[NSETM-2226] Add NodeSets adapter to support custom node_sets_file (#22)

Support custom node_sets_file in extraction, neuron_classes and trial_steps

Author: GianlucaFicarelli

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Changelog
 =========
 
+Version 0.8.0
+-------------
+
+New Features
+~~~~~~~~~~~~
+
+- Support custom node_sets_file in extraction, neuron_classes and trial_steps [NSETM-2226]
+
+
 Version 0.7.1
 -------------
 

pyproject.toml

@@ -123,7 +123,7 @@ branch = true
 parallel = false
 omit = [
  "*/blueetl/_version.py",
- "*/blueetl/adapters/bluepy/*.py",
+ "*/blueetl/adapters/impl/bluepy/*.py",
  "*/blueetl/external/**/*.py",
 ]
 

src/blueetl/adapters/base.py

@@ -1,13 +1,14 @@
 """Base Adapter."""
 
 from abc import ABC, abstractmethod
+from pathlib import Path
 from typing import Any, Generic, Optional, TypeVar
 
 from blueetl.adapters.interfaces.circuit import CircuitInterface
+from blueetl.adapters.interfaces.node_sets import NodeSetsInterface
 from blueetl.adapters.interfaces.simulation import SimulationInterface
-from blueetl.types import StrOrPath
 
-InterfaceT = TypeVar("InterfaceT", CircuitInterface, SimulationInterface)
+InterfaceT = TypeVar("InterfaceT", CircuitInterface, SimulationInterface, NodeSetsInterface)
 BaseAdapterT = TypeVar("BaseAdapterT", bound="BaseAdapter")
 
 
@@ -18,13 +19,14 @@ class AdapterError(Exception):
 class BaseAdapter(Generic[InterfaceT], ABC):
  """Base Adapter to be subclassed by other adapters."""
 
- def __init__(self, config: StrOrPath) -> None:
- """Init the adapter from the specified config."""
- self._impl: Optional[InterfaceT] = self._load_impl(str(config))
+ def __init__(self, _impl: Optional[InterfaceT]) -> None:
+ """Init the adapter from the specified implementation."""
+ self._impl: Optional[InterfaceT] = _impl
 
+ @classmethod
  @abstractmethod
- def _load_impl(self, config: str) -> Optional[InterfaceT]:
- """Load and return the implementation object, or None if the config file doesn't exist."""
+ def from_file(cls, filepath: Optional[Path]) -> "BaseAdapter":
+ """Load and return a new object from file."""
 
  @property
  def _ensure_impl(self) -> InterfaceT:
@@ -41,10 +43,3 @@ def exists(self) -> bool:
  def instance(self) -> Any:
  """Return the wrapped instance, or None if it doesn't exist."""
  return self._impl.instance if self._impl is not None else None
-
- @classmethod
- def from_impl(cls: type[BaseAdapterT], impl: InterfaceT) -> BaseAdapterT:
- """Return a new adapter with the specified implementation."""
- result = object.__new__(cls)
- result._impl = impl
- return result

src/blueetl/adapters/circuit.py

@@ -6,22 +6,25 @@
 
 from blueetl.adapters.base import BaseAdapter
 from blueetl.adapters.interfaces.circuit import CircuitInterface, NodePopulationInterface
+from blueetl.adapters.node_sets import NodeSetsAdapter
 
 
 class CircuitAdapter(BaseAdapter[CircuitInterface]):
  """Circuit Adapter."""
 
- def _load_impl(self, config: str) -> Optional[CircuitInterface]:
- """Load and return the implementation object, or None if the config file doesn't exist."""
+ @classmethod
+ def from_file(cls, filepath: Optional[Path]) -> "CircuitAdapter":
+ """Load and return a new object from file."""
  # pylint: disable=import-outside-toplevel
- if not config or not Path(config).exists():
- return None
+ if not filepath or not filepath.exists():
+ return cls(None)
  CircuitImpl: type[CircuitInterface]
- if config.endswith(".json"):
- from blueetl.adapters.bluepysnap.circuit import Circuit, CircuitImpl
+ if filepath.suffix == ".json":
+ from blueetl.adapters.impl.bluepysnap.circuit import Circuit, CircuitImpl
  else:
- from blueetl.adapters.bluepy.circuit import Circuit, CircuitImpl
- return CircuitImpl(Circuit(config))
+ from blueetl.adapters.impl.bluepy.circuit import Circuit, CircuitImpl
+ impl = CircuitImpl(Circuit(str(filepath)))
+ return cls(impl)
 
  def checksum(self) -> str:
  """Return a checksum of the relevant keys in the circuit configuration."""
@@ -31,3 +34,13 @@ def checksum(self) -> str:
  def nodes(self) -> Mapping[Optional[str], NodePopulationInterface]:
  """Return the nodes as a dict: population -> nodes."""
  return self._ensure_impl.nodes
+
+ @property
+ def node_sets_file(self) -> Optional[Path]:
+ """Returns the NodeSets file used by the circuit."""
+ return self._ensure_impl.node_sets_file
+
+ @property
+ def node_sets(self) -> NodeSetsAdapter:
+ """Returns the NodeSets file used by the circuit."""
+ return NodeSetsAdapter(self._ensure_impl.node_sets)

src/blueetl/adapters/impl/__init__.py

@@ -0,0 +1 @@
+"""Implementations."""

src/blueetl/adapters/bluepy/__init__.py …blueetl/adapters/impl/bluepy/__init__.pysrc/blueetl/adapters/bluepy/__init__.py renamed to src/blueetl/adapters/impl/bluepy/__init__.py src/blueetl/adapters/bluepy/__init__.py renamed to src/blueetl/adapters/impl/bluepy/__init__.py

@@ -1,11 +1,13 @@
 """Bluepy circuit implementation."""
 
 from collections.abc import Mapping
+from pathlib import Path
 from typing import Optional
 
 from bluepy import Circuit
 
 from blueetl.adapters.interfaces.circuit import CircuitInterface, NodePopulationInterface
+from blueetl.adapters.interfaces.node_sets import NodeSetsInterface
 from blueetl.utils import checksum_json
 
 
@@ -40,3 +42,13 @@ def nodes(self) -> Mapping[Optional[str], NodePopulationInterface]:
         The population name in the returned dict is always None, because undefined in the config.
         """
  return {None: self._circuit.cells}
+
+ @property
+ def node_sets_file(self) -> Optional[Path]:
+ """Returns the NodeSets file used by the circuit."""
+ raise NotImplementedError
+
+ @property
+ def node_sets(self) -> NodeSetsInterface:
+ """Returns the NodeSets used by the circuit."""
+ raise NotImplementedError

src/blueetl/adapters/bluepy/circuit.py …/blueetl/adapters/impl/bluepy/circuit.pysrc/blueetl/adapters/bluepy/circuit.py renamed to src/blueetl/adapters/impl/bluepy/circuit.py src/blueetl/adapters/bluepy/circuit.py renamed to src/blueetl/adapters/impl/bluepy/circuit.py

@@ -12,7 +12,7 @@
 from bluepy.impl.spike_report import SpikeReport
 from bluepy.simulation import PathHelpers
 
-from blueetl.adapters.bluepy.circuit import CircuitImpl
+from blueetl.adapters.impl.bluepy.circuit import CircuitImpl
 from blueetl.adapters.interfaces.circuit import CircuitInterface
 from blueetl.adapters.interfaces.simulation import (
  PopulationReportInterface,

src/blueetl/adapters/bluepy/simulation.py …ueetl/adapters/impl/bluepy/simulation.pysrc/blueetl/adapters/bluepy/simulation.py renamed to src/blueetl/adapters/impl/bluepy/simulation.py src/blueetl/adapters/bluepy/simulation.py renamed to src/blueetl/adapters/impl/bluepy/simulation.py

@@ -1,11 +1,14 @@
 """Bluepysnap circuit implementation."""
 
 from collections.abc import Mapping
+from pathlib import Path
 from typing import Optional
 
 from bluepysnap import Circuit
 
+from blueetl.adapters.impl.bluepysnap.node_sets import NodeSetsImpl
 from blueetl.adapters.interfaces.circuit import CircuitInterface, NodePopulationInterface
+from blueetl.adapters.interfaces.node_sets import NodeSetsInterface
 from blueetl.utils import checksum_json
 
 
@@ -23,3 +26,14 @@ def checksum(self) -> str:
  def nodes(self) -> Mapping[Optional[str], NodePopulationInterface]:
  """Return the nodes as a dict: population -> nodes."""
  return self._circuit.nodes
+
+ @property
+ def node_sets_file(self) -> Optional[Path]:
+ """Returns the NodeSets file used by the circuit."""
+ path = self._circuit.to_libsonata.node_sets_path
+ return Path(path) if path else None
+
+ @property
+ def node_sets(self) -> NodeSetsInterface:
+ """Returns the NodeSets used by the circuit."""
+ return NodeSetsImpl(self._circuit.node_sets)