passagemath-modules 10.5.46__cp310-cp310-macosx_14_0_arm64.whl → 10.6.20__cp310-cp310-macosx_14_0_arm64.whl

sage/stats/hmm/chmm.pyx

@@ -8,22 +8,22 @@ AUTHOR:
 - William Stein, 2010-03
 """
 
-#*****************************************************************************
+# ***************************************************************************
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 2 of the License, or
 # (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#*****************************************************************************
+#                  https://www.gnu.org/licenses/
+# ***************************************************************************
 
 from cpython.object cimport PyObject_RichCompare
 from libc.math cimport log, sqrt, exp, isnormal, isfinite, M_PI
 cdef double sqrt2pi = sqrt(2*M_PI)
 from cysignals.signals cimport sig_on, sig_off
 
-from sage.misc.flatten  import flatten
+from sage.misc.flatten import flatten
 from sage.structure.element import Matrix
 
 from sage.stats.time_series cimport TimeSeries
@@ -331,10 +331,10 @@ cdef class GaussianHiddenMarkovModel(HiddenMarkovModel):
             sage: hmm.GaussianHiddenMarkovModel([[.1,.9],[.5,.5]], [(1,.5), (-1,3)], [.1,.9]).__repr__()
             'Gaussian Hidden Markov Model with 2 States\nTransition matrix:\n[0.1 0.9]\n[0.5 0.5]\nEmission parameters:\n[(1.0, 0.5), (-1.0, 3.0)]\nInitial probabilities: [0.1000, 0.9000]'
         """
-        s = "Gaussian Hidden Markov Model with %s States"%self.N
-        s += '\nTransition matrix:\n%s'%self.transition_matrix()
-        s += '\nEmission parameters:\n%s'%self.emission_parameters()
-        s += '\nInitial probabilities: %s'%self.initial_probabilities()
+        s = "Gaussian Hidden Markov Model with %s States" % self.N
+        s += '\nTransition matrix:\n%s' % self.transition_matrix()
+        s += '\nEmission parameters:\n%s' % self.emission_parameters()
+        s += '\nInitial probabilities: %s' % self.initial_probabilities()
         return s
 
     def generate_sequence(self, Py_ssize_t length, starting_state=None):
@@ -422,7 +422,7 @@ cdef class GaussianHiddenMarkovModel(HiddenMarkovModel):
         else:
             q = starting_state
             if q < 0 or q>= self.N:
-                raise ValueError("starting state must be between 0 and %s"%(self.N-1))
+                raise ValueError("starting state must be between 0 and %s" % (self.N-1))
 
         states._values[0] = q
         obs._values[0] = self.random_sample(q, rstate)
@@ -1144,10 +1144,10 @@ cdef class GaussianMixtureHiddenMarkovModel(GaussianHiddenMarkovModel):
             sage: hmm.GaussianMixtureHiddenMarkovModel([[.9,.1],[.4,.6]], [[(.4,(0,1)), (.6,(1,0.1))],[(1,(0,1))]], [.7,.3]).__repr__()
             'Gaussian Mixture Hidden Markov Model with 2 States\nTransition matrix:\n[0.9 0.1]\n[0.4 0.6]\nEmission parameters:\n[0.4*N(0.0,1.0) + 0.6*N(1.0,0.1), 1.0*N(0.0,1.0)]\nInitial probabilities: [0.7000, 0.3000]'
         """
-        s = "Gaussian Mixture Hidden Markov Model with %s States"%self.N
-        s += '\nTransition matrix:\n%s'%self.transition_matrix()
-        s += '\nEmission parameters:\n%s'%self.emission_parameters()
-        s += '\nInitial probabilities: %s'%self.initial_probabilities()
+        s = "Gaussian Mixture Hidden Markov Model with %s States" % self.N
+        s += '\nTransition matrix:\n%s' % self.transition_matrix()
+        s += '\nEmission parameters:\n%s' % self.emission_parameters()
+        s += '\nInitial probabilities: %s' % self.initial_probabilities()
         return s
 
     def __reduce__(self):

sage/stats/hmm/distributions.pxd

@@ -1,10 +1,10 @@
 # sage_setup: distribution = sagemath-modules
-#############################################################################
+# ##########################################################################
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  The full text of the GPL is available at:
-#                  http://www.gnu.org/licenses/
-#############################################################################
+#                  https://www.gnu.org/licenses/
+# ##########################################################################
 
 from sage.stats.time_series cimport TimeSeries
 from sage.stats.intlist cimport IntList

sage/stats/hmm/distributions.pyx

@@ -13,12 +13,12 @@ AUTHOR:
 - William Stein, 2010-03
 """
 
-#############################################################################
+# ##########################################################################
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  The full text of the GPL is available at:
-#                  http://www.gnu.org/licenses/
-#############################################################################
+#                  https://www.gnu.org/licenses/
+# ##########################################################################
 
 from cpython.object cimport PyObject_RichCompare
 

sage/stats/hmm/hmm.pxd

@@ -1,10 +1,10 @@
 # sage_setup: distribution = sagemath-modules
-#############################################################################
+# ##########################################################################
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #  Distributed under the terms of the GNU General Public License (GPL) v2+.
 #  The full text of the GPL is available at:
-#                  http://www.gnu.org/licenses/
-#############################################################################
+#                  https://www.gnu.org/licenses/
+# ##########################################################################
 
 
 from sage.stats.time_series cimport TimeSeries

sage/stats/hmm/hmm.pyx

@@ -444,13 +444,13 @@ cdef class DiscreteHiddenMarkovModel(HiddenMarkovModel):
             sage: m.__repr__()
             'Discrete Hidden Markov Model with 2 States and 2 Emissions\nTransition matrix:\n[0.4 0.6]\n[0.1 0.9]\nEmission matrix:\n[0.1 0.9]\n[0.5 0.5]\nInitial probabilities: [0.2000, 0.8000]'
         """
-        s = "Discrete Hidden Markov Model with %s States and %s Emissions"%(
+        s = "Discrete Hidden Markov Model with %s States and %s Emissions" % (
             self.N, self.n_out)
-        s += '\nTransition matrix:\n%s'%self.transition_matrix()
-        s += '\nEmission matrix:\n%s'%self.emission_matrix()
-        s += '\nInitial probabilities: %s'%self.initial_probabilities()
+        s += '\nTransition matrix:\n%s' % self.transition_matrix()
+        s += '\nEmission matrix:\n%s' % self.emission_matrix()
+        s += '\nInitial probabilities: %s' % self.initial_probabilities()
         if self._emission_symbols is not None:
-            s += '\nEmission symbols: %s'%self._emission_symbols
+            s += '\nEmission symbols: %s' % self._emission_symbols
         return s
 
     def _emission_symbols_to_IntList(self, obs):
@@ -774,7 +774,7 @@ cdef class DiscreteHiddenMarkovModel(HiddenMarkovModel):
         else:
             q = starting_state
             if q < 0 or q >= self.N:
-                raise ValueError("starting state must be between 0 and %s"%(self.N-1))
+                raise ValueError("starting state must be between 0 and %s" % (self.N-1))
 
         states._values[0] = q
         # Generate a symbol from state q

sage/stats/hmm/util.pyx

@@ -5,19 +5,20 @@ Hidden Markov Models -- Utility functions
 
 AUTHOR:
 
-   - William Stein, 2010-03
+- William Stein, 2010-03
 """
 
-#############################################################################
+# ##########################################################################
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #  Distributed under the terms of the GNU General Public License (GPL) v2+.
 #  The full text of the GPL is available at:
-#                  http://www.gnu.org/licenses/
-#############################################################################
+#                  https://www.gnu.org/licenses/
+# ##########################################################################
 
 
 from sage.structure.element import Matrix
-from sage.misc.flatten  import flatten
+from sage.misc.flatten import flatten
+
 
 cdef class HMM_Util:
     """
@@ -124,7 +125,6 @@ cdef class HMM_Util:
         This function is used internally by the ``__init__`` methods of
         Hidden Markov Models to make a transition matrix from ``A``.
 
-
         INPUT:
 
         - ``A`` -- matrix, list, list of lists, or :class:`TimeSeries`

sage/stats/intlist.pxd

@@ -1,10 +1,10 @@
 # sage_setup: distribution = sagemath-modules
-#############################################################################
+# ##########################################################################
 #       Copyright (C) 2010 William Stein <wstein@gmail.com>
 #  Distributed under the terms of the GNU General Public License (GPL) v2+.
 #  The full text of the GPL is available at:
-#                  http://www.gnu.org/licenses/
-#############################################################################
+#                  https://www.gnu.org/licenses/
+# ##########################################################################
 
 cdef class IntList:
     cdef int* _values

sage/tensor/modules/alternating_contr_tensor.py

@@ -28,14 +28,14 @@ REFERENCES:
 - Chap. 23 of R. Godement : *Algebra* [God1968]_
 - Chap. 15 of S. Lang : *Algebra* [Lan2002]_
 """
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2017 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 from sage.tensor.modules.free_module_tensor import FreeModuleTensor
 from sage.tensor.modules.comp import Components, CompFullyAntiSym

sage/tensor/modules/comp.py

@@ -233,7 +233,7 @@ In case of symmetries, only non-redundant components are stored::
     {(0, 1): 3}
 """
 
-# *****************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2015 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #       Copyright (C) 2015 Michal Bejger <bejger@camk.edu.pl>
 #       Copyright (C) 2015 Marco Mancini <marco.mancini@obspm.fr>
@@ -241,8 +241,8 @@ In case of symmetries, only non-redundant components are stored::
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 from sage.structure.sage_object import SageObject
 from sage.rings.integer import Integer

sage/tensor/modules/ext_pow_free_module.py

@@ -46,14 +46,14 @@ REFERENCES:
 - \K. Conrad: *Exterior powers* [Con2013]_
 - Chap. 19 of S. Lang: *Algebra* [Lan2002]_
 """
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2017 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 from sage.misc.cachefunc import cached_method
 from sage.rings.integer import Integer

sage/tensor/modules/format_utilities.py

@@ -11,15 +11,15 @@ AUTHORS:
 - Michael Jung (2020): extended usage of :func:`is_atomic()`
 """
 
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2015 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #       Copyright (C) 2015 Michal Bejger <bejger@camk.edu.pl>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

sage/tensor/modules/free_module_linear_group.py

@@ -20,14 +20,14 @@ REFERENCES:
 
 - Chap. 15 of R. Godement : *Algebra* [God1968]_
 """
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2015 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 from sage.misc.cachefunc import cached_method
 from sage.structure.unique_representation import UniqueRepresentation

sage/tensor/modules/free_module_morphism.py

@@ -1359,7 +1359,6 @@ class FiniteRankFreeModuleEndomorphism(FiniteRankFreeModuleMorphism):
             sage: latex(phi)
             \mathrm{Id}
         """
-        from sage.matrix.special import identity_matrix
         from sage.misc.constant_function import ConstantFunction
 
         fmodule = parent.domain()

sage/tensor/modules/tensor_free_module.py

@@ -48,15 +48,15 @@ REFERENCES:
 - Chap. 21 (Exer. 4) of R. Godement: *Algebra* [God1968]_
 - Chap. 16 of S. Lang: *Algebra* [Lan2002]_
 """
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2015 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #       Copyright (C) 2015 Michal Bejger <bejger@camk.edu.pl>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 from sage.categories.modules import Modules
 from sage.misc.cachefunc import cached_method

sage/tensor/modules/tensor_free_submodule.py

@@ -13,7 +13,7 @@ AUTHORS:
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
+#                  https://www.gnu.org/licenses/
 # ******************************************************************************
 
 import itertools

sage/tensor/modules/tensor_free_submodule_basis.py

@@ -13,7 +13,7 @@ AUTHORS:
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
+#                  https://www.gnu.org/licenses/
 # ******************************************************************************
 
 from sage.tensor.modules.free_module_basis import Basis_abstract

sage/tensor/modules/tensor_with_indices.py

@@ -8,19 +8,19 @@ AUTHORS:
 - Eric Gourgoulhon, Michal Bejger (2014-2015): initial version
 - Léo Brunswic (2019): add multiple symmetries and multiple contractions
 """
-#******************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2015 Eric Gourgoulhon <eric.gourgoulhon@obspm.fr>
 #       Copyright (C) 2015 Michal Bejger <bejger@camk.edu.pl>
 #
 #  Distributed under the terms of the GNU General Public License (GPL)
 #  as published by the Free Software Foundation; either version 2 of
 #  the License, or (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#******************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
+from itertools import combinations
+import re
 
 from sage.structure.sage_object import SageObject
-import re
-from itertools import combinations
 
 # Regular expression for the allowed characters in index notation.
 # This includes Unicode word constituents but excludes digits and underscores.