[BBPBGLIB-1120] Remove node loaders for MVD3 and NCS (#117)

## Context
After deprecating BlueConfig files, we no longer support legacy node
format, MVD3 or NCS. Therefore, this PR removes the corresponding node
loaders.

## Scope
In `cell_reader.py`: keeping only `load_sonata` and removing the other
readers.
In `metype.py`: removing `Cell_V5`.


## Testing
Adapt the current unit tests to use SONATA nodes.

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [x] Unit/Scientific test added
* [x] Updated Readme, in-code, developer documentation

docs/api/subpackages/io.rst

@@ -14,10 +14,7 @@ neurodamus.io.cell\_readers
 
    .. autosummary::
 
-      load_mvd3
-      load_ncs
-      load_nodes_mvd3
-      load_combo_metypes
+      load_sonata
       split_round_robin
 
    .. rubric:: Exceptions

docs/architecture.rst

@@ -103,7 +103,7 @@ BBP v6 circuits would define its own cell hoc templates (/classes, one for each
 based on Cell.hoc.
 
 Morphologically detailed neurons are the heart of a Neuron simulation. Neurodamus will read the
-cells metadata from a node file (start.ncs, circuit.mvd3 or nodes.h5 sonata) and instantiate each
+cells metadata from a node file in SONATA format and instantiate each
 individual cell by:
 
 - loading the morphology and instantiate the respective sections
@@ -138,7 +138,7 @@ Due to extensively different logic, both these cell types inherit directly from
 must be handled by their own cell manager classes. To these modules implementing a new `Cell`,
 `CellManagers` and eventually `ConnectionManager` types we call **Engine** - more on this later.
 
-For the record, `Cell_V5/V6` and the corresponding `CellDistributor` and `SynapseRuleManager`
+For the record, `Cell_V6` and the corresponding `CellDistributor` and `SynapseRuleManager`
 were also made components of a special engine: the `METypeEngine`, obviously built-in (find it
 in node.py).
 
@@ -180,7 +180,6 @@ considered a cell manager, but by far lighter than a full cell manager.
 
   * `CellType`: The default cell class this manager handles.
   * `_node_loader`: The default loader function for nodes (cell metadata)
-  * `_node_format`: The default file format of nodes, .e.g. Sonata
 
 - Instance properties:
 

docs/examples.rst

@@ -85,7 +85,7 @@ Dry run mode
 ~~~~~~~~~~~~
 In order to obtain a more accurate estimation of the resources needed for a simulation,
 users can also run Neurodamus in dry run mode. This functionality is only available
-for libsonata circuits. MVD3 circuits are not supported.
+for SONATA circuits.
 
 This mode will partially instantiate cells and synapses to get a statistical overview
 of the memory used but won't run the actual simulation.

neurodamus/cell_distributor.py

@@ -8,7 +8,6 @@
 import os
 import weakref
 from contextlib import contextmanager
-from enum import Enum
 from io import StringIO
 from os import path as ospath
 from pathlib import Path
@@ -24,19 +23,13 @@
 from .core.nodeset import NodeSet
 from .io import cell_readers
 from .lfp_manager import LFPManager
-from .metype import Cell_V5, Cell_V6, EmptyCell
+from .metype import Cell_V6, EmptyCell
 from .target_manager import TargetSpec
 from .utils import compat
 from .utils.logging import log_verbose, log_all
 from .utils.memory import DryRunStats, get_mem_usage_kb
 
 
-class NodeFormat(Enum):
-    NCS = 1
-    MVD3 = 2
-    SONATA = 3
-
-
 class VirtualCellPopulation:
     """
     A virtual cell population offers a compatible interface with Cell Manager,
@@ -110,15 +103,11 @@ class CellManagerBase(_CellManager):
     """
 
     _node_loader = None
-    """Default function implementing the loading of nodes data, a.k.a. MVD
+    """Default function implementing the loading of nodes data
 
     signature:
         load(circuit_conf, gidvec, stride=1, stride_offset=0)
     """
-
-    _node_format = NodeFormat.SONATA  # NCS, Mvd, Sonata...
-    """Default Node file format"""
-
     def __init__(self, circuit_conf, target_manager, _run_conf=None, **_kw):
         """Initializes CellDistributor
 
@@ -179,12 +168,11 @@ def get_final_gids(self):
         return numpy.array(self.local_nodes.final_gids())
 
     def _init_config(self, circuit_conf, pop):
-        if self._node_format == NodeFormat.SONATA:
-            if not ospath.isabs(circuit_conf.CellLibraryFile):
-                circuit_conf.CellLibraryFile = find_input_file(circuit_conf.CellLibraryFile)
-            if not pop:   # Last attempt to get pop name
-                pop = self._get_sonata_population_name(circuit_conf.CellLibraryFile)
-                logging.info(" -> Discovered node population name: %s", pop)
+        if not ospath.isabs(circuit_conf.CellLibraryFile):
+            circuit_conf.CellLibraryFile = find_input_file(circuit_conf.CellLibraryFile)
+        if not pop:   # Last attempt to get pop name
+            pop = self._get_sonata_population_name(circuit_conf.CellLibraryFile)
+            logging.info(" -> Discovered node population name: %s", pop)
         if not pop and circuit_conf._name:
             pop = circuit_conf._name
             logging.warning("(Compat) Assuming population name from Circuit: %s", pop)
@@ -520,28 +508,11 @@ class CellDistributor(CellManagerBase):
         Instantiated cells are stored locally (.cells property)
     """
 
-    _cell_loaders = {
-        "start.ncs": cell_readers.load_ncs,
-        "circuit.mvd3": cell_readers.load_mvd3,
-    }
-
     _sonata_with_extra_attrs = True  # Enable search extra node attributes
 
     def _init_config(self, circuit_conf, _pop):
         if not circuit_conf.CellLibraryFile:
-            logging.warning("CellLibraryFile not set. Assuming legacy 'start.ncs'")
-            circuit_conf.CellLibraryFile = "start.ncs"
-        if circuit_conf.CellLibraryFile.endswith(".ncs"):
-            self._node_format = NodeFormat.NCS
-        elif circuit_conf.CellLibraryFile.endswith(".mvd3"):
-            self._node_format = NodeFormat.MVD3
-
-        self._is_v5_circuit = circuit_conf.CellLibraryFile == "start.ncs" or (
-            circuit_conf.nrnPath and ospath.isfile(ospath.join(circuit_conf.nrnPath, "start.ncs"))
-            and not ospath.isfile(ospath.join(circuit_conf.CircuitPath, "circuit.mvd3"))
-        )
-        if self._is_v5_circuit and self._circuit_conf.DetailedAxon:
-            raise ConfigurationError("V5 circuits don't support keeping detailed axons")
+            raise ConfigurationError("CellLibraryFile not set")
 
         super()._init_config(circuit_conf, _pop)
 
@@ -553,19 +524,12 @@ def load_nodes(self, load_balancer=None, **kw):
         cell_requirements = all_cell_requirements.get(self._population_name) or (
             self.is_default and all_cell_requirements.get(None)
         )
-        if self._node_format == NodeFormat.SONATA:
-            loader = cell_readers.load_sonata
-            loader_opts["node_population"] = self._population_name  # mandatory in Sonata
-            loader_opts["load_dynamic_props"] = cell_requirements
-            loader_opts["has_extra_data"] = self._sonata_with_extra_attrs
-        else:
-            if cell_requirements:
-                raise Exception('Additional cell properties only available with SONATA')
-            nodes_filename = self._circuit_conf.CellLibraryFile
-            loader = self._cell_loaders.get(nodes_filename, cell_readers.load_mvd3)
-            loader_opts = {}
+        loader = cell_readers.load_sonata
+        loader_opts["node_population"] = self._population_name  # mandatory in Sonata
+        loader_opts["load_dynamic_props"] = cell_requirements
+        loader_opts["has_extra_data"] = self._sonata_with_extra_attrs
 
-        log_verbose("Nodes Format: %s, Loader: %s", self._node_format, loader.__name__)
+        log_verbose("Nodes Format: SONATA , Loader: %s", loader.__name__)
         return super().load_nodes(load_balancer, _loader=loader, loader_opts=loader_opts)
 
     def _instantiate_cells(self, dry_run_stats_obj: DryRunStats = None, **opts):
@@ -578,7 +542,7 @@ def _instantiate_cells(self, dry_run_stats_obj: DryRunStats = None, **opts):
         if self.CellType is not NotImplemented:
             return super()._instantiate_cells(self.CellType)
         conf = self._circuit_conf
-        CellType = Cell_V5 if self._is_v5_circuit else Cell_V6
+        CellType = Cell_V6
         if conf.MorphologyType:
             CellType.morpho_extension = conf.MorphologyType
 

neurodamus/core/configuration.py

@@ -545,9 +545,6 @@ def _make_circuit_config(config_dict, req_morphology=True):
         config_dict["MorphologyPath"] = False
     elif config_dict.get("nrnPath") == "<NONE>":
         config_dict["nrnPath"] = False
-        if config_dict.get("CellLibraryFile", "start.ncs") == "start.ncs":
-            raise ConfigurationError(
-                "ncs circuits don't support disabling connectivity with nrnPath='<NONE>'")
     _validate_circuit_morphology(config_dict, req_morphology)
     _validate_file_extension(config_dict.get("CellLibraryFile"))
     _validate_file_extension(config_dict.get("nrnPath"))