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Changelog¶

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