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[0.9.6] nest extension: doc generation in CMakeLists.txt #704

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sanjayankur31 opened this issue Jan 11, 2021 · 3 comments
Open

[0.9.6] nest extension: doc generation in CMakeLists.txt #704

sanjayankur31 opened this issue Jan 11, 2021 · 3 comments
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future

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@sanjayankur31
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Hello,

While building version 0.9.6 from source for inclusion in NeuroFedora, I get this error:

CMake Error: Error processing file: /usr/share/doc/nest/generate_help.cmake

I checked my NEST installation, and I don't see a generate_help.cmake file there. I also grepped the travis log and the NEST build there doesn't seem to include this file either. So I was wondering if the CMakeLists.txt bit on installing nest extension documentation still relevant?

PyNN/pyNN/nest/extensions/CMakeLists.txt

Line 251 in 377787c

set( HELPDIRS "${PROJECT_SOURCE_DIR}:${PROJECT_SOURCE_DIR}/sli" )

@apdavison
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Hi @sanjayankur31

How are you building it? i.e. how can I reproduce this error?

@sanjayankur31
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Hi @apdavison :

I'm entering the nest extensions folder and running the standard cmake commands :

cmake .
cmake --build .
cmake --install .

Here's an example run against master (377787c):

(ins)[asinha@ankur  PyNN(master=)]$ cd pyNN/nest/extensions/
(ins)[asinha@ankur  extensions(master=)]$ ls
CMakeLists.txt  pynn_extensions.cpp  pynn_extensions.h  simple_stochastic_connection.h  sli  stochastic_stp_connection.h  stochastic_stp_connection_impl.h
(ins)[asinha@ankur  extensions(master=)]$ mkdir build
(ins)[asinha@ankur  extensions(master=)]$ cd build/
(ins)[asinha@ankur  build(master=)]$ cmake ../
-- The CXX compiler identification is GNU 10.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done

-------------------------------------------------------
pynn_extensions Configuration Summary
-------------------------------------------------------

C++ compiler         : /usr/bin/g++
Build static libs    : OFF
C++ compiler flags   : -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
NEST compiler flags  : -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -O2 -Wall -fopenmp -fdiagnostics-color=auto
NEST include dirs    : -I/builddir/build/BUILD/nest-simulator-2.20.1/nest-simulator-2.20.1/conngen  -I/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/include
NEST libraries flags : -L/usr//usr/lib64 -lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp /lib64/libltdl.so /lib64/libreadline.so /lib64/libncurses.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /usr/lib64/libneurosim.so /usr/lib64/libpy3neurosim.so

-------------------------------------------------------

You can build and install pynn_extensions now, using
  make
  make install

pynn_extensions will be installed to: /usr/lib64/nest

-- Configuring done
-- Generating done
-- Build files have been written to: /home/asinha/Documents/02_Code/01_others/PyNN/pyNN/nest/extensions/build

(ins)[asinha@ankur  build(master=)]$ cmake --build .
Scanning dependencies of target pynn_extensions_lib
[ 25%] Building CXX object CMakeFiles/pynn_extensions_lib.dir/pynn_extensions.cpp.o
[ 50%] Linking CXX shared library libpynn_extensions.so
[ 50%] Built target pynn_extensions_lib
Scanning dependencies of target pynn_extensions_module
[ 75%] Building CXX object CMakeFiles/pynn_extensions_module.dir/pynn_extensions.cpp.o
[100%] Linking CXX shared module pynn_extensions.so
[100%] Built target pynn_extensions_module

(ins)[asinha@ankur  build(master=)]$ DESTDIR=/home/asinha/dump/cmake-test/ cmake --install .
-- Install configuration: ""
-- Installing: /home/asinha/dump/cmake-test/usr/lib64/nest/pynn_extensions.so
-- Installing: /home/asinha/dump/cmake-test/usr/lib64/nest/libpynn_extensions.so
-- Installing: /home/asinha/dump/cmake-test/usr/include/pynn_extensions.h
-- Installing: /home/asinha/dump/cmake-test/usr/share/nest/sli
-- Installing: /home/asinha/dump/cmake-test/usr/share/nest/sli/pynn_extensions-init.sli
CMake Error: Error processing file: /usr/share/doc/nest/generate_help.cmake

I also get this if I run sudo python setup.py build in the root directory. (Expected since my NEST installation does not have a
generate_help.cmake file):

$ 
(ins)(.venv) [asinha@ankur  PyNN(master *%=)]$ sudo python setup.py build
[sudo] password for asinha:
/usr/lib/python3.9/site-packages/setuptools/dist.py:458: UserWarning: Normalizing '0.10.0.dev' to '0.10.0.dev0'
  warnings.warn(tmpl.format(**locals()))
running build
running build_py
creating build
creating build/lib
creating build/lib/pyNN
copying pyNN/models.py -> build/lib/pyNN
copying pyNN/network.py -> build/lib/pyNN
copying pyNN/__init__.py -> build/lib/pyNN
copying pyNN/errors.py -> build/lib/pyNN
copying pyNN/random.py -> build/lib/pyNN
copying pyNN/parameters.py -> build/lib/pyNN
copying pyNN/multisim.py -> build/lib/pyNN
copying pyNN/connectors.py -> build/lib/pyNN
copying pyNN/space.py -> build/lib/pyNN
copying pyNN/core.py -> build/lib/pyNN
creating build/lib/pyNN/nest
copying pyNN/nest/synapses.py -> build/lib/pyNN/nest
copying pyNN/nest/__init__.py -> build/lib/pyNN/nest
copying pyNN/nest/random.py -> build/lib/pyNN/nest
copying pyNN/nest/simulator.py -> build/lib/pyNN/nest
copying pyNN/nest/cells.py -> build/lib/pyNN/nest
copying pyNN/nest/conversion.py -> build/lib/pyNN/nest
copying pyNN/nest/recording.py -> build/lib/pyNN/nest
copying pyNN/nest/nineml.py -> build/lib/pyNN/nest
copying pyNN/nest/connectors.py -> build/lib/pyNN/nest
copying pyNN/nest/projections.py -> build/lib/pyNN/nest
copying pyNN/nest/electrodes.py -> build/lib/pyNN/nest
copying pyNN/nest/populations.py -> build/lib/pyNN/nest
creating build/lib/pyNN/neuron
copying pyNN/neuron/__init__.py -> build/lib/pyNN/neuron
copying pyNN/neuron/random.py -> build/lib/pyNN/neuron
copying pyNN/neuron/simulator.py -> build/lib/pyNN/neuron
copying pyNN/neuron/cells.py -> build/lib/pyNN/neuron
copying pyNN/neuron/recording.py -> build/lib/pyNN/neuron
copying pyNN/neuron/nineml.py -> build/lib/pyNN/neuron
copying pyNN/neuron/connectors.py -> build/lib/pyNN/neuron
copying pyNN/neuron/projections.py -> build/lib/pyNN/neuron
copying pyNN/neuron/populations.py -> build/lib/pyNN/neuron
creating build/lib/pyNN/brian2
copying pyNN/brian2/__init__.py -> build/lib/pyNN/brian2
copying pyNN/brian2/simulator.py -> build/lib/pyNN/brian2
copying pyNN/brian2/cells.py -> build/lib/pyNN/brian2
copying pyNN/brian2/recording.py -> build/lib/pyNN/brian2
copying pyNN/brian2/projections.py -> build/lib/pyNN/brian2
copying pyNN/brian2/populations.py -> build/lib/pyNN/brian2
creating build/lib/pyNN/common
copying pyNN/common/__init__.py -> build/lib/pyNN/common
copying pyNN/common/procedural_api.py -> build/lib/pyNN/common
copying pyNN/common/projections.py -> build/lib/pyNN/common
copying pyNN/common/control.py -> build/lib/pyNN/common
copying pyNN/common/populations.py -> build/lib/pyNN/common
creating build/lib/pyNN/mock
copying pyNN/mock/__init__.py -> build/lib/pyNN/mock
copying pyNN/mock/simulator.py -> build/lib/pyNN/mock
copying pyNN/mock/standardmodels.py -> build/lib/pyNN/mock
copying pyNN/mock/recording.py -> build/lib/pyNN/mock
copying pyNN/mock/projections.py -> build/lib/pyNN/mock
copying pyNN/mock/populations.py -> build/lib/pyNN/mock
creating build/lib/pyNN/neuroml
copying pyNN/neuroml/__init__.py -> build/lib/pyNN/neuroml
copying pyNN/neuroml/simulator.py -> build/lib/pyNN/neuroml
copying pyNN/neuroml/recording.py -> build/lib/pyNN/neuroml
copying pyNN/neuroml/projections.py -> build/lib/pyNN/neuroml
copying pyNN/neuroml/populations.py -> build/lib/pyNN/neuroml
creating build/lib/pyNN/recording
copying pyNN/recording/__init__.py -> build/lib/pyNN/recording
copying pyNN/recording/files.py -> build/lib/pyNN/recording
creating build/lib/pyNN/standardmodels
copying pyNN/standardmodels/synapses.py -> build/lib/pyNN/standardmodels
copying pyNN/standardmodels/__init__.py -> build/lib/pyNN/standardmodels
copying pyNN/standardmodels/cells.py -> build/lib/pyNN/standardmodels
copying pyNN/standardmodels/electrodes.py -> build/lib/pyNN/standardmodels
creating build/lib/pyNN/descriptions
copying pyNN/descriptions/__init__.py -> build/lib/pyNN/descriptions
creating build/lib/pyNN/nest/standardmodels
copying pyNN/nest/standardmodels/synapses.py -> build/lib/pyNN/nest/standardmodels
copying pyNN/nest/standardmodels/__init__.py -> build/lib/pyNN/nest/standardmodels
copying pyNN/nest/standardmodels/cells.py -> build/lib/pyNN/nest/standardmodels
copying pyNN/nest/standardmodels/electrodes.py -> build/lib/pyNN/nest/standardmodels
creating build/lib/pyNN/neuroml/standardmodels
copying pyNN/neuroml/standardmodels/synapses.py -> build/lib/pyNN/neuroml/standardmodels
copying pyNN/neuroml/standardmodels/__init__.py -> build/lib/pyNN/neuroml/standardmodels
copying pyNN/neuroml/standardmodels/cells.py -> build/lib/pyNN/neuroml/standardmodels
copying pyNN/neuroml/standardmodels/electrodes.py -> build/lib/pyNN/neuroml/standardmodels
creating build/lib/pyNN/neuron/standardmodels
copying pyNN/neuron/standardmodels/synapses.py -> build/lib/pyNN/neuron/standardmodels
copying pyNN/neuron/standardmodels/__init__.py -> build/lib/pyNN/neuron/standardmodels
copying pyNN/neuron/standardmodels/cells.py -> build/lib/pyNN/neuron/standardmodels
copying pyNN/neuron/standardmodels/electrodes.py -> build/lib/pyNN/neuron/standardmodels
creating build/lib/pyNN/brian2/standardmodels
copying pyNN/brian2/standardmodels/synapses.py -> build/lib/pyNN/brian2/standardmodels
copying pyNN/brian2/standardmodels/__init__.py -> build/lib/pyNN/brian2/standardmodels
copying pyNN/brian2/standardmodels/cells.py -> build/lib/pyNN/brian2/standardmodels
copying pyNN/brian2/standardmodels/electrodes.py -> build/lib/pyNN/brian2/standardmodels
creating build/lib/pyNN/utility
copying pyNN/utility/plotting.py -> build/lib/pyNN/utility
copying pyNN/utility/__init__.py -> build/lib/pyNN/utility
creating build/lib/pyNN/nineml
copying pyNN/nineml/synapses.py -> build/lib/pyNN/nineml
copying pyNN/nineml/__init__.py -> build/lib/pyNN/nineml
copying pyNN/nineml/simulator.py -> build/lib/pyNN/nineml
copying pyNN/nineml/cells.py -> build/lib/pyNN/nineml
copying pyNN/nineml/standardmodels.py -> build/lib/pyNN/nineml
copying pyNN/nineml/recording.py -> build/lib/pyNN/nineml
copying pyNN/nineml/utility.py -> build/lib/pyNN/nineml
copying pyNN/nineml/connectors.py -> build/lib/pyNN/nineml
copying pyNN/nineml/projections.py -> build/lib/pyNN/nineml
copying pyNN/nineml/read.py -> build/lib/pyNN/nineml
copying pyNN/nineml/populations.py -> build/lib/pyNN/nineml
creating build/lib/pyNN/serialization
copying pyNN/serialization/__init__.py -> build/lib/pyNN/serialization
copying pyNN/serialization/sonata.py -> build/lib/pyNN/serialization
creating build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/adexp.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/vecstim.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stdwa_guetig.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stochastic_tsodyksmarkram.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/tmgsyn.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/poisson_stim_refractory.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/gammastim.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/expisyn.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/gsfa_grr.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stochastic_synapse.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stdwa_songabbott.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/izhikevich.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stdwa_softlimits.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/gap.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/tsodyksmarkram.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/hh_traub.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/alphasyn.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/refrac.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/tmisyn.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/reset.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stdwa_symm.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/gif.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/stdwa_vogels2011.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/quantal_stp.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/netstim2.mod -> build/lib/pyNN/neuron/nmodl
copying pyNN/neuron/nmodl/alphaisyn.mod -> build/lib/pyNN/neuron/nmodl
creating build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/simple_stochastic_connection.h -> build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/stochastic_stp_connection.h -> build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/stochastic_stp_connection_impl.h -> build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/pynn_extensions.h -> build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/pynn_extensions.cpp -> build/lib/pyNN/nest/extensions
copying pyNN/nest/extensions/CMakeLists.txt -> build/lib/pyNN/nest/extensions
creating build/lib/pyNN/nest/extensions/sli
copying pyNN/nest/extensions/sli/pynn_extensions-init.sli -> build/lib/pyNN/nest/extensions/sli
creating build/lib/pyNN/descriptions/templates
creating build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/population_old.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/population_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/projection_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/assembly_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/synapsedynamics_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/modeltype_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
copying pyNN/descriptions/templates/jinja2/populationview_default.txt -> build/lib/pyNN/descriptions/templates/jinja2
creating build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/population_old.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/population_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/projection_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/assembly_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/synapsedynamics_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/modeltype_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
copying pyNN/descriptions/templates/cheetah/populationview_default.txt -> build/lib/pyNN/descriptions/templates/cheetah
creating build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/population_default.txt -> build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/projection_default.txt -> build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/assembly_default.txt -> build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/synapsedynamics_default.txt -> build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/modeltype_default.txt -> build/lib/pyNN/descriptions/templates/string
copying pyNN/descriptions/templates/string/populationview_default.txt -> build/lib/pyNN/descriptions/templates/string
Unable to find nrnivmodl. It will not be possible to use the pyNN.neuron module.
nest-config found at /usr/bin/nest-config
  -- The CXX compiler identification is GNU 10.2.1
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/g++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done

  -------------------------------------------------------
  pynn_extensions Configuration Summary
  -------------------------------------------------------

  C++ compiler         : /usr/bin/g++
  Build static libs    : OFF
  C++ compiler flags   :
  NEST compiler flags  : -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -O2 -Wall -fopenmp -fdiagnostics-color=auto
  NEST include dirs    : -I/builddir/build/BUILD/nest-simulator-2.20.1/nest-simulator-2.20.1/conngen  -I/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/include
  NEST libraries flags : -L/usr//usr/lib64 -lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp /lib64/libltdl.so /lib64/libreadline.so /lib64/libncurses.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /usr/lib64/libneurosim.so /usr/lib64/libpy3neurosim.so

  -------------------------------------------------------

  You can build and install pynn_extensions now, using
    make
    make install

  pynn_extensions will be installed to: /usr/lib64/nest

  -- Configuring done
  -- Generating done
  -- Build files have been written to: /home/asinha/Documents/02_Code/01_others/PyNN/build/lib/pyNN/nest/_build

  Scanning dependencies of target pynn_extensions_lib
  [ 25%] Building CXX object CMakeFiles/pynn_extensions_lib.dir/pynn_extensions.cpp.o
  [ 50%] Linking CXX shared library libpynn_extensions.so
  [ 50%] Built target pynn_extensions_lib
  Scanning dependencies of target pynn_extensions_module
  [ 75%] Building CXX object CMakeFiles/pynn_extensions_module.dir/pynn_extensions.cpp.o
  [100%] Linking CXX shared module pynn_extensions.so
  [100%] Built target pynn_extensions_module

  [ 50%] Built target pynn_extensions_lib
  [100%] Built target pynn_extensions_module
  Install the project...
  -- Install configuration: ""
  -- Installing: /usr/lib64/nest/pynn_extensions.so
  -- Installing: /usr/lib64/nest/libpynn_extensions.so
  -- Installing: /usr/include/pynn_extensions.h
  -- Up-to-date: /usr/share/nest/sli
  -- Installing: /usr/share/nest/sli/pynn_extensions-init.sli
  CMake Error: Error processing file: /usr/share/doc/nest/generate_help.cmake

Successfully compiled NEST extensions.

I've rebuilt my NEST installation from scratch too and a generate_help.cmake file isn't generated or installed during the build here.

@sanjayankur31
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Dug around a bit more. Looks like generate_help.cmake bit was removed in favour of python based help generation in this commit:

nest/nest-simulator@db0e3d7

The example CMakeLists.txt file was updated too:

nest/nest-simulator@db0e3d7#diff-d42b9b3d193317396a8f276754f716a1eccd6b96bb88581750ef3933190d72a2L271

@apdavison apdavison added this to the future milestone Dec 1, 2021
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