eryn 1.2.5__py3-none-any.whl → 1.2.6__py3-none-any.whl

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-1.2.5.dist-info → eryn-1.2.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: eryn
-Version: 1.2.5
+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-1.2.5.dist-info → eryn-1.2.6.dist-info}/RECORD

@@ -3,7 +3,7 @@ eryn/__init__.py,sha256=eMxCEUQyqtaUM8zTr6kDCxeuFWpxZsfY41TefWUNHXI,821
 eryn/backends/__init__.py,sha256=yRQszA4WSofDDsSpTsA1V9eNw-pLVO_qalP5wpKjyZQ,380
 eryn/backends/backend.py,sha256=Udw_29TelVxAZsMNfsMiuIOUSlEUIRKTqXhfpNwnIng,47327
 eryn/backends/hdfbackend.py,sha256=dYJZtgTyNmW7zGpN6bVP8iY16hViDq2Gj2h970_w-pw,30062
-eryn/ensemble.py,sha256=OmwaLQHjIxe9LFkNM_tTUeXmwbTI0R-bm2S5yApyncI,72325
+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
@@ -26,12 +26,13 @@ eryn/moves/tempering.py,sha256=e2doT8jVWSuaPpVUKIkWQjRe20T0i98w70wi-dz7buo,23977
 eryn/pbar.py,sha256=uDDn8dMVHLD6EqZyk6vGhkOQwxgFm21Us9dz-nZE4oI,1330
 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/__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=PqtGG__DAtIuRJm2SR9_ZuRyPvlUmh-eplgbpmZZghQ,9467
-eryn/utils/updates.py,sha256=U3T9UxPLabJzJuuB9s2OuX3vMD_2P7486SkgaFEkbLw,2137
-eryn/utils/utility.py,sha256=mgmfoL0BFFb3hho7OAQSJLO7T_erx6f6t38V-5yKSA4,11296
-eryn-1.2.5.dist-info/WHEEL,sha256=eh7sammvW2TypMMMGKgsM83HyA_3qQ5Lgg3ynoecH3M,79
-eryn-1.2.5.dist-info/METADATA,sha256=rex8RemF1bUpmVV86ZezubBZXxCZhyjneOmKd7qdbqA,6240
-eryn-1.2.5.dist-info/RECORD,,
+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,,