Update license

.gitignore

@@ -76,3 +76,6 @@ timings*.json
 # Shell and python scripts
 *.script.sh
 *.script.py
+
+# Jupyter checkpoints
+.ipynb_checkpoints/

LICENSE

@@ -1,15 +1,31 @@
-BitBirch-Tools Python Package
-Copyright (C) 2025  Miranda-Quintana Lab
+BitBirch-Tools Python Package: An open-source clustering module based on iSIM.
 
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+If you find this code useful, please cite the BitBirch paper:
+https://doi.org/10.1039/D5DD00030K
 
-This program 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 General Public License for more details.
+Copyright (C) 2025  The Miranda-Quintana Lab BitBirch developers, including:
 
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+- Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+- Krisztina Zsigmond <kzsigmond@ufl.edu>
+- Ignacio Pickering <ipickering@chem.ufl.edu>
+- Kenneth Lopez Perez <klopezperez@chem.ufl.edu>
+- Miroslav Lzicar <miroslav.lzicar@deepmedchem.com>
+- Vicky (Vic) Jung <jungvicky@ufl.edu>
+- Kate Huddleston <kdavis2@chem.ufl.edu>
+
+This program is free software: you can redistribute it and/or modify it under the terms
+of the GNU General Public License as published by the Free Software Foundation, version
+3 (SPDX-License-Identifier: GPL-3.0-only). Portions of the file ./bbtools/bb_lean.py are
+licensed under the BSD 3-Clause License Copyright (c) 2007-2024 The scikit-learn
+developers. All rights reserved. (SPDX-License-Identifier: BSD-3-Clause). Copies or
+reproductions of code in the ./bbtools/bb_lean.py file must in addition adhere to the
+BSD-3-Clause license terms. A copy of the BSD-3-Clause license can be located at the
+root of this repository, under ./LICENSES/BSD-3-Clause.txt.
+
+This program 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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this
+program. This copy can be located at the root of this repository, under
+./LICENSES/GPL-3.0-only.txt.  If not, see <http://www.gnu.org/licenses/gpl-3.0.html>.

LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2007-2024 The scikit-learn developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,15 +1,13 @@
-# bbtools
+# BitBirch-Tools
 
 ## Overview
 
 ## Installation
 
-From source:
-
-First install submodules, afterwards run:
+From source, using a conda environment:
 
 ```bash
-# conda|mamba env create --file ./environment.yaml
+conda env create --file ./environment.yaml
 pip install -e .
 ```
 

_examples_NOT_PORTED/README.md

@@ -0,0 +1,5 @@
+# BitBirch Examples
+
+TODO: Examples have not yet been ported from the BitBirch repo
+Currently they are here as a reference only
+Refinement functionality and plotting_utils have not been ported either