diff-grok 1.0.8 → 1.0.10

package/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a bug in diff-grok
+title: "[BUG] "
+labels: bug
+assignees: ""
+
+---
+
+**What happened?**  
+A clear and concise description of the problem.
+
+**How to reproduce?**  
+Provide a minimal reproducible example (code snippet, inputs, parameters, Node/TS version, OS).
+
+**What did you expect to happen?**  
+Describe the expected behavior.
+
+**What actually happened?**  
+Describe the actual behavior, error messages, stack trace, wrong output, etc.
+
+**Environment:**  
+- diff-grok version:  
+- Node / TypeScript version:  
+- OS / Platform:  
+- Additional context (e.g. dependency versions):  
+
+(optional) **Example / Test case:**  
+Provide a minimal code snippet or scenario where bug occurs.

package/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest a new feature or improvement
+title: "[FEATURE] "
+labels: enhancement
+assignees: ""
+
+---
+
+**What problem would this feature solve?**  
+Describe the motivation, use-cases, or scenarios.
+
+**Proposed solution / API idea (if any):**  
+Give a rough idea how this could look (function signature, parameters, return type, etc.).  
+
+**Alternatives / Workarounds:**  
+Describe any existing workaround or alternative that motivated this.  
+
+**Additional context (optional):**  
+Remarks, performance considerations, backward-compatibility notes, etc.

package/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+## Description
+
+Please describe what this PR does and why it is needed.
+
+## Related Issue(s) / Motivation
+
+Closes / Addresses / References: #[issue number] (if applicable)
+
+## Type of change
+
+- [ ] Bug fix  
+- [ ] New feature  
+- [ ] Update / improvement  
+- [ ] Documentation / example update  
+
+## Checklist
+
+- [ ] I have read CONTRIBUTING.md  
+- [ ] My code follows project style (lint + formatting)  
+- [ ] I added / updated tests or examples (if applicable)  
+- [ ] All existing tests pass  
+- [ ] I updated documentation / README (if applicable)  

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

@@ -0,0 +1,15 @@
+name: Deploy Docs
+on:
+  push:
+    branches: [ main ]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: npm ci
+      - run: npx typedoc
+      - uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs

package/.github/workflows/test.yaml

@@ -0,0 +1,19 @@
+name: Run tests
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+       
+    steps:
+      - uses: actions/checkout@v4      
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      
+      - name: Install dependencies
+        run: npm install
+      
+      - name: Run tests
+        run: npm test

package/CONTRIBUTING.md

@@ -0,0 +1,74 @@
+# Contributing to diff-grok 🚀
+
+Thank you for your interest in contributing to diff-grok!  
+We welcome bug reports, documentation improvements, new features, and help with tests or examples.
+
+## ✅ How to contribute
+
+### Reporting issues
+
+- Please search existing issues before creating a new one — your problem or idea may already be discussed or solved.  
+- When reporting a bug, include as much information as possible: error messages, minimal reproducible example, environment (Node version, OS, TypeScript version), and expected vs actual behavior.  
+- For feature requests — describe the motivation, proposed API (if relevant), and possible use-cases.
+
+### Submitting pull requests (PR)
+
+1. Fork the repository and create a branch:  
+   `feat/your-feature` or `fix/bug-description` or `docs/update-readme`  
+2. Make sure your code follows the existing style (TypeScript, ESLint, Prettier — as used in the repo).  
+3. Add or update tests/examples if applicable.  
+4. Run linter and tests before committing:
+
+```bash
+   npm install  
+   npm run lint  
+   npm test
+```
+
+5. Commit with a clear message. Prefer descriptive messages, e.g.:
+
+```bash
+feat: add new Rosenbrock method,
+fix: correct edge behaviour in solver,
+docs: improve README example for ODE usage.
+```
+
+6. Rebase or merge main upstream if needed; make sure no conflicts remain.
+
+7. Create a PR, describing what you’ve changed and referencing related issues (if any).
+
+## 🧑‍💻 Code style & conventions
+
+Project uses TypeScript.
+
+Follow the existing coding conventions and folder structure.
+
+Keep changes focused and minimal — avoid mixing unrelated changes (e.g. code + formatting + docs) in one PR.
+
+Write clear, self-contained commits.
+
+## 📚 Documentation & Examples
+
+If you fix or add public API — update README or add an example.
+
+For new features — prefer adding minimal examples or tests demonstrating usage.
+
+If you change behavior in edge cases — mention it clearly in docs/README.
+
+## 🗣 Communication & Etiquette
+
+Use GitHub Issues and Pull Requests for all discussions.
+
+Be respectful and patient: contributors and maintainers may be in different timezones or busy.
+
+Before opening an Issue or PR — read existing content (README, issues, pull requests) to avoid duplicates.
+
+## 🔧 CI, Tests, and Quality
+
+Ensure all existing tests pass; add new tests if adding functionality.
+
+Code should pass linting/formatting checks.
+
+If your change is substantial — consider adding a test or example illustrating it.
+
+Thank you for helping make diff-grok better! 🎉

package/README.MD

@@ -18,8 +18,34 @@ A lightweight TypeScript library for solving initial value problem ([IVP](https:
 
 ## Installation
 
+To install via npm:
+
 ```bash
-npm i diff-grok
+npm install diff-grok
+```
+
+Minimal "Hello World" example:
+
+```typescript
+// example.ts
+
+import {ODEs, mrt} from 'diff-grok';
+
+const task: ODEs = {
+  name: 'Example',
+  arg: {name: 't', start: 0, finish: 1, step: 0.1},
+  initial: [1, -1],
+  func: (t: number, y: Float64Array, output: Float64Array) => {
+    out[0] = y[0] - t;
+  },
+  tolerance: 1e-7,
+  solutionColNames: ['y(t)'],
+};
+
+const solution = mrt(task);
+
+console.log('t:', solution[0]);
+console.log('y(t):', solution[1]);
 ```
 
 ## Solving
@@ -74,7 +100,7 @@ y(0) = -1
 To solve it on the segment $[0, 2]$ with the step $0.01$ using the [MRT](https://doi.org/10.1137/S1064827594276424) method with the tolerance $10^{-7}$, we start with imports:
 
 ```typescript
-import {ODEs, mrt} from '@datagrok-ai/diff-studio-tools';
+import {ODEs, mrt} from 'diff-grok';
 ```
 
 Next, we create
@@ -152,7 +178,39 @@ The MRT, ROS3PRw and ROS34PRw methods demonstrate the following time performance
 |[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|[0, 10E+13]|40K|1E-6|14|17|8|
 |[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|[0, 60]|30K|1E-6|36|50|23|
 
-Run [check-methods.ts](./src/examples/check-methods.ts) to check results.
+Maximum absolute deviations (MADs) from the reference solutions obtained using SciPy (Radau) are summarized in the table below:
+
+|Problem|MRT|ROS3PRw|ROS34PRw|
+|-|-|-|-|
+|[Rober](https://archimede.uniba.it/~testset/report/rober.pdf)|1.87e-8|1.88e-8|1.88e-8|
+|[HIRES](https://archimede.uniba.it/~testset/report/hires.pdf)|4.80e-11|1.05e-14|2.87e-14|
+|[VDPOL](https://archimede.uniba.it/~testset/report/vdpol.pdf)|5.12e-4|5.12e-4|5.12e-4|
+|[OREGO](https://archimede.uniba.it/~testset/report/orego.pdf)|3.05e-5|3.45e-7|2.31e-6|
+|[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|1.12e-19| 1.33e-19|3.40e-17|
+|[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|4.06e-10|9.16e-12|1.58e-10|
+
+Run [check-methods.ts](./src/examples/check-methods.ts) to reproduce these results (see [here](#examples) how to run scripts standalone).
+
+The following charts compare the Diff Grok and Radau solutions for the **van der Pol** system:
+
+![Pollution](images/VDPOL.png)
+
+The following graphs present a comparison of the Diff Grok and Radau solutions for the **Pollution** model, highlighting a portion of the functions:
+
+![Pollution](images/POLL.png)
+
+Run benchmark models and find the reference solutions via the following links to the [Datagrok](https://public.datagrok.ai) platform:
+
+|Problem|Diff Grok|Radau|
+|-|-|-|
+|Rober|[ROBER.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/ROBER.ivp)|[ROBER.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/ROBER-using-Radau.csv?browse=files)|
+|HIRES|[HIRES.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/HIRES.ivp)|[HIRES.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/HIRES-using-Radau.csv?browse=files)|
+|VDPOL|[VDPOL.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/VDPOL.ivp)|[VDPOL.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/VANDERPOL-using-Radau.csv?browse=files)|
+|OREGO|[OREGO.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/OREGO.ivp)|[OREGO.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/OREGO-using-Radau.csv?browse=files)|
+|E5|[E5.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/E5.ivp)|[E5.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/E5-using-Radau.csv?browse=files)|
+|Pollution|[POLL.ivp](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/POLL.ivp)|[POLL.csv](https://public.datagrok.ai/file/System.AppData/DiffStudio/benchmarks/POLL-using-Radau.csv?browse=files)|
+
+In the file [print-benchmark.ts](./src/examples/print-benchmark.ts), you can find standalone functions that print the solutions of these problems to the console, as well as Python scripts for computing the solutions using SciPy.
 
 ## Scripting
 
@@ -262,7 +320,7 @@ To transform any model to JavaScript code with an appropriate specification of `
 1. Import the parsing and code generating tools:
 
 ```typescript
-import {getIVP, getJScode} from '@datagrok-ai/diff-studio-tools';
+import {getIVP, getJScode} from 'diff-grok';
 ```
 
 2. Define a string with a model specification, use a simple [model syntax](#model-components-and-syntax):
@@ -302,7 +360,7 @@ Diff Grok **pipeline** is a powerful feature for complex process simulation and
 1. Start with imports:
 
 ```typescript
-import * as DGL from '@datagrok/diff-grok';
+import * as DGL from 'diff-grok';
 ```
 
 2. Define your model:
@@ -394,3 +452,123 @@ Learn more
  * Diff Studio example [models](https://datagrok.ai/help/compute/models)
  * [Parameters optimization](https://datagrok.ai/help/compute/function-analysis#parameter-optimization)
  * [Sensitivity analysis](https://datagrok.ai/help/compute/function-analysis#sensitivity-analysis)
+
+## Environment Requirements
+
+### Development & Build
+
+* **Node.js ≥ 19.3.0** (required for development and building the library)
+* **npm** or **yarn** package manager
+
+### Runtime Environments
+
+#### Server-Side (Node.js)
+
+* **Node.js ≥ 16.0.0** (for server-side usage)
+  * Requires support for ES modules
+  * `Float64Array` and typed arrays support (available since Node.js 0.10+)
+
+#### Operating Systems
+
+* Windows (x64, ARM64)
+* macOS (Intel & Apple Silicon)
+* Linux (most common distributions)
+
+#### Browser Support
+
+The library runs in all modern browsers with ES2015+ support. Key requirements:
+
+* **ES Modules** (native `import`/`export`)
+* **Typed Arrays** (`Float64Array`, `Uint8Array`)
+* **WebWorkers** (for pipeline computations)
+* **ArrayBuffer** support
+
+| Browser                | Minimum Version | Supported? | Notes                                           |
+| ---------------------- | --------------- | ---------- | ----------------------------------------------- |
+| **Chrome**             | 63+             | ✔️ Yes      | Full ES2015+ and WebWorker support              |
+| **Firefox**            | 60+             | ✔️ Yes      | Full ES2015+ and WebWorker support              |
+| **Safari (macOS/iOS)** | 11.1+           | ✔️ Yes      | Native ES module and WebWorker support          |
+| **Edge (Chromium)**    | 79+             | ✔️ Yes      | Same support level as Chrome                    |
+| **Opera**              | 50+             | ✔️ Yes      | Chromium-based, full support                    |
+| **Legacy Browsers**    | -               | ❌ No       | IE 11, pre-Chromium Edge, old Android browsers  |
+
+**Browser Feature Requirements:**
+* ES2015 (ES6) JavaScript support
+* Native ES modules (`<script type="module">`)
+* `Float64Array` and other typed arrays
+* `WebWorker` API (for parallel computations)
+* `Promise` support
+* `Math` object with standard functions (`exp`, `sin`, `cos`, etc.)
+
+**Notes:**
+* For older browsers, consider using a transpiler (Babel) and bundler (Webpack/Rollup)
+* TypeScript compilation target should be ES2015 or higher
+* WebWorker support is required for pipeline computations; without it, computations run on the main thread
+
+### Bundler Configuration
+
+When bundling for browsers, ensure:
+* ES module output format is preserved or properly transformed
+* TypedArray polyfills are not included (not needed for target browsers)
+* WebWorker files are properly handled by your bundler
+
+### Polyfills
+
+No polyfills required for target environments. All required features are natively supported in the minimum browser versions listed above.
+
+## Examples
+
+Diff Grok contains a set of examples located in the folder [src/examples](./src/examples/):
+
+|File|Features|
+|-|-|
+|[basic-use.ts](./src/examples/basic-use.ts)|Minimal "Hello World" example. Illustrates the use of the [MRT](https://doi.org/10.1137/S1064827594276424) method.|
+|[check-methods.ts](./src/examples/check-methods.ts)| Checks the [performance](#performance) of numerical methods.|
+|[corr-probs.ts](./src/examples/corr-probs.ts)|Solves a set of problems with exact solutions and evaluate the deviation.|
+|[cyclic-model.ts](./src/examples/cyclic-model.ts)| Considers pharmacokinetic-pharmacodynamic (PK-PD) simulation and shows how to apply pipelines and cyclic models.|
+|[model-updates.ts](./src/examples/model-updates.ts)|Considers gluconic acid (GA) production by Aspergillus niger modeling and shows how to apply pipelines and models with updates.|
+|[pipeline-use.ts](./src/examples/pipeline-use.ts)|Considers modeling queues and shows shows how to apply pipelines and models with customized outputs.|
+|[scripting.ts](./src/examples/scripting.ts)|Shows how to generate JS-script from Diff Grok model.|
+
+To run examples standalone:
+
+1. Install TypeScript locally. If your project does not already include TypeScript:
+```bash
+npm install --save-dev typescript
+```
+
+2. Create a tsconfig.json. If you do not have one yet:
+```bash
+npx tsc --init
+```
+Recommended configuration:
+```json
+{
+  "compilerOptions": {
+    "target": "es6",
+    "lib": ["ES2022", "dom"],
+    "sourceMap": true,
+    "strict": true,
+    "moduleResolution": "node",
+    "types": ["jest", "node"],
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+  }
+}
+```
+
+3. Compile the TypeScript file:
+```bash
+tsc src/examples/basic-use.ts
+```
+
+4. Run:
+```bash
+node src/examples/basic-use.js
+```
+
+## Contributing
+
+We welcome contributions of all kinds - bug reports, feature requests, documentation updates, and pull requests.
+
+Before contributing, please read our [Contributing Guidelines](./CONTRIBUTING.md).

package/docs/.nojekyll

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