https://github.com/bluebrain/snap - v3.0.1

Bug Fixes

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

Improvements

• Made morphology directory available via MorphHelper.get_morphology_dir

- Python
Published by joni-herttuainen over 2 years ago

https://github.com/bluebrain/snap - 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

- Python
Published by edasubert over 2 years ago

https://github.com/bluebrain/snap - v2.0.2

Improvements

• Readded compatibility with jsonschema<4.18

- Python
Published by joni-herttuainen over 2 years ago

https://github.com/bluebrain/snap - v2.0.1

Bug Fixes

• fixed pylint cyclic-import issues
• fixed docstrings of Nodes.get, Edges.get
• did small fixes and added basic testing to _plotting.py

- Python
Published by joni-herttuainen over 2 years ago

https://github.com/bluebrain/snap - 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

- Python
Published by joni-herttuainen almost 3 years ago

https://github.com/bluebrain/snap - 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.

- Python
Published by GianlucaFicarelli about 3 years ago

https://github.com/bluebrain/snap - 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.

- Python
Published by mgeplf about 3 years ago

https://github.com/bluebrain/snap - 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

- Python
Published by mgeplf over 3 years ago

https://github.com/bluebrain/snap - v1.0.4

Bug Fixes

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

- Python
Published by GianlucaFicarelli over 3 years ago

https://github.com/bluebrain/snap - v1.0.3

Improvements

• schemas can return datatypes for attributes for the nodes and edges

- Python
Published by mgeplf over 3 years ago

https://github.com/bluebrain/snap - v1.0.2

Improvements

Renamed population_config to config for backwards compatibility

- Python
Published by joni-herttuainen over 3 years ago

https://github.com/bluebrain/snap - v1.0.1

New Features

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

- Python
Published by joni-herttuainen over 3 years ago

https://github.com/bluebrain/snap - v.1.0.0

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
• the old pointneuron_ spec 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

- Python
Published by joni-herttuainen over 3 years ago

https://github.com/bluebrain/snap - Release v0.13.2

Changes: * add restriction libsonata<0.1.15 as from that version the handling of circuit config may introduce unexpected changes to snap behavior

- Python
Published by joni-herttuainen almost 4 years ago

https://github.com/bluebrain/snap - Update tutorials, drop python 3.6, add python 3.9, bump requirements

What's Changed

• Minor sync of CHANGELOG.rst by @asanin-epfl in https://github.com/BlueBrain/snap/pull/145
• Add authors by @mgeplf in https://github.com/BlueBrain/snap/pull/146
• Remove restriction pylint==2.4.4 by @joni-herttuainen in https://github.com/BlueBrain/snap/pull/147
• Updated the tutorials by @joni-herttuainen in https://github.com/BlueBrain/snap/pull/148
• Bump click requirement by @GianlucaFicarelli in https://github.com/BlueBrain/snap/pull/149
• Drop python3.6 support by @GianlucaFicarelli in https://github.com/BlueBrain/snap/pull/150
• Add python 3.9 tests and ensure int64 in reports by @GianlucaFicarelli in https://github.com/BlueBrain/snap/pull/151

Full Changelog: https://github.com/BlueBrain/snap/compare/v0.13.0...v0.13.1

- Python
Published by GianlucaFicarelli over 4 years ago

https://github.com/bluebrain/snap - Added alternate_morphologies, components and type

• Added support for Sonata BBP spec. See CHANGELOG.rst for details (#142) (https://github.com/AllenInstitute/sonata/pull/130)
• Fixed: morphologies skipped in validation if rotation fields are not present (#143)

- Python
Published by joni-herttuainen almost 5 years ago

https://github.com/bluebrain/snap - Adding file accessors to Node/Edge storages

• Adding the h5 and csv files as properties from Storage (#139)
• Fix the morphology/model access using a numpy int (#137)
• Update copyright (#135)

- Python
Published by tomdele about 5 years ago

https://github.com/bluebrain/snap - Use morphio as a morphology reader

• Use morphio for the morphologies (#134)
• Pinned major versions of dependencies (#131)
• Re-enable codecov (#132)

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Implement queries mechanism for edges

• Implement queries mechanism for edges (#129)
• Pinned major versions of dependencies (#131)

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Add NeuronModelsHelper

• Add NeuronModelsHelper, analog to MorphHelper (#123)
• Add changelog (#117)
• Fix "Returning ids with get/properties" warning (#119)
• Ensure the dtype for the ids (#121)
• Move query functionality to a standalone module (#127)
• Improve perf for positional mask (#128)

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Add Edges interface

• Add a Edges interface to query edges regardless of the population names (#112)
• Add a CircuitEdgeIds object to contain the edge circuit ids (#112)
• Add a ids function to the EdgePopulation class to keep the Edge/Node class homogeneous (#112, #115)
• Add a get function to replace the properties function to the EdgePopulation class to keep the Edge/Node class homogeneous (#113)
• Add a network.py module with a NetworkObject abstract class to factorize the Nodes and Edges classes (#113, #114)
• Deprecation of the properties function from the EdgePopulation (#113)
• Add a _doctool.py module with a DocSubstitutionMeta class to update inherited class docstrings (#113)

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Dropping python2

• Python2 drop (#109)
  • remove python2 tox
  • remove python2 dependencies and bump deps version
  • removed the python2 switches in setup.py
  • added the python3.8 toxenv
  • fix circuit validation for h5py>=3.0.0
  • remove all deprecates

*Remove six dependency (#110)

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Add dict config for the Config class

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

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Adds a circuit node interface to the circuit and circuit node ids

• Adds a circuit node interface (#99)
  • Adds the CircuitNodeId/CircuitNodeIds
  • Add the Node class
• All functions can use the CircuitNodeId/CircuitNodeIds

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Fix tests on Mac. Improve validation of virtual node groups.

• Update of the example notebooks (#88)
• Improve checkids performance (#92)
• Fix unit tests on Mac, fix doc indentation (#91)
• Add the info about the python3.7 support (#93)
• Fix validation of required datasets of virtual node groups (#98)
• Fix h5py dependency to be less than 3.0 (#98)
• New Ci

- Python
Published by tomdele over 5 years ago

https://github.com/bluebrain/snap - Better config handling and "components" not mandatory by validation

• Better config paths handling (#85)
  • can use all the "." + something (i.e: ., ./dir, ../, ./../, ../../something, etc) as paths
  • add 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 .
• Improve circuit validation for virtual nodes (#86)
  • "components" is mandatory by the validation only if the circuit contains nodes other than virtual nodes
• Fix error when sampling an empty group in NodePopulation.ids (#83)

- Python
Published by tomdele almost 6 years ago

https://github.com/bluebrain/snap - Use new libsonata report API and better circuit validation

• Propagate changes from the new libsonata.ElementReport API (#62)
• Bump the libsonata version to 0.1.4 (#62)
• Generalize multiple sonata groups validation of edges and nodes (#79)
• Adapt validation to the sonata original repository examples (#81)
• Improved validation for edge_group_id, edge_group_index and node_population edge's attributes (#82)

- Python
Published by tomdele about 6 years ago

https://github.com/bluebrain/snap - Add '$target' to nodes queries

• Add '$target' to nodes queries
• Reducing memory usage for fields from @library
• Fix circuit validation of implicit node ids

- Python
Published by asanin-epfl about 6 years ago

https://github.com/bluebrain/snap - Add source/target_in_edges and better circuit validation

• Add the source/target_in_edges that returns set of edge population names that use this node population as source/target
• Remove the mechanisms_dir as a mandatory directory for the circuit validation
• Check morphology and model_template fields in both @library or normal group.
• Removed some dependencies to NodePopulation mocks in the different tests

- Python
Published by tomdele about 6 years ago

https://github.com/bluebrain/snap - Fix circuit validation and biophysical properties

• Fix circuit validation when edgegroupid/index are missing (allow missing edgegroupid/index for single group population)
• Fix circuit validation when model_type is part of @library
• Check if a node population contains biophysical nodes before calling .morph
• Add source/target to the available properties for edges
• Improved testing for the morph.py module (removed unneeded mocks)

- Python
Published by tomdele about 6 years ago

https://github.com/bluebrain/snap - Plots for reports

• Adding the filtered class for the spike and frame reports
• Adding the plots for the filtered spike/frame reports
• Fix empty dict / array for reports query
• Use categoritical values for attr in @library
• Fixing edge iterconnection with uniquenode_ids

- Python
Published by tomdele about 6 years ago

https://github.com/bluebrain/snap - Fix empty group queries in nodes and simulation reports

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

- Python
Published by tomdele over 6 years ago

https://github.com/bluebrain/snap - Node set's full support

• Node sets file has its own class
• Compound node sets can be used in node sets file
• Add population and node_id keys in node sets and node's queries
• Add the $and and $or operators to the node's queries
• Node sets are now part of the circuit and not part of the node storage anymore
• Add the node_sets_file in the circuit_config and remove it from the node storage

- Python
Published by tomdele over 6 years ago

https://github.com/bluebrain/snap - Simulations support

This version support the sonata simulations. User can now read frame and spike reports from a common public object: Simulation.

- Python
Published by tomdele over 6 years ago

https://github.com/bluebrain/snap - Multi-population support

• Add the multi-population support for circuits
• Add a sonata circuit validator
• Update the constant containers
• Implement "node_id" in node set files

- Python
Published by tomdele over 6 years ago

https://github.com/bluebrain/snap - add dynamics_params to EdgePopulation

• Add "@dynamics:" parameters for edges.
• Always use the node_id naming convention in code.

- Python
Published by tomdele almost 7 years ago