Remove SynapseReader.mod and SynReaderNRN (#122)

## Context
After removing BlueConfig, we only support SONATA edges files loaded via
`libsonata` API. This PR removes the synpase loaders that were used to
support non-SONATA files.

## Scope
Remove `SynapseReader.mod`. 
In `synapse_reader.py`, remove class `SynReaderNRN` which was used to
load non-SONATA .h5 files via `HDF5Reader`.

## Testing
Remove the test for `SynReaderNRN`

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

core/mod/coreneuron_modlist.txt

@@ -6,5 +6,4 @@ netstim_inhpoisson.mod
 SonataReportHelper.mod
 SonataReports.mod
 SpikeWriter.mod
-SynapseReader.mod
 VecStim.mod

docs/api/subpackages/io.rst

@@ -35,8 +35,7 @@ neurodamus.io.synapse\_reader
    .. autosummary::
       SynapseParameters
       SynapseReader
-      SynReaderNRN
-
+      SonataReader
 
    .. rubric:: Exceptions
 

neurodamus/connection_manager.py

@@ -15,6 +15,7 @@
 from .core import run_only_rank0
 from .core.configuration import GlobalConfig, SimConfig, ConfigurationError, find_input_file
 from .connection import Connection, ReplayMode
+from .io.sonata_config import ConnectionTypes
 from .io.synapse_reader import SynapseReader
 from .target_manager import TargetManager, TargetSpec
 from .utils import compat, bin_search, dict_filter_map
@@ -286,18 +287,16 @@ def __str__(self):
     def open_edge_location(self, syn_source, circuit_conf, **kw):
         edge_file, *pop = syn_source.split(":")
         pop_name = pop[0] if pop else None
-        n_files = circuit_conf.get("NumSynapseFiles")
         src_pop_id = _get_projection_population_id(circuit_conf)
-        return self.open_synapse_file(edge_file, pop_name, n_files, src_pop_id=src_pop_id, **kw)
+        return self.open_synapse_file(edge_file, pop_name, src_pop_id=src_pop_id, **kw)
 
-    def open_synapse_file(self, synapse_file, edge_population, n_files=1, *,
-                          src_pop_id=None, src_name=None, **_kw):
+    def open_synapse_file(self, synapse_file, edge_population, *, src_pop_id=None, src_name=None,
+                          **_kw):
         """Initializes a reader for Synapses config objects and associated population
 
         Args:
             synapse_file: The nrn/edge file. For old nrn files it may be a dir.
             edge_population: The population of the edges
-            n_files: (nrn only) the number of nrn files in the directory (without nrn.h5)
             src_pop_id: (compat) Allow overriding the src population ID
             src_name: The source pop name, normally matching that of the source cell manager
         """
@@ -307,11 +306,9 @@ def open_synapse_file(self, synapse_file, edge_population, n_files=1, *,
         if not ospath.exists(synapse_file):
             raise ConfigurationError("Connectivity (Edge) file not found: {}".format(synapse_file))
         if ospath.isdir(synapse_file):
-            logging.warning("Edges source is a directory (legacy nrn.h5 only)")
-            if ospath.isfile(ospath.join(synapse_file, "nrn.h5")):
-                n_files = 1
+            raise ConfigurationError("Edges source is a directory")
 
-        self._synapse_reader = self._open_synapse_file(synapse_file, edge_population, n_files)
+        self._synapse_reader = self._open_synapse_file(synapse_file, edge_population)
         if self._load_offsets:
             if not self._synapse_reader.has_property("synapse_index"):
                 raise Exception("Synapse offsets required but not available. "
@@ -322,12 +319,10 @@ def open_synapse_file(self, synapse_file, edge_population, n_files=1, *,
         return synapse_file
 
     # - override if needed
-    def _open_synapse_file(self, synapse_file, pop_name, n_nrn_files=None):
+    def _open_synapse_file(self, synapse_file, pop_name):
         logging.debug("Opening Synapse file %s, population: %s", synapse_file, pop_name)
         return self.SynapseReader.create(
-            synapse_file, self.CONNECTIONS_TYPE, pop_name,
-            n_nrn_files, self._raw_gids,  # Used eventually by NRN reader
-            extracellular_calcium=SimConfig.extracellular_calcium
+            synapse_file, pop_name, extracellular_calcium=SimConfig.extracellular_calcium
         )
 
     def _init_conn_population(self, src_pop_name, pop_id_override):
@@ -1202,7 +1197,7 @@ class SynapseRuleManager(ConnectionManagerBase):
     created.
     """
 
-    CONNECTIONS_TYPE = SynapseReader.SYNAPSES
+    CONNECTIONS_TYPE = ConnectionTypes.Synaptic
 
     def __init__(self, circuit_conf, target_manager, cell_manager, src_cell_manager=None, **kw):
         """Initializes a Connection/Edge manager for standard METype synapses

neurodamus/gap_junction.py

@@ -2,14 +2,13 @@
 Main module for handling and instantiating synaptical connections
 """
 from __future__ import absolute_import
-import logging
 import numpy as np
 from os import path as ospath
 
 from .connection_manager import ConnectionManagerBase
 from .core.configuration import ConfigurationError
-from .io.synapse_reader import SynapseReader, SynReaderNRN, SonataReader, SynapseParameters, \
-    FormatNotSupported
+from .io.sonata_config import ConnectionTypes
+from .io.synapse_reader import SonataReader, SynapseParameters
 from .utils import compat
 from .utils.logging import log_verbose
 
@@ -25,28 +24,7 @@ def create_array(cls, length):
         return npa
 
 
-class GapJunctionSynapseReader(SynapseReader):
-    """ Derived from SynapseReader, used for reading GapJunction synapses.
-        Factory create() will attempt to instantiate GapJunctionSynToolReader,
-        followed by SynReaderNRN.
-    """
-
-    @classmethod
-    def create(cls, syn_src, conn_type, population=None, *args, **kw):
-        """Instantiates a synapse reader, giving preference to GapJunctionSynToolReader
-        """
-        if fn := cls._get_sonata_circuit(syn_src):
-            log_verbose("[SynReader] Using SonataReader.")
-            return GapJunctionSonataReader(fn, conn_type, population, **kw)
-
-        # Syn2 support dropped (July 2023)
-        if not ospath.isdir(syn_src) and not syn_src.endswith(".h5"):
-            raise FormatNotSupported("File: {syn_src}")
-        logging.info("[GapJunctionSynReader] Attempting legacy hdf5 reader.")
-        return SynReaderNRN(syn_src, conn_type, None, *args, **kw)
-
-
-class GapJunctionSonataReader(SonataReader):
+class GapJunctionSynapseReader(SonataReader):
     Parameters = GapJunctionConnParameters
     parameter_mapping = {
         "weight": "conductance",
@@ -64,7 +42,7 @@ class GapJunctionManager(ConnectionManagerBase):
     The user will have the capacity to scale the conductance weights.
     """
 
-    CONNECTIONS_TYPE = SynapseReader.GAP_JUNCTIONS
+    CONNECTIONS_TYPE = ConnectionTypes.GapJunction
     _gj_offsets = None
     SynapseReader = GapJunctionSynapseReader
 

neurodamus/io/sonata_config.py

@@ -5,6 +5,15 @@
 import libsonata
 import logging
 import os.path
+from enum import StrEnum
+
+
+class ConnectionTypes(StrEnum):
+    Synaptic = "Synaptic"
+    GapJunction = "GapJunction"
+    NeuroModulation = "NeuroModulation"
+    NeuroGlial = "NeuroGlial"
+    GlioVascular = "GlioVascular"
 
 
 class SonataConfig:
@@ -289,11 +298,11 @@ def make_circuit(nodes_file, node_pop_name, population_info):
     @property
     def parsedProjections(self):
         projection_type_convert = dict(
-            chemical="Synaptic",
-            electrical="GapJunction",
-            synapse_astrocyte="NeuroGlial",
-            endfoot="GlioVascular",
-            neuromodulatory="NeuroModulation"
+            chemical=ConnectionTypes.Synaptic,
+            electrical=ConnectionTypes.GapJunction,
+            synapse_astrocyte=ConnectionTypes.NeuroGlial,
+            endfoot=ConnectionTypes.GlioVascular,
+            neuromodulatory=ConnectionTypes.NeuroModulation
         )
         internal_edge_pops = set(c_conf["nrnPath"] for c_conf in self._bc_circuits.values())
         projections = {}
@@ -323,10 +332,10 @@ def parsedProjections(self):
                     Type=projection_type_convert.get(pop_type)
                 )
                 # Reverse projection direction for Astrocyte projection: from neurons to astrocytes
-                if projection.get("Type") == "NeuroGlial":
+                if projection.get("Type") == ConnectionTypes.NeuroGlial:
                     projection["Source"], projection["Destination"] = projection["Destination"], \
                         projection["Source"]
-                if projection.get("Type") == "GlioVascular":
+                if projection.get("Type") == ConnectionTypes.GlioVascular:
                     for node_file_info in self._circuit_networks["nodes"]:
                         for _, pop_info in node_file_info["populations"].items():
                             if pop_info.get("type") == "vasculature":