Merge pull request #5 from yaricom/goNeat-v4-migration

Updated to use the latest version of `goNEAT`. Bump version.

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Set up Go
       uses: actions/setup-go@v2
       with:
-        go-version: 1.17
+        go-version: 1.21
 
     - name: Build
       run: go build -v ./...

README.md

@@ -3,8 +3,8 @@
 [![version](https://img.shields.io/github/v/tag/yaricom/goNEAT_NS.svg?sort=semver)](https://github.com/yaricom/goNEAT_NS/releases/latest)
 [![Build Status](https://travis-ci.org/yaricom/goNEAT_NS.svg?branch=master)](https://travis-ci.org/yaricom/goNEAT_NS) [![GoDoc](https://godoc.org/github.com/yaricom/goNEAT_NS/neatns?status.svg)](https://godoc.org/github.com/yaricom/goNEAT_NS/neatns) [![Go version](https://img.shields.io/badge/go-1.17-blue.svg)](https://github.com/moovweb/gvm) [![license](https://img.shields.io/github/license/yaricom/goNEAT_NS.svg)](https://github.com/yaricom/goNEAT_NS/blob/master/LICENSE) [![yaricom/goNEAT](https://tokei.rs/b1/github/yaricom/goNEAT_NS?category=lines)](https://github.com/yaricom/goNEAT_NS)
 
-| Branch | Tests                                                                                      | Coverage                                                                                                                             | Linting                                                                    | Code Security                                                                    |
-|--------|--------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------|----------------------------------------------------------------------------|
+| Branch | Tests                                                                                                                                           | Coverage                                                                                                                                      | Linting                                                                                                                                               | Code Security                                                                                                                                                                 |
+|--------|-------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | master | [![CI](https://github.com/yaricom/goNEAT_NS/actions/workflows/ci.yml/badge.svg)](https://github.com/yaricom/goNEAT_NS/actions/workflows/ci.yml) | [![codecov](https://codecov.io/gh/yaricom/goNEAT_NS/branch/master/graph/badge.svg?token=as31613DnV)](https://codecov.io/gh/yaricom/goNEAT_NS) | [![Lint](https://github.com/yaricom/goNEAT_NS/actions/workflows/lint.yml/badge.svg)](https://github.com/yaricom/goNEAT_NS/actions/workflows/lint.yml) | [![CodeQL](https://github.com/yaricom/goNEAT_NS/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/yaricom/goNEAT_NS/actions/workflows/codeql-analysis.yml) |
 
 ## Overview
@@ -24,7 +24,7 @@ research is to test this hypothesis.
 
 ## Minimum Requirements
 
-The source code written and compiled against GO 1.17.x.
+The source code written and compiled against GO 1.21.x.
 
 ## Installation
 

codecov.yml

@@ -0,0 +1,4 @@
+# Ignore maze runners
+ignore:
+  - "examples/maze/maze_ns.go"
+  - "examples/maze/maze_obj.go"

examples/maze/common.go

@@ -4,10 +4,11 @@ package maze
 
 import (
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT/v3/neat/network"
-	"github.com/yaricom/goNEAT_NS/v3/neatns"
+	"github.com/pkg/errors"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT/v4/neat/network"
+	"github.com/yaricom/goNEAT_NS/v4/neatns"
 	"math"
 )
 
@@ -49,7 +50,11 @@ func mazeSimulationEvaluate(env *Environment, org *genetics.Organism, record *Ag
 	nItem := neatns.NewNoveltyItem()
 
 	// get Organism phenotype's network depth
-	netDepth, err := org.Phenotype.MaxActivationDepthFast(1) // The max depth of the network to be activated
+	phenotype, err := org.Phenotype()
+	if err != nil {
+		return nil, false, err
+	}
+	netDepth, err := phenotype.MaxActivationDepthWithCap(1) // The max depth of the network to be activated
 	if err != nil {
 		neat.DebugLog(fmt.Sprintf(
 			"Failed to estimate maximal depth of the network. Using default depth: %d", netDepth))
@@ -62,15 +67,15 @@ func mazeSimulationEvaluate(env *Environment, org *genetics.Organism, record *Ag
 
 	// initialize maze simulation's environment specific to the provided organism - this will be a copy
 	// of primordial environment provided
-	orgEnv, err := mazeSimulationInit(*env, org, netDepth)
+	orgEnv, err := mazeSimulationInit(*env, phenotype, netDepth)
 	if err != nil {
 		return nil, false, err
 	}
 
 	// do a specified amount of time steps emulations or while exit not found
 	steps := 0
 	for i := 0; i < orgEnv.TimeSteps && !orgEnv.ExitFound; i++ {
-		if err = mazeSimulationStep(orgEnv, org, netDepth); err != nil {
+		if err = mazeSimulationStep(orgEnv, phenotype, netDepth); err != nil {
 			return nil, false, err
 		}
 		// store agent path points at given sample size
@@ -117,9 +122,9 @@ func mazeSimulationEvaluate(env *Environment, org *genetics.Organism, record *Ag
 
 // To initialize the maze simulation within provided environment copy and for given organism.
 // Returns new environment for simulation against given organism
-func mazeSimulationInit(env Environment, org *genetics.Organism, netDepth int) (*Environment, error) {
+func mazeSimulationInit(env Environment, phenotype *network.Network, netDepth int) (*Environment, error) {
 	// flush the neural net
-	if _, err := org.Phenotype.Flush(); err != nil {
+	if _, err := phenotype.Flush(); err != nil {
 		neat.ErrorLog("Failed to flush phenotype")
 		return nil, err
 	}
@@ -132,14 +137,14 @@ func mazeSimulationInit(env Environment, org *genetics.Organism, netDepth int) (
 	// create neural net inputs from environment
 	if inputs, err := env.GetInputs(); err != nil {
 		return nil, err
-	} else if err = org.Phenotype.LoadSensors(inputs); err != nil { // load into neural net
+	} else if err = phenotype.LoadSensors(inputs); err != nil { // load into neural net
 		return nil, err
 	}
 
 	// propagate input through the phenotype net
 
 	// Use depth to ensure full relaxation
-	if _, err := org.Phenotype.ForwardSteps(netDepth); err != nil && err != network.ErrNetExceededMaxActivationAttempts {
+	if _, err := phenotype.ForwardSteps(netDepth); err != nil && !errors.Is(err, network.ErrNetExceededMaxActivationAttempts) {
 		neat.ErrorLog(fmt.Sprintf("Failed to activate network at simulation init: %s", err))
 		return nil, err
 	}
@@ -148,21 +153,21 @@ func mazeSimulationInit(env Environment, org *genetics.Organism, netDepth int) (
 }
 
 // To execute a time step of the maze simulation evaluation within given Environment for provided Organism
-func mazeSimulationStep(env *Environment, org *genetics.Organism, netDepth int) error {
+func mazeSimulationStep(env *Environment, phenotype *network.Network, netDepth int) error {
 	// get simulation parameters as inputs to organism's network
 	if inputs, err := env.GetInputs(); err != nil {
 		return err
-	} else if err = org.Phenotype.LoadSensors(inputs); err != nil {
+	} else if err = phenotype.LoadSensors(inputs); err != nil {
 		neat.ErrorLog("Failed to load sensors")
 		return err
 	}
-	if _, err := org.Phenotype.ForwardSteps(netDepth); err != nil && err != network.ErrNetExceededMaxActivationAttempts {
+	if _, err := phenotype.ForwardSteps(netDepth); err != nil && !errors.Is(err, network.ErrNetExceededMaxActivationAttempts) {
 		neat.ErrorLog(fmt.Sprintf("Failed to activate network at simulation init: %s", err))
 		return err
 	}
 
 	// use the net's outputs to change heading and velocity of maze agent
-	if err := env.ApplyOutputs(org.Phenotype.Outputs[0].Activation, org.Phenotype.Outputs[1].Activation); err != nil {
+	if err := env.ApplyOutputs(phenotype.Outputs[0].Activation, phenotype.Outputs[1].Activation); err != nil {
 		neat.ErrorLog("Failed to apply outputs")
 		return err
 	}

examples/maze/common_test.go

@@ -2,7 +2,7 @@ package maze
 
 import (
 	"github.com/stretchr/testify/assert"
-	"github.com/yaricom/goNEAT/v3/neat"
+	"github.com/yaricom/goNEAT/v4/neat"
 	"testing"
 )
 

examples/maze/maze_ns.go

@@ -3,11 +3,12 @@ package maze
 import (
 	"context"
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/experiment/utils"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT_NS/v3/neatns"
+	"github.com/pkg/errors"
+	"github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/experiment/utils"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT_NS/v4/neatns"
 	"math"
 	"os"
 )
@@ -48,7 +49,7 @@ type noveltySearchEvaluator struct {
 	compatAdjustFreq int
 }
 
-func (e noveltySearchEvaluator) TrialRunStarted(trial *experiment.Trial) {
+func (e *noveltySearchEvaluator) TrialRunStarted(trial *experiment.Trial) {
 	opts := neatns.DefaultNoveltyArchiveOptions()
 	opts.KNNNoveltyScore = 10
 	trialSim = mazeSimResults{
@@ -58,17 +59,17 @@ func (e noveltySearchEvaluator) TrialRunStarted(trial *experiment.Trial) {
 	}
 }
 
-func (e noveltySearchEvaluator) TrialRunFinished(_ *experiment.Trial) {
+func (e *noveltySearchEvaluator) TrialRunFinished(_ *experiment.Trial) {
 	// the last epoch executed
 	e.storeRecorded()
 }
 
-func (e noveltySearchEvaluator) EpochEvaluated(_ *experiment.Trial, _ *experiment.Generation) {
+func (e *noveltySearchEvaluator) EpochEvaluated(_ *experiment.Trial, _ *experiment.Generation) {
 	// just stub
 }
 
 // GenerationEvaluate this method evaluates one epoch for given population and prints results into output directory if any.
-func (e noveltySearchEvaluator) GenerationEvaluate(ctx context.Context, pop *genetics.Population, epoch *experiment.Generation) error {
+func (e *noveltySearchEvaluator) GenerationEvaluate(ctx context.Context, pop *genetics.Population, epoch *experiment.Generation) error {
 	options, ok := neat.FromContext(ctx)
 	if !ok {
 		return neat.ErrNEATOptionsNotFound
@@ -110,9 +111,7 @@ func (e noveltySearchEvaluator) GenerationEvaluate(ctx context.Context, pop *gen
 	if epoch.Solved {
 		// print winner organism
 		org := epoch.Champion
-		if depth, err := org.Phenotype.MaxActivationDepthFast(0); err == nil {
-			neat.InfoLog(fmt.Sprintf("Activation depth of the winner: %d\n", depth))
-		}
+		utils.PrintActivationDepth(org, true)
 
 		genomeFile := "mazens_winner"
 		// Prints the winner organism's Genome to the file!
@@ -189,7 +188,7 @@ func (e *noveltySearchEvaluator) orgEvaluate(org *genetics.Organism, pop *geneti
 	// evaluate individual organism and get novelty point
 	nItem, solved, err := mazeSimulationEvaluate(e.mazeEnv, org, &record, nil)
 	if err != nil {
-		if err == ErrOutputIsNaN {
+		if errors.Is(err, ErrOutputIsNaN) {
 			// corrupted genome, but OK to continue evolutionary process
 			return false, nil
 		}

examples/maze/maze_obj.go

@@ -3,11 +3,12 @@ package maze
 import (
 	"context"
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/experiment/utils"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT_NS/v3/neatns"
+	"github.com/pkg/errors"
+	"github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/experiment/utils"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT_NS/v4/neatns"
 	"os"
 )
 
@@ -38,25 +39,25 @@ type objectiveEvaluator struct {
 	compatAdjustFreq int
 }
 
-func (e objectiveEvaluator) TrialRunStarted(trial *experiment.Trial) {
+func (e *objectiveEvaluator) TrialRunStarted(trial *experiment.Trial) {
 	trialSim = mazeSimResults{
 		trialID: trial.Id,
 		records: new(RecordStore),
 		archive: neatns.NewNoveltyArchive(archiveThresh, noveltyMetric, neatns.DefaultNoveltyArchiveOptions()),
 	}
 }
 
-func (e objectiveEvaluator) TrialRunFinished(_ *experiment.Trial) {
+func (e *objectiveEvaluator) TrialRunFinished(_ *experiment.Trial) {
 	// the last epoch executed
 	e.storeRecorded()
 }
 
-func (e objectiveEvaluator) EpochEvaluated(_ *experiment.Trial, _ *experiment.Generation) {
+func (e *objectiveEvaluator) EpochEvaluated(_ *experiment.Trial, _ *experiment.Generation) {
 	// just stub
 }
 
 // GenerationEvaluate evaluates one epoch for given population and prints results into output directory if any.
-func (e objectiveEvaluator) GenerationEvaluate(ctx context.Context, pop *genetics.Population, epoch *experiment.Generation) error {
+func (e *objectiveEvaluator) GenerationEvaluate(ctx context.Context, pop *genetics.Population, epoch *experiment.Generation) error {
 	options, ok := neat.FromContext(ctx)
 	if !ok {
 		return neat.ErrNEATOptionsNotFound
@@ -90,9 +91,7 @@ func (e objectiveEvaluator) GenerationEvaluate(ctx context.Context, pop *genetic
 	if epoch.Solved {
 		// print winner organism
 		org := epoch.Champion
-		if depth, err := org.Phenotype.MaxActivationDepthFast(0); err == nil {
-			neat.InfoLog(fmt.Sprintf("Activation depth of the winner: %d\n", depth))
-		}
+		utils.PrintActivationDepth(org, true)
 
 		genomeFile := "maze_obj_winner"
 		// Prints the winner organism to file!
@@ -154,7 +153,7 @@ func (e *objectiveEvaluator) orgEvaluate(org *genetics.Organism, _ *genetics.Pop
 	// evaluate individual organism and get novelty point holding simulation results
 	nItem, solved, err := mazeSimulationEvaluate(e.mazeEnv, org, &record, nil)
 	if err != nil {
-		if err == ErrOutputIsNaN {
+		if errors.Is(err, ErrOutputIsNaN) {
 			// corrupted genome, but OK to continue evolutionary process
 			return false, nil
 		}

executor.go

@@ -4,10 +4,10 @@ import (
 	"context"
 	"flag"
 	"fmt"
-	"github.com/yaricom/goNEAT/v3/experiment"
-	"github.com/yaricom/goNEAT/v3/neat"
-	"github.com/yaricom/goNEAT/v3/neat/genetics"
-	"github.com/yaricom/goNEAT_NS/v3/examples/maze"
+	"github.com/yaricom/goNEAT/v4/experiment"
+	"github.com/yaricom/goNEAT/v4/neat"
+	"github.com/yaricom/goNEAT/v4/neat/genetics"
+	"github.com/yaricom/goNEAT_NS/v4/examples/maze"
 	"log"
 	"math/rand"
 	"os"

go.mod

@@ -1,22 +1,22 @@
-module github.com/yaricom/goNEAT_NS/v3
+module github.com/yaricom/goNEAT_NS/v4
 
-go 1.17
+go 1.21
 
 require (
 	github.com/fogleman/gg v1.3.0
-	github.com/stretchr/testify v1.7.1
-	github.com/yaricom/goNEAT/v3 v3.0.1
+	github.com/pkg/errors v0.9.1
+	github.com/stretchr/testify v1.8.4
+	github.com/yaricom/goNEAT/v4 v4.0.1
 )
 
 require (
-	github.com/davecgh/go-spew v1.1.0 // indirect
+	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 // indirect
-	github.com/pkg/errors v0.9.1 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
-	github.com/sbinet/npyio v0.6.0 // indirect
-	github.com/spf13/cast v1.5.0 // indirect
-	golang.org/x/exp v0.0.0-20191002040644-a1355ae1e2c3 // indirect
-	golang.org/x/image v0.0.0-20220302094943-723b81ca9867 // indirect
-	gonum.org/v1/gonum v0.11.0 // indirect
+	github.com/sbinet/npyio v0.7.0 // indirect
+	github.com/spf13/cast v1.5.1 // indirect
+	golang.org/x/exp v0.0.0-20230321023759-10a507213a29 // indirect
+	golang.org/x/image v0.6.0 // indirect
+	gonum.org/v1/gonum v0.13.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 )