eryn 1.2.5__tar.gz → 1.2.6__tar.gz

{eryn-1.2.5 → eryn-1.2.6}/PKG-INFO

@@ -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 → eryn-1.2.6}/README.md

@@ -42,7 +42,7 @@ 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
 
@@ -98,17 +98,6 @@ 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 → eryn-1.2.6}/pyproject.toml

@@ -8,7 +8,7 @@ requires = [
 [project]
 name = "eryn" #@NAMESUFFIX@
 
-version = "1.2.5"
+version = "1.2.6"
 
 description = "Eryn: an omni-MCMC sampling package."
 
@@ -17,7 +17,7 @@ readme = "README.md"
 authors = [
   { name = "Michael Katz", email = "mikekatz04@gmail.com" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 classifiers = [
   "License :: OSI Approved :: Apache Software License",
@@ -25,7 +25,6 @@ classifiers = [
   "Programming Language :: C++",
   "Programming Language :: Cython",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
@@ -38,6 +37,9 @@ dependencies = [
   "jsonschema",                            # To validate content of file registry
   "matplotlib",
   "numpy",
+  "pandas",
+  "corner",
+  "seaborn",                               # for runtime plots
   "nvidia-ml-py",                          # To detect CUDA version if any
   "platformdirs",                          # To locate config and data dir on all platforms
   "pydantic",                              # To handle citations and references with advanced dataclasses
@@ -68,6 +70,7 @@ optional-dependencies.testing = [
   "matplotlib",
   "corner",
   "chainconsumer",
+  "scienceplots",                          # for runtime plots
 ]
 
 [tool.pyproject-fmt]

{eryn-1.2.5 → eryn-1.2.6}/src/eryn/ensemble.py

@@ -13,7 +13,7 @@ from .pbar import get_progress_bar
 from .state import State
 from .prior import ProbDistContainer
 
-# from .utils import PlotContainer
+from .utils import PlotContainer
 from .utils import PeriodicContainer
 from .utils.utility import groups_from_inds
 
@@ -233,7 +233,7 @@ class EnsembleSampler(object):
         blobs_dtype=None,  # TODO check this
         plot_iterations=-1,  # TODO: do plot stuff?
         plot_generator=None,
-        plot_name=None,
+        plot_folder=None,
         periodic=None,
         update_fn=None,
         update_iterations=-1,
@@ -662,18 +662,15 @@ class EnsembleSampler(object):
         self.plot_iterations = plot_iterations
 
         if plot_generator is None and self.plot_iterations > 0:
-            raise NotImplementedError
             # set to default if not provided
-            if plot_name is not None:
-                name = plot_name
-            else:
-                name = "output"
+            if plot_folder is  None:
+                plot_folder = "./runtime_plots"
             self.plot_generator = PlotContainer(
-                fp=name, backend=self.backend, thin_chain_by_ac=True
+                backend=self.backend, plots=['base', 'rj'], parent_folder=plot_folder, discard=0.2
             )
         elif self.plot_iterations > 0:
-            raise NotImplementedError
             self.plot_generator = plot_generator
+            self.plot_generator.backend = self.backend # make sure backend is correctly set
 
         # prepare stopping functions
         self.stopping_fn = stopping_fn
@@ -1107,7 +1104,7 @@ class EnsembleSampler(object):
             # diagnostic plots
             # TODO: adjust diagnostic plots
             if self.plot_iterations > 0 and (i + 1) % (self.plot_iterations) == 0:
-                self.plot_generator.generate_plot_info()  # TODO: remove defaults
+                self.plot_generator.produce_plots(sampler=self)  # TODO: remove defaults
 
             # check for stopping before updating
             if (

{eryn-1.2.5 → eryn-1.2.6}/src/eryn/utils/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# from .plot import PlotContainer
+from .plot import PlotContainer
 from .utility import *
 from .periodic import *
 from .transform import *