[BBPBGLIB-1127] Remove SpikeWriter.mod and out.dat (#123)

## Context
After the deprecation of BlueConfig files, out.dat is not generated
anymore.
Remove the SpikeWriter mod file and the code that was handling the old
out.dat spike file.

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

core/mod/coreneuron_modlist.txt

@@ -5,5 +5,4 @@ lookupTableV2.mod
 netstim_inhpoisson.mod
 SonataReportHelper.mod
 SonataReports.mod
-SpikeWriter.mod
 VecStim.mod

examples/test_neurodamus.py

@@ -57,8 +57,7 @@ def test_node_run(trace=False):
     logging.info("Run")
     node.run_all()
 
-    logging.info("Simulation finished. Gather spikes then clean up.")
-    node.spike2file("out.dat")
+    logging.info("Simulation finished.")
     node.cleanup()
 
 

neurodamus/core/_neurodamus.py

@@ -106,7 +106,7 @@ def check_load_lib(mech, env_lib_path):
         # which might not bring the model (support for split neurodamus) in which case
         # we should load only the model libs pointed by BGLIBPY_MOD_LIBRARY_PATH.
 
-        if not check_load_lib("SpikeWriter", "NRNMECH_LIB_PATH"):
+        if not check_load_lib("SonataReport", "NRNMECH_LIB_PATH"):
             logging.error("Could not load neurodamus core mechs from NRNMECH_LIB_PATH")
             sys.exit(1)
         if not check_load_lib("ProbAMPANMDA_EMS", "BGLIBPY_MOD_LIBRARY_PATH"):

neurodamus/node.py

@@ -12,7 +12,6 @@
 from os import path as ospath
 from collections import namedtuple, defaultdict
 from contextlib import contextmanager
-from shutil import copyfileobj, move
 
 from .core import MPI, mpi_no_errors, return_neuron_timings, run_only_rank0
 from .core import NeurodamusCore as Nd
@@ -1335,15 +1334,11 @@ def run_all(self):
         timings = None
         if SimConfig.use_neuron:
             timings = self._run_neuron()
-            if not SimConfig.is_sonata_config:
-                self.spike2file("out.dat")
             self.sonata_spikes()
         if SimConfig.use_coreneuron:
             print_mem_usage()
             self.clear_model(avoid_clearing_queues=False)
             self._run_coreneuron()
-            if not SimConfig.is_sonata_config:
-                self.adapt_spikes("out.dat")
         return timings
 
     # -
@@ -1487,36 +1482,6 @@ def clear_model(self, avoid_creating_objs=False, avoid_clearing_queues=True):
     #  output
     # -------------------------------------------------------------------------
 
-    @run_only_rank0
-    def adapt_spikes(self, outfile):
-        """Prepend /scatter to spikes file after coreneuron sim finishes.
-        """
-        output_root = SimConfig.output_root
-        outfile = ospath.join(output_root, outfile)
-        tmpfile = ospath.join(output_root, 'tmp.out')
-        with open(outfile, 'r') as f_src:
-            with open(tmpfile, 'w') as f_dest:
-                f_dest.write("/scatter\n")
-                copyfileobj(f_src, f_dest)
-        move(tmpfile, outfile)
-
-    @mpi_no_errors
-    def spike2file(self, outfile):
-        """ Write the spike events that occured on each node into a single output file.
-        Nodes will write in order, one after the other.
-        """
-        logging.info("Writing spikes to %s", outfile)
-        output_root = SimConfig.output_root
-        outfile = ospath.join(output_root, outfile)
-        spikevec = Nd.Vector()
-        idvec = Nd.Vector()
-        # merge spike_vecs and id_vecs for SpikeWriter
-        for spikes, ids in self._spike_vecs:
-            spikevec.append(spikes)
-            idvec.append(ids)
-        spikewriter = Nd.SpikeWriter()
-        spikewriter.write(spikevec, idvec, outfile)
-
     def sonata_spikes(self):
         """ Write the spike events that occured on each node into a single output SONATA file.
         """

neurodamus/replay.py

@@ -14,7 +14,7 @@ class SpikeManager:
     """ Holds and manages gid spike time information, specially for Replay.
 
     A SynapseReplay stim can be used for a single gid that has all the synapses instantiated.
-    Given an out.dat file from a previous run, this object uses a NetStim object to retrigger
+    Given a spikes file from a previous run, this object uses a NetStim object to retrigger
     the synapses at the appropriate time as though the presynaptic cells were present and active.
 
     Internally the spikes are stored in a :py:class:`neurodamus.utils.multimap.GroupedMultiMap`