From 1383860a21a274ab65ce3674d09059d68adce603 Mon Sep 17 00:00:00 2001 From: Matt Graham Date: Thu, 20 Aug 2020 17:38:17 +0100 Subject: [PATCH] Bumping version and regenerating HTML docs --- docs/docs/adapters.html | 56 +++--- docs/docs/autodiff.html | 4 +- docs/docs/autograd_wrapper.html | 12 +- docs/docs/errors.html | 18 +- docs/docs/index.html | 2 +- docs/docs/integrators.html | 12 +- docs/docs/matrices.html | 328 +++++++++++++------------------- docs/docs/progressbars.html | 88 ++++----- docs/docs/samplers.html | 326 +++++++++++++++++++++++++++---- docs/docs/solvers.html | 14 +- docs/docs/stagers.html | 14 +- docs/docs/states.html | 50 ++--- docs/docs/systems.html | 128 ++++++------- docs/docs/transitions.html | 48 ++--- docs/docs/utils.html | 16 +- docs/index.html | 63 ++++++ setup.py | 2 +- 17 files changed, 725 insertions(+), 456 deletions(-) diff --git a/docs/docs/adapters.html b/docs/docs/adapters.html index 2107d49..a7ef924 100644 --- a/docs/docs/adapters.html +++ b/docs/docs/adapters.html @@ -102,7 +102,7 @@

Module mici.adapters

Expand source code -Browse git +Browse git 
"""Methods for adaptively setting algorithmic parameters of transitions."""
 
@@ -276,7 +276,7 @@ 
Module mici.adapters

         }
         init_step_size = (
             self._find_and_set_init_step_size(chain_state, system, integrator)
-            if integrator.step_size is None else integrator.step_size)
+        )
         if self.log_step_size_reg_target is None:
             adapt_state['log_step_size_reg_target'] = log(10 * init_step_size)
         else:
@@ -317,14 +317,17 @@ 
Module mici.adapters

         """
         init_state = state.copy()
         h_init = system.h(init_state)
+        if np.isnan(h_init):
+            raise AdaptationError('Hamiltonian evaluating to NaN at initial state.')
         integrator.step_size = 1
         delta_h_threshold = log(2)
         for s in range(self.max_init_step_size_iters):
             try:
                 state = integrator.step(init_state)
                 delta_h = abs(h_init - system.h(state))
-                if s == 0:
-                    step_size_too_big = delta_h > delta_h_threshold
+                if s == 0 or np.isnan(delta_h):
+                    step_size_too_big = (
+                        np.isnan(delta_h) or delta_h > delta_h_threshold)
                 if (step_size_too_big and delta_h <= delta_h_threshold) or (
                         not step_size_too_big and delta_h > delta_h_threshold):
                     return integrator.step_size
@@ -606,7 +609,7 @@ 
Classes

 

 
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+Browse git
 
 
class Adapter(ABC):
     """Abstract adapter for implementing schemes to adapt transition parameters.
@@ -706,7 +709,7 @@ 
Instance variables

 

 
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@property
 @abstractmethod
@@ -747,7 +750,7 @@ 
Returns

 

 
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@abstractmethod
 def initialize(self, chain_state, transition):
@@ -793,7 +796,7 @@ 
Args

 

 
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@abstractmethod
 def update(self, adapt_state, chain_state, trans_stats, transition):
@@ -839,7 +842,7 @@ 
Args

 

 
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@abstractmethod
 def finalize(self, adapt_state, transition):
@@ -932,7 +935,7 @@ 
Args

 

 
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class DualAveragingStepSizeAdapter(Adapter):
     """Dual averaging integrator step size adapter.
@@ -1019,7 +1022,7 @@ 
Args

         }
         init_step_size = (
             self._find_and_set_init_step_size(chain_state, system, integrator)
-            if integrator.step_size is None else integrator.step_size)
+        )
         if self.log_step_size_reg_target is None:
             adapt_state['log_step_size_reg_target'] = log(10 * init_step_size)
         else:
@@ -1060,14 +1063,17 @@ 
Args

         """
         init_state = state.copy()
         h_init = system.h(init_state)
+        if np.isnan(h_init):
+            raise AdaptationError('Hamiltonian evaluating to NaN at initial state.')
         integrator.step_size = 1
         delta_h_threshold = log(2)
         for s in range(self.max_init_step_size_iters):
             try:
                 state = integrator.step(init_state)
                 delta_h = abs(h_init - system.h(state))
-                if s == 0:
-                    step_size_too_big = delta_h > delta_h_threshold
+                if s == 0 or np.isnan(delta_h):
+                    step_size_too_big = (
+                        np.isnan(delta_h) or delta_h > delta_h_threshold)
                 if (step_size_too_big and delta_h <= delta_h_threshold) or (
                         not step_size_too_big and delta_h > delta_h_threshold):
                     return integrator.step_size
@@ -1152,7 +1158,7 @@ 
Returns

 

 
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+Browse git
 
 
def initialize(self, chain_state, transition):
     integrator = transition.integrator
@@ -1164,7 +1170,7 @@ 
Returns

     }
     init_step_size = (
         self._find_and_set_init_step_size(chain_state, system, integrator)
-        if integrator.step_size is None else integrator.step_size)
+    )
     if self.log_step_size_reg_target is None:
         adapt_state['log_step_size_reg_target'] = log(10 * init_step_size)
     else:
@@ -1200,7 +1206,7 @@ 
Args

 

 
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def update(self, adapt_state, chain_state, trans_stats, transition):
     adapt_state['iter'] += 1
@@ -1242,7 +1248,7 @@ 
Args

 

 
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def finalize(self, adapt_state, transition):
     if isinstance(adapt_state, dict):
@@ -1301,7 +1307,7 @@ 
Args

 

 
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class OnlineVarianceMetricAdapter(Adapter):
     """Diagonal metric adapter using online variance estimates.
@@ -1448,7 +1454,7 @@ 
Returns

 

 
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def initialize(self, chain_state, transition):
     return {
@@ -1485,7 +1491,7 @@ 
Args

 

 
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def update(self, adapt_state, chain_state, trans_stats, transition):
     # Use Welford (1962) incremental algorithm to update statistics to
@@ -1523,7 +1529,7 @@ 
Args

 

 
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def finalize(self, adapt_state, transition):
     if isinstance(adapt_state, dict):
@@ -1605,7 +1611,7 @@ 
Args

 

 
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class OnlineCovarianceMetricAdapter(Adapter):
     """Dense metric adapter using online covariance estimates.
@@ -1755,7 +1761,7 @@ 
Returns

 

 
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def initialize(self, chain_state, transition):
     dim_pos = chain_state.pos.shape[0]
@@ -1794,7 +1800,7 @@ 
Args

 

 
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def update(self, adapt_state, chain_state, trans_stats, transition):
     # Use Welford (1962) incremental algorithm to update statistics to
@@ -1832,7 +1838,7 @@ 
Args

 

 
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def finalize(self, adapt_state, transition):
     if isinstance(adapt_state, dict):
diff --git a/docs/docs/autodiff.html b/docs/docs/autodiff.html
index 37b4e1d..4be6cab 100644
--- a/docs/docs/autodiff.html
+++ b/docs/docs/autodiff.html
@@ -47,7 +47,7 @@ 
Module mici.autodiff

 

 
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"""Automatic differentation fallback for constructing derivative functions."""
 
@@ -148,7 +148,7 @@ 
Returns

 

 
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def autodiff_fallback(diff_func, func, diff_op_name, name):
     """Generate derivative function automatically if not provided.
diff --git a/docs/docs/autograd_wrapper.html b/docs/docs/autograd_wrapper.html
index a186f16..a4b98d8 100644
--- a/docs/docs/autograd_wrapper.html
+++ b/docs/docs/autograd_wrapper.html
@@ -51,7 +51,7 @@ 
Module mici.autograd_wrapper

 

 
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"""Additional autograd differential operators."""
 
@@ -195,7 +195,7 @@ 
Functions

 

 
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@_wrapped_unary_to_nary
 def grad_and_value(fun, x):
@@ -220,7 +220,7 @@ 
Functions

 

 
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@_wrapped_unary_to_nary
 def jacobian_and_value(fun, x):
@@ -262,7 +262,7 @@ 
Functions

 

 
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@_wrapped_unary_to_nary
 def mhp_jacobian_and_value(fun, x):
@@ -300,7 +300,7 @@ 
Functions

 

 
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@_wrapped_unary_to_nary
 def hessian_grad_and_value(fun, x):
@@ -342,7 +342,7 @@ 
Functions

 

 
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@_wrapped_unary_to_nary
 def mtp_hessian_grad_and_value(fun, x):
diff --git a/docs/docs/errors.html b/docs/docs/errors.html
index 37d2c21..1782a6e 100644
--- a/docs/docs/errors.html
+++ b/docs/docs/errors.html
@@ -70,7 +70,7 @@ 
Module mici.errors

 

 
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+Browse git
 
 
"""Exception types."""
 
@@ -125,7 +125,7 @@ 
Classes

 

 
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class Error(RuntimeError):
     """Base class for errors."""

@@ -153,7 +153,7 @@ 
Subclasses

 

 
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class IntegratorError(Error):
     """Error raised when integrator step fails."""

@@ -181,7 +181,7 @@ 
Subclasses

 

 
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class NonReversibleStepError(IntegratorError):
     """Error raised when integrator step fails reversibility check."""

@@ -204,7 +204,7 @@ 
Ancestors

 

 
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class ConvergenceError(IntegratorError):
     """Error raised when solver fails to converge within allowed iterations."""

@@ -227,7 +227,7 @@ 
Ancestors

 

 
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class LinAlgError(Error):
     """Error raised when a matrix operation raises a linear algebra error."""

@@ -249,7 +249,7 @@ 
Ancestors

 

 
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class HamiltonianDivergenceError(IntegratorError):
     """Error raised when integration of Hamiltonian dynamics diverges."""

@@ -272,7 +272,7 @@ 
Ancestors

 

 
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class AdaptationError(Error):
     """Error raised when adaptation of transition parameters fails."""

@@ -294,7 +294,7 @@ 
Ancestors

 

 
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class ReadOnlyStateError(Error):
     """Error raised when writing to attributes of read-only chain state."""

diff --git a/docs/docs/index.html b/docs/docs/index.html
index 5045714..ceec3d1 100644
--- a/docs/docs/index.html
+++ b/docs/docs/index.html
@@ -55,7 +55,7 @@ 
Package mici

 

 
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+Browse git
 
 
# -*- coding: utf-8 -*-
 """ MCMC samplers based on simulating Hamiltonian dynamics on a manifold. """
diff --git a/docs/docs/integrators.html b/docs/docs/integrators.html
index 68e7df4..db41e60 100644
--- a/docs/docs/integrators.html
+++ b/docs/docs/integrators.html
@@ -70,7 +70,7 @@ 
Module mici.integrators

 

 
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"""Symplectic integrators for simulation of Hamiltonian dynamics."""
 
@@ -457,7 +457,7 @@ 
Args

 

 
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class Integrator(ABC):
     """Base class for integrators."""
@@ -536,7 +536,7 @@ 
Returns

 

 
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def step(self, state):
     """Perform a single integrator step from a supplied state.
@@ -588,7 +588,7 @@ 
Args

 

 
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class LeapfrogIntegrator(Integrator):
     r"""
@@ -704,7 +704,7 @@ 
Args

 

 
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class ImplicitLeapfrogIntegrator(Integrator):
     r"""
@@ -947,7 +947,7 @@ 
Args

 

 
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class ConstrainedLeapfrogIntegrator(Integrator):
     r"""
diff --git a/docs/docs/matrices.html b/docs/docs/matrices.html
index 6873140..0de8ec9 100644
--- a/docs/docs/matrices.html
+++ b/docs/docs/matrices.html
@@ -674,6 +674,8 @@
 
  • array
    • 
 
  • transpose
    • 
 
  • T
    • 
+
  • eigval
    • 
+
  • eigvec
    • 
 
 
    
 
@@ -821,7 +823,7 @@ 
    Module mici.matrices
    
 
    
 
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+Browse git
 
 
    """Structured matrix classes implementing basic linear algebra operations."""
 
@@ -862,12 +864,6 @@ 
    Module mici.matrices
    
 
     __array_priority__ = 1
 
-    """Set of attributes required for class to be considered a subclass"""
-    _required_subclass_attrs = {
-        'array', 'shape', 'T', 'diagonal', '__array__', '__mul__', '__rmul__',
-        '__truediv__', '__neg__', '__matmul__', '__rmatmul__'
-    }
-
     def __init__(self, shape, **kwargs):
         """
         Args:
@@ -1000,25 +996,6 @@ 
    Module mici.matrices
    
     def __repr__(self):
         return type(self).__name__ + str(self)
 
-    @classmethod
-    def _get_required_subclass_attrs(cls):
-        """Compute set of required subclass attributes."""
-        req = set()
-        for C in cls.__mro__:
-            if hasattr(C, '_required_subclass_attrs'):
-                req |= C._required_subclass_attrs
-        return req
-
-    @classmethod
-    def __subclasshook__(cls, C):
-        # Customize isinstance / issubclass behaviour to also return True for
-        # classes / objects with classes which have all required attributes
-        # without being direct subclasses
-        if hasattr(cls, '_get_required_subclass_attrs'):
-            if all(any(attr in B.__dict__ for B in C.__mro__)
-                   for attr in cls._get_required_subclass_attrs()):
-                return True
-        return NotImplemented
 
     @abc.abstractmethod
     def _compute_hash(self):
@@ -1162,8 +1139,6 @@ 
    Module mici.matrices
    
 class SquareMatrix(Matrix):
     """Base class for matrices with equal numbers of rows and columns."""
 
-    _required_subclass_attrs = {'log_abs_det'}
-
     def __init__(self, shape, **kwargs):
         if shape[0] != shape[1]:
             raise ValueError(
@@ -1206,7 +1181,6 @@ 
    Module mici.matrices
    
 class InvertibleMatrix(SquareMatrix):
     """Base class for non-singular square matrices."""
 
-    _required_subclass_attrs = {'inv'}
 
     def __init__(self, shape, **kwargs):
         super().__init__(shape, **kwargs)
@@ -1257,8 +1231,6 @@ 
    Module mici.matrices
    
 class SymmetricMatrix(SquareMatrix):
     """Base class for square matrices which are equal to their transpose."""
 
-    _required_subclass_attrs = {'eigval', 'eigvec'}
-
     def __init__(self, shape, **kwargs):
         self._eigval = None
         self._eigvec = None
@@ -1293,8 +1265,6 @@ 
    Module mici.matrices
    
 class PositiveDefiniteMatrix(SymmetricMatrix, InvertibleMatrix):
     """Base class for positive definite matrices."""
 
-    _required_subclass_attrs = {'sqrt'}
-
     def __init__(self, shape, **kwargs):
         self._sqrt = None
         super().__init__(shape, **kwargs)
@@ -1411,8 +1381,6 @@ 
    Module mici.matrices
    
     same shapes and with the same indices / keys.
     """
 
-    _required_subclass_attrs = {'grad_log_abs_det', 'grad_quadratic_form_inv'}
-
     @property
     @abc.abstractmethod
     def grad_log_abs_det(self):
@@ -2503,7 +2471,7 @@ 
    Module mici.matrices
    
         return sum(block.log_abs_det for block in self._blocks)
 
 
-class SymmetricBlockDiagonalMatrix(SquareBlockDiagonalMatrix):
+class SymmetricBlockDiagonalMatrix(SquareBlockDiagonalMatrix, SymmetricMatrix):
     """Symmetric specialisation of `SquareBlockDiagonalMatrix`.
 
     All matrix blocks in diagonal are restricted to be symmetric, i.e.
@@ -2531,7 +2499,7 @@ 
    Module mici.matrices
    
 
 
 class PositiveDefiniteBlockDiagonalMatrix(
-        SymmetricBlockDiagonalMatrix, PositiveDefiniteMatrix,
+        SquareBlockDiagonalMatrix, PositiveDefiniteMatrix, 
         DifferentiableMatrix):
     """Positive definite specialisation of `SymmetricBlockDiagonalMatrix`.
 
@@ -2560,6 +2528,9 @@ 
    Module mici.matrices
    
         else:
             return super()._scalar_multiply(scalar)
 
+    def _construct_transpose(self):
+        return self
+
     def _construct_sqrt(self):
         return SquareBlockDiagonalMatrix(
             tuple(block.sqrt for block in self._blocks))
@@ -3087,7 +3058,7 @@ 
    Args
    
 
    
 
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+Browse git
 
 
    class Matrix(abc.ABC):
     """Base class for matrix-like objects.
@@ -3099,12 +3070,6 @@ 
    Args
    
 
     __array_priority__ = 1
 
-    """Set of attributes required for class to be considered a subclass"""
-    _required_subclass_attrs = {
-        'array', 'shape', 'T', 'diagonal', '__array__', '__mul__', '__rmul__',
-        '__truediv__', '__neg__', '__matmul__', '__rmatmul__'
-    }
-
     def __init__(self, shape, **kwargs):
         """
         Args:
@@ -3237,25 +3202,6 @@ 
    Args
    
     def __repr__(self):
         return type(self).__name__ + str(self)
 
-    @classmethod
-    def _get_required_subclass_attrs(cls):
-        """Compute set of required subclass attributes."""
-        req = set()
-        for C in cls.__mro__:
-            if hasattr(C, '_required_subclass_attrs'):
-                req |= C._required_subclass_attrs
-        return req
-
-    @classmethod
-    def __subclasshook__(cls, C):
-        # Customize isinstance / issubclass behaviour to also return True for
-        # classes / objects with classes which have all required attributes
-        # without being direct subclasses
-        if hasattr(cls, '_get_required_subclass_attrs'):
-            if all(any(attr in B.__dict__ for B in C.__mro__)
-                   for attr in cls._get_required_subclass_attrs()):
-                return True
-        return NotImplemented
 
     @abc.abstractmethod
     def _compute_hash(self):
@@ -3292,7 +3238,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def shape(self):
@@ -3306,7 +3252,7 @@ 
    Instance variables
    
 
    
 
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    @property
 @abc.abstractmethod
@@ -3320,7 +3266,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def transpose(self):
@@ -3336,7 +3282,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def transpose(self):
@@ -3352,7 +3298,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def diagonal(self):
@@ -3376,7 +3322,7 @@ 
    Args
    
 
    
 
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    class ExplicitArrayMatrix(Matrix):
     """Matrix with an explicit array representation."""
@@ -3426,7 +3372,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def array(self):
@@ -3465,7 +3411,7 @@ 
    Args
    
 
    
 
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    class ImplicitArrayMatrix(Matrix):
     """Matrix with an implicit array representation."""
@@ -3529,7 +3475,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def array(self):
@@ -3581,7 +3527,7 @@ 
    Args
    
 
    
 
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    class MatrixProduct(ImplicitArrayMatrix):
     """Matrix implicitly defined as a product of a sequence of matrices.
@@ -3661,7 +3607,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def matrices(self):
@@ -3707,13 +3653,11 @@ 
    Args
    
 
    
 
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    class SquareMatrix(Matrix):
     """Base class for matrices with equal numbers of rows and columns."""
 
-    _required_subclass_attrs = {'log_abs_det'}
-
     def __init__(self, shape, **kwargs):
         if shape[0] != shape[1]:
             raise ValueError(
@@ -3752,7 +3696,7 @@ 
    Instance variables
    
 
    
 
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    @property
 @abc.abstractmethod
@@ -3806,7 +3750,7 @@ 
    Args
    
 
    
 
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    class SquareMatrixProduct(MatrixProduct, SquareMatrix):
     """Matrix implicitly defined as a product of a sequence of square matrices.
@@ -3852,7 +3796,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def log_abs_det(self):
@@ -3898,12 +3842,11 @@ 
    Args
    
 
    
 
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    class InvertibleMatrix(SquareMatrix):
     """Base class for non-singular square matrices."""
 
-    _required_subclass_attrs = {'inv'}
 
     def __init__(self, shape, **kwargs):
         super().__init__(shape, **kwargs)
@@ -3968,7 +3911,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def inv(self):
@@ -4032,7 +3975,7 @@ 
    Args
    
 
    
 
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    class InvertibleMatrixProduct(SquareMatrixProduct, InvertibleMatrix):
     """Matrix defined as a product of a sequence of invertible matrices.
@@ -4117,13 +4060,11 @@ 
    Args
    
 
    
 
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    class SymmetricMatrix(SquareMatrix):
     """Base class for square matrices which are equal to their transpose."""
 
-    _required_subclass_attrs = {'eigval', 'eigvec'}
-
     def __init__(self, shape, **kwargs):
         self._eigval = None
         self._eigvec = None
@@ -4168,6 +4109,7 @@ 
    Subclasses
    
 
  • mici.matrices._BaseTriangularFactoredDefiniteMatrix
    • 
 
  • DenseSymmetricMatrix
    • 
 
  • EigendecomposedSymmetricMatrix
    • 
+
  • SymmetricBlockDiagonalMatrix
    • 
 
  • SymmetricLowRankUpdateMatrix
    • 
 
 
    Instance variables
    
@@ -4178,7 +4120,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def eigval(self):
@@ -4194,7 +4136,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def eigvec(self):
@@ -4213,7 +4155,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def log_abs_det(self):
@@ -4256,13 +4198,11 @@ 
    Args
    
 
    
 
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    class PositiveDefiniteMatrix(SymmetricMatrix, InvertibleMatrix):
     """Base class for positive definite matrices."""
 
-    _required_subclass_attrs = {'sqrt'}
-
     def __init__(self, shape, **kwargs):
         self._sqrt = None
         super().__init__(shape, **kwargs)
@@ -4318,7 +4258,7 @@ 
    Instance variables
    
 
    
 
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    @property
 def sqrt(self):
@@ -4397,7 +4337,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class IdentityMatrix(PositiveDefiniteMatrix, ImplicitArrayMatrix):
     """Matrix representing identity operator on a vector space.
@@ -4482,7 +4422,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigval(self):
@@ -4495,7 +4435,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigvec(self):
@@ -4508,7 +4448,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -4524,7 +4464,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -4594,7 +4534,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DifferentiableMatrix(InvertibleMatrix):
     """Parameterically defined matrix defining gradient of scalar operations.
@@ -4620,8 +4560,6 @@ 
    Args
    
     same shapes and with the same indices / keys.
     """
 
-    _required_subclass_attrs = {'grad_log_abs_det', 'grad_quadratic_form_inv'}
-
     @property
     @abc.abstractmethod
     def grad_log_abs_det(self):
@@ -4661,7 +4599,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 @abc.abstractmethod
@@ -4721,7 +4659,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @abc.abstractmethod
 def grad_quadratic_form_inv(self, vector):
@@ -4758,7 +4696,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class ScaledIdentityMatrix(
         SymmetricMatrix, DifferentiableMatrix, ImplicitArrayMatrix):
@@ -4866,7 +4804,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def scalar(self):
@@ -4880,7 +4818,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigval(self):
@@ -4893,7 +4831,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigvec(self):
@@ -4906,7 +4844,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -4922,7 +4860,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -4939,7 +4877,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -4987,7 +4925,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     return -np.sum(vector**2) / self._scalar**2
    
@@ -5015,7 +4953,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class PositiveScaledIdentityMatrix(
         ScaledIdentityMatrix, PositiveDefiniteMatrix):
@@ -5145,7 +5083,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DiagonalMatrix(
         SymmetricMatrix, DifferentiableMatrix, ImplicitArrayMatrix):
@@ -5229,7 +5167,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -5242,7 +5180,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigvec(self):
@@ -5255,7 +5193,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigval(self):
@@ -5268,7 +5206,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -5323,7 +5261,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     return -(self.inv @ vector)**2
    
@@ -5346,7 +5284,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class PositiveDiagonalMatrix(DiagonalMatrix, PositiveDefiniteMatrix):
     """Specialisation of `DiagonalMatrix` with positive diagonal parameter.
@@ -5480,7 +5418,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class TriangularMatrix(InvertibleMatrix, ExplicitArrayMatrix):
     """Matrix with non-zero values only in lower or upper triangle elements."""
@@ -5542,7 +5480,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def lower(self):
@@ -5558,7 +5496,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -5620,7 +5558,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class InverseTriangularMatrix(InvertibleMatrix, ImplicitArrayMatrix):
     """Triangular matrix implicitly specified by its inverse."""
@@ -5709,7 +5647,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def lower(self):
@@ -5722,7 +5660,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -5738,7 +5676,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -5807,7 +5745,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class TriangularFactoredDefiniteMatrix(
         _BaseTriangularFactoredDefiniteMatrix, DifferentiableMatrix,
@@ -5905,7 +5843,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -5972,7 +5910,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     inv_factor_vector = self.factor.inv @ vector
@@ -6015,7 +5953,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class TriangularFactoredPositiveDefiniteMatrix(
         TriangularFactoredDefiniteMatrix, PositiveDefiniteMatrix):
@@ -6178,7 +6116,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DenseDefiniteMatrix(_BaseTriangularFactoredDefiniteMatrix,
                           DifferentiableMatrix, ExplicitArrayMatrix):
@@ -6266,7 +6204,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def factor(self):
@@ -6286,7 +6224,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -6353,7 +6291,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     inv_matrix_vector = self.inv @ vector
@@ -6384,7 +6322,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DensePositiveDefiniteMatrix(DenseDefiniteMatrix, PositiveDefiniteMatrix):
     """Positive-definite matrix specified by a dense 2D array."""
@@ -6532,7 +6470,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DensePositiveDefiniteProductMatrix(DensePositiveDefiniteMatrix):
     """Positive-definite matrix specified as a signed symmetric product.
@@ -6603,7 +6541,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -6682,7 +6620,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     inv_matrix_vector = self.inv @ vector
@@ -6718,7 +6656,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DenseSquareMatrix(InvertibleMatrix, ExplicitArrayMatrix):
     """Dense non-singular square matrix."""
@@ -6790,7 +6728,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def lu_and_piv(self):
@@ -6810,7 +6748,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -6873,7 +6811,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class InverseLUFactoredSquareMatrix(InvertibleMatrix, ImplicitArrayMatrix):
     """Square matrix implicitly defined by LU factorisation of inverse."""
@@ -6956,7 +6894,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -7018,7 +6956,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DenseSymmetricMatrix(
         SymmetricMatrix, InvertibleMatrix, ExplicitArrayMatrix):
@@ -7122,7 +7060,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class OrthogonalMatrix(InvertibleMatrix, ExplicitArrayMatrix):
     """Square matrix with columns and rows that are orthogonal unit vectors."""
@@ -7166,7 +7104,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -7224,7 +7162,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class ScaledOrthogonalMatrix(InvertibleMatrix, ImplicitArrayMatrix):
     """Matrix corresponding to orthogonal matrix multiplied by a scalar.
@@ -7295,7 +7233,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -7311,7 +7249,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -7371,7 +7309,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class EigendecomposedSymmetricMatrix(
         SymmetricMatrix, InvertibleMatrix, ImplicitArrayMatrix):
@@ -7521,7 +7459,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class EigendecomposedPositiveDefiniteMatrix(
         EigendecomposedSymmetricMatrix, PositiveDefiniteMatrix):
@@ -7650,7 +7588,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class SoftAbsRegularizedPositiveDefiniteMatrix(
         EigendecomposedPositiveDefiniteMatrix, DifferentiableMatrix):
@@ -7727,7 +7665,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def grad_log_abs_det(self):
@@ -7796,7 +7734,7 @@ 
    Methods
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def softabs(self, x):
     """Smooth approximation to absolute function."""
@@ -7811,7 +7749,7 @@ 
    Methods
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_softabs(self, x):
     """Derivative of smooth approximation to absolute function."""
@@ -7834,7 +7772,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def grad_quadratic_form_inv(self, vector):
     num_j_mtx = self.eigval[:, None] - self.eigval[None, :]
@@ -7863,7 +7801,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class BlockMatrix(ImplicitArrayMatrix):
     """Matrix with non-zero entries defined by a series of submatrix blocks."""
@@ -7903,7 +7841,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 @abc.abstractmethod
@@ -7952,7 +7890,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class SquareBlockDiagonalMatrix(InvertibleMatrix, BlockMatrix):
     """Square matrix with non-zero values only in blocks along diagonal."""
@@ -8039,6 +7977,7 @@ 
    Ancestors
    
 
    Subclasses
    
 
 
    Instance variables
    
 
    
@@ -8048,7 +7987,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def blocks(self):
@@ -8062,7 +8001,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def diagonal(self):
@@ -8075,7 +8014,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigval(self):
@@ -8088,7 +8027,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def eigvec(self):
@@ -8105,7 +8044,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def log_abs_det(self):
@@ -8156,9 +8095,9 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
-
    class SymmetricBlockDiagonalMatrix(SquareBlockDiagonalMatrix):
+
    class SymmetricBlockDiagonalMatrix(SquareBlockDiagonalMatrix, SymmetricMatrix):
     """Symmetric specialisation of `SquareBlockDiagonalMatrix`.
 
     All matrix blocks in diagonal are restricted to be symmetric, i.e.
@@ -8188,16 +8127,13 @@ 
    Ancestors
    
 
-
    Subclasses
    
-
 
    Instance variables
    
 
    
 
    var blocks
    
@@ -8239,6 +8175,14 @@ 
    Instance variables
    
 
    
 
    Transpose of matrix.
    
 
    
+
    var eigval
    
+
    
+
    Eigenvalues of matrix as a 1D array.
    
+
    
+
    var eigvec
    
+
    
+
    Eigenvectors of matrix stacked as columns of a Matrix object.
    
+
    
 
    
 
 
    
@@ -8258,10 +8202,10 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class PositiveDefiniteBlockDiagonalMatrix(
-        SymmetricBlockDiagonalMatrix, PositiveDefiniteMatrix,
+        SquareBlockDiagonalMatrix, PositiveDefiniteMatrix, 
         DifferentiableMatrix):
     """Positive definite specialisation of `SymmetricBlockDiagonalMatrix`.
 
@@ -8290,6 +8234,9 @@ 
    Args
    
         else:
             return super()._scalar_multiply(scalar)
 
+    def _construct_transpose(self):
+        return self
+
     def _construct_sqrt(self):
         return SquareBlockDiagonalMatrix(
             tuple(block.sqrt for block in self._blocks))
@@ -8313,7 +8260,6 @@ 
    Args
    
 
    
 
    Ancestors
    
 
      
-
    • SymmetricBlockDiagonalMatrix
      • 
 
    • SquareBlockDiagonalMatrix
      • 
 
    • PositiveDefiniteMatrix
      • 
 
    • SymmetricMatrix
      • 
@@ -8333,7 +8279,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def grad_log_abs_det(self):
@@ -8415,7 +8361,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def grad_quadratic_form_inv(self, vector):
     if self.is_differentiable:
@@ -8443,7 +8389,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class DenseRectangularMatrix(ExplicitArrayMatrix):
     """Dense rectangular matrix."""
@@ -8507,7 +8453,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class BlockRowMatrix(BlockMatrix):
     """Matrix composed of horizontal concatenation of a series of blocks."""
@@ -8568,7 +8514,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def blocks(self):
@@ -8617,7 +8563,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class BlockColumnMatrix(BlockMatrix):
     """Matrix composed of vertical concatenation of a series of blocks."""
@@ -8678,7 +8624,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def blocks(self):
@@ -8769,7 +8715,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class SquareLowRankUpdateMatrix(InvertibleMatrix, ImplicitArrayMatrix):
     """Square matrix equal to a low-rank update to a square matrix.
@@ -8942,7 +8888,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def capacitance_matrix(self):
@@ -8960,7 +8906,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def diagonal(self):
@@ -8978,7 +8924,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def log_abs_det(self):
@@ -9068,7 +9014,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class SymmetricLowRankUpdateMatrix(
         SquareLowRankUpdateMatrix, SymmetricMatrix, InvertibleMatrix):
@@ -9193,7 +9139,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def capacitance_matrix(self):
@@ -9306,7 +9252,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class PositiveDefiniteLowRankUpdateMatrix(
         SymmetricLowRankUpdateMatrix, PositiveDefiniteMatrix,
@@ -9446,7 +9392,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def capacitance_matrix(self):
@@ -9465,7 +9411,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def grad_log_abs_det(self):
@@ -9540,7 +9486,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def grad_quadratic_form_inv(self, vector):
     inv_matrix_vector = self.inv @ vector
diff --git a/docs/docs/progressbars.html b/docs/docs/progressbars.html
index 2b3bdcd..b705525 100644
--- a/docs/docs/progressbars.html
+++ b/docs/docs/progressbars.html
@@ -125,7 +125,7 @@ 
      Module mici.progressbars
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      """Progress bar classes for tracking progress of chains."""
 
@@ -821,7 +821,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class BaseProgressBar(abc.ABC):
     """Base class defining expected interface for progress bars."""
@@ -909,7 +909,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def sequence(self):
@@ -923,7 +923,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def n_iter(self):
@@ -951,7 +951,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @abc.abstractmethod
 def update(self, iter_count, iter_dict, refresh=True):
@@ -990,7 +990,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class DummyProgressBar(BaseProgressBar):
     """Placeholder progress bar which does not display progress updates."""
@@ -1030,7 +1030,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def update(self, iter_count, iter_dict, refresh=True):
     pass
      
@@ -1077,7 +1077,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class ProgressBar(BaseProgressBar):
     """Iterable object for tracking progress of an iterative task.
@@ -1343,7 +1343,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def description(self):
@@ -1357,7 +1357,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def counter(self):
@@ -1371,7 +1371,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def prop_complete(self):
@@ -1385,7 +1385,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def perc_complete(self):
@@ -1399,7 +1399,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def elapsed_time(self):
@@ -1413,7 +1413,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def iter_rate(self):
@@ -1433,7 +1433,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def est_remaining_time(self):
@@ -1451,7 +1451,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def n_block_filled(self):
@@ -1465,7 +1465,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def n_block_empty(self):
@@ -1479,7 +1479,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def prop_partial_block(self):
@@ -1493,7 +1493,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def filled_blocks(self):
@@ -1507,7 +1507,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def empty_blocks(self):
@@ -1524,7 +1524,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def partial_block(self):
@@ -1541,7 +1541,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def progress_bar(self):
@@ -1555,7 +1555,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def bar_color(self):
@@ -1574,7 +1574,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def stats(self):
@@ -1588,7 +1588,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def prefix(self):
@@ -1604,7 +1604,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def postfix(self):
@@ -1631,7 +1631,7 @@ 
      Methods
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def reset(self):
     """Reset progress bar state."""
@@ -1659,7 +1659,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def update(self, iter_count, iter_dict=None, refresh=True):
     """Update progress bar state
@@ -1692,7 +1692,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def refresh(self):
     """Refresh visual display(s) of progress bar."""
@@ -1732,7 +1732,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class LabelledSequenceProgressBar(BaseProgressBar):
     """Iterable object for tracking progress of a sequence of labelled tasks."""
@@ -1929,7 +1929,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def counter(self):
@@ -1943,7 +1943,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def description(self):
@@ -1957,7 +1957,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def stats(self):
@@ -1971,7 +1971,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def prefix(self):
@@ -1985,7 +1985,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def postfix(self):
@@ -1999,7 +1999,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def completed_labels(self):
@@ -2015,7 +2015,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def current_label(self):
@@ -2029,7 +2029,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def unstarted_labels(self):
@@ -2043,7 +2043,7 @@ 
      Instance variables
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      @property
 def progress_bar(self):
@@ -2069,7 +2069,7 @@ 
      Methods
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def reset(self):
     """Reset progress bar state."""
@@ -2097,7 +2097,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def update(self, iter_count, iter_dict=None, refresh=True):
     """Update progress bar state
@@ -2129,7 +2129,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def refresh(self):
     """Refresh visual display(s) of status bar."""
@@ -2161,7 +2161,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class FileDisplay:
     """Use file which supports ANSI escape sequences as an updatable display"""
@@ -2224,7 +2224,7 @@ 
      Methods
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def update(self, obj):
     self._move_line(self._position[0] - self._position[1])
diff --git a/docs/docs/samplers.html b/docs/docs/samplers.html
index 930a78b..169483a 100644
--- a/docs/docs/samplers.html
+++ b/docs/docs/samplers.html
@@ -130,7 +130,7 @@ 
      Module mici.samplers
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      """Monte Carlo sampler classes for peforming inference."""
 
@@ -166,6 +166,21 @@ 
      Module mici.samplers
      
     from multiprocessing.managers import SyncManager
     MULTIPROCESS_AVAILABLE = False
 
+try:
+    from threadpoolctl import threadpool_limits
+    THREADPOOLCTL_AVAILABLE = True
+except ImportError:
+    THREADPOOLCTL_AVAILABLE = False
+
+try:
+    from contextlib import nullcontext
+except ImportError:
+    # Fallback for nullcontext context manager for Python 3.6
+    # https://stackoverflow.com/a/55902915
+    @contextmanager
+    def nullcontext():
+        yield None
+
 
 logger = logging.getLogger(__name__)
 
@@ -651,6 +666,7 @@ 
      Module mici.samplers
      
 def _sample_chains_sequential(init_states, rngs, chain_iterators, **kwargs):
     """Sample multiple chains sequentially in a single process."""
     chain_outputs = []
+    exception = None
     for chain_index, (init_state, rng, chain_iterator) in enumerate(
             zip(init_states, rngs, chain_iterators)):
         *outputs, exception = _sample_chain(
@@ -678,11 +694,15 @@ 
      Module mici.samplers
      
         try:
             chain_index, init_state, rng, n_iter, kwargs = chain_queue.get(
                 block=False)
-            *outputs, exception = _sample_chain(
-                init_state=init_state, rng=rng, chain_index=chain_index,
-                chain_iterator=_ProxyProgressBar(
-                    range(n_iter), chain_index, iter_queue),
-                parallel_chains=True, **kwargs)
+            max_threads = kwargs.pop('max_threads_per_process', None)
+            context = (threadpool_limits(limits=max_threads)
+                       if THREADPOOLCTL_AVAILABLE else nullcontext())
+            with context:
+                *outputs, exception = _sample_chain(
+                    init_state=init_state, rng=rng, chain_index=chain_index,
+                    chain_iterator=_ProxyProgressBar(
+                        range(n_iter), chain_index, iter_queue),
+                    parallel_chains=True, **kwargs)
             # Returned exception being AdaptationError indicates chain
             # terminated due to adapter initialisation failing therefore do not
             # store returned chain outputs and put None value on iteration queue
@@ -972,6 +992,15 @@ 
      Module mici.samplers
      
                 output of `os.cpu_count()`.
 
         Kwargs:
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             memmap_enabled (bool): Whether to memory-map arrays used to store
                 chain data to files on disk to avoid excessive system memory
                 usage for long chains and/or large chain states. The chain data
@@ -1039,6 +1068,7 @@ 
      Module mici.samplers
      
             n_iter, kwargs.pop('progress_bar_class'), n_chain)
         if n_process == 1:
             # Using single process therefore run chains sequentially
+            kwargs.pop('max_threads_per_process', None)
             *states_traces_stats, adapter_states, _ = _sample_chains_sequential(
                 init_states=init_states, rngs=rngs,
                 chain_iterators=chain_iterators, transitions=self.transitions,
@@ -1072,7 +1102,7 @@ 
      Module mici.samplers
      
 
         Args:
             n_warm_up_iter (int): Number of adaptive warm up iterations per
-                chain. Depending on the `mici.stages.Stager` instance specified
+                chain. Depending on the `mici.stagers.Stager` instance specified
                 by the `stage arguments the warm up iterations may be split
                 between one or more adaptive stages.
             n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -1121,6 +1151,15 @@ 
      Module mici.samplers
      
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             memmap_enabled (bool): Whether to memory-map arrays used to store
                 chain data to files on disk to avoid excessive system memory
                 usage for long chains and/or large chain states. The chain data
@@ -1183,6 +1222,7 @@ 
      Module mici.samplers
      
             common_sample_chains_kwargs['n_process'] = n_process
         else:
             sample_chains_func = _sample_chains_sequential
+            common_sample_chains_kwargs.pop('max_threads_per_process', None)
         if stager is None:
             if all(a.is_fast for a_list in adapters.values() for a in a_list):
                 stager = WarmUpStager()
@@ -1423,6 +1463,15 @@ 
      Module mici.samplers
      
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
                 List of functions which compute the variables to be recorded at
                 each chain iteration, with each trace function being passed the
@@ -1516,7 +1565,7 @@ 
      Module mici.samplers
      
 
         Args:
             n_warm_up_iter (int): Number of adaptive warm up iterations per
-                chain. Depending on the `mici.stages.Stager` instance specified
+                chain. Depending on the `mici.stagers.Stager` instance specified
                 by the `stage arguments the warm up iterations may be split
                 between one or more adaptive stages.
             n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -1536,6 +1585,15 @@ 
      Module mici.samplers
      
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
                 List of functions which compute the variables to be recorded at
                 each chain iteration during the main non-adaptive sampling
@@ -1987,7 +2045,7 @@ 
      Args
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      class MarkovChainMonteCarloMethod(object):
     """Generic Markov chain Monte Carlo (MCMC) sampler.
@@ -2153,6 +2211,15 @@ 
      Args
      
                 output of `os.cpu_count()`.
 
         Kwargs:
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             memmap_enabled (bool): Whether to memory-map arrays used to store
                 chain data to files on disk to avoid excessive system memory
                 usage for long chains and/or large chain states. The chain data
@@ -2220,6 +2287,7 @@ 
      Args
      
             n_iter, kwargs.pop('progress_bar_class'), n_chain)
         if n_process == 1:
             # Using single process therefore run chains sequentially
+            kwargs.pop('max_threads_per_process', None)
             *states_traces_stats, adapter_states, _ = _sample_chains_sequential(
                 init_states=init_states, rngs=rngs,
                 chain_iterators=chain_iterators, transitions=self.transitions,
@@ -2253,7 +2321,7 @@ 
      Args
      
 
         Args:
             n_warm_up_iter (int): Number of adaptive warm up iterations per
-                chain. Depending on the `mici.stages.Stager` instance specified
+                chain. Depending on the `mici.stagers.Stager` instance specified
                 by the `stage arguments the warm up iterations may be split
                 between one or more adaptive stages.
             n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -2302,6 +2370,15 @@ 
      Args
      
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             memmap_enabled (bool): Whether to memory-map arrays used to store
                 chain data to files on disk to avoid excessive system memory
                 usage for long chains and/or large chain states. The chain data
@@ -2364,6 +2441,7 @@ 
      Args
      
             common_sample_chains_kwargs['n_process'] = n_process
         else:
             sample_chains_func = _sample_chains_sequential
+            common_sample_chains_kwargs.pop('max_threads_per_process', None)
         if stager is None:
             if all(a.is_fast for a_list in adapters.values() for a in a_list):
                 stager = WarmUpStager()
@@ -2501,7 +2579,7 @@ 
      Returns
      
 
      
 
 Expand source code
-Browse git
+Browse git
 
 
      def sample_chain(self, n_iter, init_state, trace_funcs, **kwargs):
     """Sample a Markov chain from a given initial state.
@@ -2641,6 +2719,16 @@ 
      Args
      
 
    
 
    Kwargs
    
 
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    memmap_enabled : bool
    
 
    Whether to memory-map arrays used to store
 chain data to files on disk to avoid excessive system memory
@@ -2715,7 +2803,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def sample_chains(self, n_iter, init_states, trace_funcs, n_process=1,
                   **kwargs):
@@ -2751,6 +2839,15 @@ 
    Returns
    
             output of `os.cpu_count()`.
 
     Kwargs:
+        max_threads_per_process (int or None): If `threadpoolctl` is
+            available this argument may be used to limit the maximum number
+            of threads that can be used in thread pools used in libraries
+            supported by `threadpoolctl`, which include BLAS and OpenMP
+            implementations. This argument will only have an effect if
+            `n_process > 1` such that chains are being run on multiple
+            processes and only if `threadpoolctl` is installed in the
+            current Python environment. If set to `None` (the default) no
+            limits are set.
         memmap_enabled (bool): Whether to memory-map arrays used to store
             chain data to files on disk to avoid excessive system memory
             usage for long chains and/or large chain states. The chain data
@@ -2818,6 +2915,7 @@ 
    Returns
    
         n_iter, kwargs.pop('progress_bar_class'), n_chain)
     if n_process == 1:
         # Using single process therefore run chains sequentially
+        kwargs.pop('max_threads_per_process', None)
         *states_traces_stats, adapter_states, _ = _sample_chains_sequential(
             init_states=init_states, rngs=rngs,
             chain_iterators=chain_iterators, transitions=self.transitions,
@@ -2852,7 +2950,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -2911,6 +3009,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    memmap_enabled : bool
    
 
    Whether to memory-map arrays used to store
 chain data to files on disk to avoid excessive system memory
@@ -2975,7 +3083,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def sample_chains_with_adaptive_warm_up(
         self, n_warm_up_iter, n_main_iter, init_states, trace_funcs,
@@ -2995,7 +3103,7 @@ 
    Returns
    
 
     Args:
         n_warm_up_iter (int): Number of adaptive warm up iterations per
-            chain. Depending on the `mici.stages.Stager` instance specified
+            chain. Depending on the `mici.stagers.Stager` instance specified
             by the `stage arguments the warm up iterations may be split
             between one or more adaptive stages.
         n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -3044,6 +3152,15 @@ 
    Returns
    
             dynamically assign the chains across multiple processes. If set
             to `None` then the number of processes will be set to the
             output of `os.cpu_count()`. Default is `n_process=1`.
+        max_threads_per_process (int or None): If `threadpoolctl` is
+            available this argument may be used to limit the maximum number
+            of threads that can be used in thread pools used in libraries
+            supported by `threadpoolctl`, which include BLAS and OpenMP
+            implementations. This argument will only have an effect if
+            `n_process > 1` such that chains are being run on multiple
+            processes and only if `threadpoolctl` is installed in the
+            current Python environment. If set to `None` (the default) no
+            limits are set.
         memmap_enabled (bool): Whether to memory-map arrays used to store
             chain data to files on disk to avoid excessive system memory
             usage for long chains and/or large chain states. The chain data
@@ -3106,6 +3223,7 @@ 
    Returns
    
         common_sample_chains_kwargs['n_process'] = n_process
     else:
         sample_chains_func = _sample_chains_sequential
+        common_sample_chains_kwargs.pop('max_threads_per_process', None)
     if stager is None:
         if all(a.is_fast for a_list in adapters.values() for a in a_list):
             stager = WarmUpStager()
@@ -3196,7 +3314,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class HamiltonianMCMC(MarkovChainMonteCarloMethod):
     """Wrapper class for Hamiltonian Markov chain Monte Carlo (H-MCMC) methods.
@@ -3408,6 +3526,15 @@ 
    Args
    
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
                 List of functions which compute the variables to be recorded at
                 each chain iteration, with each trace function being passed the
@@ -3501,7 +3628,7 @@ 
    Args
    
 
         Args:
             n_warm_up_iter (int): Number of adaptive warm up iterations per
-                chain. Depending on the `mici.stages.Stager` instance specified
+                chain. Depending on the `mici.stagers.Stager` instance specified
                 by the `stage arguments the warm up iterations may be split
                 between one or more adaptive stages.
             n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -3521,6 +3648,15 @@ 
    Args
    
                 dynamically assign the chains across multiple processes. If set
                 to `None` then the number of processes will be set to the
                 output of `os.cpu_count()`. Default is `n_process=1`.
+            max_threads_per_process (int or None): If `threadpoolctl` is
+                available this argument may be used to limit the maximum number
+                of threads that can be used in thread pools used in libraries
+                supported by `threadpoolctl`, which include BLAS and OpenMP
+                implementations. This argument will only have an effect if
+                `n_process > 1` such that chains are being run on multiple
+                processes and only if `threadpoolctl` is installed in the
+                current Python environment. If set to `None` (the default) no
+                limits are set.
             trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
                 List of functions which compute the variables to be recorded at
                 each chain iteration during the main non-adaptive sampling
@@ -3722,7 +3858,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def sample_chain(self, n_iter, init_state, **kwargs):
     """Sample a Markov chain from a given initial state.
@@ -3843,6 +3979,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -3923,7 +4069,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def sample_chains(self, n_iter, init_states, **kwargs):
     """Sample one or more Markov chains from given initial states.
@@ -3951,6 +4097,15 @@ 
    Returns
    
             dynamically assign the chains across multiple processes. If set
             to `None` then the number of processes will be set to the
             output of `os.cpu_count()`. Default is `n_process=1`.
+        max_threads_per_process (int or None): If `threadpoolctl` is
+            available this argument may be used to limit the maximum number
+            of threads that can be used in thread pools used in libraries
+            supported by `threadpoolctl`, which include BLAS and OpenMP
+            implementations. This argument will only have an effect if
+            `n_process > 1` such that chains are being run on multiple
+            processes and only if `threadpoolctl` is installed in the
+            current Python environment. If set to `None` (the default) no
+            limits are set.
         trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
             List of functions which compute the variables to be recorded at
             each chain iteration, with each trace function being passed the
@@ -4045,7 +4200,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -4069,6 +4224,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -4165,7 +4330,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def sample_chains_with_adaptive_warm_up(
         self, n_warm_up_iter, n_main_iter, init_states, **kwargs):
@@ -4189,7 +4354,7 @@ 
    Returns
    
 
     Args:
         n_warm_up_iter (int): Number of adaptive warm up iterations per
-            chain. Depending on the `mici.stages.Stager` instance specified
+            chain. Depending on the `mici.stagers.Stager` instance specified
             by the `stage arguments the warm up iterations may be split
             between one or more adaptive stages.
         n_main_iter (int): Number of iterations (samples to draw) per chain
@@ -4209,6 +4374,15 @@ 
    Returns
    
             dynamically assign the chains across multiple processes. If set
             to `None` then the number of processes will be set to the
             output of `os.cpu_count()`. Default is `n_process=1`.
+        max_threads_per_process (int or None): If `threadpoolctl` is
+            available this argument may be used to limit the maximum number
+            of threads that can be used in thread pools used in libraries
+            supported by `threadpoolctl`, which include BLAS and OpenMP
+            implementations. This argument will only have an effect if
+            `n_process > 1` such that chains are being run on multiple
+            processes and only if `threadpoolctl` is installed in the
+            current Python environment. If set to `None` (the default) no
+            limits are set.
         trace_funcs (Iterable[Callable[[ChainState], Dict[str, array]]]):
             List of functions which compute the variables to be recorded at
             each chain iteration during the main non-adaptive sampling
@@ -4352,7 +4526,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class StaticMetropolisHMC(HamiltonianMCMC):
     """Static integration time H-MCMC implementation with Metropolis sampling.
@@ -4427,7 +4601,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def n_step(self):
@@ -4567,6 +4741,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -4667,7 +4851,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -4691,6 +4875,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -4844,7 +5038,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class RandomMetropolisHMC(HamiltonianMCMC):
     """Random integration time H-MCMC with Metropolis sampling of new state.
@@ -4927,7 +5121,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def n_step_range(self):
@@ -5067,6 +5261,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -5167,7 +5371,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -5191,6 +5395,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -5372,7 +5586,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DynamicMultinomialHMC(HamiltonianMCMC):
     """Dynamic integration time H-MCMC with multinomial sampling of new state.
@@ -5488,7 +5702,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def max_tree_depth(self):
@@ -5502,7 +5716,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def max_delta_h(self):
@@ -5642,6 +5856,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -5742,7 +5966,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -5766,6 +5990,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -5945,7 +6179,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class DynamicSliceHMC(HamiltonianMCMC):
     """Dynamic integration time H-MCMC with slice sampling of new state.
@@ -6059,7 +6293,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def max_tree_depth(self):
@@ -6073,7 +6307,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @property
 def max_delta_h(self):
@@ -6213,6 +6447,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
@@ -6313,7 +6557,7 @@ 
    Args
    
 
    
 
    n_warm_up_iter : int
    
 
    Number of adaptive warm up iterations per
-chain. Depending on the mici.stages.Stager instance specified
+chain. Depending on the Stager instance specified
 by the `stage arguments the warm up iterations may be split
 between one or more adaptive stages.
    
 
    n_main_iter : int
    
@@ -6337,6 +6581,16 @@ 
    Kwargs
    
 dynamically assign the chains across multiple processes. If set
 to None then the number of processes will be set to the
 output of os.cpu_count(). Default is n_process=1.
    
+
    max_threads_per_process : int or None
    
+
    If threadpoolctl is
+available this argument may be used to limit the maximum number
+of threads that can be used in thread pools used in libraries
+supported by threadpoolctl, which include BLAS and OpenMP
+implementations. This argument will only have an effect if
+n_process > 1 such that chains are being run on multiple
+processes and only if threadpoolctl is installed in the
+current Python environment. If set to None (the default) no
+limits are set.
    
 
    trace_funcs : Iterable[Callable[[ChainState], Dict[str, array]]]
    
 
    
 
    List of functions which compute the variables to be recorded at
diff --git a/docs/docs/solvers.html b/docs/docs/solvers.html
index cdfdb04..157f024 100644
--- a/docs/docs/solvers.html
+++ b/docs/docs/solvers.html
@@ -52,7 +52,7 @@ 
    Module mici.solvers
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    """Solvers for non-linear systems of equations for implicit integrators."""
 
@@ -363,7 +363,7 @@ 
    Functions
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def euclidean_norm(vct):
     """Calculate the Euclidean (L-2) norm of a vector."""
@@ -378,7 +378,7 @@ 
    Functions
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def maximum_norm(vct):
     """Calculate the maximum (L-infinity) norm of a vector."""
@@ -420,7 +420,7 @@ 
    Raises
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def solve_fixed_point_direct(
         func, x0, convergence_tol=1e-9, divergence_tol=1e10, max_iters=100,
@@ -505,7 +505,7 @@ 
    Raises
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def solve_fixed_point_steffensen(
         func, x0, convergence_tol=1e-9, divergence_tol=1e10, max_iters=100,
@@ -628,7 +628,7 @@ 
    Raises
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def solve_projection_onto_manifold_quasi_newton(
         state, state_prev, dt, system, constraint_tol=1e-9, position_tol=1e-8,
@@ -784,7 +784,7 @@ 
    Raises
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def solve_projection_onto_manifold_newton(
         state, state_prev, dt, system, constraint_tol=1e-9, position_tol=1e-8,
diff --git a/docs/docs/stagers.html b/docs/docs/stagers.html
index 31ca3e9..3885d10 100644
--- a/docs/docs/stagers.html
+++ b/docs/docs/stagers.html
@@ -72,7 +72,7 @@ 
    Module mici.stagers
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    """Classes for controlling sampling of Markov chains split into stages."""
 
@@ -317,7 +317,7 @@ 
    Instance variables
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class Stager(abc.ABC):
     """Abstract chain iteration stager."""
@@ -432,7 +432,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @abc.abstractmethod
 def stages(self, n_warm_up_iter, n_main_iter, adapters, trace_funcs):
@@ -499,7 +499,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class WarmUpStager(Stager):
     """Chain iteration stager with a single adaptive warm up stage.
@@ -584,7 +584,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def stages(self, n_warm_up_iter, n_main_iter, adapters, trace_funcs):
     # adaptive warm up stage
@@ -660,7 +660,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class WindowedWarmUpStager(Stager):
     """Chain iteration stager with a hierarchy of adaptive warm up stages.
@@ -840,7 +840,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def stages(self, n_warm_up_iter, n_main_iter, adapters, trace_funcs):
     fast_adapters = {
diff --git a/docs/docs/states.html b/docs/docs/states.html
index 32417d7..472f722 100644
--- a/docs/docs/states.html
+++ b/docs/docs/states.html
@@ -58,7 +58,7 @@ 
    Module mici.states
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    """Objects for recording state of a Markov chain and caching computations."""
 
@@ -78,7 +78,7 @@ 
    Module mici.states
    
 def cache_in_state(*depends_on):
     """Memoizing decorator for system methods.
 
-    Used to decorate `mici.system.System` methods which compute a function of
+    Used to decorate `mici.systems.System` methods which compute a function of
     one or more chain state variable(s), with the decorated method caching the
     value returned by the method being wrapped in the `ChainState` object to
     prevent the need for recomputation on future calls if the state variables
@@ -86,8 +86,8 @@ 
    Module mici.states
    
 
     Additionally for `ChainState` instances initialized with a `_call_counts`
     argument, the memoized method will update a counter for the method in the
-    `ChainState._call_counts` attribute every time the method being decorated is
-    called (i.e. when there isn't a valid cached value available).
+    `_call_counts` attribute every time the method being decorated is called
+    (i.e. when there isn't a valid cached value available).
 
     Args:
        *depends_on: One or more strings corresponding to the names of any state
@@ -115,7 +115,7 @@ 
    Module mici.states
    
 def cache_in_state_with_aux(depends_on, auxiliary_outputs):
     """Memoizing decorator for system methods with possible auxiliary outputs.
 
-    Used to decorate `mici.system.System` methods which compute a function of
+    Used to decorate `mici.systems.System` methods which compute a function of
     one or more chain state variable(s), with the decorated method caching the
     value or values returned by the method being wrapped in the `ChainState`
     object to prevent the need for recomputation on future calls if the state
@@ -142,8 +142,8 @@ 
    Module mici.states
    
 
     Additionally for `ChainState` instances initialized with a `_call_counts`
     argument, the memoized method will update a counter for the method in the
-    `ChainState._call_counts` attribute every time the method being decorated is
-    called (i.e. when there isn't a valid cached value available).
+    `_call_counts` attribute every time the method being decorated is called
+    (i.e. when there isn't a valid cached value available).
 
     Args:
         depends_on (str or Tuple[str]): A string or tuple of strings, with each
@@ -265,7 +265,7 @@ 
    Module mici.states
    
             _cache = {}
         self.__dict__['_cache'] = _cache
         self.__dict__['_call_counts'] = (
-            Counter(_call_counts) if isinstance(_call_counts, dict)
+            Counter(_call_counts) if not isinstance(_call_counts, Counter)
             else _call_counts)
         self.__dict__['_read_only'] = _read_only
 
@@ -346,15 +346,15 @@ 
    Functions
    
     
 
    
 
    Memoizing decorator for system methods.
    
-
    Used to decorate mici.system.System methods which compute a function of
+
    Used to decorate System methods which compute a function of
 one or more chain state variable(s), with the decorated method caching the
 value returned by the method being wrapped in the ChainState object to
 prevent the need for recomputation on future calls if the state variables
 the returned value depends on have not been changed in between the calls.
    
 
    Additionally for ChainState instances initialized with a _call_counts
 argument, the memoized method will update a counter for the method in the
-ChainState._call_counts attribute every time the method being decorated is
-called (i.e. when there isn't a valid cached value available).
    
+_call_counts attribute every time the method being decorated is called
+(i.e. when there isn't a valid cached value available).
    
 
    Args
    
 
    
 
    *depends_on
    
@@ -367,12 +367,12 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def cache_in_state(*depends_on):
     """Memoizing decorator for system methods.
 
-    Used to decorate `mici.system.System` methods which compute a function of
+    Used to decorate `mici.systems.System` methods which compute a function of
     one or more chain state variable(s), with the decorated method caching the
     value returned by the method being wrapped in the `ChainState` object to
     prevent the need for recomputation on future calls if the state variables
@@ -380,8 +380,8 @@ 
    Args
    
 
     Additionally for `ChainState` instances initialized with a `_call_counts`
     argument, the memoized method will update a counter for the method in the
-    `ChainState._call_counts` attribute every time the method being decorated is
-    called (i.e. when there isn't a valid cached value available).
+    `_call_counts` attribute every time the method being decorated is called
+    (i.e. when there isn't a valid cached value available).
 
     Args:
        *depends_on: One or more strings corresponding to the names of any state
@@ -411,7 +411,7 @@ 
    Args
    
     
 
    
 
    Memoizing decorator for system methods with possible auxiliary outputs.
    
-
    Used to decorate mici.system.System methods which compute a function of
+
    Used to decorate System methods which compute a function of
 one or more chain state variable(s), with the decorated method caching the
 value or values returned by the method being wrapped in the ChainState
 object to prevent the need for recomputation on future calls if the state
@@ -436,8 +436,8 @@ 
    Args
    
 depend on have not been changed in between.
    
 
    Additionally for ChainState instances initialized with a _call_counts
 argument, the memoized method will update a counter for the method in the
-ChainState._call_counts attribute every time the method being decorated is
-called (i.e. when there isn't a valid cached value available).
    
+_call_counts attribute every time the method being decorated is called
+(i.e. when there isn't a valid cached value available).
    
 
    Args
    
 
    
 
    depends_on : str or Tuple[str]
    
@@ -461,12 +461,12 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def cache_in_state_with_aux(depends_on, auxiliary_outputs):
     """Memoizing decorator for system methods with possible auxiliary outputs.
 
-    Used to decorate `mici.system.System` methods which compute a function of
+    Used to decorate `mici.systems.System` methods which compute a function of
     one or more chain state variable(s), with the decorated method caching the
     value or values returned by the method being wrapped in the `ChainState`
     object to prevent the need for recomputation on future calls if the state
@@ -493,8 +493,8 @@ 
    Args
    
 
     Additionally for `ChainState` instances initialized with a `_call_counts`
     argument, the memoized method will update a counter for the method in the
-    `ChainState._call_counts` attribute every time the method being decorated is
-    called (i.e. when there isn't a valid cached value available).
+    `_call_counts` attribute every time the method being decorated is called
+    (i.e. when there isn't a valid cached value available).
 
     Args:
         depends_on (str or Tuple[str]): A string or tuple of strings, with each
@@ -614,7 +614,7 @@ 
    Kwargs
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class ChainState(object):
     """Markov chain state.
@@ -689,7 +689,7 @@ 
    Kwargs
    
             _cache = {}
         self.__dict__['_cache'] = _cache
         self.__dict__['_call_counts'] = (
-            Counter(_call_counts) if isinstance(_call_counts, dict)
+            Counter(_call_counts) if not isinstance(_call_counts, Counter)
             else _call_counts)
         self.__dict__['_read_only'] = _read_only
 
@@ -779,7 +779,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def copy(self, read_only=False):
     """Create a deep copy of the state object.
diff --git a/docs/docs/systems.html b/docs/docs/systems.html
index 7f71344..cacd524 100644
--- a/docs/docs/systems.html
+++ b/docs/docs/systems.html
@@ -355,7 +355,7 @@ 
    Module mici.systems
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    """Hamiltonian systems encapsulating energy functions and their derivatives."""
 
@@ -2017,7 +2017,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class System(ABC):
     r"""Base class for Hamiltonian systems.
@@ -2222,7 +2222,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @cache_in_state('pos')
 def neg_log_dens(self, state):
@@ -2256,7 +2256,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @cache_in_state_with_aux('pos', 'neg_log_dens')
 def grad_neg_log_dens(self, state):
@@ -2290,7 +2290,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def h1(self, state):
     """Hamiltonian component depending only on position.
@@ -2322,7 +2322,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def dh1_dpos(self, state):
     """Derivative of `h1` Hamiltonian component with respect to position.
@@ -2352,7 +2352,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def h1_flow(self, state, dt):
     """Apply exact flow map corresponding to `h1` Hamiltonian component.
@@ -2384,7 +2384,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @abstractmethod
 def h2(self, state):
@@ -2416,7 +2416,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @abstractmethod
 def dh2_dmom(self, state):
@@ -2448,7 +2448,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def h(self, state):
     """Hamiltonian function for system.
@@ -2480,7 +2480,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def dh_dpos(self, state):
     """Derivative of Hamiltonian with respect to position.
@@ -2515,7 +2515,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def dh_dmom(self, state):
     """Derivative of Hamiltonian with respect to momentum.
@@ -2548,7 +2548,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    @abstractmethod
 def sample_momentum(self, state, rng):
@@ -2621,7 +2621,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class EuclideanMetricSystem(System):
     r"""Hamiltonian system with a Euclidean metric on the position space.
@@ -2760,7 +2760,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
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    @cache_in_state('mom')
 def h2(self, state):
@@ -2785,7 +2785,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('mom')
 def dh2_dmom(self, state):
@@ -2808,7 +2808,7 @@ 
    Args
    
 
    
 
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    def h2_flow(self, state, dt):
     """Apply exact flow map corresponding to `h2` Hamiltonian component.
@@ -2846,7 +2846,7 @@ 
    Returns
    
 
    
 
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    def dh2_flow_dmom(self, dt):
     """Derivatives of `h2_flow` flow map with respect to input momentum.
@@ -2885,7 +2885,7 @@ 
    Returns
    
 
    
 
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    def sample_momentum(self, state, rng):
     return self.metric.sqrt @ rng.standard_normal(state.pos.shape)
    
@@ -3091,7 +3091,7 @@ 
    Args
    
 
    
 
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    class GaussianEuclideanMetricSystem(EuclideanMetricSystem):
     r"""Euclidean Hamiltonian system with a tractable Gaussian component.
@@ -3225,7 +3225,7 @@ 
    Returns
    
 
    
 
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    def h2(self, state):
     return (0.5 * state.pos @ state.pos +
@@ -3250,7 +3250,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('mom')
 def dh2_dmom(self, state):
@@ -3265,7 +3265,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('mom')
 def dh2_dpos(self, state):
@@ -3288,7 +3288,7 @@ 
    Args
    
 
    
 
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    def h2_flow(self, state, dt):
     omega = 1. / self.metric.eigval**0.5
@@ -3327,7 +3327,7 @@ 
    Returns
    
 
    
 
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    def dh2_flow_dmom(self, dt):
     omega = 1. / self.metric.eigval**0.5
@@ -3636,7 +3636,7 @@ 
    Args
    
 
    
 
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    class ConstrainedEuclideanMetricSystem(EuclideanMetricSystem):
     r"""Base class for Euclidean Hamiltonian systems subject to constraints.
@@ -3955,7 +3955,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def constr(self, state):
@@ -3988,7 +3988,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state_with_aux('pos', 'constr')
 def jacob_constr(self, state):
@@ -4028,7 +4028,7 @@ 
    Args
    
 
    
 
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    @abstractmethod
 def jacob_constr_inner_product(
@@ -4073,7 +4073,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def gram(self, state):
@@ -4115,7 +4115,7 @@ 
    Returns
    
 
    
 
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    def inv_gram(self, state):
     """Inverse of Gram matrix at current position.
@@ -4138,7 +4138,7 @@ 
    Returns
    
 
    
 
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    def log_det_sqrt_gram(self, state):
     """Value of (half of) log-determinant of Gram matrix."""
@@ -4164,7 +4164,7 @@ 
    Returns
    
 
    
 
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    @abstractmethod
 def grad_log_det_sqrt_gram(self, state):
@@ -4197,7 +4197,7 @@ 
    Returns
    
 
    
 
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    def h1(self, state):
     if self.dens_wrt_hausdorff:
@@ -4224,7 +4224,7 @@ 
    Returns
    
 
    
 
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    def dh1_dpos(self, state):
     if self.dens_wrt_hausdorff:
@@ -4256,7 +4256,7 @@ 
    Returns
    
 
    
 
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    def project_onto_cotangent_space(self, mom, state):
     """Project a momentum on to the co-tangent space at a position.
@@ -4297,7 +4297,7 @@ 
    Returns
    
 
    
 
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    def sample_momentum(self, state, rng):
     mom = super().sample_momentum(state, rng)
@@ -4602,7 +4602,7 @@ 
    Args
    
 
    
 
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    class DenseConstrainedEuclideanMetricSystem(ConstrainedEuclideanMetricSystem):
     r"""Euclidean Hamiltonian system subject to a dense set of constraints.
@@ -4777,7 +4777,7 @@ 
    Methods
    
 
    
 
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    @cache_in_state_with_aux('pos', ('jacob_constr', 'constr'))
 def mhp_constr(self, state):
@@ -4809,7 +4809,7 @@ 
    Args
    
 
    
 
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    def jacob_constr_inner_product(
         self, jacob_constr_1, inner_product_matrix, jacob_constr_2=None):
@@ -4840,7 +4840,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def grad_log_det_sqrt_gram(self, state):
@@ -5270,7 +5270,7 @@ 
    Args
    
 
    
 
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    class GaussianDenseConstrainedEuclideanMetricSystem(
         GaussianEuclideanMetricSystem, DenseConstrainedEuclideanMetricSystem):
@@ -5427,7 +5427,7 @@ 
    Args
    
 
    
 
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    def jacob_constr_inner_product(
         self, jacob_constr_1, inner_product_matrix, jacob_constr_2=None):
@@ -5880,7 +5880,7 @@ 
    Args
    
 
    
 
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    class RiemannianMetricSystem(System):
     r"""Riemannian Hamiltonian system with a position-dependent metric.
@@ -6119,7 +6119,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def metric_func(self, state):
@@ -6158,7 +6158,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state_with_aux('pos', 'metric_func')
 def vjp_metric_func(self, state):
@@ -6201,7 +6201,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def metric(self, state):
@@ -6239,7 +6239,7 @@ 
    Returns
    
 
    
 
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    def h(self, state):
     return self.h1(state) + self.h2(state)
    
@@ -6263,7 +6263,7 @@ 
    Returns
    
 
    
 
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    def h1(self, state):
     return self.neg_log_dens(state) + 0.5 * self.metric(state).log_abs_det
    
@@ -6287,7 +6287,7 @@ 
    Returns
    
 
    
 
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    def dh1_dpos(self, state):
     # Evaluate VJP of metric function before metric as metric value will
@@ -6315,7 +6315,7 @@ 
    Returns
    
 
    
 
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    def h2(self, state):
     return 0.5 * state.mom @ self.metric(state).inv @ state.mom
    
@@ -6329,7 +6329,7 @@ 
    Returns
    
 
    
 
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    def dh2_dpos(self, state):
     # Evaluate VJP of metric function before metric as metric value will
@@ -6357,7 +6357,7 @@ 
    Returns
    
 
    
 
 Expand source code
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    def dh2_dmom(self, state):
     return self.metric(state).inv @ state.mom
    
@@ -6382,7 +6382,7 @@ 
    Returns
    
 
    
 
 Expand source code
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    def sample_momentum(self, state, rng):
     return self.metric(state).sqrt @ rng.normal(size=state.pos.shape)
    
@@ -6537,7 +6537,7 @@ 
    Args
    
 
    
 
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    class ScalarRiemannianMetricSystem(RiemannianMetricSystem):
     """Riemannian-metric system with scaled identity matrix representation.
@@ -6637,7 +6637,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state('pos')
 def metric(self, state):
@@ -6928,7 +6928,7 @@ 
    Args
    
 
    
 
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    class DiagonalRiemannianMetricSystem(RiemannianMetricSystem):
     """Riemannian-metric system with diagonal matrix representation.
@@ -7304,7 +7304,7 @@ 
    Args
    
 
    
 
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    class CholeskyFactoredRiemannianMetricSystem(RiemannianMetricSystem):
     """Riemannian-metric system with Cholesky-factored matrix representation.
@@ -7681,7 +7681,7 @@ 
    Args
    
 
    
 
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    class DenseRiemannianMetricSystem(RiemannianMetricSystem):
     """Riemannian-metric system with dense matrix representation.
@@ -8098,7 +8098,7 @@ 
    Args
    
 
    
 
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    class SoftAbsRiemannianMetricSystem(RiemannianMetricSystem):
     """SoftAbs Riemmanian metric Hamiltonian system.
@@ -8292,7 +8292,7 @@ 
    Returns
    
 
    
 
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    def metric_func(self, state):
     return self.hess_neg_log_dens(state)
    
@@ -8321,7 +8321,7 @@ 
    Returns
    
 
    
 
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    def vjp_metric_func(self, state):
     return self.mtp_neg_log_dens(state)
    
@@ -8348,7 +8348,7 @@ 
    Returns
    
 
    
 
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    @cache_in_state_with_aux('pos', ('grad_neg_log_dens', 'neg_log_dens'))
 def hess_neg_log_dens(self, state):
@@ -8396,7 +8396,7 @@ 
    Returns
    
 
    
 
 Expand source code
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    @cache_in_state_with_aux(
     'pos', ('hess_neg_log_dens', 'grad_neg_log_dens', 'neg_log_dens'))
diff --git a/docs/docs/transitions.html b/docs/docs/transitions.html
index a038d15..ff0ba9c 100644
--- a/docs/docs/transitions.html
+++ b/docs/docs/transitions.html
@@ -195,7 +195,7 @@ 
    Module mici.transitions
    
 
    
 
 Expand source code
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+Browse git
 
 
    """Markov transition kernels."""
 
@@ -932,7 +932,7 @@ 
    References
    
 
    
 
 Expand source code
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    def euclidean_no_u_turn_criterion(system, state_1, state_2, sum_mom):
     """No-U-turn termination criterion for Euclidean manifolds [1].
@@ -1002,7 +1002,7 @@ 
    References
    
 
    
 
 Expand source code
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+Browse git
 
 
    def riemannian_no_u_turn_criterion(system, state_1, state_2, sum_mom):
     """Generalized no-U-turn termination criterion on Riemannian manifolds [2].
@@ -1052,7 +1052,7 @@ 
    Classes
    
 
    
 
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    class Transition(ABC):
     """Base class for Markov transition kernels.
@@ -1109,7 +1109,7 @@ 
    Instance variables
    
 
    
 
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    @abstractproperty
 def state_variables(self):
@@ -1129,7 +1129,7 @@ 
    Instance variables
    
 
    
 
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    @abstractproperty
 def statistic_types(self):
@@ -1172,7 +1172,7 @@ 
    Returns
    
 
    
 
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    @abstractmethod
 def sample(self, state, rng):
@@ -1211,7 +1211,7 @@ 
    Args
    
 
    
 
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    class MomentumTransition(Transition):
     """Base class for momentum transitions.
@@ -1312,7 +1312,7 @@ 
    Returns
    
 
    
 
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    @abstractmethod
 def sample(self, state, rng):
@@ -1354,7 +1354,7 @@ 
    Args
    
 
    
 
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    class IndependentMomentumTransition(MomentumTransition):
     """Independent momentum transition.
@@ -1426,7 +1426,7 @@ 
    Returns
    
 
    
 
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    def sample(self, state, rng):
     state.mom = self.system.sample_momentum(state, rng)
@@ -1477,7 +1477,7 @@ 
    Args
    
 
    
 
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    class CorrelatedMomentumTransition(MomentumTransition):
     """Correlated (partial) momentum transition.
@@ -1590,7 +1590,7 @@ 
    Returns
    
 
    
 
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    def sample(self, state, rng):
     if self.mom_resample_coeff == 1:
@@ -1625,7 +1625,7 @@ 
    Args
    
 
    
 
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    class IntegrationTransition(Transition):
     """Base class for integration transtions.
@@ -1733,7 +1733,7 @@ 
    Returns
    
 
    
 
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    @abstractmethod
 def sample(self, state, rng):
@@ -1783,7 +1783,7 @@ 
    Args
    
 
    
 
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    class MetropolisIntegrationTransition(IntegrationTransition):
     """Base for HMC methods using a Metropolis accept step to sample new state.
@@ -1929,7 +1929,7 @@ 
    Args
    
 
    
 
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    class MetropolisStaticIntegrationTransition(MetropolisIntegrationTransition):
     """Static integration transition with Metropolis sampling of new state.
@@ -2021,7 +2021,7 @@ 
    Returns
    
 
    
 
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    def sample(self, state, rng):
     return self._sample_n_step(state, self.n_step, rng)
    
@@ -2065,7 +2065,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
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    class MetropolisRandomIntegrationTransition(MetropolisIntegrationTransition):
     """Random integration transition with Metropolis sampling of new state.
@@ -2165,7 +2165,7 @@ 
    Returns
    
 
    
 
 Expand source code
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+Browse git
 
 
    def sample(self, state, rng):
     n_step = rng.integers(*self.n_step_range)
@@ -2242,7 +2242,7 @@ 
    Args
    
 
    
 
 Expand source code
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+Browse git
 
 
    class DynamicIntegrationTransition(IntegrationTransition):
     """Base class for dynamic integration transitions.
@@ -2517,7 +2517,7 @@ 
    Returns
    
 
    
 
 Expand source code
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+Browse git
 
 
    def sample(self, state, rng):
     stats = {'n_step': 0, 'sum_metrop_accept_prob': 0., 'reject_prob': 1.}
@@ -2636,7 +2636,7 @@ 
    Args
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    class MultinomialDynamicIntegrationTransition(DynamicIntegrationTransition):
     """Dynamic integration transition with multinomial sampling of new state.
@@ -2796,7 +2796,7 @@ 
    Args
    
 
    
 
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-Browse git
+Browse git
 
 
    class SliceDynamicIntegrationTransition(DynamicIntegrationTransition):
     """Dynamic integration transition with slice sampling of new state.
diff --git a/docs/docs/utils.html b/docs/docs/utils.html
index 2b6a530..2184250 100644
--- a/docs/docs/utils.html
+++ b/docs/docs/utils.html
@@ -61,7 +61,7 @@ 
    Module mici.utils
    
 
    
 
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+Browse git
 
 
    """Utility functions and classes."""
 
@@ -292,7 +292,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def hash_array(array):
     """Compute hash of a NumPy array by hashing data as a byte sequence.
@@ -326,7 +326,7 @@ 
    Returns
    
 
    
 
 Expand source code
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+Browse git
 
 
    def log1p_exp(val):
     """Numerically stable implementation of `log(1 + exp(val))`."""
@@ -344,7 +344,7 @@ 
    Returns
    
 
    
 
 Expand source code
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+Browse git
 
 
    def log1m_exp(val):
     """Numerically stable implementation of `log(1 - exp(val))`."""
@@ -364,7 +364,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def log_sum_exp(val1, val2):
     """Numerically stable implementation of `log(exp(val1) + exp(val2))`."""
@@ -384,7 +384,7 @@ 
    Returns
    
 
    
 
 Expand source code
-Browse git
+Browse git
 
 
    def log_diff_exp(val1, val2):
     """Numerically stable implementation of `log(exp(val1) - exp(val2))`."""
@@ -414,7 +414,7 @@ 
    Classes
    
 
    
 
 Expand source code
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+Browse git
 
 
    class LogRepFloat(object):
     """Numerically stable logarithmic representation of positive float values.
@@ -549,7 +549,7 @@ 
    Instance variables
    
 
    
 
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+Browse git
 
 
    @property
 def val(self):
diff --git a/docs/index.html b/docs/index.html
index bc0173c..477e32e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -88,6 +88,7 @@
 
  • Why Mici?
    • 
 
  • Related projects
    • 
 
  • Overview of package
    • 
+
  • Notebooks
    • 
 
  • Example: sampling on a torus
    • 
 
  • References
    • 
 
@@ -158,6 +159,68 @@ 
    Overview of package
    
 
  • DynamicSliceHMC - dynamic integration time Hamiltonian Monte Carlo with slice sampling from trajectory, equivalent to the original 'NUTS' algorithm (Hoffman and Gelman, 2014).
    • 
 
  • DynamicMultinomialHMC - dynamic integration time Hamiltonian Monte Carlo with multinomial sampling from trajectory, equivalent to the current default MCMC algorithm in Stan (Hoffman and Gelman, 2014; Betancourt, 2017).
    • 
 
+
    Notebooks
    
+
    The manifold MCMC methods implemented in Mici have been used in several research projects. Below links are provided to a selection of Jupyter notebooks associated with these projects as demonstrations of how to use Mici and to illustrate some of the settings in which manifold MCMC methods can be computationally advantageous.
    
+
+  
+    
+  
+  
+    
+    
+  
+  
+    
+    
+  
+  
+    
+    
+  
+
     Manifold lifting: MCMC in the vanishing noise regime
    Open non-interactive version with nbviewer
+      
+        Render with nbviewer
+      
+    
    Open interactive version with Binder
+      
+        Launch with Binder
+      
+    
    Open interactive version with Google Colab
+      
+        Open in Colab
+        
+    
    
+
+
+  
+    
+  
+  
+    
+    
+  
+  
+    
+    
+  
+  
+    
+    
+  
+
    Manifold MCMC methods for inference in diffusion models
    Open non-interactive version with nbviewer
+      
+        Render with nbviewer
+      
+    
    Open interactive version with Binder
+      
+        Launch with Binder
+      
+    
    Open interactive version with Google Colab
+      
+        Open in Colab
+        
+    
    
+
 
    Example: sampling on a torus
    
 
 
diff --git a/setup.py b/setup.py
index 2f60a58..a3cf39e 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name='mici',
-    version='0.1.8',
+    version='0.1.9',
     author='Matt Graham',
     description=(
         'MCMC samplers based on simulating Hamiltonian dynamics on a manifold'