Fix CoreNEURON reports restore

 - Update 'save' report.conf with new tstop instead of creating a new one

neurodamus/core/coreneuron_configuration.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from ._utils import run_only_rank0
 from . import NeurodamusCore as Nd
+from .configuration import ConfigurationError
 from ..report import get_section_index
 
 
@@ -85,6 +86,47 @@ class _CoreNEURONConfig(object):
     def instantiate_artificial_cell(self):
         self.artificial_cell_object = Nd.CoreNEURONArtificialCell()
 
+    @run_only_rank0
+    def update_tstop(self, report_name, nodeset_name, tstop):
+        # Try current directory first
+        report_conf = Path(self.output_root) / self.report_config_file
+        if not report_conf.exists():
+            # Try one level up from output_root
+            parent_report_conf = Path(self.output_root) / ".." / self.report_config_file
+            if parent_report_conf.exists():
+                # Copy the file to current location
+                report_conf.write_bytes(parent_report_conf.read_bytes())
+            else:
+                raise ConfigurationError(f"Report config file not found in {report_conf} "
+                                         f"or {parent_report_conf}")
+
+        # Read all content
+        with report_conf.open('rb') as f:
+            lines = f.readlines()
+
+        # Find and update the matching line
+        found = False
+        for i, line in enumerate(lines):
+            try:
+                parts = line.decode().split()
+                # Report name and target name must match in order to update the tstop
+                if parts[0:2] == [report_name, nodeset_name]:
+                    parts[9] = f"{tstop:.6f}"
+                    lines[i] = (' '.join(parts) + '\n').encode()
+                    found = True
+                    break
+            except (UnicodeDecodeError, IndexError):
+                # Ignore lines that cannot be decoded (binary data)
+                continue
+
+        if not found:
+            raise ConfigurationError(f"Report '{report_name}' with target '{nodeset_name}' "
+                                     "not matching any report in the 'save' execution")
+
+        # Write back
+        with report_conf.open('wb') as f:
+            f.writelines(lines)
+
     @run_only_rank0
     def write_report_config(
             self, report_name, target_name, report_type, report_variable,

neurodamus/node.py

@@ -825,7 +825,7 @@ def enable_reports(self):
             pop_offsets_alias = self._circuits.get_population_offsets()
         else:
             pop_offsets_alias = CircuitManager.read_population_offsets()
-        if SimConfig.use_coreneuron:
+        if SimConfig.use_coreneuron and not SimConfig.restore_coreneuron:
             CoreConfig.write_report_count(len(reports_conf))
 
         for rep_name, rep_conf in reports_conf.items():
@@ -839,7 +839,7 @@ def enable_reports(self):
                 continue
 
             if SimConfig.use_coreneuron and MPI.rank == 0:
-                if not self._report_write_coreneuron_config(rep_name, rep_conf, target, rep_params):
+                if not self._report_write_coreneuron_config(rep_conf, target, rep_params):
                     n_errors += 1
                     continue
 
@@ -940,35 +940,38 @@ def _report_build_params(self, rep_name, rep_conf, target, pop_offsets_alias_pop
         )
 
     #
-    def _report_write_coreneuron_config(self, rep_name, rep_conf, target, rep_params):
+    def _report_write_coreneuron_config(self, rep_conf, target, rep_params):
         target_spec = TargetSpec(rep_conf["Target"])
 
-        # for sonata config, compute target_type from user inputs
-        if "Sections" in rep_conf and "Compartments" in rep_conf:
-            def _compute_corenrn_target_type(section_type, compartment_type):
-                sections = ["all", "soma", "axon", "dend", "apic"]
-                compartments = ["center", "all"]
-                if section_type not in sections:
-                    raise ConfigurationError(f"Report: invalid section type '{section_type}'")
-                if compartment_type not in compartments:
-                    raise ConfigurationError(f"Report: invalid compartment type {compartment_type}")
-                if section_type == "all":  # for "all sections", support only target_type=0
-                    return 0
-                # 0=Compartment, Section { 2=Soma, 3=Axon, 4=Dendrite, 5=Apical, 6=SomaAll ... }
-                return sections.index(section_type)+1+4*compartments.index(compartment_type)
-
-            section_type = rep_conf.get("Sections")
-            compartment_type = rep_conf.get("Compartments")
-            target_type = _compute_corenrn_target_type(section_type, compartment_type)
-
-        reporton_comma_separated = ",".join(rep_params.report_on.split())
-        core_report_params = (
-            (os.path.basename(rep_conf.get("FileName", rep_name)),
-                target_spec.name, rep_params.rep_type, reporton_comma_separated)
-            + rep_params[3:5] + (target_type,) + rep_params[5:8]
-            + (target.get_gids(), SimConfig.corenrn_buff_size)
-        )
-        CoreConfig.write_report_config(*core_report_params)
+        if SimConfig.restore_coreneuron:
+            CoreConfig.update_tstop(rep_params.name, target_spec.name, rep_params.end)
+        else:
+            # for sonata config, compute target_type from user inputs
+            if "Sections" in rep_conf and "Compartments" in rep_conf:
+                def _compute_corenrn_target_type(section_type, compartment_type):
+                    sections = ["all", "soma", "axon", "dend", "apic"]
+                    compartments = ["center", "all"]
+                    if section_type not in sections:
+                        raise ConfigurationError(f"Report: invalid section type '{section_type}'")
+                    if compartment_type not in compartments:
+                        raise ConfigurationError(f"Report: invalid compartment type "
+                                                 f"{compartment_type}")
+                    if section_type == "all":  # for "all sections", support only target_type=0
+                        return 0
+                    # 0=Compartment, Section { 2=Soma, 3=Axon, 4=Dendrite, 5=Apical, 6=SomaAll ... }
+                    return sections.index(section_type)+1+4*compartments.index(compartment_type)
+
+                section_type = rep_conf.get("Sections")
+                compartment_type = rep_conf.get("Compartments")
+                target_type = _compute_corenrn_target_type(section_type, compartment_type)
+
+            reporton_comma_separated = ",".join(rep_params.report_on.split())
+            core_report_params = (
+                (rep_params.name, target_spec.name, rep_params.rep_type, reporton_comma_separated)
+                + rep_params[3:5] + (target_type,) + rep_params[5:8]
+                + (target.get_gids(), SimConfig.corenrn_buff_size)
+            )
+            CoreConfig.write_report_config(*core_report_params)
         return True
 
     def _report_setup(self, report, rep_conf, target, rep_type):
@@ -1008,8 +1011,10 @@ def _report_setup(self, report, rep_conf, target, rep_type):
                 report.add_synapse_report(cell, point, spgid, pop_name, pop_offset)
 
     def _reports_init(self, pop_offsets_alias):
-        pop_offsets = pop_offsets_alias[0]
+        if SimConfig.restore_coreneuron:
+            return
 
+        pop_offsets = pop_offsets_alias[0]
         if SimConfig.use_coreneuron:
             # write spike populations
             if hasattr(CoreConfig, "write_population_count"):