- Support for
numpy>=2 - Made
EdgesandEdgePopulationgetfunctions more consistent- Both now return
self.ids(query)ifproperties=None propertiesis now a keyword argument inEdgePopulation.get
- Both now return
- Added
EdgePopulation.statswith two methods:divergence,convergence - Added new notebooks covering node sets as well as node and edge queries
- Added the possibility to query Edge IDs and Node IDs based on edge/node population type using query key
population_type- the types conform to node types and edge types defined in the sonata specification
- teach the bluepysnap validate-circuit and bluepysnap validate-simulation the ability to --ignore-datatype-errors so that mismatches of datatypes to the specification are ignored
- Update simulation validation to conform to the SONATA spec
synapse_replay.sourceand.datspike input files are no longer supported
- Support morphology containers
- Fixed a bug causing some iterables (e.g., tuples) in queries not to work as expected
- Added simulation config validation
- Added a new commandline subcommands:
validate-simulation,validate-circuit
- Edge populations'
iter_connectionsreturnsCircuitNodeIdinstead ofint - Removed the commandline subcommand
validatein favor of newvalidate-circuitcommand
- Readded compatibility with
jsonschema<4.18
- Fixed pylint
cyclic-importissues - Fixed docstrings of
Nodes.get,Edges.get - Added basic testing to
_plotting.py
NodeSetsobject can be instantiated with three methods:from_file,from_string,from_dict- Simulation inputs are now accessible with
Simulation.inputs libsonatareader ofsynapse_replayfiles can now be accessed withsimulation.inputs["<input_name>"].reader- only
h5format is supported
- only
- 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_propertytoNodePopulation.get - Undeprecated calling
Edges.getandEdgePopulation.getwithproperties=None
- Fixed the Same property with different dtype issue with
nodes.get,edges.get
nodes.getandedges.get(andnetwork.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))
- returns a generator yielding tuples of
- Removed
Network.property_dtypes,CircuitIds.index_schema Circuit.node_sets,Simulation.node_setsreturnsNodeSetsobject initialized with empty dict when node sets file is not presentNodeSet.resolvedis no longer availableFrameReport.node_setreturns node_set name instead of resolved node set query- Removed
Edges.properties,EdgePopulation.propertiesthat were already supposed to be removed in v1.0.0
- Added
CircuitIds.intersectionto take the intersection of twoCircuitIds.
- Improve performance when querying a population with get() and ids().
- Fix CircuitIds.sample() to always return different samples.
- Ensure that the report DataFrames have the same schema even when empty.
- 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.
- Add python 3.10 tests, and update GitHub actions.
- Add pickling to classes with caching, to reduce chances of blowup on cached methods
- Remove NeuroM and lazy-object-proxy dependency leftovers.
- 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
- Set recursive autodoc generation to include 'nodes' and 'edges'.
- Renamed population_config to config for backwards compatibility
- Access the population configs for node/edge populations via population_config property
- Spatial index for segments and synapses
- jsonschema based validation of h5 files and circuit configuration
- checks for required attributes and data types of attributes (in h5 files)
- 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
- 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
- Add python 3.9 tests.
- Ensure that ids in frame reports are always np.int64 even when using libsonata 0.1.10.
- Fix deprecation warnings.
- Drop python 3.6 support.
- 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
- Update circuit validation for the current BBP sonata spec
- Fix circuit validation. Validation of morphologies was skipped when no rotations fields were present.
- Adding the h5 and csv file accessors to the Node/EdgeStorage classes.
- Fix the morphology/model access using a numpy int (using a numpy integer to access the morphology/model used to fail).
- Update the copyright.
- removing the MORPH_CACHE_SIZE
- removing neurom as the main reader for morphologies
- adding morphio as the main reader for the morphologies
- Implement queries mechanism for edges
- Pinned major versions of dependencies.
- Pinned major versions of neuroM to <2.0.0.
- Added NeuronModelsHelper to access nodes neuron models
- Moved nodes query mechanism to a separate module
- Ensure the dtypes as int64 for the node/edge ids (#121).
- 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)
- Deprecated the properties function from the EdgePopulation (#113)
- Added the python3.8 toxenv
- 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)
- Fixed circuit validation for h5py>=3.0.0
- Allowed usage of config dict instead of file only (#108)
- Added a circuit node interface (#99)
- Added the CircuitNodeId/CircuitNodeIds
- Added Nodes class
- All functions can use the CircuitNodeId/CircuitNodeIds
- 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)
- 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)
- 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 .
- Improved circuit validation for virtual nodes (#86)
- "components" is mandatory by the validation only if the circuit contains nodes other than virtual nodes
- Fixed error when sampling an empty group in NodePopulation.ids (#83)
- 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)
- Added '$node_set' to nodes queries
- Reduced memory usage for fields from @library
- Fixed circuit validation of implicit node ids
- Added the source/target_in_edges that returns set of edge population names that use this node population as source/target
- Checked morphology and model_template fields in both @library or normal group.
- Removed some dependencies to NodePopulation mocks in the different tests
- Removed the mechanisms_dir as a mandatory directory for the circuit validation
- Added source/target node ids to the available properties for edges
- Checked if a node population contains biophysical nodes before calling .morph
- Improved testing for the morph.py module (removed unneeded mocks)
- 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
- Added the FilteredFrameReport and FilteredSpikeReport classes used as lazy and cached results for simulation queries.
- Added plots to the filtered spike/frame reports
- Added the filtered class for the spike and frame reports
- Used categoritical values for attr in @library
- Fixed empty dict / array for reports query
- Fixed edge iter_connection with unique_node_ids
- Fixed the empty list/array/dict in simulation reports and in node.ids()
- 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
- 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
- Added the Simulation support
- Simulation config support
- Spike reports support
- Frame reports support
- Added the multi-population support for circuits
- Added a sonata circuit validator
- Implement "node_id" in node set files
- Updated the constant containers
- Added "@dynamics:" parameters for edges.
- Always use the node_id naming convention in code docstrings.
- Run deploy step in Travis only for Python 3.6
- Initial commit