bandframework · mpratola · Jun 25, 2026 · Jun 25, 2026 · Jun 25, 2026 · Jun 29, 2026
diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2025 Matthew Pratola and John Yannotty
+Copyright (c) 2025 Matthew T. Pratola and John Yannotty
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,142 +1,58 @@
-# Open Bayesian Trees Project
-This repository includes new developments with Bayesian Additive Regression Trees and extends the original OpenBT repository created by Matt Pratola (https://bitbucket.org/mpratola/openbt/src/master/).
-Such extensions include Bayesian Model Mixing and Bayesian Calibration. 
-All of the Bayesian Tree code is written in C++. User interfaces constructed in R and Python allow one to easily run the software.
-The BART Model Mixing software has been implemented in the [Taweret](https://github.com/bandframework/Taweret/tree/main) Python package in conjunction with the [BAND](https://bandframework.github.io/) collaboration.
-
-
-# Installation
-The heart of OpenBT is a set of C++ tools that can be used directly via
-the command line or indirectly through the Python and R packages, which wrap
-them.  Typically these tools are built with an implementation of the Message
-Passing Interface (MPI) such as [Open MPI](https://www.open-mpi.org) or
-[MPICH](https://www.mpich.org) to enable distributed parallelization of
-computations.  In particular, the Python wrapper package is always built with
-MPI support.
-
-The software and its distribution scheme have been developed to allow users to
-use OpenBT with the MPI installation of their choice.  For instance, it
-can be built with MPI installations on leadership class platforms and clusters
-that were installed by experts and optimized for their specific platform.  As a
-result, however, the software is not distributed as prebuilt binaries or wheels,
-but rather must be built for each case with the compiler suite and matching MPI
-implementation provided by the user.
-
-## Requirements
-Before building and installing the Python package, users
-must provide
-* a compiler suite that includes a C++ compiler that supports the C++14
-  standard,
-* an MPI installation that is compatible with the compiler suite, and
-* optionally the [Eigen software package](https://gitlab.com/libeigen/eigen).
-
-Note that if installing MPI using a package manager, related developer library
-packages such as ``libopenmpi-dev`` or ``libmpich-dev`` might need to be
-installed in addition to the base MPI packages such as ``openmpi-bin`` or
-``mpich``.
-
-To build and install just the bare C++ tools, users must provide in addition to
-the above
-* the [Meson build system](https://mesonbuild.com) and its prerequisites such as
-  Python 3 and [ninja](https://ninja-build.org).
-
-While both Meson and ninja are used internally to build the Python package, they
-are installed automatically just for building the package.
-
-The Meson build system is setup to automatically detect the compiler suite and
-MPI installation to use.  If Eigen already exists in the system and Meson can
-find it, then Meson will use it for the build.  Otherwise, Meson will
-automatically obtain a copy of Eigen for internal use.
-
-We presently test OpenBT with both Open MPI and MPICH.  In addition, we
-have successfully tested with the Intel MPI implementation and have used the
-Python package with MPI implementations installed
-* via package managers such as Ubuntu's Advanced Packaging Tool (`apt`) and
-  [homebrew](https://brew.sh) on macOS;
-* by experts on clusters and that are available as modules; and
-* with `conda` from the prebuilt conda forge
-  [openmpi](https://anaconda.org/conda-forge/openmpi) package.
-
-## Meson installation
-The Meson build system documentation suggests installing Meson via package
-manager when possible.  Please refer to that documentation for detailed and
-up-to-date installation information.
-
-If Meson cannot be installed by package manager or the manager's version is too
-old, the following is contrary to Meson suggestions but has been used
-successfully to install Meson with Python into a dedicated virtual environment
-as well as to install `meson` in the `PATH` for use without needing to activate
-that virtual environment.
-```
-$ /path/to/target/python -m venv ~/local/venv/meson
-$ . ~/local/venv/meson/bin/activate
-$ which python
-$ python -m pip install --upgrade pip
-$ python -m pip install meson
-$ python -m pip list
-$ ln -s ~/local/venv/meson/bin/meson ~/local/bin
-<add ~/local/bin to PATH if desired and appropriate>
-$ deactivate
-$ which meson
-$ meson --version
-```
-Note that this `meson` virtual environment is for installing **just** the Meson
-build system.  Attempts to install `openbt` into this virtual environment
-will likely fail with an error that the `mesonbuild` module cannot be found.
-
-## Python package
-The OpenBT Python package is **not** currently distributed on PyPI since the
-[PyPI OpenBT package](https://pypi.org/project/openbt/) already exists.  This
-package will eventually be transferred to this project so that distribution of
-modern versions of this package will be enabled by PyPI under the name `openbt`.
-
-<!--
-The OpenBTMixing Python package is distributed on
-[PyPI](https://pypi.org/project/openbtmixing/) as a source distribution that
-contains the C++ code and files needed by Meson to build the dedicated,
-standalone command line tools that the package will use.  The tools are built
-and installed automatically by Meson as part of executing
-```
-python -m pip install openbt
-```
-By default, `pip install` does not show any of Meson's progress.  Users and
-developers interested in seeing how Meson satisfies dependencies and reviewing
-compiler output should pass `-v` to `pip install`.
--->
+# OpenBT
 
-Instead the package should be built and installed from a clone of this repository with
-```
-$ cd /path/to/OpenBT/openbt_pypkg
-$ python -m pip install .
-```
-Developers can install in developer/editable mode with verbose logging of the
-build process and installation with
-```
-$ cd /path/to/OpenBT/openbt_pypkg
-$ python -m pip install -v -e .
-```
-In this latter case, the command line tools are built automatically and
-installed at `/path/to/OpenBT/openbt_pypkg/src/openbt/bin`.  The
-Python package is hardcoded to use those tools so that the existence of another
-set of tools in the system and in `PATH` should not cause issues.
+TODO: Copy info from landing page of sphinx docs here.
 
-OpenBT package installations can be minimally tested with
-```
-$ python
->>> import openbt
->>> openbt.__version__
-'<version>'
->>> openbt.test()
-```
+### Repository
+TODO: Add general badges
+
+### Python
+TODO: Add Python-specific badges
+
+## License & Copyright
 
-## C++ library & command line tool interface
-Developers and C++ users can directly build and install the command line tools,
-an OpenBT library, and library tests with `tools/build_openbt_clt.sh`.
-Note that these do **not** need to be built in order to use the Python package.
+TODO: Copy license & copyright info from landing page of sphinx docs here
 
-## R package
-**TODO**: Needs to be written based on current state of affairs.
+## Support
 
-# Examples
+To
 
-The examples from the article "Model Mixing Using Bayesian Additive Regression Trees" are reproduced in the jupyter notebook BART_BMM_Technometrics.ipynb. This notebook can be run locally or in a virtual environment such as google colab.
+* report potential problems with OpenBT or any of the packages derived from it,
+* propose a change, or
+* request a new feature,
+
+please check if a related [Issue](https://github.com/bandframework/OpenBT/issues)
+already exists before creating a new issue.  For all other communication, please
+send an email to the OpenBT development team
+
+ * TODO: Matt's contact info
+ * TODO: John's contact info
+
+## Documentation
+
+[User and Developer Guides](https://openbt.readthedocs.io) are hosted on
+ReadTheDocs.  Please refer to those documents for information regarding
+examples.
+
+## Installation & Testing
+
+Refer to the getting started sections in the User Guide related to the tool or
+package that you intend to use.
+
+## Contributing to IBCDFO
+
+Contributions are welcome in a variety of forms; see
+[Contributing](https://openbt.readthedocs.io/en/latest/contributing.html) in the
+Developer Guide.
+
+## Cite OpenBT
+
+```
+@techreport{openbt2026,
+  author      = {Matt Pratola and John Yannotty},
+  title       = {{OpenBT 1.2.0} Users Manual},
+  institution = {TBD},
+  number      = {Version 1.2.0},
+  year        = {2026},
+  url         = {https://openbt.readthedocs.io/}
+}
+```
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -2,5 +2,10 @@ Contributing
 ============
 General Information
 -------------------
-.. todo::
-    Sarthak to write this
+    The Open Bayesian Trees (OpenBT) project evolved from an initial C + MPI codebase written from scratch in 2010 through two subsequent ground-up rewrites culminating in the current C++ codebase with R and Python wrappers. Matt Pratola (mpratola@iu.edu) has served as the primary author and architect for OpenBT. John Yannotty (jcyannotty@gmail.com) made significant contributions to the project including BART-based model mixing, the Random Path BART (RPBART) model and RPBART-based model mixing, integrating the Eigen library, and writing Python wrapper code.  Jared O'Neal (joneal@anl.gov) led the move from Autotools to Meson and built out the various Github and Python integrations as part of folding OpenBT into BAND. Akira Horiguchi (ahoriguchi@ucdavis.edu) made contributions with Sobol sensitivity indices and Shapley indices as well as Pareto front-based multiobjective optimization. Clark van Lieshout (clarkvan33@gmail.com) contributed Python wrapper code. Robert McCulloch (robert.mcculloch@asu.edu) made contributions in the early days with the random number generators and log gamma approximation.
+
+    The current repo, now housed within the wider BAND project, becomes the long-term home for OpenBT.
+
+    Contributions of source code, documentation, and fixes are accepted via github pull requests.  Contributors should branch from, and make pull requests to, the develop branch of `https://github.com/bandframework/openbt <https://github.com/bandframework/openbt>`__.  Please see `https://bandframework.github.io/software/ <https://bandframework.github.io/software/>`__ or email a member of the `BAND <https://bandframework.github.io/team>`__ team for more information.
+
+
diff --git a/docs/images/openbt_logo_rect.png b/docs/images/openbt_logo_rect.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,14 +3,21 @@
 .. _Open MPI: https://www.open-mpi.org
 .. _MPICH: https://www.mpich.org
 .. _framework: https://bandframework.github.io
+.. _Issue 35: https://github.com/bandframework/OpenBT/issues/35
+.. _OpenBT repository: https://bitbucket.org/mpratola/openbt/src/master
+.. _OpenBTMixing repository: https://github.com/jcyannotty/OpenBT
 
-.. todo::
-    Write high-level description, explain development history, and motivate
-    breakdown of documents presented here.  License, copyright, responsibilities
-    of user, etc.
+
+.. image:: images/openbt_logo_rect.png
+    :align: center
+    :alt: OpenBT
+    :height: 165
+    :width: 451
+
+|openbt| is an extensible software project that implements a variety of Bayesian tree models for scientific and industry applications, including regression, model mixing, sensitivity analysis and multiobjective optimization.  
 
 The heart of |openbt| is a set of C++ tools that can be used directly |via| the
-command line or indirectly through the ``openbt`` Python package, which wraps
+command line or indirectly through the ``openbt`` Python package or ``RopenBT'' R package, which wraps
 them.  Typically these tools are built with an implementation of the Message
 Passing Interface (MPI), such as `Open MPI`_ or MPICH_, to enable distributed
 parallelization of computations.  In particular, the Python wrapper package is
@@ -22,12 +29,18 @@ it can be built with MPI installed on a laptop using the system's package
 manager or with MPI installations on leadership class platforms and clusters
 that were installed by experts and optimized for their specific platform.
 
+This repository was established by merging the contents of the original Bitbucket
+`OpenBT repository`_ with the `OpenBTMixing repository`_, which was based off of
+the former.  It, therefore, will supersede those two repositories, which will be
+frozen.
+
+This repository and its contents are being established and developed as part of
+|band| framework_.
+
 .. note::
     While an R wrapper does exist for the original |openbt| and |openbtmixing|
     repositories, that functionality has not yet been included in this new,
-    combined repository (Issue #XYZ).
-
-This package is being developed as part of |band| framework_.
+    combined repository (`Issue 35`_).
 
 .. toctree::
    :numbered:

diff --git a/docs/release_procedure.rst b/docs/release_procedure.rst
@@ -128,8 +128,8 @@ Otherwise,
    * One side effect of the use of ``setuptools-scm`` is that by default it
      includes in the distribution all files located within ``openbt_pypkg``.
      However, many files and folders in that space do **not** need to be
-     distributed (|eg| Flake8 configuration files and OpenBT command line tools
-     installed during development in ``src/openbt/bin``).  This is what
+     distributed (|eg| Flake8 configuration files and |openbt| command line
+     tools installed during development in ``src/openbt/bin``).  This is what
      "minimal" means above.  Files and folders that should not be included in
      the distribution are specified in ``MANIFEST.in``.
    * Review the metadata to ensure correct and complete.  This should include

diff --git a/includes/ambrt.h b/includes/ambrt.h
@@ -1,26 +1,4 @@
 //     ambrt.h: Additive mean BART model class definition.
-//     Copyright (C) 2012-2016 Matthew T. Pratola, Robert E. McCulloch and Hugh A. Chipman
-//
-//     This file is part of OpenBT.
-//
-//     OpenBT is free software: you can redistribute it and/or modify
-//     it under the terms of the GNU Affero General Public License as published by
-//     the Free Software Foundation, either version 3 of the License, or
-//     (at your option) any later version.
-//
-//     OpenBT is distributed in the hope that it will be useful,
-//     but WITHOUT ANY WARRANTY; without even the implied warranty of
-//     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//     GNU Affero General Public License for more details.
-//
-//     You should have received a copy of the GNU Affero General Public License
-//     along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-//     Author contact information
-//     Matthew T. Pratola: mpratola@gmail.com
-//     Robert E. McCulloch: robert.e.mculloch@gmail.com
-//     Hugh A. Chipman: hughchipman@gmail.com
-
 
 #ifndef GUARD_ambrt_h
 #define GUARD_ambrt_h

diff --git a/includes/amxbrt.h b/includes/amxbrt.h
@@ -1,3 +1,5 @@
+//     amxbrt.h: BART-based model mixing model class definition.
+
 #ifndef GUARD_amxbrt_h
 #define GUARD_amxbrt_h
 

diff --git a/includes/brt.h b/includes/brt.h
@@ -1,26 +1,4 @@
 //     brt.h: Base BT model class definition.
-//     Copyright (C) 2012-2016 Matthew T. Pratola, Robert E. McCulloch and Hugh A. Chipman
-//
-//     This file is part of OpenBT.
-//
-//     OpenBT is free software: you can redistribute it and/or modify
-//     it under the terms of the GNU Affero General Public License as published by
-//     the Free Software Foundation, either version 3 of the License, or
-//     (at your option) any later version.
-//
-//     OpenBT is distributed in the hope that it will be useful,
-//     but WITHOUT ANY WARRANTY; without even the implied warranty of
-//     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//     GNU Affero General Public License for more details.
-//
-//     You should have received a copy of the GNU Affero General Public License
-//     along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-//     Author contact information
-//     Matthew T. Pratola: mpratola@gmail.com
-//     Robert E. McCulloch: robert.e.mculloch@gmail.com
-//     Hugh A. Chipman: hughchipman@gmail.com
-
 
 #ifndef GUARD_brt_h
 #define GUARD_brt_h

diff --git a/includes/brtfuns.h b/includes/brtfuns.h
@@ -1,26 +1,4 @@
 //     brtfuns.h: Base BT model class help functions header file.
-//     Copyright (C) 2012-2016 Matthew T. Pratola, Robert E. McCulloch and Hugh A. Chipman
-//
-//     This file is part of OpenBT.
-//
-//     OpenBT is free software: you can redistribute it and/or modify
-//     it under the terms of the GNU Affero General Public License as published by
-//     the Free Software Foundation, either version 3 of the License, or
-//     (at your option) any later version.
-//
-//     OpenBT is distributed in the hope that it will be useful,
-//     but WITHOUT ANY WARRANTY; without even the implied warranty of
-//     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//     GNU Affero General Public License for more details.
-//
-//     You should have received a copy of the GNU Affero General Public License
-//     along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-//     Author contact information
-//     Matthew T. Pratola: mpratola@gmail.com
-//     Robert E. McCulloch: robert.e.mculloch@gmail.com
-//     Hugh A. Chipman: hughchipman@gmail.com
-
 
 #ifndef GUARD_brtfuns_h
 #define GUARD_brtfuns_h

diff --git a/includes/crn.h b/includes/crn.h
@@ -1,26 +1,4 @@
 //     crn.h: Random number generator class definition.
-//     Copyright (C) 2012-2016 Matthew T. Pratola, Robert E. McCulloch and Hugh A. Chipman
-//
-//     This file is part of OpenBT.
-//
-//     OpenBT is free software: you can redistribute it and/or modify
-//     it under the terms of the GNU Affero General Public License as published by
-//     the Free Software Foundation, either version 3 of the License, or
-//     (at your option) any later version.
-//
-//     OpenBT is distributed in the hope that it will be useful,
-//     but WITHOUT ANY WARRANTY; without even the implied warranty of
-//     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//     GNU Affero General Public License for more details.
-//
-//     You should have received a copy of the GNU Affero General Public License
-//     along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-//     Author contact information
-//     Matthew T. Pratola: mpratola@gmail.com
-//     Robert E. McCulloch: robert.e.mculloch@gmail.com
-//     Hugh A. Chipman: hughchipman@gmail.com
-
 
 #ifndef CRN_H
 #define CRN_H