fix docs, remove Cell_V5

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).
 

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

@@ -24,7 +24,7 @@
 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
@@ -523,8 +523,6 @@ def _init_config(self, circuit_conf, _pop):
         if not circuit_conf.CellLibraryFile:
             raise ConfigurationError("CellLibraryFile not set")
 
-        # self._is_v5_circuit alwaysFalse for sonata
-
         super()._init_config(circuit_conf, _pop)
 
     def load_nodes(self, load_balancer=None, **kw):
@@ -553,7 +551,7 @@ 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/io/cell_readers.py

@@ -9,9 +9,9 @@
 from os import path as ospath
 
 from ..core import NeurodamusCore as Nd
-from ..core.configuration import ConfigurationError, SimConfig
+from ..core.configuration import SimConfig
 from ..core import run_only_rank0
-from ..metype import METypeManager, METypeItem
+from ..metype import METypeManager
 from ..utils.logging import log_verbose
 
 EMPTY_GIDVEC = np.empty(0, dtype="uint32")
@@ -198,58 +198,6 @@ def validate_property(prop_name):
     return gidvec, meinfos, fullsize
 
 
-def load_combo_metypes(combo_file, gidvec, combo_list, morph_list):
-    """ Read file with mecombo info, retaining only those that are local to this node
-    Args:
-        combo_file: Path to the combo file to read metype info from
-        gidvec: local gids to load info about
-        combo_list: comboList Combos corresponding to local gids
-        morph_list: morphList Morpholgies corresponding to local gids
-    """
-    if not combo_file:
-        logging.error("Missing BlueConfig field 'MEComboInfoFile' which has gid:mtype:emodel.")
-        raise ConfigurationError("MEComboInfoFile not specified")
-
-    # Optimization: index combos
-    combo_ids = defaultdict(list)
-    for i, c in enumerate(combo_list):
-        combo_ids[c].append(i)
-
-    log_verbose("Loading emodel+additional info from Combo f %s", combo_file)
-    f = open(combo_file)
-    next(f)  # Skip Header
-
-    me_manager = METypeManager()
-    for tstr in f:
-        vals = tstr.strip().split()
-        if len(vals) not in (6, 8):
-            wmsg = ("Could not parse line %s from MEComboInfoFile %s."
-                    "Expecting 6 (hippocampus) or 8 (somatosensory) fields")
-            logging.warning(wmsg, tstr, combo_file)
-
-        # metypes may be reused by several cells
-        # We create a single item and later assign to each matching gid
-        meitem = METypeItem(*vals)
-        for i in combo_ids[meitem.combo_name]:
-            if morph_list[i] == meitem.morph_name:
-                me_manager[int(gidvec[i])] = meitem
-
-    # confirm that all gids have been matched.
-    # Otherwise, print combo + morph info to help finding issues
-    nerr = 0
-    for gid in gidvec:
-        gid = int(gid)
-        if gid not in me_manager:
-            logging.error("MEComboInfoFile: No MEInfo for gid %d", gid)
-            nerr += 1
-    if nerr > 0:
-        logging.error("gidvec: " + str(gidvec))
-        logging.error("Memap: " + str(me_manager.gids))
-        raise CellReaderError("Errors found during processing of mecombo file. See log")
-
-    return me_manager
-
-
 def _getNeededAttributes(node_reader, etype_path, emodels, gidvec):
     """
     Read additional attributes required by emodel templates global var <emodel>__NeededAttributes

neurodamus/metype.py

@@ -195,87 +195,6 @@ def __getattr__(self, item):
         return prop
 
 
-class Cell_V5(METype):
-    __slots__ = ('_rng_list',)
-
-    def __init__(self, gid, meinfo, circuit_conf):
-        # In NCS, meinfo is simply the metype filename (string)
-        mepath = circuit_conf.METypePath
-        morpho_path = circuit_conf.MorphologyPath
-        if isinstance(meinfo, METypeItem):
-            meinfo = meinfo.emodel_tpl  # Compat with loading V5 cells from Sonata Nodes
-        melabel = self._load_template(meinfo, mepath)
-        super().__init__(gid, mepath, melabel, morpho_path)
-
-    def _instantiate_cell(self, gid, _etype_path, emodel, morpho_path, _meinfos, _axon):
-        """Instantiates a cell v5 or older. Assumes emodel hoc templates are loaded
-        """
-        EModel = getattr(Nd, emodel)
-        logging.debug("Loading Gid %d: emodel: %s", gid, emodel)
-        try:
-            # For this step, do not call mpi_abort in neuron and let neurodamus handle and abort,
-            # NB: Do not re-raise as ConfigurationError, neurodamus doesn't call mpi_abort so hangs
-            old_flag = Nd.pc.mpiabort_on_error(0)
-            self._ccell = ccell = EModel(gid, morpho_path)
-            Nd.pc.mpiabort_on_error(old_flag)
-        except Exception as e:
-            raise Exception("Error when loading Gid %d: emodel: %s, morpho_path: %s"
-                            % (gid, emodel, morpho_path)) from e
-        self._cellref = ccell.CellRef
-        self._synapses = ccell.CellRef.synlist
-        self._syn_helper_list = ccell.CellRef.synHelperList
-        self._threshold_current = ccell.getThreshold()
-        try:
-            self._hypAmp_current = ccell.getHypAmp()
-        except Exception:
-            pass
-
-    def re_init_rng(self, ion_seed):
-        if not hasattr(self._ccell, "re_init_rng"):
-            return  # dont apply on cells without re_init_rng func
-        rng = SimConfig.rng_info
-        rng_mode = rng.getRNGMode()
-
-        if rng_mode == rng.COMPATIBILITY:
-            return super().re_init_rng(ion_seed)
-        if rng_mode == rng.RANDOM123:
-            Nd.rng123ForStochKvInit(self._ccell)
-            return
-        # otherwise rng_mode is mcellran4
-        self._rng_list = Nd.rngForStochKvInit(self._ccell)
-        gid = self._cellref.gid
-        if gid > 400000:
-            logging.warning("mcellran4 cannot initialize properly with large gids: %d", gid)
-
-    @staticmethod
-    def _load_template(tpl_filename, tpl_location=None):
-        """Helper function which loads the template into NEURON and returns its name.
-        The actual template name will have any hyphens (e.g.: R-C261296A-P1_repaired)
-        replaced with underscores as hyphens must not appear in template names.
-
-        Args:
-            tpl_filename: the template file to load
-            tpl_location: (Optional) path for the templates
-        Returns:
-            The name of the template as it appears inside the file (sans hyphens)
-        """
-        #  start.ncs gives metype names with hyphens, but the templates themselves
-        #  have those hyphens replaced with underscores.
-        tpl_path = ospath.join(tpl_location, tpl_filename) \
-            if tpl_location else tpl_filename
-
-        # first open the file manually to get the hoc template name
-        tpl_name = None
-        with open(tpl_path + ".hoc", "r") as templateReader:
-            for line in templateReader:
-                line = line.strip()
-                if line.startswith("begintemplate"):
-                    tpl_name = line.split()[1]
-                    break
-        Nd.load_hoc(tpl_path)
-        return tpl_name
-
-
 class EmptyCell(BaseCell):
     """
     Class representing an empty cell, e.g. an artificial cell

tests/scientific/conftest.py

@@ -3,8 +3,6 @@
 
 assert os.environ.get("NEURODAMUS_NEOCORTEX_ROOT"), \
     "Test requires loading a neocortex model to run"
-assert os.path.isfile("/gpfs/bbp.cscs.ch/project/proj83/circuits/Bio_M/20200805/circuit.mvd3"), \
-    "Circuit file not available"
 
 pytestmark = [
     pytest.mark.forked,