pynamicalsys 1.3.0__tar.gz → 1.3.1__tar.gz

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/CHANGELOG.md

@@ -5,7 +5,13 @@ 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).
 
-## [v1.3.0] 2025-08-23
+## [v1.3.1] - 2025-08-24
+
+### Modified
+
+- Removed `cache=True` from the low level methods that was leading to cache compilation errors.
+
+## [v1.3.0] - 2025-08-23
 
 ### Added
 

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.3.0
+Version: 1.3.1
 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

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/__version__.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.3.0'
-__version_tuple__ = version_tuple = (1, 3, 0)
+__version__ = version = '1.3.1'
+__version_tuple__ = version_tuple = (1, 3, 1)
 
-__commit_id__ = commit_id = 'g138b5d22a'
+__commit_id__ = commit_id = 'g3102ffa8b'

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/common/recurrence_quantification_analysis.py

@@ -91,7 +91,7 @@ class RTEConfig:
             raise ValueError("metric must be 'supremum', 'euclidean' or 'manhattan'")
 
 
-@njit(cache=True)
+@njit
 def _recurrence_matrix(
     arr: NDArray[np.float64], threshold: float, metric_id: int
 ) -> NDArray[np.uint8]:

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/common/utils.py

@@ -21,7 +21,7 @@ from numpy.typing import NDArray
 from numba import njit
 
 
-@njit(cache=True)
+@njit
 def qr(M: NDArray[np.float64]) -> Tuple[NDArray[np.float64], NDArray[np.float64]]:
     """
     Perform numerically stable QR decomposition using modified Gram-Schmidt with reorthogonalization.
@@ -92,7 +92,7 @@ def qr(M: NDArray[np.float64]) -> Tuple[NDArray[np.float64], NDArray[np.float64]
     return Q, R
 
 
-@njit(cache=True)
+@njit
 def householder_qr(
     M: NDArray[np.float64],
 ) -> Tuple[NDArray[np.float64], NDArray[np.float64]]:
@@ -184,7 +184,7 @@ def householder_qr(
     return Q, R
 
 
-@njit(cache=True)
+@njit
 def finite_difference_jacobian(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/continuous_time/chaotic_indicators.py

@@ -25,7 +25,7 @@ from pynamicalsys.continuous_time.trajectory_analysis import step, evolve_system
 from pynamicalsys.continuous_time.numerical_integrators import rk4_step_wrapped
 
 
-# @njit(cache=True)
+# @njit
 def lyapunov_exponents(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -136,7 +136,7 @@ def lyapunov_exponents(
         return [result]
 
 
-@njit(cache=True)
+@njit
 def SALI(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -238,7 +238,7 @@ def SALI(
         return [[time, sali]]
 
 
-# @njit(cache=True)
+# @njit
 def LDI(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/continuous_time/numerical_integrators.py

@@ -23,7 +23,7 @@ from numba import njit, prange
 from pynamicalsys.continuous_time.models import variational_equations
 
 
-@njit(cache=True)
+@njit
 def rk4_step(
     t: float,
     u: NDArray[np.float64],
@@ -43,7 +43,7 @@ def rk4_step(
     return u_next
 
 
-@njit(cache=True)
+@njit
 def variational_rk4_step(
     t: float,
     u: NDArray[np.float64],
@@ -115,7 +115,7 @@ RK45_B4 = np.array(
 )
 
 
-@njit(cache=True)
+@njit
 def rk45_step(t, u, parameters, equations_of_motion, time_step, atol=1e-6, rtol=1e-3):
     """Single adaptive step of RK45 (Dormand-Prince).
 
@@ -163,7 +163,7 @@ def rk45_step(t, u, parameters, equations_of_motion, time_step, atol=1e-6, rtol=
     return u5, t + time_step, time_step_new, accept
 
 
-@njit(cache=True)
+@njit
 def variational_rk45_step(
     t,
     u,
@@ -227,7 +227,7 @@ def variational_rk45_step(
     return u5, t + time_step, time_step_new, accept
 
 
-@njit(cache=True)
+@njit
 def rk4_step_wrapped(
     t: float,
     u: NDArray[np.float64],
@@ -265,7 +265,7 @@ def rk4_step_wrapped(
     return u_next, t_next, h_next, accept
 
 
-@njit(cache=True)
+@njit
 def rk45_step_wrapped(
     t: float,
     u: NDArray[np.float64],
@@ -302,7 +302,7 @@ def rk45_step_wrapped(
         )
 
 
-@njit(cache=True)
+@njit
 def estimate_initial_step(
     t0: float,
     u0: np.ndarray,

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/continuous_time/trajectory_analysis.py

@@ -24,7 +24,7 @@ from numpy.typing import NDArray
 from pynamicalsys.continuous_time.numerical_integrators import rk4_step_wrapped
 
 
-@njit(cache=True)
+@njit
 def step(
     time: np.float64,
     u: NDArray[np.float64],
@@ -68,7 +68,7 @@ def step(
     return u_new, time_new, time_step_new
 
 
-@njit(cache=True)
+@njit
 def evolve_system(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -102,7 +102,7 @@ def evolve_system(
     return u
 
 
-@njit(cache=True)
+@njit
 def generate_trajectory(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/discrete_time/dynamical_indicators.py

@@ -32,7 +32,7 @@ from pynamicalsys.discrete_time.trajectory_analysis import (
 from pynamicalsys.common.utils import qr, householder_qr, fit_poly, wedge_norm
 
 
-@njit(cache=True)
+@njit
 def lyapunov_1D(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -120,7 +120,7 @@ def lyapunov_1D(
     return history if return_history else np.array([exponent / sample_size])
 
 
-@njit(cache=True)
+@njit
 def lyapunov_er(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -246,7 +246,7 @@ def lyapunov_er(
         return aux_exponents, u_contig
 
 
-@njit(cache=True)
+@njit
 def maximum_lyapunov_er(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -367,7 +367,7 @@ def maximum_lyapunov_er(
         return np.array([exponent / sample_size]), u_contig
 
 
-@njit(cache=True)
+@njit
 def lyapunov_qr(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -701,7 +701,7 @@ def dig(
     return -np.log10(abs(WB0 - WB1))
 
 
-@njit(cache=True)
+@njit
 def SALI(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -761,7 +761,7 @@ def SALI(
     - Uses QR decomposition to initialize orthonormal deviation vectors.
     - Computes both Parallel (PAI) and Antiparallel (AAI) Alignment Indices.
     - Early termination occurs if SALI < `tol` (indicating chaotic behavior).
-    - Optimized with `@njit(cache=True)` for performance.
+    - Optimized with `@njit` for performance.
     """
 
     np.random.seed(seed)  # For reproducibility
@@ -1047,7 +1047,7 @@ def GALI_k(
         return np.array([gali])
 
 
-@njit(cache=True)
+@njit
 def hurst_exponent(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -1224,13 +1224,13 @@ def finite_time_hurst_exponent(
         return H_values
 
 
-@njit(cache=True)
+@njit
 def lyapunov_vectors():
     # ! To be implemented...
     pass
 
 
-@njit(cache=True)
+@njit
 def lagrangian_descriptors(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/discrete_time/models.py

@@ -408,7 +408,7 @@ def logistic_map_jacobian(
 # ! ------------------ !
 
 
-@njit(cache=True)
+@njit
 def rulkov_map(
     u: NDArray[np.float64], parameters: Union[NDArray[np.float64], Sequence[float]]
 ) -> NDArray[np.float64]:
@@ -419,7 +419,7 @@ def rulkov_map(
     return np.array([x_new, y_new])
 
 
-@njit(cache=True)
+@njit
 def rulkov_map_jacobian(
     u: NDArray[np.float64],
     parameters: Union[NDArray[np.float64], Sequence[float]],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/discrete_time/trajectory_analysis.py

@@ -22,7 +22,7 @@ from numba import njit, prange
 from numpy.typing import NDArray
 
 
-@njit(cache=True)
+@njit
 def iterate_mapping(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -78,7 +78,7 @@ def iterate_mapping(
     return u
 
 
-@njit(cache=True)
+@njit
 def generate_trajectory(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -331,7 +331,7 @@ def bifurcation_diagram(
         return param_values, results
 
 
-@njit(cache=True)
+@njit
 def period_counter(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -415,7 +415,7 @@ def period_counter(
     return -1
 
 
-@njit(cache=True)
+@njit
 def rotation_number(
     u: Union[NDArray[np.float64], Sequence[float], float],
     parameters: Union[NDArray[np.float64], Sequence[float], float],
@@ -438,7 +438,7 @@ def rotation_number(
     return rn
 
 
-@njit(cache=True)
+@njit
 def escape_basin_and_time_entering(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -515,7 +515,7 @@ def escape_basin_and_time_entering(
     return -1, max_time
 
 
-@njit(cache=True)
+@njit
 def escape_time_exiting(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -584,7 +584,7 @@ def escape_time_exiting(
     return -1, max_time  # No escape
 
 
-@njit(cache=True)
+@njit
 def survival_probability(
     escape_times: NDArray[np.int32],
     max_time: np.int32,
@@ -659,7 +659,7 @@ def survival_probability(
     return t_values, survival_probs
 
 
-@njit(cache=True)
+@njit
 def is_periodic(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -811,7 +811,7 @@ def scan_phase_space(
     return result
 
 
-@njit(cache=True)
+@njit
 def scan_symmetry_line(
     points: NDArray[np.float64],
     parameters: NDArray[np.float64],
@@ -1095,7 +1095,7 @@ def find_periodic_orbit(
     return periodic_orbit
 
 
-@njit(cache=True)
+@njit
 def eigenvalues_and_eigenvectors(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys/discrete_time/transport.py

@@ -390,7 +390,7 @@ def mean_squared_displacement(
     return output
 
 
-@njit(cache=True)
+@njit
 def recurrence_times(
     u: NDArray[np.float64],
     parameters: NDArray[np.float64],

{pynamicalsys-1.3.0 → pynamicalsys-1.3.1}/src/pynamicalsys.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.3.0
+Version: 1.3.1
 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