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BlueBrain
The Blue Brain Pythonic Simulation and Network Analysis Productivity layer
Oftentimes, the naming of `afferent_edges`/`efferent_edges`/`afferent_nodes`/`efferent_nodes` cause confusion among our users. Also, quite frankly, I always have to look them up too as they don't feel intuitive. It's not clear what...
`firing_rate_histogram` is limited to only consider gids within the report (see: [here](https://github.com/BlueBrain/snap/blob/16986bf0b78f73f016335751ca9042496fa345e5/bluepysnap/_plotting.py#L82)). `bluepy` did not have the same behavior in it's implementation of the plot. Therefore, to ease the comparison...
When using get-like functions (edges.pathway_edges, nodes.get) it is common to concatenate the outputs of the functions to mimic the old bluepysnap interface. However, if no nodes/edges satisfy the query, instead...
@edasubert approached me with a question as to why does this happen: ```python >>> list(circuit.edges.iter_connections(source="Excitatory")) Traceback (most recent call last): File "/gpfs/bbp.cscs.ch/ssd/apps/bsd/2023-02-23/stage_applications/install_gcc-12.2.0-skylake/py-bluepysnap-2.0.2-hmbi6r/lib/python3.10/site-packages/bluepysnap/node_sets.py", line 52, in get_ids return self._node_sets.materialize(self._name, population).flatten() libsonata._libsonata.SonataError:...
WIP This is an initial experiment to convert a query to node_sets, to be able to use libsonata to get the ids. Possible benefits: - it seems faster than using...
Calls to circ.edges.afferent_edges even for one target neuron is filling my 32GB of ram almost instantly.  Is this expected behaviour? What is the correct way to get synapse properties...
Registered a Thalamus simulation to nse/test2 in Nexus to be used instead of the hard-coded path. * requires `bluepyentity` to run simulation notebooks Requires https://github.com/BlueBrain/bluepyentity/pull/27 * to use entity.instance to...
When CircuitNodeIds is converted to a numpy array it turns into a (N, 2) array rather than an array of N unique identifiers. This causes issues when using e.g. np.isin,...
