Merge pull request #1 from yaricom/v2

V2

Author: yaricom

.github/FUNDING.yml

@@ -1,3 +1,4 @@
 # These are supported funding model platforms
 
 patreon: io42
+custom: ["https://www.buymeacoffee.com/io42"]

.github/release-drafter.yml

@@ -0,0 +1,31 @@
+name-template: 'v$RESOLVED_VERSION 🌈'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    label: 'chore'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES

.github/workflows/ci.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Go
+      uses: actions/setup-go@v2
+      with:
+        go-version: 1.15
+
+    - name: Build
+      run: go build -v ./...
+      env:
+        GO111MODULE: on
+
+    - name: Run coverage
+      run: go test -coverprofile=coverage.txt -covermode=atomic -timeout 40m -v ./...
+      env:
+        GO111MODULE: on
+        
+    - name: Upload coverage to Codecov
+      run: bash <(curl -s https://codecov.io/bash)

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '19 8 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'go' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/drafter.yml

@@ -0,0 +1,32 @@
+# The release drafter
+# https://github.com/release-drafter/release-drafter
+#
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - master
+  # pull_request event is required only for autolabeler
+  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+    types: [opened, reopened, synchronize]
+
+jobs:
+  update_release_draft:
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/lint.yml

@@ -0,0 +1,29 @@
+name: Lint
+# Lint runs golangci-lint over the entire Tendermint repository
+# This workflow is run on every pull request and push to master
+# The `golangci` job will pass without running if no *.{go, mod, sum} files have been modified.
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+jobs:
+  golangci:
+    name: golangci-lint
+    runs-on: ubuntu-latest
+    timeout-minutes: 8
+    steps:
+      - uses: actions/checkout@v2
+      - uses: technote-space/get-diff-action@v4
+        with:
+          PATTERNS: |
+            **/**.go
+            go.mod
+            go.sum
+      - uses: golangci/[email protected]
+        with:
+          # Required: the version of golangci-lint is required and must be specified without patch version: we always use the latest patch version.
+          version: v1.38
+          args: --timeout 10m
+          github-token: ${{ secrets.github_token }}
+        if: env.GIT_DIFF

data/maze.neat

@@ -30,9 +30,6 @@ print_every 100
 babies_stolen 0
 num_runs 1
 num_generations 2000
-log_level 1
-
-
-linktrait_mut_sig 1.0
-nodetrait_mut_sig 0.5
-recur_prob 0.15
+log_level info
+epoch_executor sequential
+genome_compat_method linear

examples/common.go

@@ -0,0 +1,2 @@
+// Package examples package holds various examples with NEAT Novelty Search.
+package examples

experiments/maze/common.go examples/maze/common.goexperiments/maze/common.go renamed to examples/maze/common.go

@@ -1,12 +1,13 @@
-// The maze solving experiments based on NEAT methodology with Novelty Search and Fitness based optimization
+// Package maze provides the maze solving experiments based on NEAT methodology with Novelty Search and Fitness
+// based optimization.
 package maze
 
 import (
 	"fmt"
-	"github.com/yaricom/goNEAT/neat"
-	"github.com/yaricom/goNEAT/neat/genetics"
-	"github.com/yaricom/goNEAT/neat/network"
-	"github.com/yaricom/goNEAT_NS/neatns"
+	"github.com/yaricom/goNEAT/v2/neat"
+	"github.com/yaricom/goNEAT/v2/neat/genetics"
+	"github.com/yaricom/goNEAT/v2/neat/network"
+	"github.com/yaricom/goNEAT_NS/v2/neatns"
 	"math"
 )
 
@@ -42,18 +43,29 @@ func histDiff(left, right []float64) float64 {
 func mazeSimulationEvaluate(env *Environment, org *genetics.Organism, record *AgentRecord, pathPoints []Point) (*neatns.NoveltyItem, bool, error) {
 	nItem := neatns.NewNoveltyItem()
 
+	// get Organism phenotype's network depth
+	netDepth, err := org.Phenotype.MaxActivationDepthFast(1) // The max depth of the network to be activated
+	if err != nil {
+		neat.WarnLog(fmt.Sprintf(
+			"Failed to estimate maximal depth of the network:\n%s\nUsing default depth: %d",
+			org.Genotype, netDepth))
+	}
+	neat.DebugLog(fmt.Sprintf("Network depth: %d for organism: %d\n", netDepth, org.Genotype.Id))
+	if netDepth == 0 {
+		neat.DebugLog(fmt.Sprintf("ALERT: Network depth is ZERO for Genome: %s", org.Genotype))
+	}
+
 	// initialize maze simulation's environment specific to the provided organism - this will be a copy
 	// of primordial environment provided
-	orgEnv, err := mazeSimulationInit(*env, org)
+	orgEnv, err := mazeSimulationInit(*env, org, netDepth)
 	if err != nil {
 		return nil, false, err
 	}
 
-	// do specified amount of time steps emulations or while exit not found
+	// do a specified amount of time steps emulations or while exit not found
 	steps := 0
 	for i := 0; i < orgEnv.TimeSteps && !orgEnv.ExitFound; i++ {
-		err := mazeSimulationStep(orgEnv, org)
-		if err != nil {
+		if err = mazeSimulationStep(orgEnv, org, netDepth); err != nil {
 			return nil, false, err
 		}
 		// store agent path points at given sample size
@@ -100,88 +112,58 @@ 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) (*Environment, error) {
-
-	// get Organism phenotype's network depth
-	netDepth, err := org.Phenotype.MaxDepth() // The max depth of the network to be activated
-	if err != nil {
-		if err != network.NetErrDepthCalculationFailedLoopDetected {
-			return nil, err
-		} else {
-			neat.InfoLog(fmt.Sprintf("Network loop detected, using default depth: %d for organism: %d\n",
-				netDepth, org.Genotype.Id))
-		}
-	}
-	neat.DebugLog(fmt.Sprintf("Network depth: %d for organism: %d\n", netDepth, org.Genotype.Id))
-	if netDepth == 0 {
-		neat.DebugLog(fmt.Sprintf("ALERT: Network depth is ZERO for Genome: %s", org.Genotype))
-	}
-
+func mazeSimulationInit(env Environment, org *genetics.Organism, netDepth int) (*Environment, error) {
 	// flush the neural net
-	if _, err = org.Phenotype.Flush(); err != nil {
+	if _, err := org.Phenotype.Flush(); err != nil {
 		neat.ErrorLog("Failed to flush phenotype")
 		return nil, err
 	}
 	// update the maze
-	err = env.Update()
-	if err != nil {
+	if err := env.Update(); err != nil {
 		neat.ErrorLog("Failed to update environment")
 		return nil, err
 	}
 
 	// create neural net inputs from environment
-	inputs, err := env.GetInputs()
-	if err != nil {
+	if inputs, err := env.GetInputs(); err != nil {
 		return nil, err
-	}
-
-	// load into neural net
-	if err = org.Phenotype.LoadSensors(inputs); err != nil {
+	} else if err = org.Phenotype.LoadSensors(inputs); err != nil { // load into neural net
 		return nil, err
 	}
 
 	// propagate input through the phenotype net
 
-	// Relax phenotype net and get output
-	if _, err = org.Phenotype.Activate(); err != nil && err != network.NetErrExceededMaxActivationAttempts {
-		neat.ErrorLog("Failed to activate network init 1")
+	// Use depth to ensure full relaxation
+	if _, err := org.Phenotype.ForwardSteps(netDepth); err != nil && err != network.ErrNetExceededMaxActivationAttempts {
+		neat.ErrorLog(fmt.Sprintf("Failed to activate network at simulation init: %s", err))
 		return nil, err
 	}
 
-	// use depth to ensure relaxation at each layer
-	for relax := 0; relax <= netDepth; relax++ {
-		if _, err = org.Phenotype.Activate(); err != nil && err != network.NetErrExceededMaxActivationAttempts {
-			neat.ErrorLog("Failed to activate network init 2")
-			return nil, err
-		}
-	}
-
 	return &env, nil
 }
 
 // To execute a time step of the maze simulation evaluation within given Environment for provided Organism
-func mazeSimulationStep(env *Environment, org *genetics.Organism) error {
+func mazeSimulationStep(env *Environment, org *genetics.Organism, 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 {
 		neat.ErrorLog("Failed to load sensors")
 		return err
 	}
-	_, err := org.Phenotype.Activate()
-	if err != nil && err != network.NetErrExceededMaxActivationAttempts {
-		neat.ErrorLog("Failed to activate network simulation")
+	if _, err := org.Phenotype.ForwardSteps(netDepth); err != nil && 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(org.Phenotype.Outputs[0].Activation, org.Phenotype.Outputs[1].Activation); err != nil {
 		neat.ErrorLog("Failed to apply outputs")
 		return err
 	}
 
 	// update the environment
-	if err = env.Update(); err != nil {
+	if err := env.Update(); err != nil {
 		neat.ErrorLog("Failed to update environment")
 		return err
 	}