bayesmbar 0.0.5__tar.gz

bayesmbar-0.0.5/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package to PyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/BayesMBAR
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4.1.7
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+

bayesmbar-0.0.5/.github/workflows/sphinx.yml

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+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12' 
+
+    - name: Install pandoc
+      run: sudo apt-get install -y pandoc
+      
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r ./docs/requirements.txt
+    
+    - name: Build Sphinx documentation
+      run: |
+        cd docs
+        make html
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/build/html

bayesmbar-0.0.5/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# 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/
+
+.DS_Store

bayesmbar-0.0.5/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: docs/requirements.txt
+  

bayesmbar-0.0.5/LICENSE

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+MIT License
+
+Copyright (c) 2023 The Ding Research Group at the Tufts University
+
+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.

bayesmbar-0.0.5/PKG-INFO

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+Metadata-Version: 2.3
+Name: bayesmbar
+Version: 0.0.5
+Summary: Add your description here
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: blackjax>=1.2.3
+Requires-Dist: ipython>=8.27.0
+Requires-Dist: jax>=0.4.33
+Requires-Dist: jaxlib==0.4.33
+Requires-Dist: marimo>=0.8.15
+Requires-Dist: nbsphinx>=0.9.5
+Requires-Dist: networkx>=3.3
+Requires-Dist: pytest>=8.3.2
+Requires-Dist: sphinx-autoapi>=3.3.1
+Requires-Dist: sphinx-book-theme>=1.1.3
+Requires-Dist: sphinx-copybutton>=0.5.2
+Requires-Dist: sphinx>=8.0.2
+Requires-Dist: tqdm>=4.66.5
+Description-Content-Type: text/markdown
+
+# Bayesian Multistate Bennett Acceptance Ratio Method
+
+This repository contains the code for the Bayesian Multistate Bennett Acceptance Ratio Method as described in the [paper](https://doi.org/10.1021/acs.jctc.3c01212). BayesMBAR is a Bayesion generalization of the Multistate Bennett Acceptance Ratio (MBAR) method for computing free energy differences between multiple states. 
+
+Besides its theoretical interest, BayesMBAR has two practical advantages over MBAR. First, it provides a more accurate uncertainty estimate, especially when the number of samples is small or the phase space overlap between states is poor. Second, it allows for the incorporation of prior information to improve the accuracy of the free energy estimates. For example, when the free energy surface over a collective variable is known to be smooth, BayesMBAR can use this information to improve the accuracy of the free energy estimates.  The [paper](https://doi.org/10.1021/acs.jctc.3c01212) has more details on the method and its applications.
+
+We are committed to making the code as user-friendly as possible. We are actively working on improving the [documentation](http://xdinglab.com/BayesMBAR/) and adding more examples. If you have any questions or suggestions, please feel free to open an issue or [contact us](mailto:Xinqiang.Ding@tufts.edu) directly. 

bayesmbar-0.0.5/README.md

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+# Bayesian Multistate Bennett Acceptance Ratio Method
+
+This repository contains the code for the Bayesian Multistate Bennett Acceptance Ratio Method as described in the [paper](https://doi.org/10.1021/acs.jctc.3c01212). BayesMBAR is a Bayesion generalization of the Multistate Bennett Acceptance Ratio (MBAR) method for computing free energy differences between multiple states. 
+
+Besides its theoretical interest, BayesMBAR has two practical advantages over MBAR. First, it provides a more accurate uncertainty estimate, especially when the number of samples is small or the phase space overlap between states is poor. Second, it allows for the incorporation of prior information to improve the accuracy of the free energy estimates. For example, when the free energy surface over a collective variable is known to be smooth, BayesMBAR can use this information to improve the accuracy of the free energy estimates.  The [paper](https://doi.org/10.1021/acs.jctc.3c01212) has more details on the method and its applications.
+
+We are committed to making the code as user-friendly as possible. We are actively working on improving the [documentation](http://xdinglab.com/BayesMBAR/) and adding more examples. If you have any questions or suggestions, please feel free to open an issue or [contact us](mailto:Xinqiang.Ding@tufts.edu) directly. 

bayesmbar-0.0.5/build.sh

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+python3 -m build
+python3 -m twine upload --repository-url https://upload.pypi.org/legacy/ dist/*

bayesmbar-0.0.5/docs/.gitignore

@@ -0,0 +1 @@
+./build/*

bayesmbar-0.0.5/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   ?= uv run 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)

bayesmbar-0.0.5/docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

bayesmbar-0.0.5/docs/requirements.txt

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+uv
+furo==2021.11.16
+pandoc

bayesmbar-0.0.5/docs/source/API.rst

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+API
+===
+
+.. automodule:: bayesmbar
+   :members:
+   :undoc-members:
+   :show-inheritance:

bayesmbar-0.0.5/docs/source/_static/four_harmonics.html

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+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <base href='/' />
+    <meta charset="utf-8" />
+    <link rel="icon" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/favicon.ico" />
+    <!-- Preload is necessary because we show these images when we disconnect from the server,
+    but at that point we cannot load these images from the server -->
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/gradient-yHQUC_QB.png" as="image" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/noise-60BoTA8O.png" as="image" />
+    <!-- Preload the fonts -->
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/Lora-VariableFont_wght-B2ootaw-.ttf" as="font" crossorigin="anonymous" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/PTSans-Regular-CxL0S8W7.ttf" as="font" crossorigin="anonymous" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/PTSans-Bold-D9fedIX3.ttf" as="font" crossorigin="anonymous" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/FiraMono-Regular-BTCkDNvf.ttf" as="font" crossorigin="anonymous" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/FiraMono-Medium-DU3aDxX5.ttf" as="font" crossorigin="anonymous" />
+    <link rel="preload" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/FiraMono-Bold-CLVRCuM9.ttf" as="font" crossorigin="anonymous" />
+
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="theme-color" content="#000000" />
+    <meta name="description" content="a marimo app" />
+    <link rel="apple-touch-icon" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/apple-touch-icon.png" />
+    <link rel="manifest" crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/manifest.json" />
+
+    <script data-marimo="true">
+      function __resizeIframe(obj) {
+        var scrollbarHeight = 20; // Max between windows, mac, and linux
+
+        function setHeight() {
+          var element = obj.contentWindow.document.documentElement;
+          // If there is no vertical scrollbar, we don't need to resize the iframe
+          if (element.scrollHeight === element.clientHeight) {
+            return;
+          }
+
+          // Create a new height that includes the scrollbar height if it's visible
+          var hasHorizontalScrollbar = element.scrollWidth > element.clientWidth;
+          var newHeight = element.scrollHeight + (hasHorizontalScrollbar ? scrollbarHeight : 0);
+
+          // Only update the height if it's different from the current height
+          if (obj.style.height !== `${newHeight}px`) {
+            obj.style.height = `${newHeight}px`;
+          }
+        }
+
+        // Resize the iframe to the height of the content and bottom scrollbar height
+        setHeight();
+
+        // Resize the iframe when the content changes
+        const resizeObserver = new ResizeObserver((entries) => {
+          setHeight();
+        });
+        resizeObserver.observe(obj.contentWindow.document.body);
+      }
+    </script>
+    <marimo-filename hidden>/Users/xding07/Library/CloudStorage/OneDrive-Tufts/Research/Projects_on_Github/BayesMBAR/docs/source/examples/four_harmonics.py</marimo-filename>
+    <marimo-mode data-mode='read' hidden></marimo-mode>
+    <marimo-version data-version='0.8.15' hidden></marimo-version>
+    <marimo-user-config data-config='{"completion": {"activate_on_typing": true, "copilot": false}, "display": {"cell_output": "above", "code_editor_font_size": 16, "dataframes": "rich", "default_width": "medium", "theme": "light"}, "formatting": {"line_length": 79}, "keymap": {"overrides": {}, "preset": "default"}, "package_management": {"manager": "pip"}, "runtime": {"auto_instantiate": true, "auto_reload": "off", "on_cell_change": "autorun"}, "save": {"autosave": "after_delay", "autosave_delay": 1000, "format_on_save": false}, "server": {"browser": "default", "follow_symlink": false}}' hidden></marimo-user-config>
+    <marimo-app-config data-config='{"width": "medium"}' hidden></marimo-app-config>
+    <marimo-server-token data-token='static' hidden></marimo-server-token>
+    <title>four harmonics</title>
+    <script type="module" crossorigin crossorigin="anonymous" src="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/index-Bh_LkwFB.js"></script>
+    <link rel="stylesheet" crossorigin crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/@marimo-team/frontend@0.8.15/dist/assets/index-wucNfsJm.css">
+  
+<script data-marimo="true">
+    window.__MARIMO_STATIC__ = {};
+    window.__MARIMO_STATIC__.version = "0.8.15";
+    window.__MARIMO_STATIC__.notebookState = {"cellIds": ["Hbol", "sXTe", "MJUe", "GCuS", "DECB"], "cellNames": ["X18=", "X18=", "X18=", "X18=", "X18="], "cellCodes": ["aW1wb3J0JTIwbnVtcHklMjBhcyUyMG5wJTBBZnJvbSUyMGJheWVzbWJhciUyMGltcG9ydCUyMENCYXllc01CQVI=", 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+    window.__MARIMO_STATIC__.files = {};
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+</head>
+  <body>
+    <div id="root"></div>
+  
+    <marimo-code hidden="">
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+    </marimo-code>
+    </body>
+</html>

bayesmbar-0.0.5/docs/source/conf.py

@@ -0,0 +1,64 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "BayesMBAR"
+copyright = "2024, Xinqiang Ding"
+author = "Xinqiang Ding"
+# release = '0.0.1'
+
+# -- 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.path.insert(0, os.path.abspath("../../"))
+sys.path.insert(0, os.path.abspath("../../../"))
+
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+    "nbsphinx",
+#    "autoapi.extension",
+]
+
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# autodoc_default_options = {
+#     'member-order': 'bysource',
+# }
+autoclass_content = 'both'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_book_theme"
+html_logo = "_static/logo.png"
+html_static_path = ["_static"]
+html_theme_options = {
+    'show_toc_level': 2,
+    'repository_url': 'https://github.com/DingGroup/BayesMBAR',
+    'use_repository_button': True,     # add a "link to repository" button
+    'navigation_with_keys': False,
+}
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"