff May 25, 2024
8165986
implement drand48() for windows for MB solver - needed for Chombo also
jcschaff May 25, 2024
461304e
use _getpid for getpid on windows
jcschaff May 25, 2024
33a235b
move include for windows earlier for MB solver
jcschaff May 25, 2024
ad7ca1a
disable build for windows moving boundary for now
jcschaff May 25, 2024
6f630d1
fix graphvis failure on windows, don't build docs on windows
jcschaff May 25, 2024
bb4fe00
fix artifact upload for macos_x86_64 and macos_arm64
jcschaff May 25, 2024
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Attempting to remove static link flags
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CodeByDrescher committed Jan 25, 2024
commit 87d84e081cebed83254253b48893c46f592ae532
10 changes: 6 additions & 4 deletions smoldyn-2.38/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -167,10 +167,12 @@ elseif (OPTION_MINGW)
include_directories(${MINGWDIR}/include windows)
link_directories(${MINGWDIR}/lib)
#list(APPEND DEP_LIBS opengl32 glu32 freeglut z)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -static")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static")
set(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS} -static -s")
set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS} -static -s")
# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -static")
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static")
# set(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS} -static -s")
# set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS} -static -s")
set(CMAKE_SHARED_LIBRARY_LINK_C_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS} -s")
set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "${CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS}-s")
endif()

set(APPLE_BUILD 0)
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