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* generate typed dict * generate entitycore schemas * entitycore * build_model * fetching assets * download morphologies, hoc_files, mechanisms * pyright * single_neuron_simulation * entitycore routes * bimodal * Typings * Migrating Nexus helper to entitycore helper * fetch morphology * fetch mechanisms * Retrieve morphology entitycore * download * FORMAT PRIORITY * direct current plot * simulation * remove dendrogram for now * clean up 1 * add vlab info * add vlab, project id * run_simulation service * model_factory * simulation routes use prject contexts * lint * check token * Headers * morphology, plot * clean up * naming * naming * feedback * typo * types * typing * Typging * Types and linting * authors * authors * format * comment * response models * type error * format * updated schemas * cureate schemas * remove trailing / * add sinaptome * Keep codegenerator for reference * ass * traling slash * migrate synaptome to entitycore --------- Co-authored-by: Gil Arturo Barrios del Villar <gilarturo.barriosdelvillar@openbraininstitute.org> Co-authored-by: g-bar <gbarv2@gmail.com>
…rcuit simulation * Add current changes * Make single cell sim distributed * Add circuit route and sim code draft * Add current changes * Add current progress * Futher refactoring * Futher refactoring * Add simulation code, docker setup * Fix container tag * Provide ENVIRONMENT var to docker build * Fix missing env vars * Add current changes * Convert to async, refactor * Remove unused deps * Make route handlers async * Other changes * Remove ARM platfor build from api * Some improvements for the docker setup * Ensure user group is created * Use arm64 for api * Entitycore integration: model download * Auth and other fixes * Register Simulation execution and results * Provide custom libnrnmech path * Fix output dir, add comments, enable NWB save * Have a better name for ready marker file * Refctor saving the results * Rename artefacts, cleanu p * Check the the status * Add current changes * Try using qemu and buildx * Try to build arm image in a different way * Temporarily isable Qemu and buildx * Put back normal build from makefile * Set platform in docker compose to amd64 * Add missing IMAGE_NAME * Add test script to run MPI in a container * Add missing module init files * Debug issue with storage * Clean up app storage debug code * Add was_generated_by field to generated NWBs * Process on_failure and on_success from the api service * Add sending the pending status to the redis stream * Upgrade bluecellulab and entitysdk * Use 8 workers to download circuit * Update simulation script to correctly gather sim reports with MPI * Use time rate for NWB instead of supplying time series data * Make sure sim exec status is getting set to error if simulation fails * Provide input spike files with absolute path * Add production build (for now from the current branch) * Update labels * Fix image tag in prod, disable staging build for now * Fix img tag suffix env resolution * Disable prod deployment, enable staging deployment * Dynamicly determine number of MPI processes * Disable adding projections to allow BCL set up local synapses * Build production image * Add more logs * Build in staging * Call pc.quit() after simulation ended * Provide v_init, init spikes dicts * Remove hippocampus projections * Add NWB compression * Send queue position in extra prop * Build for current tag * Disable build from the current branch * Refactor job_position fn into job monitoring fn to run callbacks * Remove nexus, part 1 * Remove nexus, part 2 * Remove nexus, part 3 * Refactor Github actions * Remove sample circuit * Fix all checks * Fix typo * Pass exec id as string * Clean up * Better error handling and clean up * Rename single_cell to single_neuron to be consistent * Another round of clean up * Migrate most of single cell functions * Fix synapse generation * Remove redundant endpoints, clean up * validation and small fixes * Final touches * Add comment about glibc version conflict * Split single neuron calibration and validation tasks * Add accounting for small circuit simulations * Integrate accounting for circuit simulations, make validation a single job * Correct exc_type types * Fix sync/async call in on_failed handler * Clean up, add job fn reference check * Clean up #2 * Upgrade deps * Update pull request GH action * Fix types for asset label and content type * Clean up some entitycore types * Fix some other types * Provide default accounting base URL * Add makefile entry to start job monitor * Refactor circuit simulations, add timestamp to JobMessage * Fix simulation constructor args * Upgrade BlueCelluLab to use validation multiprocessing from released version * Move logic between job - service, renaem send_one to send_once
* Better logs for a missing hoc file * Make sure single neuron models have the same structure * Bump ready marker version (to invalidate current cache)
* Small init model improvements, more logs and clean up * Remove arch MD doc
* Add WIP * Add endpoint to fetch output files * Enable authentication * Clean up, organize imports * Add Ultralizer repo clone, test build * Clean up * Ignore missing dep for now * Temporarily disable job-fn-reference check * Finalize Github actions
* update entitysdk version * uv lock
* Make sure only external entitySDK client is used * Datamodel code generator dependency
* Add current recordings * Use combination of sec and seg to index current recordings
Collaborator
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Relates to Bluenaas implementation of IC Simulator. |
pgetta
previously approved these changes
Mar 12, 2026
Contributor
Author
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@pgetta is there a reason that the python version is locked at 3.12.13 now? Because I was unable to run uv lock with my python version. I can install it if this necessary. |
Contributor
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EDIT: we would need this obi-one version to be used: https://github.com/openbraininstitute/obi-one/releases/tag/2026.3.6 |
darshanmandge
previously approved these changes
Mar 13, 2026
Collaborator
In general I like versions fixed, had too many issues with things suddenly not working in the past. I've updated it to the latest patch. I remember trying to use 3.13 - but some packages failed, maybe the situation is different now, will try to upgrade at some point. With UV, if I'm not mistaken, you can run |
Contributor
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New release made for obi-one: https://github.com/openbraininstitute/obi-one/releases/tag/2026.3.7 |
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Add support for exporting current report variables to a separate current_report.nwb.
Current densities recorded from the simulation are converted to currents using the segment area of the recorded compartment and stored as VoltageClampSeries.
If a SEClamp stimulus is present in the simulation configuration, the command waveform is reconstructed and written to the NWB stimulus group.
The simulation script was also refactored to rely on the BlueCellulab report helper pipeline instead of manually configuring recordings. This depends on the corresponding BlueCellulab API changes (report payload updates including segment area and time) and should be merged after that PR.