pynamicalsys 1.4.0__tar.gz → 1.4.5__tar.gz

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/CHANGELOG.md

@@ -5,7 +5,19 @@ 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).
 
-## [Unreleased]
+## [v1.4.4] - 17-09-2025
+
+### Modified
+
+- `DiscreteDynamicalSystem` class:
+    - Fixed problems in the `finite_hurst_exponent`
+
+- `ContinuousDynamicalSystem` and `HamiltonianSystem` classes:
+    - Fixed the output of the `recurrence_time_entropy` method when `return_final_state=True`.
+
+[v1.4.3]: https://github.com/mrolims/pynamicalsys/compare/v1.4.1...v1.4.4
+
+## [v1.4.1] - 2025-09-15
 
 ### Added
 
@@ -42,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `ContinuousDynamicalSystem` class:
     - `lyapunov` method now uses a specific function to compute only the maximum Lyapunov exponent when `num_exponents=1`.
 
-[Unreleased]: https://github.com/mrolims/pynamicalsys/compare/v1.3.1...HEAD
+[v1.4.1]: https://github.com/mrolims/pynamicalsys/compare/v1.3.1...v1.4.1
 
 ## [v1.3.1] - 2025-08-24
 

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/MANIFEST.in

@@ -1,7 +1,7 @@
 # MANIFEST.in
 
 # Exclude tests and notebooks
-prune discrete-time-tests
+prune tests
 prune paper
 
 # Exclude docs (if you have a docs folder)

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.4.0
+Version: 1.4.5
 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
@@ -677,7 +677,6 @@ License:                     GNU GENERAL PUBLIC LICENSE
         the library.  If this is what you want to do, use the GNU Lesser General
         Public License instead of this License.  But first, please read
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Operating System :: OS Independent

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/pyproject.toml

@@ -6,7 +6,6 @@ authors = [{ name = "Matheus Rolim Sales", email = "rolim.sales.m@gmail.com" }]
 readme = "README.md"
 license = { file = "LICENSE" }
 classifiers = [
-    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Operating System :: OS Independent",
@@ -25,11 +24,18 @@ dependencies = [
 requires-python = ">=3.8"
 
 [build-system]
-requires = ["setuptools>=61.0", "setuptools-scm>=8"]
+requires = ["setuptools>=77.0", "setuptools-scm>=9"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
-packages = ["pynamicalsys"]
+packages = [
+    "pynamicalsys",
+    "pynamicalsys.common",
+    "pynamicalsys.continuous_time",
+    "pynamicalsys.core",
+    "pynamicalsys.discrete_time",
+    "pynamicalsys.hamiltonian_systems",
+]
 package-dir = { "" = "src" }
 license-files = []
 

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/__version__.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.4.0'
-__version_tuple__ = version_tuple = (1, 4, 0)
+__version__ = version = '1.4.5'
+__version_tuple__ = version_tuple = (1, 4, 5)
 
-__commit_id__ = commit_id = 'g99b46b31b'
+__commit_id__ = commit_id = 'gb18384e86'

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/continuous_time/chaotic_indicators.py

@@ -657,7 +657,7 @@ def recurrence_time_entropy(
     # Prepare output
     result = [rte]
     if config.return_final_state:
-        result.append(points[-1])
+        result.append(points[-1, 1:])
     if config.return_recmat:
         result.append(recmat)
     if config.return_p:

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/core/hamiltonian_systems.py

@@ -440,14 +440,15 @@ class HamiltonianSystem:
             Value at which the section is taken.
         crossing : {-1, 0, 1}, default=1
             Direction of crossing:
-            -1 : downward
-             0 : all crossings
-             1 : upward
+
+            - -1 : downward
+            - 0 : all crossings
+            - 1 : upward
 
         Returns
         -------
         section_points : ndarray
-            Points of the trajectory lying on the Poincaré section.
+            Points of the trajectory lying on the Poincaré section. The first column is the time of each crossing.
 
         Raises
         ------

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/discrete_time/dynamical_indicators.py

@@ -1122,12 +1122,10 @@ def finite_time_hurst_exponent(
 
     # Compute Hurst exponent for each window
     for i in range(num_windows):
-        result = hurst_exponent(
-            u, parameters, finite_time, mapping, wmin=wmin, return_last=True
-        )
-        H_values[i] = result[: len(u)]
-        phase_space_points[i] = u
-        u = result[len(u) :]
+        time_series = generate_trajectory(u, parameters, finite_time, mapping)
+        H_values[i] = hurst_exponent(time_series, wmin=wmin)
+        phase_space_points[i] = time_series[-1, :]
+        u = time_series[-1, :]
 
     if return_points:
         return H_values, phase_space_points

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/hamiltonian_systems/chaotic_indicators.py

@@ -591,7 +591,7 @@ def recurrence_time_entropy(
     # Prepare output
     result = [rte]
     if config.return_final_state:
-        result.append(points[-1])
+        result.append(points[-1, 1:])
     if config.return_recmat:
         result.append(recmat)
     if config.return_p:

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys/hamiltonian_systems/trajectory_analysis.py

@@ -270,11 +270,11 @@ def ensemble_poincare_section(
 
     Returns
     -------
-    section_points : NDArray[np.float64], shape (num_ic, num_intersections, 2*dof)
-        Poincaré section points for each initial condition.
+    section_points : NDArray[np.float64], shape (num_ic, num_intersections, 2*dof + 1)
+        Poincaré section points for each initial condition with the first column being the time at each crossing.
     """
     num_ic, dof = q.shape
-    section_points = np.zeros((num_ic, num_intersections, 2 * dof))
+    section_points = np.zeros((num_ic, num_intersections, 2 * dof + 1))
     for i in prange(num_ic):
         section_points[i] = generate_poincare_section(
             q[i],

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.4.0
+Version: 1.4.5
 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
@@ -677,7 +677,6 @@ License:                     GNU GENERAL PUBLIC LICENSE
         the library.  If this is what you want to do, use the GNU Lesser General
         Public License instead of this License.  But first, please read
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Operating System :: OS Independent

{pynamicalsys-1.4.0 → pynamicalsys-1.4.5}/src/pynamicalsys.egg-info/SOURCES.txt

@@ -42,35 +42,4 @@ src/pynamicalsys/hamiltonian_systems/chaotic_indicators.py
 src/pynamicalsys/hamiltonian_systems/models.py
 src/pynamicalsys/hamiltonian_systems/numerical_integrators.py
 src/pynamicalsys/hamiltonian_systems/trajectory_analysis.py
-src/pynamicalsys/hamiltonian_systems/validators.py
-tests/continuous_time/test_RTE.ipynb
-tests/continuous_time/test_SALI_and_LDI.ipynb
-tests/continuous_time/test_basin_of_attraction.ipynb
-tests/continuous_time/test_hurst_exponent.ipynb
-tests/continuous_time/test_lyapunov.ipynb
-tests/continuous_time/test_poincare_section.ipynb
-tests/continuous_time/test_trajectory.ipynb
-tests/discrete-time/test_FTLE.ipynb
-tests/discrete-time/test_RTE.ipynb
-tests/discrete-time/test_SALI.ipynb
-tests/discrete-time/test_SALI.py
-tests/discrete-time/test_bif_diagram.ipynb
-tests/discrete-time/test_chaotic_saddle.ipynb
-tests/discrete-time/test_dig.ipynb
-tests/discrete-time/test_ensemble_statistics.ipynb
-tests/discrete-time/test_escape.ipynb
-tests/discrete-time/test_fractal_dimension.ipynb
-tests/discrete-time/test_hurst_exponent.ipynb
-tests/discrete-time/test_lyapunov.ipynb
-tests/discrete-time/test_lyapunov_exponents.ipynb
-tests/discrete-time/test_manifold.ipynb
-tests/discrete-time/test_manifolds.ipynb
-tests/discrete-time/test_period_counter.ipynb
-tests/discrete-time/test_phase_space.ipynb
-tests/discrete-time/test_step.py
-tests/hamiltonian_systems/test_RTE.ipynb
-tests/hamiltonian_systems/test_alignment_indices.ipynb
-tests/hamiltonian_systems/test_hurst_exponent.ipynb
-tests/hamiltonian_systems/test_lyapunov.ipynb
-tests/hamiltonian_systems/test_poincare_section.ipynb
-tests/hamiltonian_systems/test_trajectory.ipynb
+src/pynamicalsys/hamiltonian_systems/validators.py