mcsamplers 2026.9.4__tar.gz

mcsamplers-2026.9.4/.gitignore

@@ -0,0 +1,181 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.txt
+*.h5
+*.json
+*.pkl
+*.pdf
+*.orig
+*.txt
+*.png
+*.json
+*.gwf
+*.h5
+*.hdf5
+*.log
+# C extensions
+*.so
+*.npy
+*.npz
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# The packaging framework (hatch-requirements-txt) READS these at build time,
+# so a blanket *.txt above would leave a clone unbuildable: pip clones, hatch
+# looks for requirements.txt, and metadata generation fails with
+# FileNotFoundError. They must be tracked.
+!requirements.txt
+!optional-requirements.txt

mcsamplers-2026.9.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020-2026 Vaishak Prasad
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mcsamplers-2026.9.4/PKG-INFO

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+Metadata-Version: 2.5
+Name: mcsamplers
+Version: 2026.9.4
+Summary: Monte-Carlo samplers for gravitational-wave parameter estimation: nested sampling and MCMC
+Project-URL: Homepage, https://gitlab.com/vaishakp/parameter-estimation
+Project-URL: Bug Tracker, https://gitlab.com/vaishakp/parameter-estimation/-/issues
+Author-email: Vaishak Prasad <vaishakprasad@gmail.com>
+License: MIT
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.11
+Requires-Dist: corner
+Requires-Dist: h5py
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: psutil
+Requires-Dist: scipy
+Requires-Dist: sympy
+Requires-Dist: tqdm
+Requires-Dist: waveformtools
+Provides-Extra: opt
+Requires-Dist: pytest; extra == 'opt'
+Requires-Dist: schwimmbad; extra == 'opt'
+Description-Content-Type: text/markdown
+
+# mcsamplers
+
+Monte-Carlo stochastic samplers for gravitational-wave parameter estimation:
+nested sampling and MCMC, built around a small `Model` base class that you
+subclass with your own likelihood.
+
+```bash
+pip install mcsamplers
+```
+
+Requires Python 3.11+.
+
+## The `Model` contract
+
+Everything here works against one abstraction. Subclass `Model`, implement
+`evaluate_logliklihood`, and the reduced-coordinate machinery comes with it:
+the samplers explore the unit cube `[0, 1]^ndim`, and `Model` maps those
+points onto your physical priors before calling you.
+
+```python
+import numpy as np
+from mcsamplers.model import Model
+
+class Gaussian(Model):
+    def evaluate_logliklihood(self, parameters):
+        return -0.5 * float(np.sum(np.asarray(parameters) ** 2))
+
+model = Gaussian(
+    xdata=np.linspace(0, 1, 64),
+    ydata=np.zeros(64),
+    initial_guess=[0.5, 0.5],
+    parameter_priors_dict={"a": [0.0, 2.0], "b": [-1.0, 1.0]},
+)
+
+# Unit cube in, physical parameters out: (0.5, 0.5) -> (1.0, 0.0)
+model.evaluate_logliklihood_reduced(np.array([0.5, 0.5]))
+```
+
+Priors are uniform boxes given as `{name: [min, max]}`. `Model` also supplies
+`evaluate_liklihood`, `ln_prior_probability`, `pushforward_samples` and the
+pickle round trip the samplers use for checkpointing.
+
+## Nested sampling
+
+```python
+from mcsamplers.nested.sampler import NestedSampler
+
+sampler = NestedSampler(n_live=500, n_dim=2, n_iter=5000, Model=model)
+sampler.run()
+
+samples = sampler.posterior_samples
+log_z = sampler.logevidence
+```
+
+New live points are drawn according to `random_sample_method`, one of
+`prior`, `mcmc`, `random-distance` or `relative-centroid`. Runs can be
+checkpointed and resumed with `restart=True` and `checkpoint_time_stamps`.
+
+## MCMC
+
+`mcsamplers.markov_chain.yumcee` is a Metropolis–Hastings sampler with
+multiple walkers:
+
+```python
+from mcsamplers.markov_chain.yumcee import yumcee_run
+
+samples = yumcee_run(loglik, iguess, ndim, nwalkers, nsteps, prop_sigma)
+```
+
+`yumcee_p` is a parallel variant intended to run across nodes, and
+`yumcee_utils` holds autocorrelation, corner-plot and sample-statistics
+helpers.
+
+## Tests
+
+```bash
+pip install mcsamplers[opt]
+pytest --pyargs mcsamplers.tests
+```
+
+## Status and caveats
+
+This is research code — used in anger, but not hardened for general use. The
+test suite pins the `Model` contract, not sampling correctness: the samplers
+themselves have no numerical regression tests.
+
+## Licence
+
+MIT. See [LICENSE](LICENSE).

mcsamplers-2026.9.4/README.md

@@ -0,0 +1,89 @@
+# mcsamplers
+
+Monte-Carlo stochastic samplers for gravitational-wave parameter estimation:
+nested sampling and MCMC, built around a small `Model` base class that you
+subclass with your own likelihood.
+
+```bash
+pip install mcsamplers
+```
+
+Requires Python 3.11+.
+
+## The `Model` contract
+
+Everything here works against one abstraction. Subclass `Model`, implement
+`evaluate_logliklihood`, and the reduced-coordinate machinery comes with it:
+the samplers explore the unit cube `[0, 1]^ndim`, and `Model` maps those
+points onto your physical priors before calling you.
+
+```python
+import numpy as np
+from mcsamplers.model import Model
+
+class Gaussian(Model):
+    def evaluate_logliklihood(self, parameters):
+        return -0.5 * float(np.sum(np.asarray(parameters) ** 2))
+
+model = Gaussian(
+    xdata=np.linspace(0, 1, 64),
+    ydata=np.zeros(64),
+    initial_guess=[0.5, 0.5],
+    parameter_priors_dict={"a": [0.0, 2.0], "b": [-1.0, 1.0]},
+)
+
+# Unit cube in, physical parameters out: (0.5, 0.5) -> (1.0, 0.0)
+model.evaluate_logliklihood_reduced(np.array([0.5, 0.5]))
+```
+
+Priors are uniform boxes given as `{name: [min, max]}`. `Model` also supplies
+`evaluate_liklihood`, `ln_prior_probability`, `pushforward_samples` and the
+pickle round trip the samplers use for checkpointing.
+
+## Nested sampling
+
+```python
+from mcsamplers.nested.sampler import NestedSampler
+
+sampler = NestedSampler(n_live=500, n_dim=2, n_iter=5000, Model=model)
+sampler.run()
+
+samples = sampler.posterior_samples
+log_z = sampler.logevidence
+```
+
+New live points are drawn according to `random_sample_method`, one of
+`prior`, `mcmc`, `random-distance` or `relative-centroid`. Runs can be
+checkpointed and resumed with `restart=True` and `checkpoint_time_stamps`.
+
+## MCMC
+
+`mcsamplers.markov_chain.yumcee` is a Metropolis–Hastings sampler with
+multiple walkers:
+
+```python
+from mcsamplers.markov_chain.yumcee import yumcee_run
+
+samples = yumcee_run(loglik, iguess, ndim, nwalkers, nsteps, prop_sigma)
+```
+
+`yumcee_p` is a parallel variant intended to run across nodes, and
+`yumcee_utils` holds autocorrelation, corner-plot and sample-statistics
+helpers.
+
+## Tests
+
+```bash
+pip install mcsamplers[opt]
+pytest --pyargs mcsamplers.tests
+```
+
+## Status and caveats
+
+This is research code — used in anger, but not hardened for general use. The
+test suite pins the `Model` contract, not sampling correctness: the samplers
+themselves have no numerical regression tests.
+
+## Licence
+
+MIT. See [LICENSE](LICENSE).

mcsamplers-2026.9.4/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

mcsamplers-2026.9.4/docs/code.rst

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+Serial Monte Carlo intro
+========================
+.. automodule:: MCMC.readme
+   :members:
+
+
+Serial Monte Carlo sampler
+==========================
+.. automodule:: MCMC.yumcee
+   :members:
+
+Monte Carlo utils
+=================
+.. automodule:: MCMC.yumcee_utils
+   :members:
+
+
+Parallel Monte Carlo sampler
+============================
+.. automodule:: MCMC.yumcee_p
+   :members:

mcsamplers-2026.9.4/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

mcsamplers-2026.9.4/docs/source/README

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+Markov Chain Monte Carlo project: yumcee.
+
+yumcee: Serial MCMC
+yumcee_p : MCMC implemented with mpi4py
+yumcee_utils: Various utilities for Statistics of samples
+
+
+This library contains Monte Carlo samplers.
+
+1. Serial Markov chain Monte Carlo.
+2. Parallel Markov chain Monte Carlo.
+3. Setial Nested sampler.
+
+
+The MCMC is a very basic MCMC samplers with a static poposal sigma, which can be controlled. This is capable of running multi dimensional, multi walker MCMC.
+
+The Nested smapler is under construction.
+
+More details can be found in the wiki page of the gitlab repository.

mcsamplers-2026.9.4/docs/source/conf.py

@@ -0,0 +1,65 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+sys.setrecursionlimit(1500)
+
+
+# -- Project information -----------------------------------------------------
+
+project = "Parameter estimation"
+copyright = "2020, Vaishak P"
+author = "Vaishak P"
+
+# The full version, including alpha/beta/rc tags
+release = "2020"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["rinoh.frontend.sphinx", "sphinx.ext.autodoc"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    "papersize": "letterpaper",
+    "pointsize": "10pt",
+    "preamble": "",
+    "figure_align": "htbp",
+}

mcsamplers-2026.9.4/docs/source/index.rst

@@ -0,0 +1,60 @@
+.. Parameter estimation documentation master file, created by
+   sphinx-quickstart on Wed Jul  8 14:13:27 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Parameter estimation's documentation!
+================================================
+
+*yumcee*, is a very basic, working,  MPI based- Monte-Carlo sampler and a set of tools for barrying out Bayesian parameter estimation. 
+
+It is implemented in python using MPI for parallelism, and thus scalable to large systems. It consists of:
+
+    1.  A markov chain Monte-Carlo (MCMC) sampler.
+    
+    2.  A nested Monte-Carlo sampler (in works).
+
+    3.  Tools for parameter-estimation.
+
+    4.  Retreiving the statistical properties of the posteriors from the chains: 
+ 
+       
+        a). mean/mode.
+
+        b). standard deviation.
+
+    6.  Plotting the posteriors.
+
+    7.  Miscellaneous tools
+        
+        Saving the chains, results to the disk.
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Serial Monte Carlo intro
+========================
+.. include:: README
+.. automodule:: MCMC.README
+   :members:
+   :download: `<README>`
+
+
+Serial Monte Carlo sampler
+==========================
+.. automodule:: MCMC.yumcee
+   :members:
+
+Monte Carlo utils
+=================
+.. automodule:: MCMC.yumcee_utils
+   :members:
+
+Parallel Monte Carlo sampler
+============================
+.. automodule:: MCMC.yumcee_p
+   :members:

mcsamplers-2026.9.4/mcsamplers/__init__.py

@@ -0,0 +1,6 @@
+"""Monte-Carlo samplers: nested sampling and MCMC."""
+
+# Written in PEP 440 normal form. A zero-padded "2026.09.04" would normalise
+# to "2026.9.4" on the built distribution, leaving __version__ disagreeing
+# with importlib.metadata.version("mcsamplers") for the life of the release.
+__version__ = "2026.9.4"

mcsamplers-2026.9.4/mcsamplers/markov_chain/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2020] [Vaishak Prasad]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mcsamplers-2026.9.4/mcsamplers/markov_chain/README

@@ -0,0 +1,19 @@
+Markov Chain Monte Carlo project: yumcee.
+
+yumcee: Serial MCMC
+yumcee_p : MCMC implemented with mpi4py
+yumcee_utils: Various utilities for Statistics of samples
+
+
+This library contains Monte Carlo samplers.
+
+1. Serial Markov chain Monte Carlo.
+2. Parallel Markov chain Monte Carlo.
+3. Setial Nested sampler.
+
+
+The MCMC is a very basic MCMC samplers with a static poposal sigma, which can be controlled. This is capable of running multi dimensional, multi walker MCMC.
+
+The Nested smapler is under construction.
+
+More details can be found in the wiki page of the gitlab repository.

mcsamplers-2026.9.4/mcsamplers/markov_chain/README.md

@@ -0,0 +1,5 @@
+Markov Chain Monte Carlo project: yumcee.
+
+yumcee: Serial MCMC
+yumcee_p : MCMC implemented with mpi4py
+yumcee_utils: Various utilities for Statistics of samples

mcsamplers-2026.9.4/mcsamplers/markov_chain/__init__.py

@@ -0,0 +1 @@
+"""Markov-chain Monte Carlo samplers (yumcee, serial and parallel)."""