@reicek/neataptic-ts 0.1.0

package/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a bug report to help us improve NeatapticTS
+title: ''
+labels: bug
+assignees: ''
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Run '...'
+3. See error
+
+**Expected behavior**
+What you expected to happen.
+
+**Minimal repro (code)**
+Please include a small snippet or a link to a minimal repo/example that reproduces the issue.
+
+**Environment (please complete the following information):**
+- OS: (e.g. Windows 10 / macOS / Linux)
+- Node version: (e.g. v16.20.0)
+- NeatapticTS commit / tag:
+
+**Logs / stack traces**
+If applicable, add logs or stack traces to help diagnosis.
+
+**Additional context**
+Add any other context about the problem here.

package/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of the problem the feature would solve.
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Example usage**
+Provide a short code snippet or example of how the new API/feature would be used.
+
+**Alternatives considered**
+Describe alternatives you've considered and why they are insufficient.
+
+**Acceptance criteria**
+- [ ] Clear behavior described
+- [ ] Backwards-compatibility considerations noted
+- [ ] Tests or examples to demonstrate the new feature
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

package/.github/PULL_REQUEST_TEMPLATE.md

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+<!-- Brief title: keep under 60 chars -->
+
+## Summary
+<!-- One-line summary of the change -->
+
+## Related issue
+<!-- Link to the issue number this PR addresses, if any -->
+
+## What I changed
+- 
+- 
+
+## Why this is needed
+<!-- Short motivation / user-visible impact -->
+
+## Checklist
+- [ ] I have read the CONTRIBUTING guide
+- [ ] The change is covered by tests (new or updated) and `npm test` passes
+- [ ] I regenerated docs where applicable (`npm run docs`) and committed generated README changes if API/JSDoc changed
+- [ ] Relevant files were linted / typechecked
+- [ ] I added/update examples if applicable
+
+## Testing notes
+<!-- How to reproduce / run the tests for this change -->
+
+## Screenshots (optional)
+
+<!-- Add short notes for reviewers, and any breaking changes -->

package/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, refactor ]
+  pull_request:
+    branches: [ main, refactor ]
+
+jobs:
+  build-test:
+    runs-on: ubuntu-latest
+    env:
+      QLTY_COVERAGE_TOKEN: ${{ secrets.QLTY_COVERAGE_TOKEN }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Use Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+    - name: Install dependencies
+      run: npm ci
+    - name: Run tests
+      run: npm test
+    - name: Check for coverage file
+      id: cov
+      run: |
+        if [ -f coverage/lcov.info ]; then
+          echo "found=true" >> $GITHUB_OUTPUT
+        else
+          echo "found=false" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Upload coverage to Qlty
+      if: ${{ steps.cov.outputs.found == 'true' && env.QLTY_COVERAGE_TOKEN != '' }}
+      uses: qltysh/qlty-action/coverage@v2
+      with:
+        token: ${{ env.QLTY_COVERAGE_TOKEN }}
+        files: coverage/lcov.info
+    - name: Build
+      run: npm run build

package/.github/workflows/deploy-pages.yml

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+name: Deploy docs to GitHub Pages
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Use Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+
+    - name: Install dependencies
+      run: npm ci
+
+    - name: Build docs
+      run: npm run docs
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs
+        publish_branch: gh-pages

package/.github/workflows/manual_release_pipeline.yml

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+name: Manual release pipeline
+
+on:
+  workflow_dispatch:
+    inputs:
+      level:
+        description: 'Version bump level (patch, minor, major)'
+        required: true
+        default: 'patch'
+      branch:
+        description: 'Branch to release from'
+        required: true
+        default: 'release'
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      packages: write
+      actions: write
+    env:
+      NPM_TOKEN: ${{ secrets.NPM_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.inputs.branch }}
+        fetch-depth: 0
+
+    - name: Setup Node
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+
+    - name: Install dependencies
+      run: npm ci
+
+    - name: Configure git
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+    - name: Bump version, create tag and push
+      run: |
+        npm version ${{ github.event.inputs.level }} -m "chore(release): %s [ci skip]"
+        git push origin HEAD --follow-tags
+    - name: Done
+      run: echo "Version bumped and tags pushed. The release workflows will run on tag/release publish."
+
+  publish:
+    needs: release
+    uses: ./.github/workflows/publish.yml
+    with:
+      run_publish: 'true'
+      release_tag: ${{ github.ref }}
+    secrets:
+      QLTY_COVERAGE_TOKEN: ${{ secrets.QLTY_COVERAGE_TOKEN }}
+      NPM_TOKEN: ${{ secrets.NPM_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

package/.github/workflows/publish.yml

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+name: Publish packages
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      run_publish:
+        description: 'Whether to actually publish packages'
+        required: false
+        default: 'true'
+      release_tag:
+        description: 'Optional tag to publish (used for metadata only)'
+        required: false
+  workflow_call:
+    inputs:
+      run_publish:
+        description: 'Whether to actually publish packages'
+        required: false
+        type: string
+        default: 'true'
+      release_tag:
+        description: 'Optional tag to publish (used for metadata only)'
+        required: false
+        type: string
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    env:
+      QLTY_COVERAGE_TOKEN: ${{ secrets.QLTY_COVERAGE_TOKEN }}
+      RUN_PUBLISH: ${{ github.event.inputs.run_publish || 'true' }}
+      RELEASE_TAG: ${{ github.event.inputs.release_tag || '' }}
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Use Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+        registry-url: 'https://registry.npmjs.org'
+
+    - name: Install dependencies
+      run: npm ci
+
+    - name: Build
+      run: npm run build
+
+    - name: Publish to npm
+      if: ${{ env.RUN_PUBLISH == 'true' }}
+      env:
+        NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+      run: |
+        echo "Publishing to npm..."
+        npm publish --access public
+
+    - name: Publish to GitHub Packages
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+        registry-url: 'https://npm.pkg.github.com/'
+
+    - name: Publish to GitHub Packages (scoped)
+      if: ${{ env.RUN_PUBLISH == 'true' }}
+      env:
+        NODE_AUTH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        echo "Publishing to GitHub Packages..."
+        npm publish --registry https://npm.pkg.github.com/
+
+    - name: Check for coverage file
+      id: cov
+      run: |
+        if [ -f coverage/lcov.info ]; then
+          echo "found=true" >> $GITHUB_OUTPUT
+        else
+          echo "found=false" >> $GITHUB_OUTPUT
+        fi
+
+    - name: Upload coverage to Qlty (release)
+      if: ${{ steps.cov.outputs.found == 'true' && env.QLTY_COVERAGE_TOKEN != '' }}
+      uses: qltysh/qlty-action/coverage@v2
+      with:
+        token: ${{ env.QLTY_COVERAGE_TOKEN }}
+        files: coverage/lcov.info

package/.github/workflows/release_dispatch.yml

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+name: Manual release
+
+on:
+  workflow_dispatch:
+    inputs:
+      level:
+        description: 'Version bump level (patch, minor, major)'
+        required: true
+        default: 'patch'
+
+jobs:
+  bump-and-release:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Node
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+
+    - name: Install deps
+      run: npm ci
+
+    - name: Bump version and push
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        set -e
+        git config user.name "github-actions[bot]"
+        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        npm version ${{ github.event.inputs.level }} -m "chore(release): %s [ci skip]"
+        git push origin --follow-tags
+
+    - name: Create GitHub Release (done by tag push)
+      run: echo "Tag pushed; release workflows will be triggered by the tag/release event."

package/.travis.yml

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+language: node_js
+script: 'npm run test:src'
+node_js:
+  - 'node'
+  - '7.6'

package/CONTRIBUTING.md

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+## Contributing to NeatapticTS
+
+Thank you for helping improve NeatapticTS — this project is educational and community-focused, and contributions that improve clarity, examples, tests, or API ergonomics are especially welcome.
+
+### Quick checklist
+- Fork the repo and open a branch for your work
+- Run `npm install`
+- Make code or docs changes
+- Run tests and `npm run docs` if you changed JSDoc
+- Open a pull request that links an issue (recommended)
+
+---
+
+### Setup (local)
+1. Fork this repository and clone your fork.
+2. Install dependencies:
+
+```powershell
+npm install
+```
+
+---
+
+### Running tests and docs
+- Run unit tests:
+
+```powershell
+npm test
+```
+
+- Generate the documentation and mirrored `src` READMEs (run this if you changed JSDoc comments):
+
+```powershell
+npm run docs
+```
+
+---
+
+### Code style and quality
+- Keep changes small and focused. Prefer many small PRs over one large PR.
+- Follow TypeScript types and avoid `any` unless necessary; include type updates where relevant.
+- Add or update tests for behavioral changes. Tests live in `test/` and run with `npm test`.
+
+---
+
+### Documentation
+- Update JSDoc comments in the `src/` files when changing public APIs.
+- Run `npm run docs` to regenerate per-folder `README.md` files (these are mirrored into `src/*/README.md` and the `docs/` site).
+
+---
+
+### Reporting bugs
+Open an issue with the following minimal information:
+- Repro steps or a small example
+- Error/log output and Node version (or browser/OS when applicable)
+- The expected vs actual behavior
+
+If possible, include a small runnable snippet that reproduces the problem.
+
+---
+
+### Submitting a pull request
+1. Create a descriptive branch name (e.g. `fix/activation-pool-bug` or `feat/multiobjective-telemetry`).
+2. Open an issue first for non-trivial changes and note the issue number in your PR.
+3. Ensure tests pass and run `npm run docs` if you changed JSDoc or public APIs.
+4. In your PR description include:
+   - A short summary of the change
+   - The motivation and any user-visible API changes
+   - Links to related issues
+   - Test and docs status (e.g., `tests: pass`, `docs regenerated`)
+
+---
+
+### Review and CI
+The project runs tests and basic checks on PRs. Address review comments promptly. Small style or linter failures are typically fixed during the PR review.
+
+---
+
+### Attribution & license
+This project is released under the MIT License. Core ideas and portions of code are derived from the original Neataptic (Thomas Wagenaar) and Synaptic (Juan Cazala). See `LICENSE` for details.
+
+---
+
+### Code of conduct
+We follow a community-friendly code of conduct. Be respectful in discussions and PR reviews.
+
+---
+
+### Need help?
+Open an issue describing what you'd like to change and we can advise on implementation approach and scope.
+
+Thank you for contributing!

package/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2024 Cesar Anton <reicek@gmail.com>
+Copyright (c) 2017 Thomas Wagenaar <wagenaartje@protonmail.com>
+Copyright (c) 2017 Juan Cazala (parts used from Synaptic)
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE

package/ONNX_EXPORT.md

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+# ONNX Export in NeatapticTS
+
+NeatapticTS supports exporting trained neural networks to the ONNX (Open Neural Network Exchange) format, which enables interoperability with other machine learning frameworks and tools.
+
+## Supported Network Types
+
+ONNX export in NeatapticTS supports:
+
+- **Strictly Layered, Fully Connected MLPs**:
+  - Simple MLPs (input → output)
+  - Single hidden layer MLPs (input → hidden → output)
+  - Multi-hidden layer MLPs (input → hidden₁ → hidden₂ → ... → output)
+
+Each layer must be fully connected to the next layer, with no skip or recurrent connections.
+
+## Supported Activation Functions
+
+The following activation functions are mapped to their ONNX equivalents:
+
+- `Tanh`
+- `Sigmoid` (or `Logistic`)
+- `ReLU`
+- `Identity` (or any unknown function)
+
+Unsupported activation functions will be mapped to `Identity` with a warning.
+
+## Usage Example
+
+```typescript
+import { Architect } from 'neataptic';
+
+// Create and train a network
+const network = new Architect.Perceptron(2, 3, 1);
+network.train([
+  { input: [0, 0], output: [0] },
+  { input: [0, 1], output: [1] },
+  { input: [1, 0], output: [1] },
+  { input: [1, 1], output: [0] }
+]);
+
+// Export to ONNX format
+const onnxModel = network.toONNX();
+
+// Convert to JSON string for saving or transmitting
+const onnxJson = JSON.stringify(onnxModel);
+```
+
+## Limitations
+
+- The export functionality only supports strictly layered, fully connected MLPs.
+- Networks with skip connections, recurrent connections, or non-MLP topologies are not supported.
+- LSTM, GRU, and other advanced architectures are not supported.
+- All nodes in the same layer must use the same activation function (enforced).
+
+## Example Network Structures
+
+### Simple MLP (input → output)
+```
+Input Layer (2 nodes) → Output Layer (1 node)
+```
+
+### Single Hidden Layer MLP
+```
+Input Layer (2 nodes) → Hidden Layer (3 nodes) → Output Layer (1 node)
+```
+
+### Multi-Hidden Layer MLP
+```
+Input Layer (2 nodes) → Hidden Layer 1 (4 nodes) → Hidden Layer 2 (3 nodes) → Output Layer (1 node)
+```
+
+## ONNX Model Structure
+
+The exported ONNX model includes:
+
+- Input and output tensor definitions with batch dimension
+- Weight and bias initializers for each layer
+- MatMul, Add, and Activation nodes for the computation graph
+- Producer information and ONNX version metadata
+
+## Future Enhancements
+
+Future versions may support:
+- Skip connections
+- Recurrent connections
+- Custom activation functions
+- LSTM and GRU cell types