eryn 1.2.0__tar.gz

eryn-1.2.0/PKG-INFO

@@ -0,0 +1,167 @@
+Metadata-Version: 2.3
+Name: eryn
+Version: 1.2.0
+Summary: Eryn: an omni-MCMC sampling package.
+Author: Michael Katz
+Author-email: Michael Katz <mikekatz04@gmail.com>
+Classifier: License :: OSI Approved :: Apache Software License
+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
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: exceptiongroup ; python_full_version < '3.11'
+Requires-Dist: h5py
+Requires-Dist: jsonschema
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: nvidia-ml-py
+Requires-Dist: platformdirs
+Requires-Dist: pydantic
+Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: wrapt
+Requires-Dist: ipykernel ; extra == 'doc'
+Requires-Dist: ipython ; extra == 'doc'
+Requires-Dist: ipywidgets ; extra == 'doc'
+Requires-Dist: myst-parser ; extra == 'doc'
+Requires-Dist: nbsphinx ; extra == 'doc'
+Requires-Dist: pypandoc ; extra == 'doc'
+Requires-Dist: sphinx ; extra == 'doc'
+Requires-Dist: sphinx-rtd-theme ; extra == 'doc'
+Requires-Dist: sphinx-tippy ; extra == 'doc'
+Requires-Dist: corner ; extra == 'doc'
+Requires-Dist: matplotlib ; extra == 'testing'
+Requires-Dist: corner ; extra == 'testing'
+Requires-Dist: chainconsumer ; extra == 'testing'
+Requires-Python: >=3.9
+Provides-Extra: doc
+Provides-Extra: testing
+Description-Content-Type: text/markdown
+
+# Eryn: a multi-purpose MCMC sampler
+
+Eryn is an advanced MCMC sampler. It has the capability to run with parallel tempering, multiple model types, and unknown counts within each model type using Reversible Jump MCMC techniques. Eryn is heavily based on [emcee](https://emcee.readthedocs.io/en/stable/). The `emcee` base structure with the Ensemble Sampler, State objects, proposal setup, and storage backends is carried over into Eryn with small changes to account for the increased complexity. In a simple sense, Eryn is an advanced (and slightly more complicated) version of `emcee`. 
+
+If you use Eryn in your publication, please cite the paper [arXiv:2303.02164](https://arxiv.org/abs/2303.02164), its [zenodo](https://zenodo.org/record/7705496#.ZAhzukJKjlw), and [emcee](https://emcee.readthedocs.io/en/stable/). The documentation for Eryn can be found here: [mikekatz04.github.io/Eryn](https://mikekatz04.github.io/Eryn). You will find the code on Github: [github.com/mikekatz04/Eryn](https://github.com/mikekatz04/Eryn). 
+
+## Getting Started
+
+Below is a quick set of instructions to get you started with `eryn`.
+
+```
+pip install eryn
+```
+To import eryn:
+
+```
+from eryn.ensemble import EnsembleSampler
+```
+
+See [examples notebook](https://github.com/mikekatz04/Eryn/blob/main/examples/Eryn_tutorial.ipynb) for more info. You can also navigate the [Documentation](https://mikekatz04.github.io/Eryn/html/index.html) pages.
+
+
+### Prerequisites
+
+Eryn has only a few python-based dependencies: `tqdm`, `corner` for plotting, `numpy`, `matplotlib`. 
+
+### Installing
+
+If you are not planning to develop the code, you can just install the latest version with the pip installation technique given above. Otherwise, you can just clone the repo and run `pip install .` inside of the Eryn directory. To run tests on Eryn during development, you can run the following in the main Eryn directory:
+```
+python -m unittest discover
+```
+
+
+## Running the Tests
+
+In the main directory of the package run in the terminal:
+```
+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.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/mikekatz04/Eryn/tags).
+
+## Citation
+
+When using this package, please cite at minimum the following sources:
+
+```
+@article{Karnesis:2023ras,
+    author = "Karnesis, Nikolaos and Katz, Michael L. and Korsakova, Natalia and Gair, Jonathan R. and Stergioulas, Nikolaos",
+    title = "{Eryn : A multi-purpose sampler for Bayesian inference}",
+    eprint = "2303.02164",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.IM",
+    month = "3",
+    year = "2023"
+}
+
+@software{michael_katz_2023_7705496,
+  author       = {Michael Katz and
+                  Nikolaos Karnesis and
+                  Natalia Korsakova},
+  title        = {mikekatz04/Eryn: first full release},
+  month        = mar,
+  year         = 2023,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.7705496},
+  url          = {https://doi.org/10.5281/zenodo.7705496}
+}
+
+@ARTICLE{2013PASP..125..306F,
+       author = {{Foreman-Mackey}, Daniel and {Hogg}, David W. and {Lang}, Dustin and {Goodman}, Jonathan},
+        title = "{emcee: The MCMC Hammer}",
+      journal = {\pasp},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics, Statistics - Computation},
+         year = 2013,
+        month = mar,
+       volume = {125},
+       number = {925},
+        pages = {306},
+          doi = {10.1086/670067},
+archivePrefix = {arXiv},
+       eprint = {1202.3665},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+```
+
+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.
+
+## Acknowledgments
+
+* We wish to thank S. Babak, M. Le Jeune, S. Marsat, T. Littenberg, and N. Cornish for their useful comments and very fruitful discussions. 
+* N Stergioulas and N Karnesis acknowledge  support from the Gr-PRODEX 2019 funding program (PEA 4000132310).

eryn-1.2.0/README.md

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+# Eryn: a multi-purpose MCMC sampler
+
+Eryn is an advanced MCMC sampler. It has the capability to run with parallel tempering, multiple model types, and unknown counts within each model type using Reversible Jump MCMC techniques. Eryn is heavily based on [emcee](https://emcee.readthedocs.io/en/stable/). The `emcee` base structure with the Ensemble Sampler, State objects, proposal setup, and storage backends is carried over into Eryn with small changes to account for the increased complexity. In a simple sense, Eryn is an advanced (and slightly more complicated) version of `emcee`. 
+
+If you use Eryn in your publication, please cite the paper [arXiv:2303.02164](https://arxiv.org/abs/2303.02164), its [zenodo](https://zenodo.org/record/7705496#.ZAhzukJKjlw), and [emcee](https://emcee.readthedocs.io/en/stable/). The documentation for Eryn can be found here: [mikekatz04.github.io/Eryn](https://mikekatz04.github.io/Eryn). You will find the code on Github: [github.com/mikekatz04/Eryn](https://github.com/mikekatz04/Eryn). 
+
+## Getting Started
+
+Below is a quick set of instructions to get you started with `eryn`.
+
+```
+pip install eryn
+```
+To import eryn:
+
+```
+from eryn.ensemble import EnsembleSampler
+```
+
+See [examples notebook](https://github.com/mikekatz04/Eryn/blob/main/examples/Eryn_tutorial.ipynb) for more info. You can also navigate the [Documentation](https://mikekatz04.github.io/Eryn/html/index.html) pages.
+
+
+### Prerequisites
+
+Eryn has only a few python-based dependencies: `tqdm`, `corner` for plotting, `numpy`, `matplotlib`. 
+
+### Installing
+
+If you are not planning to develop the code, you can just install the latest version with the pip installation technique given above. Otherwise, you can just clone the repo and run `pip install .` inside of the Eryn directory. To run tests on Eryn during development, you can run the following in the main Eryn directory:
+```
+python -m unittest discover
+```
+
+
+## Running the Tests
+
+In the main directory of the package run in the terminal:
+```
+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.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/mikekatz04/Eryn/tags).
+
+## Citation
+
+When using this package, please cite at minimum the following sources:
+
+```
+@article{Karnesis:2023ras,
+    author = "Karnesis, Nikolaos and Katz, Michael L. and Korsakova, Natalia and Gair, Jonathan R. and Stergioulas, Nikolaos",
+    title = "{Eryn : A multi-purpose sampler for Bayesian inference}",
+    eprint = "2303.02164",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.IM",
+    month = "3",
+    year = "2023"
+}
+
+@software{michael_katz_2023_7705496,
+  author       = {Michael Katz and
+                  Nikolaos Karnesis and
+                  Natalia Korsakova},
+  title        = {mikekatz04/Eryn: first full release},
+  month        = mar,
+  year         = 2023,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.7705496},
+  url          = {https://doi.org/10.5281/zenodo.7705496}
+}
+
+@ARTICLE{2013PASP..125..306F,
+       author = {{Foreman-Mackey}, Daniel and {Hogg}, David W. and {Lang}, Dustin and {Goodman}, Jonathan},
+        title = "{emcee: The MCMC Hammer}",
+      journal = {\pasp},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics, Statistics - Computation},
+         year = 2013,
+        month = mar,
+       volume = {125},
+       number = {925},
+        pages = {306},
+          doi = {10.1086/670067},
+archivePrefix = {arXiv},
+       eprint = {1202.3665},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+```
+
+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.
+
+## Acknowledgments
+
+* We wish to thank S. Babak, M. Le Jeune, S. Marsat, T. Littenberg, and N. Cornish for their useful comments and very fruitful discussions. 
+* N Stergioulas and N Karnesis acknowledge  support from the Gr-PRODEX 2019 funding program (PEA 4000132310).

eryn-1.2.0/pyproject.toml

@@ -0,0 +1,87 @@
+[build-system]
+build-backend = "uv_build"
+
+requires = [
+  "uv-build>=0.8.17,<0.9",
+]
+
+[project]
+name = "eryn" #@NAMESUFFIX@
+
+version = "1.2.0"
+
+description = "Eryn: an omni-MCMC sampling package."
+
+readme = "README.md"
+
+authors = [
+  { name = "Michael Katz", email = "mikekatz04@gmail.com" },
+]
+requires-python = ">=3.9"
+
+classifiers = [
+  "License :: OSI Approved :: Apache Software License",
+  "Natural Language :: English",
+  "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",
+  "Programming Language :: Python :: 3.13",
+]
+
+dependencies = [
+  "exceptiongroup; python_version<'3.11'", # To access ExceptionGroup with Python 3.9 and 3.10
+  "h5py",
+  "jsonschema",                            # To validate content of file registry
+  "matplotlib",
+  "numpy",
+  "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
+  "pyyaml",                                # To read file registry
+  "requests",                              # To download files automatically
+  "rich",                                  # To display downlaod progress bar
+  "scipy",
+  "tqdm",
+  "wrapt",
+  #@DEPS_CUPYCUDA@,
+  #@DEPS_ERYNCORE@,
+]
+
+optional-dependencies.doc = [
+  "ipykernel",
+  "ipython",
+  "ipywidgets",
+  "myst-parser",
+  "nbsphinx",
+  "pypandoc",
+  "sphinx",
+  "sphinx-rtd-theme",
+  "sphinx-tippy",
+  "corner"
+]
+
+optional-dependencies.testing = [
+  "matplotlib",
+  "corner",
+  "chainconsumer",
+]
+
+[tool.pyproject-fmt]
+max_supported_python = "3.13"
+
+[tool.coverage]
+paths.source = [
+  "src/",
+  "**/site-packages/",
+]
+
+report.omit = [
+  "*/eryn/_version.py",
+  "*/eryn/tests/*.py",
+  "*/eryn/git_version.py",
+  "*/eryn_backend_*/git_version.py",
+]

eryn-1.2.0/src/eryn/CMakeLists.txt

@@ -0,0 +1,51 @@
+# Add subdirectories which contain compiled sources
+
+# Handle Git Metadata
+get_target_property(_ERYN_WITH_CPU eryn WITH_CPU)
+get_target_property(_ERYN_WITH_GPU eryn WITH_GPU)
+
+message(CHECK_START "Building eryn.git_version metadata")
+message(CHECK_START "Find Git executable")
+find_package(Git)
+if(Git_FOUND)
+  message(CHECK_PASS "found")
+  message(CHECK_START "Checking if in Git worktree")
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} rev-parse --is-inside-work-tree
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    OUTPUT_QUIET ERROR_QUIET
+    RESULT_VARIABLE ERYN_GIT_IN_WORKTREE_CODE)
+  if(ERYN_GIT_IN_WORKTREE_CODE EQUAL "0")
+    message(CHECK_PASS "yes")
+
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} log -1 --format=%H
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      OUTPUT_VARIABLE ERYN_GIT_COMMIT_ID
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+    execute_process(
+      COMMAND ${GIT_EXECUTABLE} log -1 --format=%h
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      OUTPUT_VARIABLE ERYN_GIT_COMMIT_SHORT_ID
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+    configure_file(git_version.py.in git_version.py @ONLY)
+
+    if(_ERYN_WITH_CPU)
+      install(FILES ${CMAKE_CURRENT_BINARY_DIR}/git_version.py DESTINATION eryn)
+      install(FILES ${CMAKE_CURRENT_BINARY_DIR}/git_version.py
+              DESTINATION eryn_backend_cpu)
+    endif()
+    if(_ERYN_WITH_GPU)
+      install(FILES ${CMAKE_CURRENT_BINARY_DIR}/git_version.py
+              DESTINATION eryn_backend_cuda${CUDAToolkit_VERSION_MAJOR}x)
+    endif()
+
+    message(CHECK_PASS "done")
+  else()
+    message(CHECK_FAIL "no")
+  endif()
+else()
+  message(CHECK_FAIL "not found")
+  message(CHECK_FAIL "eryn.git_version will not be available")
+endif()

eryn-1.2.0/src/eryn/__init__.py

@@ -0,0 +1,35 @@
+"""GPU Backend Tools."""
+
+# ruff: noqa: E402
+try:
+    from eryn._version import (  # pylint: disable=E0401,E0611
+        __version__,
+        __version_tuple__,
+    )
+
+except ModuleNotFoundError:
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+
+    try:
+        __version__ = version(__name__)
+        __version_tuple__ = tuple(__version__.split("."))
+    except PackageNotFoundError:  # pragma: no cover
+        __version__ = "unknown"
+        __version_tuple__ = (0, 0, 0, "unknown")
+    finally:
+        del version, PackageNotFoundError
+
+_is_editable: bool
+try:
+    from . import _editable
+
+    _is_editable = True
+    del _editable
+except (ModuleNotFoundError, ImportError):
+    _is_editable = False
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "_is_editable",
+]

eryn-1.2.0/src/eryn/backends/__init__.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+
+from .backend import Backend
+
+from .hdfbackend import HDFBackend, TempHDFBackend
+
+__all__ = ["Backend", "HDFBackend", "TempHDFBackend", "get_test_backends"]
+
+
+def get_test_backends():
+    backends = [Backend]
+
+    try:
+        import h5py  # NOQA
+    except ImportError:
+        pass
+    else:
+        backends.append(TempHDFBackend)
+
+    return backends