Changelog

Version v3.1.0

Improvements

  • Made Edges and EdgePopulation get functions more consistent

    • Both now return self.ids(query) if properties=None

    • properties is now a keyword argument in EdgePopulation.get

  • Added EdgePopulation.stats with two methods: divergence, convergence

Version v3.0.1

Bug Fixes

  • Fixed a bug causing some iterables (e.g., tuples) in queries not to work as expected

Version v3.0.0

New Features

  • Added simulation config validation

  • Added a new commandline subcommands: validate-simulation, validate-circuit

Breaking Changes

  • Edge populations’ iter_connections returns CircuitNodeId instead of int

  • Removed the commandline subcommand validate in favor of new validate-circuit command

Version v2.0.2

Improvements

  • Readded compatibility with jsonschema<4.18

Version v2.0.1

Bug Fixes

  • Fixed pylint cyclic-import issues

  • Fixed docstrings of Nodes.get, Edges.get

  • Added basic testing to _plotting.py

Version v2.0.0

New Features

  • NodeSets object can be instantiated with three methods: from_file, from_string, from_dict

  • Simulation inputs are now accessible with Simulation.inputs

  • libsonata reader of synapse_replay files can now be accessed with simulation.inputs["<input_name>"].reader

    • only h5 format is supported

Improvements

  • Node set resolution is done by libsonata

  • Simulation node set extends Circuit node set

    • A warning is raised if any of the circuit’s node sets is overwritten

  • Added kwarg: raise_missing_property to NodePopulation.get

  • Undeprecated calling Edges.get and EdgePopulation.get with properties=None

Bug Fixes

  • Fixed the Same property with different dtype issue with nodes.get, edges.get

Breaking Changes

  • nodes.get and edges.get (and network.get) no longer return a dataframe

    • returns a generator yielding tuples of (<population_name>, <dataframe>) instead

    • to get the previous behavior (all in one dataframe): pd.concat(df for _, df in circuit.nodes.get(*args, **kwargs))

  • Removed Network.property_dtypes, CircuitIds.index_schema

  • Circuit.node_sets, Simulation.node_sets returns NodeSets object initialized with empty dict when node sets file is not present

  • NodeSet.resolved is no longer available

  • FrameReport.node_set returns node_set name instead of resolved node set query

  • Removed Edges.properties, EdgePopulation.properties that were already supposed to be removed in v1.0.0

Version v1.0.7

New Features

  • Added CircuitIds.intersection to take the intersection of two CircuitIds.

Improvements

  • Improve performance when querying a population with get() and ids().

Bug Fixes

  • Fix CircuitIds.sample() to always return different samples.

  • Ensure that the report DataFrames have the same schema even when empty.

Version v1.0.6

Improvements

  • Clarification for partial circuit configs

  • Publish version as bluepysnap.__version__

  • Support lazy loading of nodes attributes.

  • Add t_step parameter to frame reports.

  • Add python 3.11 tests.

  • Drop python 3.7 support.

Version v1.0.5

Improvements

  • Add python 3.10 tests, and update GitHub actions.

  • Add pickling to classes with caching, to reduce chances of blowup on cached methods

Version v1.0.4

Bug Fixes

  • Remove NeuroM and lazy-object-proxy dependency leftovers.

Version v1.0.3

New Features

  • Teach schemas to return datatypes for attributes for the nodes and edges.

  • Add support for spatial indices:

    • node_populations now have a “spatial_segment_index” property which gives access to the segment index

    • edge_populations now have a “spatial_synapse_index” property which gives access to the synapse index

Bug Fixes

  • Set recursive autodoc generation to include ‘nodes’ and ‘edges’.

Version v1.0.2

Improvements

  • Renamed population_config to config for backwards compatibility

Version v1.0.1

New Features

  • Access the population configs for node/edge populations via population_config property

  • Spatial index for segments and synapses

Version v1.0.0

New Features

  • jsonschema based validation of h5 files and circuit configuration

    • checks for required attributes and data types of attributes (in h5 files)

Improvements

  • Add black & isort to handle formatting

  • Use libsonata to provide more of the functionality

    • parsing config files

    • accessing data in Circuit and Simulation

  • Circuit validation changed to be more config-driven

    • it now only validates objects defined in the circuit configuration file

  • Improved performance when loading nodes and edges from a circuit.

  • Fixed warnings with Pandas 1.5.0

Breaking Changes

  • Simulation

    • run and condition properties return libsonata classes instead of dictionaries

  • non-BBP Sonata circuit validation was removed

  • The NodeStorage & EdgeStorage classes were removed

  • point_neuron is no longer supported

  • Some column data types in the nodes and edges DataFrames returned by the get() method may be float or int instead of object.

  • require libsonata>=0.1.16

Version v0.13.1

Improvements

  • Add python 3.9 tests.

Bug Fixes

  • Ensure that ids in frame reports are always np.int64 even when using libsonata 0.1.10.

  • Fix deprecation warnings.

Removed

  • Drop python 3.6 support.

Version v0.13.0

New Features

  • Sonata BBP spec:

    • Node/edge populations are now supported in config

    • Population type available in NodePopulation/EdgePopulation

    • Population config (if given) overwrites the “components” config for that population

    • Alternate morphology directories (.h5, .asc) are now supported

Improvements

  • Update circuit validation for the current BBP sonata spec

Bug Fixes

  • Fix circuit validation. Validation of morphologies was skipped when no rotations fields were present.

Version v0.12.1

New Features

  • Adding the h5 and csv file accessors to the Node/EdgeStorage classes.

Bug Fixes

  • Fix the morphology/model access using a numpy int (using a numpy integer to access the morphology/model used to fail).

Others

  • Update the copyright.

Version v0.12.0

Improvements

  • removing the MORPH_CACHE_SIZE

  • removing neurom as the main reader for morphologies

  • adding morphio as the main reader for the morphologies

Version v0.11.0

New Features

  • Implement queries mechanism for edges

Improvements

  • Pinned major versions of dependencies.

Bug Fixes

  • Pinned major versions of neuroM to <2.0.0.

Version v0.10.0

New Features

  • Added NeuronModelsHelper to access nodes neuron models

Improvements

  • Moved nodes query mechanism to a separate module

Version v0.9.1

Bug Fixes

  • Ensure the dtypes as int64 for the node/edge ids (#121).

Version v0.9.0

New Features

  • Added a Edges interface to query edges regardless of the population names (#112)

  • Added a CircuitEdgeIds object to contain the edge circuit ids (#112)

  • Added a ids function to the EdgePopulation class to keep the Edge/Node class homogeneous (#112, #115)

  • Added a get function to replace the properties function to the EdgePopulation class to keep the Edge/Node class homogeneous (#113)

  • Added a network.py module with a NetworkObject abstract class to factorize the Nodes and Edges classes (#113, #114)

  • Added a _doctool.py module with a DocSubstitutionMeta class to update inherited class docstrings (#113)

Deprecation

  • Deprecated the properties function from the EdgePopulation (#113)

Version v0.8.0

Improvements

  • Added the python3.8 toxenv

Removed

  • Dropped Python2 support (#109)

    • Removed python2 tox

    • Removed python2 dependencies and bump deps version

    • Removed the python2 switches in setup.py

  • Removed all deprecated functions

  • Removed six dependency (#110)

Bug Fixes

  • Fixed circuit validation for h5py>=3.0.0

Version v0.7.1

New Features

  • Allowed usage of config dict instead of file only (#108)

Version v0.7.0

New Features

  • Added a circuit node interface (#99)

    • Added the CircuitNodeId/CircuitNodeIds

    • Added Nodes class

  • All functions can use the CircuitNodeId/CircuitNodeIds

Version v0.6.2

Improvements

  • Update of the example notebooks (#88)

  • Improved _check_ids performance (#92)

  • Added information about the python3.7 support (#93)

  • Moved the CI from travis to GH Actions (#100, #101, #102, #103)

Bug Fixes

  • Fixed unit tests on Mac, fix doc indentation (#91)

  • Fixed validation of required datasets of virtual node groups (#98)

  • Fixed h5py dependency to be less than 3.0 (#98)

Version v0.6.1

New Features

  • Improved the configuration paths handling (#85)

    • Can use all the “.” + something (i.e: ., ./dir, ../, ./../, ../../something, etc) as paths

    • Added raises to avoid errors

    • Manifest not mandatory anymore (if no anchors in the config)

    • Config strings resolved as paths only if they contain $ or start by .

Improvements

  • Improved circuit validation for virtual nodes (#86)

    • “components” is mandatory by the validation only if the circuit contains nodes other than virtual nodes

Bug Fixes

  • Fixed error when sampling an empty group in NodePopulation.ids (#83)

Version v0.6.0

Improvements

  • Propagated changes from the new libsonata.ElementReport API (#62)

  • Bumped the libsonata version to 0.1.4 (#62)

  • Generalized multiple sonata groups validation of edges and nodes (#79)

  • Adapted validation to the sonata original repository examples (#81)

  • Improved validation for edge_group_id, edge_group_index and node_population edge’s attributes (#82)

Version v0.5.3

New Features

  • Added ‘$node_set’ to nodes queries

Improvements

  • Reduced memory usage for fields from @library

Bug Fixes

  • Fixed circuit validation of implicit node ids

Version v0.5.2

New Features

  • Added the source/target_in_edges that returns set of edge population names that use this node population as source/target

Improvements

  • Checked morphology and model_template fields in both @library or normal group.

  • Removed some dependencies to NodePopulation mocks in the different tests

Bug Fixes

  • Removed the mechanisms_dir as a mandatory directory for the circuit validation

Version v0.5.1

New Features

  • Added source/target node ids to the available properties for edges

Improvements

  • Checked if a node population contains biophysical nodes before calling .morph

  • Improved testing for the morph.py module (removed unneeded mocks)

Bug Fixes

  • Fixed circuit validation when edge_group_id/index are missing (allow missing edge_group_id/index for single group population)

  • Fixed circuit validation when model_type is part of @library

Version v0.5.0

New Features

  • Added the FilteredFrameReport and FilteredSpikeReport classes used as lazy and cached results for simulation queries.

  • Added plots to the filtered spike/frame reports

Improvements

  • Added the filtered class for the spike and frame reports

  • Used categoritical values for attr in @library

Bug Fixes

  • Fixed empty dict / array for reports query

  • Fixed edge iter_connection with unique_node_ids

Version v0.4.1

Bug Fixes

  • Fixed the empty list/array/dict in simulation reports and in node.ids()

Version v0.4.0

New Features

  • Added complete support of the node sets

  • Added population and node_id keys in node sets and node’s queries

  • Added the $and and $or operators to the node’s queries

Improvements

  • Added node sets class

  • Added support for compound node sets in the node sets files

  • Added the node_sets_file in the circuit_config and remove it from the node storage

Version v0.3.0

New Features

  • Added the Simulation support

    • Simulation config support

    • Spike reports support

    • Frame reports support

Version v0.2.0

New Features

  • Added the multi-population support for circuits

  • Added a sonata circuit validator

  • Implement “node_id” in node set files

Improvements

  • Updated the constant containers

Version v0.1.2

New Features

  • Added “@dynamics:” parameters for edges.

Improvements

  • Always use the node_id naming convention in code docstrings.

Version v0.1.1

Improvements

  • Run deploy step in Travis only for Python 3.6

Version v0.1.0

New Features

  • Initial commit