pynamicalsys 1.2.1__tar.gz → 1.3.0__tar.gz

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/CHANGELOG.md

@@ -5,7 +5,30 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v1.2.1] - 2025-06-29
+## [v1.3.0] 2025-08-23
+
+### Added
+
+- `DiscreteDynamicalSystem` class:
+  - `step` method: returns the next state of the system.
+  - `GALI` method: computes the generalized alignment index (GALI).
+
+- `ContinuousDynamicalSystem` class:
+    - `GALI` method that computes the generalized alignment index (GALI).
+
+### Modified
+
+- `DiscreteDynamicalSystem` class:
+    - Improved performance when checking sampling points by avoiding repeated searches in sample_times.
+    - Refactored the `lyapunov` method to allow computing only a subset of the Lyapunov spectrum.
+
+- `ContinuousDynamicalSystem` class:
+    - Unified integration step logic (previously duplicated across methods like trajectory and lyapunov_exponents) into a single step function.
+    - Refactored the `lyapunov` method to allow computing only a subset of the Lyapunov spectrum.
+
+[v1.3.0]: https://github.com/mrolims/pynamicalsys/compare/v1.2.2...v1.3.0
+
+## [v1.2.2] - 2025-06-29
 
 ### Added
 
@@ -16,11 +39,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Lyapunov exponents calculation.
   - The smallest aligment index (SALI) and linear dependence index (LDI) for chaos detection.
 
-## [v1.0.0] - 2025-06-16
+[v1.2.2]: https://github.com/mrolims/pynamicalsys/compare/v1.0.0...v1.2.2
+
+## v1.0.0 - 2025-06-16
 
 ### Added
 
-- `DiscreteDynamicalSystems` class for simulating and analyzing discrete nonlinear dynamical systems:
+- `DiscreteDynamicalSystem` class for simulating and analyzing discrete nonlinear dynamical systems:
   - Trajectory computation.
   - Chaotic indicators.
   - Fixed points, periodic orbits, and manifolds.
@@ -36,8 +61,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - `PlotStyler` utility class to globally configure and apply consistent styling for Matplotlib plots.
 
----
-
 <!-- Dummy heading to avoid ending on a transition -->
 
 ##

pynamicalsys-1.3.0/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to pynamicalsys
+
+We appreciate your interest in contributing to pynamicalsys! Whether you're fixing a bug, suggesting an improvement, or adding a new feature, your help is welcome.
+
+## How to Contribute
+
+1. **Fork the Repository**  
+   Create a personal copy of this repository.
+
+2. **Create a Feature Branch**  
+   Use a descriptive branch name:
+
+   ```bash
+   $ git checkout -b fix-typo-in-readme
+   ```
+
+3. **Make Changes**
+
+   Follow the coding style and ensure existing functionality it not broken. Add tests if relevant.
+
+4. **Submit a Pull Request**
+
+   Push your branch and open a pull request on GitHub. Include a clear description of your changes.
+
+5. **Wait for Review**
+
+   We'll review your PR and may request changes or offer suggestions.
+
+## Coding Style
+
+- Follow **PEP8** standards for Pycode code.
+- Use **docstrings** (PEP257) for public classes, functions, and modules.
+- Include **type hints** where appropriate.
+- Keep commits clean and descriptive.
+
+## Bug Reports & Feature Requests
+
+- Submit an [issue](https://github.com/mrolims/pynamicalsys/issues) to report bugs or suggest new features.
+- Include steps to reproduce, error messages, or use cases when possible.
+
+## Code of Conduct
+
+We strive to maintain a respectful and inclusive community. Please follow our [code of conduct](https://pynamicalsys.readthedocs.io/en/latest/) when interacting.
+
+## Thank You
+
+Your contributions help improve the project and support the community — thank you!

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.2.1
+Version: 1.3.0
 Summary: A Python toolkit for the analysis of dynamical systems
 Author-email: Matheus Rolim Sales <rolim.sales.m@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -689,6 +689,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: numpy>=1.21
 Requires-Dist: matplotlib>=3.4
 Requires-Dist: numba>=0.55
+Requires-Dist: scipy>=0.6
 
 # pynamicalsys: A Python toolkit for the analysis of dynamical systems
 
@@ -698,28 +699,28 @@ Requires-Dist: numba>=0.55
 
 ## Overview
 
-**pynamicalsys** is designed to provide a fast, flexible, and user-friendly environment for analyzing **nonlinear dynamical systems**. It is designed for students, researchers, educators, and enthusiasts who want to explore the world of chaos and dynamical systems. Beyond standard tools like trajectory generation and Lyapunov exponents calculation, pynamicalsys includes advanced features such as
+**pynamicalsys** is designed to provide a fast, flexible, and user-friendly environment for analyzing **nonlinear dynamical systems**. It is intended for students, researchers, educators, and enthusiasts who want to explore the world of chaos and dynamical systems. Beyond standard tools like trajectory generation and Lyapunov exponents calculation, **pynamicalsys** includes advanced features such as
 
--   **Linear dependence index** for chaos detection.
--   **Recurrence plots** and recurrence time statistics.
--   Chaos indicators based on **weighted Birkhoff averages**.
--   Statistical measures of **diffusion and transport** in dynamical systems.
--   Computation of **periodic orbits**, their **stability** and their **manifolds**.
--   Basin metric for **quantifying** the structure of **basins of attraction**.
--   **Plot styling** for consistent and customizable visualizations.
+- **Linear dependence index** for chaos detection.
+- **Recurrence plots** and recurrence time statistics.
+- Chaos indicators based on **weighted Birkhoff averages**.
+- Statistical measures of **diffusion and transport** in dynamical systems.
+- Computation of **periodic orbits**, their **stability** and their **manifolds**.
+- Basin metric for **quantifying** the structure of **basins of attraction**.
+- **Plot styling** for consistent and customizable visualizations.
 
-pynamicalsys is built on top of NumPy and Numba, ensuring high performance and efficiency. Thanks to Numba accelerated computation, pynamicalsys offers speedups up to **130x** compared to the original Python implementation of the algorithms. This makes it suitable for large-scale simulations and analyses.
+**pynamicalsys** is built on top of NumPy and Numba, ensuring high performance and efficiency. Thanks to Numba accelerated computation, **pynamicalsys** offers speedups up to **130x** compared to the original Python implementation of the algorithms. This makes it suitable for large-scale simulations and analyses.
 
 ## Installation
 
 ### Prerequisites
 
--   Python 3.8 or higher
--   pip (Python package installer)
+- Python 3.8 or higher
+- pip (Python package installer)
 
 ### Install via PyPI
 
-To install the latest stable release, run:
+To install the latest stable release, run in your command line:
 
 ```bash
 $ pip install pynamicalsys
@@ -727,6 +728,13 @@ $ pip install pynamicalsys
 
 > **Note:** On **Windows**, it is **strongly recommended** to use [Anaconda](https://www.anaconda.com). It simplifies dependency management and avoids potential issues with scientific libraries during installation. Be sure to run the command from the **Anaconda Prompt**, not from Command Prompt or PowerShell, to ensure the correct environment is activated.
 
+### Upgrade via PyPI
+
+To upgrade your current version of **pynamicalsys** to the latest stable release, run in your command line:
+
+```bash
+$ pip install pynamicalsys --upgrade
+```
 
 ### Install from source
 
@@ -761,19 +769,19 @@ Currently, our research paper is under review, but in the mean time, if you use
 
 ```bibtex
 @misc{pynamicalsys,
-  title={pynamicalsys: A Python toolkit for the analysis of dynamical systems}, 
+  title={pynamicalsys: A Python toolkit for the analysis of dynamical systems},
   author={Matheus Rolim Sales and Leonardo Costa de Souza and Daniel Borin and Michele Mugnaine and José Danilo Szezech Jr. and Ricardo Luiz Viana and Iberê Luiz Caldas and Edson Denis Leonel and Chris G. Antonopoulos},
   year={2025},
   eprint={2506.14044},
   archivePrefix={arXiv},
   primaryClass={nlin.CD},
-  url={https://arxiv.org/abs/2506.14044}, 
+  url={https://arxiv.org/abs/2506.14044},
 }
 ```
 
 ## Contributing
 
-We welcome contributions from the community! To get started, please see our Contributing Guidelines.
+We welcome contributions from the community! To get started, please see our [Contributing Guidelines](https://pynamicalsys.readthedocs.io/en/latest/contributing.html).
 
 ## License
 

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/README.md

@@ -6,28 +6,28 @@
 
 ## Overview
 
-**pynamicalsys** is designed to provide a fast, flexible, and user-friendly environment for analyzing **nonlinear dynamical systems**. It is designed for students, researchers, educators, and enthusiasts who want to explore the world of chaos and dynamical systems. Beyond standard tools like trajectory generation and Lyapunov exponents calculation, pynamicalsys includes advanced features such as
+**pynamicalsys** is designed to provide a fast, flexible, and user-friendly environment for analyzing **nonlinear dynamical systems**. It is intended for students, researchers, educators, and enthusiasts who want to explore the world of chaos and dynamical systems. Beyond standard tools like trajectory generation and Lyapunov exponents calculation, **pynamicalsys** includes advanced features such as
 
--   **Linear dependence index** for chaos detection.
--   **Recurrence plots** and recurrence time statistics.
--   Chaos indicators based on **weighted Birkhoff averages**.
--   Statistical measures of **diffusion and transport** in dynamical systems.
--   Computation of **periodic orbits**, their **stability** and their **manifolds**.
--   Basin metric for **quantifying** the structure of **basins of attraction**.
--   **Plot styling** for consistent and customizable visualizations.
+- **Linear dependence index** for chaos detection.
+- **Recurrence plots** and recurrence time statistics.
+- Chaos indicators based on **weighted Birkhoff averages**.
+- Statistical measures of **diffusion and transport** in dynamical systems.
+- Computation of **periodic orbits**, their **stability** and their **manifolds**.
+- Basin metric for **quantifying** the structure of **basins of attraction**.
+- **Plot styling** for consistent and customizable visualizations.
 
-pynamicalsys is built on top of NumPy and Numba, ensuring high performance and efficiency. Thanks to Numba accelerated computation, pynamicalsys offers speedups up to **130x** compared to the original Python implementation of the algorithms. This makes it suitable for large-scale simulations and analyses.
+**pynamicalsys** is built on top of NumPy and Numba, ensuring high performance and efficiency. Thanks to Numba accelerated computation, **pynamicalsys** offers speedups up to **130x** compared to the original Python implementation of the algorithms. This makes it suitable for large-scale simulations and analyses.
 
 ## Installation
 
 ### Prerequisites
 
--   Python 3.8 or higher
--   pip (Python package installer)
+- Python 3.8 or higher
+- pip (Python package installer)
 
 ### Install via PyPI
 
-To install the latest stable release, run:
+To install the latest stable release, run in your command line:
 
 ```bash
 $ pip install pynamicalsys
@@ -35,6 +35,13 @@ $ pip install pynamicalsys
 
 > **Note:** On **Windows**, it is **strongly recommended** to use [Anaconda](https://www.anaconda.com). It simplifies dependency management and avoids potential issues with scientific libraries during installation. Be sure to run the command from the **Anaconda Prompt**, not from Command Prompt or PowerShell, to ensure the correct environment is activated.
 
+### Upgrade via PyPI
+
+To upgrade your current version of **pynamicalsys** to the latest stable release, run in your command line:
+
+```bash
+$ pip install pynamicalsys --upgrade
+```
 
 ### Install from source
 
@@ -69,19 +76,19 @@ Currently, our research paper is under review, but in the mean time, if you use
 
 ```bibtex
 @misc{pynamicalsys,
-  title={pynamicalsys: A Python toolkit for the analysis of dynamical systems}, 
+  title={pynamicalsys: A Python toolkit for the analysis of dynamical systems},
   author={Matheus Rolim Sales and Leonardo Costa de Souza and Daniel Borin and Michele Mugnaine and José Danilo Szezech Jr. and Ricardo Luiz Viana and Iberê Luiz Caldas and Edson Denis Leonel and Chris G. Antonopoulos},
   year={2025},
   eprint={2506.14044},
   archivePrefix={arXiv},
   primaryClass={nlin.CD},
-  url={https://arxiv.org/abs/2506.14044}, 
+  url={https://arxiv.org/abs/2506.14044},
 }
 ```
 
 ## Contributing
 
-We welcome contributions from the community! To get started, please see our Contributing Guidelines.
+We welcome contributions from the community! To get started, please see our [Contributing Guidelines](https://pynamicalsys.readthedocs.io/en/latest/contributing.html).
 
 ## License
 

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/pyproject.toml

@@ -15,7 +15,7 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 
-dependencies = ["numpy >=1.21", "matplotlib >=3.4", "numba >=0.55"]
+dependencies = ["numpy >=1.21", "matplotlib >=3.4", "numba >=0.55", "scipy >=0.6"]
 requires-python = ">=3.8"
 
 [build-system]

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/src/pynamicalsys/__version__.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '1.2.1'
-__version_tuple__ = version_tuple = (1, 2, 1)
+__version__ = version = '1.3.0'
+__version_tuple__ = version_tuple = (1, 3, 0)
+
+__commit_id__ = commit_id = 'g138b5d22a'

{pynamicalsys-1.2.1 → pynamicalsys-1.3.0}/src/pynamicalsys/common/utils.py

@@ -257,7 +257,7 @@ def finite_difference_jacobian(
 
 
 @njit
-def wedge_product_norm(vectors: NDArray[np.float64]) -> float:
+def wedge_norm_2(vectors: NDArray[np.float64]) -> float:
     """
     Computes the norm of the wedge product of n m-dimensional vectors using the Gram determinant.
 
@@ -295,6 +295,25 @@ def wedge_product_norm(vectors: NDArray[np.float64]) -> float:
     return norm
 
 
+def wedge_norm(V: NDArray[np.float64]) -> float:
+    """
+    Computes the norm of the wedge product of k d-dimensional vectors using the Gram determinant.
+
+    Parameters:
+    vectors : NDArray[np.float64]
+        A (d, k) array where d is the dimension and k is the number of vectors.
+
+    Returns:
+    norm : float
+        The norm (magnitude) of the wedge product.
+    """
+    G = V.T @ V  # Gram matrix, shape (k, k)
+
+    det = np.linalg.det(G)
+
+    return 0 if det < 0 else np.sqrt(det)
+
+
 @njit
 def _coeff_mat(x: NDArray[np.float64], deg: int) -> NDArray[np.float64]:
     mat_ = np.zeros(shape=(x.shape[0], deg + 1))
@@ -322,23 +341,3 @@ def fit_poly(
     p = _fit_x(a, y)
     # Reverse order so p[0] is coefficient of highest order
     return p[::-1]
-
-
-if __name__ == "__main__":
-
-    v = np.random.rand(2, 2)
-    w = v.copy()
-
-    q, r = qr(v)
-    print("Q:\n", q)
-    print("R:\n", r)
-    print("QR Product:\n", np.dot(q, r))
-    print("Original Matrix:\n", v)
-
-    print()
-
-    q, r = householder_qr(v)
-    print("Q:\n", q)
-    print("R:\n", r)
-    print("QR Product:\n", np.dot(q, r))
-    print("Original Matrix:\n", v)