Codex fixes (#7)

* fix: prevent duplicate connections in pruneAndExpress recursion

Pass nil accumulator to recursive pruneAndExpress calls instead of the
growing connections slice. Previously, passing the populated slice caused
already-accumulated entries to be appended again on each recursive return,
producing duplicate connections in the substrate.

Identified by Codex code review.

* fix: close file handles in config loaders and experiment result writers

- Add defer configFile.Close() in hyperneat.LoadYAMLConfigFile
- Add defer configFile.Close() in eshyperneat.LoadYAMLConfigFile
- Add explicit Close() with error handling for both output files
  in executor.go (experiment .dat and .npz result files)

Identified by Codex code review.

* fix: correct ESIterations loop boundary for lastHidden index

The previous update collapsed lastHidden to just HiddenCount() (a local
count) by computing lastHidden + (HiddenCount() - lastHidden). This broke
multi-iteration runs by preventing subsequent passes from seeing the correct
hidden node window.

Fix: compute lastHidden = firstHidden + es.Layout.HiddenCount() to keep
the boundary consistently in global index space.

Identified by Codex code review.

* fix: eliminate deadlock and data race in experiment runner

Replace the competing dual-receiver errChan pattern with signal.NotifyContext:
- Only main now reads from errChan (single receiver, no deadlock)
- Removed signal handler goroutine that competed with main for errChan
- Removed shared outer 'err' variable written from multiple goroutines (data race)
- Print 'Press Ctrl+C to stop' synchronously before launching experiment
- Distinguish user interrupt (ctx.Err() != nil) from real errors
- Remove now-unused 'context' import

Identified by Codex code review.

Author: yaricom

cppn/evolvable_substrate.go

@@ -178,7 +178,7 @@ func (es *EvolvableSubstrate) CreateNetworkSolver(cppn *network.Network, graphBu
 
 		// move to the next window
 		firstHiddenIter = lastHidden
-		lastHidden = lastHidden + (es.Layout.HiddenCount() - lastHidden)
+		lastHidden = firstHidden + es.Layout.HiddenCount()
 	}
 
 	// Connect hidden nodes to the output
@@ -325,12 +325,12 @@ func (es *EvolvableSubstrate) pruneAndExpress(a, b, c float64, connections []*Qu
 	for _, quadNode := range node.Nodes {
 		childVariance := nodeVariance(quadNode)
 
-		if childVariance >= options.VarianceThreshold {
-			if conn, err := es.pruneAndExpress(a, b, c, connections, quadNode, outgoing, options); err != nil {
-				return nil, err
-			} else {
-				connections = append(connections, conn...)
-			}
+			if childVariance >= options.VarianceThreshold {
+				if conn, err := es.pruneAndExpress(a, b, c, nil, quadNode, outgoing, options); err != nil {
+					return nil, err
+				} else {
+					connections = append(connections, conn...)
+				}
 		} else if !options.LeoEnabled || (quadNode.Leo() > 0) {
 			// Band Pruning phase.
 			// If LEO is turned off, this should always happen.

eshyperneat/es_hyper_neat.go

@@ -61,5 +61,9 @@ func LoadYAMLConfigFile(path string) (*Options, error) {
 	if err != nil {
 		return nil, errors.Wrap(err, "failed to open ES-HyperNEAT configuration file")
 	}
+	defer func() {
+		_ = configFile.Close()
+	}()
+
 	return LoadYAMLOptions(configFile)
 }

executor.go

@@ -1,7 +1,6 @@
 package main
 
 import (
-	"context"
 	"flag"
 	"fmt"
 	"github.com/yaricom/goESHyperNEAT/v2/eshyperneat"
@@ -113,39 +112,24 @@ func main() {
 
 	// prepare to execute
 	errChan := make(chan error)
-	ctx, cancel := context.WithCancel(experimentContext)
+	fmt.Println("\nPress Ctrl+C to stop")
+	ctx, cancel := signal.NotifyContext(experimentContext, syscall.SIGHUP, syscall.SIGINT, syscall.SIGTERM, syscall.SIGQUIT)
+	defer cancel()
 
 	// run experiment in the separate GO routine
 	go func() {
-		if err = exp.Execute(ctx, startGenome, generationEvaluator, trialObserver); err != nil {
-			errChan <- err
-		} else {
-			errChan <- nil
-		}
+		errChan <- exp.Execute(ctx, startGenome, generationEvaluator, trialObserver)
 	}()
 
-	// register handler to wait for termination signals
-	//
-	go func(cancel context.CancelFunc) {
-		fmt.Println("\nPress Ctrl+C to stop")
-
-		signals := make(chan os.Signal, 1)
-		signal.Notify(signals, syscall.SIGHUP, syscall.SIGINT, syscall.SIGTERM, syscall.SIGQUIT)
-		select {
-		case <-signals:
-			// signal to stop test fixture
-			cancel()
-		case err = <-errChan:
-			// stop waiting
-		}
-	}(cancel)
-
 	// Wait for experiment completion
 	//
 	err = <-errChan
 	if err != nil {
-		// error during execution
-		log.Fatalf("Experiment execution failed: %s", err)
+		if ctx.Err() != nil {
+			fmt.Println("\nExperiment interrupted by user")
+		} else {
+			log.Fatalf("Experiment execution failed: %s", err)
+		}
 	}
 
 	// Print experiment results statistics
@@ -157,16 +141,28 @@ func main() {
 	expResPath := fmt.Sprintf("%s/%s.dat", outDir, *experimentName)
 	if expResFile, err := os.Create(expResPath); err != nil {
 		log.Fatal("Failed to create file for experiment results", err)
-	} else if err = exp.Write(expResFile); err != nil {
-		log.Fatal("Failed to save experiment results", err)
+	} else {
+		if err = exp.Write(expResFile); err != nil {
+			_ = expResFile.Close()
+			log.Fatal("Failed to save experiment results", err)
+		}
+		if err = expResFile.Close(); err != nil {
+			log.Fatal("Failed to close file for experiment results", err)
+		}
 	}
 
 	// Save experiment data in Numpy NPZ format if requested
 	//
 	npzResPath := fmt.Sprintf("%s/%s.npz", outDir, *experimentName)
 	if npzResFile, err := os.Create(npzResPath); err != nil {
 		log.Fatalf("Failed to create file for experiment results: [%s], reason: %s", npzResPath, err)
-	} else if err = exp.WriteNPZ(npzResFile); err != nil {
-		log.Fatal("Failed to save experiment results as NPZ file", err)
+	} else {
+		if err = exp.WriteNPZ(npzResFile); err != nil {
+			_ = npzResFile.Close()
+			log.Fatal("Failed to save experiment results as NPZ file", err)
+		}
+		if err = npzResFile.Close(); err != nil {
+			log.Fatalf("Failed to close file for experiment results: [%s], reason: %s", npzResPath, err)
+		}
 	}
 }

hyperneat/hyper_neat.go

@@ -57,6 +57,10 @@ func LoadYAMLConfigFile(path string) (*Options, error) {
 	if err != nil {
 		return nil, errors.Wrap(err, "failed to open HyperNEAT configuration file")
 	}
+	defer func() {
+		_ = configFile.Close()
+	}()
+
 	return LoadYAMLOptions(configFile)
 }