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Fix PyChaste Build for Chaste 2024.1 #64

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merged 42 commits into from
Apr 15, 2024
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a71cfe6
#62 Search for castxml on PATH
kwabenantim Feb 29, 2024
cf61be4
#62 Update package_info with immersed boundary
kwabenantim Feb 29, 2024
615e4fa
#62 git ignore build directory
kwabenantim Mar 4, 2024
17e1d2a
#62 remove empty src/mesh from cmake config
kwabenantim Mar 4, 2024
d60da4a
Merge branch 'develop' into release-2024.1
kwabenantim Mar 4, 2024
ad7a0e1
Prettify package info
kwabenantim Mar 9, 2024
5a1c7df
#62 restore correct custom population writer
kwabenantim Mar 12, 2024
d32f6dd
#62 set generator std=c++17
kwabenantim Mar 12, 2024
fabff5c
#62 update wrapper header collection
kwabenantim Mar 12, 2024
e8975d6
#62 update package info yaml
kwabenantim Mar 12, 2024
dccf760
#62 update module wrappers
kwabenantim Mar 12, 2024
8d4045d
#62 update wrapper header collection
kwabenantim Mar 12, 2024
39c51a1
#62 update wrapper header collection
kwabenantim Mar 12, 2024
3d71919
#62 add immersed boundary wrappers
kwabenantim Mar 12, 2024
1b00801
#62 use new PYBIND11_OVERRIDE macros
kwabenantim Mar 12, 2024
6fb613d
#62 Remove non-standard MutableElement wrappers
kwabenantim Mar 12, 2024
795f099
#62 add MutableElement<1,2> and <2,3>
kwabenantim Mar 12, 2024
6fb23f7
#62 remove missing MutableElement1_2 constructor
kwabenantim Mar 18, 2024
3fe4c00
#62 reorder cell_based registrations
kwabenantim Mar 20, 2024
c1ac439
#62 update cppwg cmake target
kwabenantim Mar 23, 2024
b9505ee
#62 simplify and annotate package info
kwabenantim Mar 23, 2024
eca7431
#62 rm missing mesh from cmake
kwabenantim Mar 25, 2024
c1461d8
#62 Add numerical method classes
kwabenantim Mar 25, 2024
a09ef78
#62 update c++ std in generation cmake
kwabenantim Mar 25, 2024
d74e09e
#62 fix numerical method wrappers
kwabenantim Mar 25, 2024
404a480
#62 add immersed boundary tutorial
kwabenantim Mar 25, 2024
de6c6f9
#62 expand immersed boundary tutorial
kwabenantim Mar 25, 2024
3964667
#62 add third part of immersed boundary tutorial
kwabenantim Mar 25, 2024
5e0d0a4
#62 update immersed boundary tutorial
kwabenantim Mar 25, 2024
d548c83
#62 update immersed boundary tutorial
kwabenantim Mar 25, 2024
587e149
#62 dont' support vtk5
kwabenantim Mar 26, 2024
52b9ed3
#62 vtk5 not supported
kwabenantim Apr 8, 2024
5c26634
#62 add immersed boundary actor generators
kwabenantim Apr 8, 2024
2591aa2
#62 add image viz to immersed boundary tutorial
kwabenantim Apr 8, 2024
bef45fe
#62 add animation to immersed boundary tutorial
kwabenantim Apr 8, 2024
1e60b9b
#62 Update immersed boundary tutorial
kwabenantim Apr 11, 2024
c238afe
#62 Fix typo in VtkScene
kwabenantim Apr 11, 2024
a17a409
#62 Regenerate immersed boundary tutorial markdown
kwabenantim Apr 11, 2024
1f56164
#62 Fix immersed boundary tutorial
kwabenantim Apr 11, 2024
942b38a
#62 Update immersed boundary tutorial
kwabenantim Apr 11, 2024
6b5643d
#62 Add immersed boundary tutorial to tests
kwabenantim Apr 11, 2024
b8fbacc
Merge branch 'develop' into release-2024.1
kwabenantim Apr 11, 2024
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2 changes: 2 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -19,3 +19,5 @@ src/python/dist*
src/python/chaste.egg-info*
# No api docs
doc/api/build*
# Build folder
build/
1 change: 0 additions & 1 deletion ProjectIncludes.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@
set(PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/cell_based)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/ode)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/mesh)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/tutorial)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/src/visualization)
list (APPEND PYCHASTE_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/dynamic)
19 changes: 8 additions & 11 deletions WrapPython.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,6 @@ add_compile_options(-Wno-unused-local-typedefs)
# Add any cmake modules defined in this project
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR} PARENT_SCOPE)

# Used for binding generation
set(CASTXML_EXE_LOC "/usr/bin/castxml" CACHE FILEPATH "Path to the castxml executable.")

# Find the Chaste and third party dependency header files.
include_directories(${Chaste_INCLUDE_DIRS} ${Chaste_THIRD_PARTY_INCLUDE_DIRS})

Expand Down Expand Up @@ -102,14 +99,14 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/doc/ DESTINATION ${CMAKE_CURRENT_BINARY_DI

# Target to generate bindings
add_custom_target(project_PyChaste_Python_Bindings)
SET(arguments ${CMAKE_SOURCE_DIR}/)
LIST(APPEND arguments ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers/)
LIST(APPEND arguments ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrapper_generators/package_info.yaml)
LIST(APPEND arguments ${CASTXML_EXE_LOC})
LIST(APPEND arguments ${PYCHASTE_INCLUDE_DIRS})
LIST(APPEND arguments ${Chaste_INCLUDE_DIRS})
LIST(APPEND arguments ${Chaste_THIRD_PARTY_INCLUDE_DIRS})
add_custom_command(TARGET project_PyChaste_Python_Bindings COMMAND python3 ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrapper_generators/generate.py ${arguments})
add_custom_command(
TARGET project_PyChaste_Python_Bindings
COMMAND cppwg ${CMAKE_SOURCE_DIR}
-w ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrappers
-p ${CMAKE_CURRENT_SOURCE_DIR}/dynamic/wrapper_generators/package_info.yaml
-i ${PYCHASTE_INCLUDE_DIRS} ${Chaste_INCLUDE_DIRS} ${Chaste_THIRD_PARTY_INCLUDE_DIRS}
--std c++17
)

# Loop through each module and create the shared library targets
list(LENGTH PYCHASTE_PYTHON_MODULES len1)
Expand Down
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