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Refactor conngen module to be a ConnBuilder #1830

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merged 51 commits into from
Nov 23, 2020
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b01620a
Remove Python 2 workaround
jougs Aug 23, 2020
b03c0f3
Refactor conngen module functionality into a ConnBuilder
jougs Aug 23, 2020
43c201c
Update conngen_interface SLI example
jougs Aug 24, 2020
b9bccbf
Update SLI documentation for ConnGen related functions
jougs Aug 24, 2020
7cc177a
Make strings consistent
jougs Aug 24, 2020
2952250
Update PyNEST example docstrings
jougs Aug 24, 2020
ea3dc97
Remove ConnGen functions from PyNEST HL API
jougs Aug 24, 2020
a202516
Update 2to3 conversion guide wrt Connect with a ConnGen
jougs Aug 24, 2020
c06c383
Formatting
jougs Aug 24, 2020
4d452e5
Protect from compilation in case libneurosim is not there
jougs Aug 26, 2020
bea0530
Force Python 3 and monkey patch CSA build scripts
jougs Aug 26, 2020
5aaaa10
Export PYTHONPATH so csa is actually available
jougs Aug 27, 2020
d286a1b
Replace old CGConnect to Connect with conngen rule and remove useless…
jougs Aug 27, 2020
9bc2d43
Formatting
jougs Aug 27, 2020
e4fff41
Merge branch 'master' of github.com:nest/nest-simulator into refactor…
jougs Nov 5, 2020
bdd6340
Update conngen documentation and move to connection management guide
jougs Nov 6, 2020
4c249c6
Fix build script for libneurosim
jougs Nov 6, 2020
23854c3
Add library search path for CSA installation
jougs Nov 6, 2020
368b805
Fix CSA tests
jougs Nov 7, 2020
8ee1ba0
Reorder initializers to avoid warning
jougs Nov 7, 2020
e87dd5e
Remove debug output
jougs Nov 7, 2020
70f92b0
Remove deleted file also from index
jougs Nov 9, 2020
8c4d8ed
Fix conngen connect using weight and delay
jougs Nov 9, 2020
e970181
Move code around and fix formatting
jougs Nov 10, 2020
0c001a4
Add check for custom synapse parameter
jougs Nov 10, 2020
c208c99
Add test for conflicting specifications of weight and delay
jougs Nov 10, 2020
2448655
Add check for conflicting specifications of weight and delay
jougs Nov 10, 2020
135bb74
Merge branch 'master' of github.com:nest/nest-simulator into refactor…
jougs Nov 10, 2020
228fb15
Move code around
jougs Nov 10, 2020
637c9f0
Make naming in CSA examples and test consistent
jougs Nov 10, 2020
ffc8e97
Rename conn_builder_conngeninterface.* to conn_builder_conngen.*
jougs Nov 10, 2020
da416da
Add libneurosim compilation information and more links
jougs Nov 10, 2020
e40c193
Remove line that crept in via a merge conflict resolution
jougs Nov 10, 2020
bb8e3c0
Apply suggestions from code review
jougs Nov 11, 2020
7ab7a68
Remove workaround for https://github.com/INCF/libneurosim/issues/19
jougs Nov 11, 2020
f844959
Update description and comments to reflect reality
jougs Nov 11, 2020
24cc546
Merge branch 'refactor_conngen_module' of github.com:jougs/nest-simul…
jougs Nov 11, 2020
e59d104
Apply suggestions from code review
jougs Nov 11, 2020
ccfae0d
nest-3ify
jougs Nov 11, 2020
824caee
Prevent ConnBuilderConngen from being used with collocated synapses
jougs Nov 11, 2020
c2b4ead
Fix formatting
jougs Nov 11, 2020
16cae4a
Merge branch 'master' of github.com:nest/nest-simulator into refactor…
jougs Nov 11, 2020
86f682c
Merge branch 'refactor_conngen_module' of github.com:jougs/nest-simul…
jougs Nov 11, 2020
1700daf
Fix formatting of Python files
jougs Nov 11, 2020
745211a
Apply suggestions from code review
jougs Nov 12, 2020
500a741
Add test case for error reporting if using collocated synapses
jougs Nov 13, 2020
02fc169
Rename for consistency with other connect tests
jougs Nov 13, 2020
d5802c9
Convert inline reference to footnote and reference section
jougs Nov 13, 2020
444695a
Merge branch 'master' of github.com:nest/nest-simulator into refactor…
jougs Nov 19, 2020
aca7b53
Set expected_warnings to 0 unconditionally
jougs Nov 20, 2020
876c69a
Fix import of renamed file
jougs Nov 20, 2020
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8 changes: 0 additions & 8 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -219,9 +219,6 @@ add_custom_target( installcheck
################## Define Subdirectories here ##################
################################################################################

if ( HAVE_LIBNEUROSIM )
add_subdirectory( conngen )
endif ()
add_subdirectory( doc )
add_subdirectory( examples )
add_subdirectory( extras )
Expand Down Expand Up @@ -314,11 +311,6 @@ foreach ( INC ${ALL_INCLUDES_tmp} ${with-includes} )
endforeach ()
set( ALL_INCLUDES "${ALL_INCLUDES} ${SIONLIB_INCLUDE}" )

if ( HAVE_LIBNEUROSIM )
set( ALL_LIBS "-lconngen ${ALL_LIBS}" )
set( ALL_INCLUDES "-I${PROJECT_SOURCE_DIR}/conngen ${ALL_INCLUDES}" )
endif ()

################################################################################
################## File generation here ##################
################################################################################
Expand Down
14 changes: 3 additions & 11 deletions cmake/FindLibNeurosim.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -35,18 +35,10 @@ find_library( NEUROSIM_LIBRARY
NAMES neurosim
HINTS ${LIBNEUROSIM_ROOT}/lib
)

if ( ${PYTHON_VERSION} VERSION_GREATER "3" )
find_library( PYNEUROSIM_LIBRARY
NAMES py3neurosim
HINTS ${LIBNEUROSIM_ROOT}/lib
)
else ()
find_library( PYNEUROSIM_LIBRARY
NAMES pyneurosim
HINTS ${LIBNEUROSIM_ROOT}/lib
find_library( PYNEUROSIM_LIBRARY
NAMES py3neurosim
HINTS ${LIBNEUROSIM_ROOT}/lib
)
endif ()

if ( EXISTS "${LIBNEUROSIM_INCLUDE_DIR}/neurosim/version.h" )
file( STRINGS "${LIBNEUROSIM_INCLUDE_DIR}/neurosim/version.h"
Expand Down
4 changes: 0 additions & 4 deletions cmake/ProcessOptions.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,6 @@ function( NEST_PROCESS_WITH_LIBNEUROSIM )
set( HAVE_LIBNEUROSIM ON PARENT_SCOPE )

include_directories( ${LIBNEUROSIM_INCLUDE_DIRS} )
# is linked in conngen/CMakeLists.txt

# export found variables to parent scope
set( LIBNEUROSIM_FOUND "${LIBNEUROSIM_FOUND}" PARENT_SCOPE )
Expand Down Expand Up @@ -629,9 +628,6 @@ function( NEST_DEFAULT_MODULES )
# requires HAVE_LIBNEUROSIM set
# Static modules
set( SLI_MODULES models )
if ( HAVE_LIBNEUROSIM )
set( SLI_MODULES ${SLI_MODULES} conngen )
endif ()
set( SLI_MODULES ${SLI_MODULES} PARENT_SCOPE )

set( SLI_MODULE_INCLUDE_DIRS )
Expand Down
48 changes: 0 additions & 48 deletions conngen/CMakeLists.txt

This file was deleted.

60 changes: 0 additions & 60 deletions conngen/conngen.h

This file was deleted.

25 changes: 0 additions & 25 deletions conngen/conngendatum.cpp

This file was deleted.

45 changes: 0 additions & 45 deletions conngen/conngendatum.h

This file was deleted.

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