eryn 1.2.4__py3-none-any.whl → 1.2.6__py3-none-any.whl

eryn/utils/transform.py

@@ -11,6 +11,10 @@ class TransformContainer:
     """Container for helpful transformations
 
     Args:
+        input_basis (list): List of integers or strings representing each 
+            basis element from the input basis.
+        output_basis (list): List of integers or strings representing each 
+            basis element for the output basis.
         parameter_transforms (dict, optional): Keys are ``int`` or ``tuple``
             of ``int`` that contain the indexes into the parameters
             that correspond to the transformation added as the Values to the
@@ -31,53 +35,70 @@ class TransformContainer:
 
     """
 
-    def __init__(self, parameter_transforms=None, fill_dict=None):
+    def __init__(self, input_basis=None, output_basis=None, parameter_transforms=None, fill_dict=None, key_map={}):
 
+        
         # store originals
         self.original_parameter_transforms = parameter_transforms
+        self.ndim_full = len(output_basis)
+        self.ndim = len(input_basis)
+
+        self.input_basis, self.output_basis = input_basis, output_basis
+
+        test_inds = []
+        for key in input_basis:
+            if key not in output_basis and key not in key_map:
+                raise ValueError("All keys in input_basis must be present in output basis, or you must provide a key_map")
+            key_in = key if key not in key_map else key_map[key]
+            test_inds.append(output_basis.index(key_in))
+
+        self.test_inds = test_inds = np.asarray(test_inds)
         if parameter_transforms is not None:
             # differentiate between single and multi parameter transformations
             self.base_transforms = {"single_param": {}, "mult_param": {}}
 
             # iterate through transforms and setup single and multiparameter transforms
             for key, item in parameter_transforms.items():
-                if isinstance(key, int):
-                    self.base_transforms["single_param"][key] = item
+                if isinstance(key, str) or isinstance(key, int):
+                    if key not in output_basis:
+                        assert key in key_map
+                        key = key_map[key]
+                    key_in = output_basis.index(key)
+                    self.base_transforms["single_param"][key_in] = item
                 elif isinstance(key, tuple):
-                    self.base_transforms["mult_param"][key] = item
+                    _tmp = []
+                    for i in range(len(key)):
+                        key_tmp = key[i]
+                        if  key_tmp not in output_basis:
+                            assert key_tmp in key_map
+                            key_tmp = key_map[key_tmp]
+                        _tmp.append(output_basis.index(key_tmp))
+                    self.base_transforms["mult_param"][tuple(_tmp)] = item
                 else:
                     raise ValueError(
-                        "Parameter transform keys must be int or tuple of ints. {} is neither.".format(
+                        "Parameter transform keys must be str (or int) or tuple of strs (or ints). {} is neither.".format(
                             key
                         )
                     )
         else:
             self.base_transforms = None
 
+        self.original_fill_dict = fill_dict
         if fill_dict is not None:
             if not isinstance(fill_dict, dict):
                 raise ValueError("fill_dict must be a dictionary.")
 
-            self.fill_dict = fill_dict
-            fill_dict_keys = list(self.fill_dict.keys())
-            for key in ["ndim_full", "fill_inds", "fill_values"]:
-                # check to make sure it has all necessary pieces
-                if key not in fill_dict_keys:
-                    raise ValueError(
-                        f"If providing fill_inds, dictionary must have {key} as a key."
-                    )
-            # check all the inputs
-            if not isinstance(fill_dict["ndim_full"], int):
-                raise ValueError("fill_dict['ndim_full'] must be an int.")
-            if not isinstance(fill_dict["fill_inds"], np.ndarray):
-                raise ValueError("fill_dict['fill_inds'] must be an np.ndarray.")
-            if not isinstance(fill_dict["fill_values"], np.ndarray):
-                raise ValueError("fill_dict['fill_values'] must be an np.ndarray.")
+            self.fill_dict = {}
+            self.fill_dict["fill_inds"] = []
+            self.fill_dict["fill_values"] = []
+            for key in fill_dict.keys():
+                self.fill_dict["fill_inds"].append(output_basis.index(key))
+                self.fill_dict["fill_values"].append(fill_dict[key])
 
             # set up test_inds accordingly
-            self.fill_dict["test_inds"] = np.delete(
-                np.arange(self.fill_dict["ndim_full"]), self.fill_dict["fill_inds"]
-            )
+            self.fill_dict["test_inds"] = test_inds
+            self.fill_dict["fill_inds"] = np.asarray(self.fill_dict["fill_inds"])
+            self.fill_dict["fill_values"] = np.asarray(self.fill_dict["fill_values"])
 
         else:
             self.fill_dict = None
@@ -134,6 +155,8 @@ class TransformContainer:
     def fill_values(self, params, xp=None):
         """fill fixed parameters
 
+        This also adjusts parameter order as needed between the two bases. 
+
         Args:
             params (np.ndarray[..., ndim]): Array with coordinates. This array is
                 filled with values according to the ``self.fill_dict`` dictionary.
@@ -152,7 +175,7 @@ class TransformContainer:
             shape = params.shape
 
             # setup new array to fill
-            params_filled = xp.zeros(shape[:-1] + (self.fill_dict["ndim_full"],))
+            params_filled = xp.zeros(shape[:-1] + (self.ndim_full,))
             test_inds = xp.asarray(self.fill_dict["test_inds"])
             # special indexing to properly fill array with params
             indexing_test_inds = tuple([slice(0, temp) for temp in shape[:-1]]) + (
@@ -179,7 +202,7 @@ class TransformContainer:
             return params
 
     def both_transforms(
-        self, params, copy=True, return_transpose=False, reverse=False, xp=None
+        self, params, copy=True, return_transpose=False, xp=None
     ):
         """Transform the parameters and fill fixed parameters
 
@@ -197,9 +220,6 @@ class TransformContainer:
                 (default: ``True``)
             return_transpose (bool, optional): If ``True``, return the transpose of the
                 array. (default: ``False``)
-            reverse (bool, optional): If ``True`` perform the filling after the transforms. This makes
-                indexing easier, but removes the ability of fixed parameters to affect transforms. 
-                (default: ``False``)
             xp (object, optional): ``numpy`` or ``cupy``. If ``None``, use ``numpy``.
                 (default: ``None``) 
 
@@ -212,15 +232,8 @@ class TransformContainer:
             xp = np
 
         # run transforms first
-        if reverse:
-            temp = self.transform_base_parameters(
-                params, copy=copy, return_transpose=return_transpose, xp=xp
-            )
-            temp = self.fill_values(temp, xp=xp)
-
-        else:
-            temp = self.fill_values(params, xp=xp)
-            temp = self.transform_base_parameters(
-                temp, copy=copy, return_transpose=return_transpose, xp=xp
-            )
+        temp = self.fill_values(params, xp=xp)
+        temp = self.transform_base_parameters(
+            temp, copy=copy, return_transpose=return_transpose, xp=xp
+        )
         return temp

eryn/utils/updates.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 from abc import ABC
+import dataclasses
 
 import numpy as np
 
@@ -20,6 +21,111 @@ class Update(ABC, object):
         """
         raise NotImplementedError
 
+class CompositeUpdate(Update):
+    """A composite update that chains multiple Update objects together."""
+    
+    def __init__(self, updates: list):
+        """
+        Args:
+            updates (list): List of Update objects to chain together.
+        """
+        self._updates = updates
+    
+    def __call__(self, iter, last_sample, sampler):
+        """Call all chained updates in sequence."""
+        for update in self._updates:
+            update(iter, last_sample, sampler)
+    
+    def __add__(self, other):
+        """Concatenate with another Update or CompositeUpdate."""
+        if isinstance(other, CompositeUpdate):
+            return CompositeUpdate(self._updates + other._updates)
+        elif isinstance(other, Update):
+            return CompositeUpdate(self._updates + [other])
+        else:
+            raise NotImplementedError
+    
+    def __radd__(self, other):
+        """Support other + self."""
+        if isinstance(other, CompositeUpdate):
+            return CompositeUpdate(other._updates + self._updates)
+        elif isinstance(other, Update):
+            return CompositeUpdate([other] + self._updates)
+        else:
+            raise NotImplementedError
+    
+    def __repr__(self):
+        return f"CompositeUpdate({self._updates})"
+
+
+@dataclasses.dataclass
+class UpdateStep(Update):
+    """
+    Base class for chainable update steps.
+    
+    Attributes:
+        nsteps (int): Base number of steps between updates.
+        increment (int): Factor by which to increase the interval.
+        increment_every (int): Number of iterations after which to increase the interval.
+        stop (int): Optional iteration to stop updates.
+    """
+    nsteps: int = 100
+    increment: int = 1
+    increment_every: int = 500
+    stop: int = None
+    
+    def __add__(self, other):
+        """Concatenate with another Update or CompositeUpdate."""
+        if isinstance(other, CompositeUpdate):
+            return CompositeUpdate([self] + other._updates)
+        elif isinstance(other, Update):
+            return CompositeUpdate([self, other])
+        else:
+            return NotImplemented
+    
+    def __radd__(self, other):
+        """Support other + self."""
+        if isinstance(other, CompositeUpdate):
+            return CompositeUpdate(other._updates + [self])
+        elif isinstance(other, Update):
+            return CompositeUpdate([other, self])
+        else:
+            return NotImplemented
+    
+    def check_step(self, iteration):
+        """Check if the update should be applied at this iteration.
+        
+        The diagnostic frequency decreases over time. The interval between
+        diagnostics is multiplied by `increment` every `increment_every` steps.
+        
+        Example with nsteps=100, increment=2, increment_every=500:
+            - iterations 0-499: check every 100 steps (but not at 0)
+            - iterations 500-999: check every 200 steps
+            - iterations 1000-1499: check every 400 steps
+            - etc.
+        """
+        if iteration == 0:
+            return False
+        
+        exponent = iteration // self.increment_every
+        interval = self.nsteps * (self.increment ** exponent)
+        
+        if self.stop is not None and iteration >= self.stop:
+            return False
+        
+        return (iteration % interval == 0)
+
+    def update(self, iteration, last_sample, sampler):
+        """Override this method in subclasses to define the update behavior."""
+        raise NotImplementedError("Subclasses must implement update() method.")
+    
+    def __call__(self, iteration, last_sample, sampler):
+        """Call the update if the step condition is met."""
+        if self.check_step(iteration):
+            print(f'Calling {self.__class__.__name__} at iteration {iteration}')
+            self.update(iteration, last_sample, sampler)
+        
+   
 
 class AdjustStretchProposalScale(Update):
     def __init__(

eryn/utils/utility.py

@@ -218,7 +218,7 @@ def stepping_stone_log_evidence(betas, logls, block_len=50, repeats=100):
 
     Based on
     a. https://arxiv.org/abs/1810.04488 and
-    b. https://pubmed.ncbi.nlm.nih.gov/21187451/.
+    b. doi: 10.1093/sysbio/syq085
 
     Args:
         betas (np.ndarray[ntemps]): The inverse temperatures to use for the quadrature.

{eryn-1.2.4.dist-info → eryn-1.2.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: eryn
-Version: 1.2.4
+Version: 1.2.6
 Summary: Eryn: an omni-MCMC sampling package.
 Author: Michael Katz
 Author-email: Michael Katz <mikekatz04@gmail.com>
@@ -9,7 +9,6 @@ Classifier: Natural Language :: English
 Classifier: Programming Language :: C++
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -19,6 +18,9 @@ Requires-Dist: h5py
 Requires-Dist: jsonschema
 Requires-Dist: matplotlib
 Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: corner
+Requires-Dist: seaborn
 Requires-Dist: nvidia-ml-py
 Requires-Dist: platformdirs
 Requires-Dist: pydantic
@@ -41,7 +43,8 @@ Requires-Dist: corner ; extra == 'doc'
 Requires-Dist: matplotlib ; extra == 'testing'
 Requires-Dist: corner ; extra == 'testing'
 Requires-Dist: chainconsumer ; extra == 'testing'
-Requires-Python: >=3.9
+Requires-Dist: scienceplots ; extra == 'testing'
+Requires-Python: >=3.10
 Provides-Extra: doc
 Provides-Extra: testing
 Description-Content-Type: text/markdown
@@ -90,7 +93,7 @@ python -m unittest discover
 
 ## Contributing
 
-Please read [CONTRIBUTING.md](CONTRIBUTING) for details on our code of conduct, and the process for submitting pull requests to us.
+Please read [CONTRIBUTING](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us. See [CONTRIBUTORS](CONTRIBUTORS.md) for those that have authored code for and contributed to Eryn.
 
 ## Versioning
 
@@ -146,17 +149,6 @@ archivePrefix = {arXiv},
 
 Depending on which proposals are used, you may be required to cite more sources. Please make sure you do this properly. 
 
-## Authors
-
-* **Michael Katz**
-* Nikos Karnesis
-* Natalia Korsakova
-* Jonathan Gair
-
-### Contibutors
-
-* Maybe you!
-
 ## License
 
 This project is licensed under the GNU License - see the [LICENSE.md](LICENSE) file for details.

{eryn-1.2.4.dist-info → eryn-1.2.6.dist-info}/RECORD

@@ -1,9 +1,9 @@
 eryn/CMakeLists.txt,sha256=rs-_qMYpJryM_FyvERto4RgQQ_NV4lkYvFzCNU7vvFc,1736
 eryn/__init__.py,sha256=eMxCEUQyqtaUM8zTr6kDCxeuFWpxZsfY41TefWUNHXI,821
 eryn/backends/__init__.py,sha256=yRQszA4WSofDDsSpTsA1V9eNw-pLVO_qalP5wpKjyZQ,380
-eryn/backends/backend.py,sha256=VitOOK3vkzVlpzYj-y-_N0Q5GA6DBdm9ZwIMKvQjBOE,47011
-eryn/backends/hdfbackend.py,sha256=njW1KA2Anw9zxpLTYLkpNErNRBgNMA4VKidZXidkh-A,29414
-eryn/ensemble.py,sha256=TqpTLun3iydLOycEi2Gtlg0enLEL2raVrPyVMIQgn-o,71998
+eryn/backends/backend.py,sha256=Udw_29TelVxAZsMNfsMiuIOUSlEUIRKTqXhfpNwnIng,47327
+eryn/backends/hdfbackend.py,sha256=dYJZtgTyNmW7zGpN6bVP8iY16hViDq2Gj2h970_w-pw,30062
+eryn/ensemble.py,sha256=-swmSbfrfxrQzP4yRUuG-GtQKvcaHPIgZMmyt595r0Q,72342
 eryn/git_version.py.in,sha256=dZ5WklaoF4dDsCVqhgw5jwr3kJCc8zjRX_LR90byZOw,139
 eryn/model.py,sha256=5TeWTI6V-Xcuy5C2LI6AmtZZU-EkRSSuA7VojXNALk8,284
 eryn/moves/__init__.py,sha256=9pWsSZSKLt05Ihd46vPASHwotTOHOPk_zEsCm8jWiw8,1081
@@ -24,14 +24,15 @@ eryn/moves/rj.py,sha256=6krjJ5EsvgLZMTMgE9rStjjKtBIW6nw87ywRYbYtROU,15915
 eryn/moves/stretch.py,sha256=auKjeN5elf9fqLR1-oDeR0pF1vdaRnKJEQcpI0mLgVU,8242
 eryn/moves/tempering.py,sha256=e2doT8jVWSuaPpVUKIkWQjRe20T0i98w70wi-dz7buo,23977
 eryn/pbar.py,sha256=uDDn8dMVHLD6EqZyk6vGhkOQwxgFm21Us9dz-nZE4oI,1330
-eryn/prior.py,sha256=x4E5NS4v7Odag7a30OXQ-kJuoU3a6M6JnJuKlWGO6F4,14393
+eryn/prior.py,sha256=3JhtkcD3TqZCpu54T_CO_M0_4wfabA9CLf_V_OVKoFA,16034
 eryn/state.py,sha256=x4HZNrGhxnR6Ia2JrVskJGDS1Uk3AgQHgxJ4384Hpzs,31456
-eryn/utils/__init__.py,sha256=HzlQs1wg3J1xdrZjIMO34QHd0ZT58SQFCKEdclj7vpM,250
-eryn/utils/periodic.py,sha256=Q07HKMNeUN8V_rauUjT7fKRwlYOd2AFsa9DekuRYUbk,4135
+eryn/utils/__init__.py,sha256=2jn40OhyhBETx0O6PExDQ104UigIe3xx76KBVZaYZSQ,248
+eryn/utils/periodic.py,sha256=w0C7YT6v7iVkvhP2OAg0UZ3aMZRUUCyLXrxAwT1pOeY,4745
+eryn/utils/plot.py,sha256=RAzhocHyk7xyxPVnisnZ4ri8OObFL16KJG7XxkSITEM,56841
 eryn/utils/stopping.py,sha256=fX1np10U3B-fpI3dGqEPZfqeYt8dc0x3PQGwrvYbbFU,5095
-eryn/utils/transform.py,sha256=wzOYow7xHjqVOi8ZQDXBeoFj9y53cCtIeLggrQuo_sc,8895
-eryn/utils/updates.py,sha256=U3T9UxPLabJzJuuB9s2OuX3vMD_2P7486SkgaFEkbLw,2137
-eryn/utils/utility.py,sha256=mgmfoL0BFFb3hho7OAQSJLO7T_erx6f6t38V-5yKSA4,11296
-eryn-1.2.4.dist-info/WHEEL,sha256=eh7sammvW2TypMMMGKgsM83HyA_3qQ5Lgg3ynoecH3M,79
-eryn-1.2.4.dist-info/METADATA,sha256=IBGDzBc3Esx7RPZ_RKSFQewgaitRnFyVEaacPn3-9MA,6240
-eryn-1.2.4.dist-info/RECORD,,
+eryn/utils/transform.py,sha256=PqtGG__DAtIuRJm2SR9_ZuRyPvlUmh-eplgbpmZZghQ,9467
+eryn/utils/updates.py,sha256=W9oWUkUXzofTX21MDx8K89GMR_x-SYJERGphvGUcGF8,6003
+eryn/utils/utility.py,sha256=9i3xe0SllA31jWvO_D39dGN_mi8r_va8Pe-dOWhasaM,11280
+eryn-1.2.6.dist-info/WHEEL,sha256=eh7sammvW2TypMMMGKgsM83HyA_3qQ5Lgg3ynoecH3M,79
+eryn-1.2.6.dist-info/METADATA,sha256=qN0g_VqhB1a9_uYFKzzSorCQBfLnecSB9MyfCU-N3gY,6290
+eryn-1.2.6.dist-info/RECORD,,