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Add native support for networks represented in SONATA format #2595

Merged
merged 237 commits into from
May 15, 2023
Merged

Add native support for networks represented in SONATA format #2595

merged 237 commits into from
May 15, 2023

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nicolossus
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This PR adds support for building and simulating networks of point neurons represented by the SONATA format.

@stinebuu
Example with creating nodes from sonata files
5230106
@stinebuu
Add cmake option for hd5f
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Connections possible
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Iterate over config files
7dcf2ef
@stinebuu
Do not hard-code "0"
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@stinebuu
Work started on sonata builder
b948ba1
@stinebuu
Rename conn_builder_sonata
e882eb0
@stinebuu
Call class correctly
0d45099
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Move functions
dd8813c
@stinebuu
Get synapse params
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@stinebuu
Separate getting attributes and creating synapse map into functions
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Create function for reading data
c6db162
@stinebuu
Create hl_api_sonata
e939346
@stinebuu
Use hl_api_sonata, plot spikes
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@stinebuu
Change edge file setup
fa0a301
@stinebuu
Get simulator parameters from simulator config file
dd98eaf
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Update dynmics correctly
2011edb
@stinebuu
Check if weight and delays are given as h5
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@stinebuu
Only set setable synapse params
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@stinebuu
node_id's not continuous
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@stinebuu
Update example
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@stinebuu
add memory function
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@stinebuu
Merge remote-tracking branch 'nest-simulator/master' into nestsonata
2530b07 
Conflicts:
	CMakeLists.txt
@stinebuu
Update how we create nodes from sonata files
2df25b1
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Debugg information
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@stinebuu
Close sonata files and delete datasets
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@stinebuu
Do not do GetConnections for GLIF example, it causes memory failure
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Create nodes when more than one virtual
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Plot for GLIF example as well
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Check node parameters
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@nicolossus
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I have merged with the current master and done the necessary updates.

@heplesser and @jessica-mitchell The documentation on configuring NEST for SONATA in nest_sonata_guide.rst is updated and I also added some context for the HDF5 option in cmake_options.rst. Do you think the documentation looks fine for now?

@jougs I have adapted the build matrix to also include HDF5 for the full NEST build. Can you check that the changes are okay?

jessica-mitchell
jessica-mitchell requested changes May 4, 2023
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@nicolossus Looks good, just noticed that the link to the example is broken because the path is incorrect (see comments), also you need to add a README to the pynest/example/sonata_example/ page for sphinx-gallery to generate output from subdirectories.

doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
doc/htmldoc/examples/index.rst Outdated Show resolved Hide resolved
doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
nicolossus and others added 2 commits May 4, 2023 13:34
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Apply suggestions from code review
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Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
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Add README.rst
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@jessica-mitchell Thanks, fixed your comments.

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jessica-mitchell approved these changes May 4, 2023
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Great, looks good!

@jougs jougs requested a review from heplesser May 4, 2023 12:40
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@nicolossus This looks very fine, I just have a few details, see inline.

doc/htmldoc/installation/cmake_options.rst Outdated Show resolved Hide resolved
doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
pynest/examples/sonata_example/300_pointneurons/circuit_config.json Outdated Show resolved Hide resolved
pynest/nest/lib/hl_api_sonata.py Outdated Show resolved Hide resolved
pynest/nest/lib/hl_api_sonata.py Show resolved Hide resolved
nestkernel/sonata_connector.cpp Outdated Show resolved Hide resolved
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@heplesser I have now addressed all your comments and suggestions. All links should now be to the most sensible destination, the consistency checks in sonata_connector.cpp have been refactored and I added some more comments on the logic in hl_api_sonata.py.

@nicolossus nicolossus requested a review from heplesser May 9, 2023 14:28
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@nicolossus Thanks a lot, looks good to me and the failing on macOS seems to be a runner problem, so I will approve now, assuming that the test will pass on re-run.

@heplesser heplesser removed the request for review from jougs May 11, 2023 07:15
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Just three minor formal changes. Otherwise this looks good to me.

doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
doc/htmldoc/nest_sonata/nest_sonata_guide.rst Outdated Show resolved Hide resolved
@jougs jougs merged commit a3623b0 into nest:master May 15, 2023
@nicolossus nicolossus deleted the nestsonata branch May 15, 2023 20:23
@terhorstd terhorstd changed the title Add native support for networks represented by the SONATA format Add native support for networks represented in SONATA format Jun 23, 2023
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@steffengraber steffengraber steffengraber left review comments

@heplesser heplesser heplesser approved these changes

@jougs jougs jougs approved these changes

@jessica-mitchell jessica-mitchell jessica-mitchell approved these changes

@clinssen clinssen clinssen approved these changes

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I: User Interface Users may need to change their code due to changes in function calls S: Normal Handle this with default priority T: Enhancement New functionality, model or documentation
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10 participants
@nicolossus @heplesser @med-ayssar @steffengraber @jougs @jessica-mitchell @clinssen @terhorstd @stinebuu @hakonsbm