V2 library release

.github/FUNDING.yml

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

.github/codecov.yml

@@ -1,2 +1,2 @@
 ignore:
-  - "examples/**/*"  # ignoring experiments folder
+  - "examples/**/*"  # ignoring examples folder

.github/linters/.jscpd.json

@@ -0,0 +1,10 @@
+{
+  "threshold": 20,
+  "reporters": [
+    "consoleFull"
+  ],
+  "ignore": [
+    "**/__snapshots__/**"
+  ],
+  "absolute": true
+}

.github/release-drafter.yml

@@ -1,4 +1,4 @@
-name-template: 'v$RESOLVED_VERSION 🌈'
+name-template: 'v$RESOLVED_VERSION 🇺🇦'
 tag-template: 'v$RESOLVED_VERSION'
 categories:
   - title: '🚀 Features'

.github/workflows/ci.yml

@@ -11,12 +11,12 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Go
       uses: actions/setup-go@v3
       with:
-        go-version: 1.17
+        go-version: 1.21
 
     - name: Build
       run: go build -v ./...
@@ -29,4 +29,9 @@ jobs:
         GO111MODULE: on
 
     - name: Upload coverage to Codecov
-      run: bash <(curl -s https://codecov.io/bash)
+      uses: codecov/codecov-action@v4
+      with:
+        files: ./coverage.txt
+        flags: unittests
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true

.github/workflows/super-linter.yml

@@ -3,28 +3,50 @@
 #
 # You can adjust the behavior by modifying this file.
 # For more information, see:
-# https://github.com/github/super-linter
+# https://github.com/golangci/golangci-lint-action
 name: Lint Code Base
-
 on:
   push:
-    branches: [ master ]
+    tags:
+      - v*
+    branches:
+      - master
+      - main
   pull_request:
-    branches: [ master ]
+permissions:
+  contents: read
+  # Optional: allow read access to pull request. Use with `only-new-issues` option.
+  # pull-requests: read
 jobs:
-  run-lint:
+  golangci:
+    name: lint
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v3
+      - uses: actions/setup-go@v5
+        with:
+          go-version: '1.19'
+      - uses: actions/checkout@v4
+      - name: golangci-lint
+        uses: golangci/golangci-lint-action@v6
         with:
-          # Full git history is needed to get a proper list of changed files within `super-linter`
-          fetch-depth: 0
+          # Optional: version of golangci-lint to use in form of v1.2 or v1.2.3 or `latest` to use the latest version
+          version: v1.60
+
+          # Optional: working directory, useful for monorepos
+          # working-directory: somedir
+
+          # Optional: golangci-lint command line arguments.
+          # args: --issues-exit-code=0
+
+          # Optional: show only new issues if it's a pull request. The default value is `false`.
+          # only-new-issues: true
+
+          # Optional: if set to true then the all caching functionality will be complete disabled,
+          #           takes precedence over all other caching options.
+          # skip-cache: true
+
+          # Optional: if set to true then the action don't cache or restore ~/go/pkg.
+          # skip-pkg-cache: true
 
-      - name: Lint Code Base
-        uses: github/super-linter/slim@v4
-        env:
-          VALIDATE_ALL_CODEBASE: false
-          DEFAULT_BRANCH: master
-          FILTER_REGEX_EXCLUDE: .*README.md
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # Optional: if set to true then the action don't cache or restore ~/.cache/go-build.
+          # skip-build-cache: true

.gitignore

@@ -6,6 +6,7 @@ vendor
 
 # The IDEA project forlder
 .idea
+/goESHyperNEAT.iml
 
 # The MacOS specific
 .DS_Store
@@ -22,3 +23,4 @@ vendor
 
 # Output of the go coverage tool, specifically when used with LiteIDE
 *.out
+

Makefile

@@ -11,7 +11,7 @@ GORUN = $(GOCMD) run
 # The common parameters
 BINARY_NAME = eshyperneat
 OUT_DIR = out
-LOG_LEVEL = -1
+LOG_LEVEL = info
 
 #
 # The retina experiment parameters

README.md

@@ -1,3 +1,5 @@
+# goESHyperNEAT 🇺🇦 [![Made in Ukraine](https://img.shields.io/badge/made_in-ukraine-ffd700.svg?labelColor=0057b7)](https://u24.gov.ua)
+
 [![Build Status](https://travis-ci.org/yaricom/goESHyperNEAT.svg?branch=master)](https://travis-ci.org/yaricom/goESHyperNEAT) [![GoDoc](https://godoc.org/github.com/yaricom/goESHyperNEAT?status.svg)](https://godoc.org/github.com/yaricom/goESHyperNEAT)
 
 ## Overview
@@ -15,32 +17,32 @@ by human before algorithm execution to reflect inherent geometrical topology of
 of hidden nodes in the network this leads to the reduction of algorithm efficiency due to lack of ability to estimate where
 CPPN generated patterns will have intersection with manually seeded nodes.
 
-This drawback is addressed by **Evolved-Substrate HyperNEAT** method which allows to encode hidden nodes position
+This drawback is addressed by **Evolvable-Substrate HyperNEAT** method which allows to encode hidden nodes position
 in the substrate in the CPPN generated patterns of weights. As additional benefit of this the substrate is able to evolve it's
 geometrical topology during training, producing regions with varying neural density, thereby providing a kind of scaffolding
 for situating cognitive structures in the biological brains.
 
 
-## References:
+## References
 
 1. The original C++ NEAT implementation created by Kenneth O. Stanley, see: [NEAT][1]
 2. Other NEAT implementations can be found at [NEAT Software Catalog][2]
 3. [The ES-HyperNEAT Users Page][3]
-4. Kenneth O. Stanley, David D’Ambrosio and Jason Gauci, [A Hypercube-Based Indirect Encoding for Evolving Large-Scale Neural Networks][4], Artificial Life journal 15(2), Cambridge, MA: MIT Press, 2009
-5. Sebastian Risi, Kenneth O. Stanley, [An Enhanced Hypercube-Based Encoding for Evolving the Placement, Density and Connectivity of Neurons][5], Artificial Life journal, Cambridge, MA: MIT Press, 2012
-6. Kenneth O. Stanley, [Ph.D. Dissertation: EFFICIENT EVOLUTION OF NEURAL NETWORKS THROUGH COMPLEXIFICATION][6], Department of Computer Sciences, The University of Texas at Austin, Technical Report~AI-TR-04–39, August 2004
-7. Kenneth O. Stanley, [Compositional Pattern Producing Networks: A Novel Abstraction of Development][7], Genetic Programming and Evolvable Machines, Special Issue on Developmental Systems, New York, NY: Springer, 2007
-8. Iaroslav Omelianenko, [The GoLang NEAT implementation][8], GitHub, 2018
+4. Kenneth O. Stanley, David D’Ambrosio and Jason Gauci, [A Hypercube-Based Indirect Encoding for Evolving Large-Scale Neural Networks][4], Artificial Life journal, Cambridge, MA: MIT Press, 2009, vol. 15, no. 2, pp. 185-212 
+5. Sebastian Risi, Kenneth O. Stanley, [An Enhanced Hypercube-Based Encoding for Evolving the Placement, Density and Connectivity of Neurons][5], Artificial Life journal, Cambridge, MA: MIT Press, 2012, vol. 18, no. 4, pp. 331-363
+6. Kenneth O. Stanley, [Ph.D. Dissertation: Efficient Evolution of Neural Networks through Complexification][6], Department of Computer Sciences, The University of Texas at Austin, Technical Report~AI-TR-04–39, August 2004
+7. Kenneth O. Stanley, [Compositional Pattern Producing Networks: A Novel Abstraction of Development][7], Genetic Programming and Evolvable Machines, Special Issue on Developmental Systems, New York, NY: Springer, 2007, vol. 8, pp. 131-162
+8. Omelianenko, Iaroslav, [The GoLang implementation of NeuroEvolution of Augmented Topologies (NEAT) algorithm][8], GitHub, Computer software
 
 This source code maintained and managed by [Iaroslav Omelianenko][9]
 
 
 [1]:http://www.cs.ucf.edu/~kstanley/neat.html
 [2]:http://eplex.cs.ucf.edu/neat_software/
 [3]:http://eplex.cs.ucf.edu/hyperNEATpage/HyperNEAT.html
-[4]:http://eplex.cs.ucf.edu/papers/stanley_alife09.pdf
-[5]:https://www.mitpressjournals.org/doi/pdfplus/10.1162/ARTL_a_00071
-[6]:http://nn.cs.utexas.edu/keyword?stanley:phd04
-[7]:http://eplex.cs.ucf.edu/papers/stanley_gpem07.pdf
-[8]:https://github.com/yaricom/goNEAT
+[4]:https://doi.org/10.1162/artl.2009.15.2.15202
+[5]:https://doi.org/10.1162/ARTL_a_00071
+[6]:https://nn.cs.utexas.edu/downloads/papers/stanley.phd04.pdf
+[7]:https://doi.org/10.1007/s10710-007-9028-8
+[8]:https://doi.org/10.5281/zenodo.13628842
 [9]:https://io42.space

cppn/common_test.go

@@ -0,0 +1,31 @@
+package cppn
+
+import (
+	"bytes"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/yaricom/goNEAT/v4/neat/network"
+	"testing"
+)
+
+func checkNetworkSolverOutputs(solver network.Solver, outExpected []float64, delta float64, t *testing.T) {
+	signals := []float64{0.9, 5.2, 1.2, 0.6}
+	err := solver.LoadSensors(signals)
+	require.NoError(t, err, "failed to load sensors")
+
+	res, err := solver.RecursiveSteps()
+	require.NoError(t, err, "failed to perform recursive activation")
+	require.True(t, res, "failed to relax network")
+
+	outs := solver.ReadOutputs()
+	for i, out := range outs {
+		assert.InDelta(t, outExpected[i], out, delta, "wrong output at: %d", i)
+	}
+}
+
+func printGraph(graph SubstrateGraphBuilder, t *testing.T) {
+	var buf bytes.Buffer
+	err := graph.Marshal(&buf)
+	assert.NoError(t, err)
+	t.Log(buf.String())
+}