maintain/ipickering/rename to bblean

.flake8

@@ -6,6 +6,6 @@ exclude =
     __pycache__,
     build,
     .eggs,
-    bbtools.egg-info,
-    bbtools/legacy/*.py,
+    bblean.egg-info,
+    bblean/legacy/*.py,
     docs,

.pre-commit-config.yaml

@@ -24,7 +24,6 @@ repos:
     hooks:
       - id: black
         files: \.py$
-        exclude: bbtools/bblean\.py$|bbtools/bblean_v1\.py$|bbtools/bb_int64\.py$
         stages: [pre-push]
 
   - repo: https://github.com/PyCQA/flake8
@@ -38,7 +37,7 @@ repos:
     hooks:
       - id: autoflake
         files: \.py$
-        exclude: bbtools/bblean\.py$|bbtools/bblean_v1\.py$|bbtools/bb_int64\.py$
+        exclude: bblean/bitbirch\.py$|bblean/legacy/bb_uint8\.py$|bblean/legacy/bb_int64_dense\.py$
         stages: [pre-push]
 
   - repo: local

LICENSE

@@ -1,27 +1,38 @@
-BitBirch-Tools Python Package: An open-source clustering module based on iSIM.
+BitBirch-Lean Python Package: An open-source clustering module based on iSIM.
 
 If you find this code useful, please cite the BitBirch paper:
 https://doi.org/10.1039/D5DD00030K
 
-Copyright (C) 2025  The Miranda-Quintana Lab BitBirch developers, including:
-
+Copyright (C) 2025  The Miranda-Quintana Lab and other BitBirch developers, including:
 - 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>
+
+Authors of ./bblean/multiround.py are:
+- Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+- Ignacio Pickering <ipickering@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 ./bblean/bitbirch.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
+./bblean/bitbirch.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.
+
+Portions of the file ./bblean/bitbirch.py were previously licensed under the LGPL 3.0
+license (SPDX-License-Identifier: LGPL-3.0-only), they are relicensed in this program
+as GPL-3.0, with permission of all original copyright holders:
+- Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
 - Vicky (Vic) Jung <jungvicky@ufl.edu>
+- Kenneth Lopez Perez <klopezperez@chem.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.

README.md

@@ -1,4 +1,4 @@
-# BitBirch-Tools
+# BitBirch-Lean
 
 ## Overview
 
@@ -8,6 +8,7 @@ From source, using a conda environment:
 
 ```bash
 conda env create --file ./environment.yaml
+conda activate bblean
 pip install -e .
 ```
 

_examples_NOT_PORTED/refinement/refine_tutorial.ipynb

@@ -205,7 +205,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#  This function can be found in bbtools.refinement\n",
     "def radius(fps):\n",
     "    bb.set_merge('radius')\n",
     "    brc = bb.BitBirch(branching_factor=branching_factor, threshold=threshold)\n",

bblean/__init__.py

@@ -0,0 +1,7 @@
+r"""
+bblean
+"""
+
+from bblean.bitbirch import BitBirch  # type: ignore
+
+__all__ = ["BitBirch"]

bbtools/_console.py → bblean/_console.py

@@ -4,7 +4,7 @@
 
 from rich.console import Console
 
-from bbtools.memory import get_peak_memory, PeakMemoryStats
+from bblean.memory import get_peak_memory, PeakMemoryStats
 
 
 class BBConsole(Console):

bbtools/bb_lean/bitbirch.py → bblean/bitbirch.py

@@ -1,60 +1,62 @@
-# type: ignore
-# BitBirch-Tools Python Package: An open-source clustering module based on iSIM.
+# BitBirch-Lean Python Package: An open-source clustering module based on iSIM.
 #
 # If you find this code useful, please cite the BitBirch paper:
 # https://doi.org/10.1039/D5DD00030K
 #
-# Copyright (C) 2025  The Miranda-Quintana Lab BitBirch developers, including:
-#
+# Copyright (C) 2025  The Miranda-Quintana Lab and other BitBirch developers, including:
 # - 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>
+#
+# Authors of ./bblean/multiround.py are:
+# - Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+# - Ignacio Pickering <ipickering@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 this file 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 this 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
+# version 3 (SPDX-License-Identifier: GPL-3.0-only).
+#
+# Portions of this file 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 this
+# 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.
 #
+# Portions of this file were previously licensed under the LGPL 3.0
+# license (SPDX-License-Identifier: LGPL-3.0-only), they are relicensed in this program
+# as GPL-3.0, with permission of all original copyright holders:
+# - Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+# - Vicky (Vic) Jung <jungvicky@ufl.edu>
+# - Kenneth Lopez Perez <klopezperez@chem.ufl.edu>
+# - Kate Huddleston <kdavis2@chem.ufl.edu>
+#
 # 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>.
-
-# TODO: remove this?
-# Parts of the BitBIRCH algorithm were previously released under the LGPL-3.0 license
-# by:
-# Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
-# Vicky (Vic) Jung <jungvicky@ufl.edu>
-# Kenneth Lopez Perez <klopezperez@chem.ufl.edu>
-# Kate Huddleston <kdavis2@chem.ufl.edu>
-
-from numpy.typing import NDArray, DTypeLike
+# type: ignore
 import typing as tp
 from collections import defaultdict
 from weakref import WeakSet
 
-import numpy as np
 from scipy import sparse
+import numpy as np
+from numpy.typing import NDArray, DTypeLike
 
-from bbtools.utils import calc_centroid, min_safe_uint
-from bbtools.packing import (
+from bblean.utils import calc_centroid, min_safe_uint
+from bblean.packing import (
     pack_fingerprints,
     unpack_fingerprints,
     popcount,
     jt_sim_packed,
 )
-from bbtools.merges import get_merge_accept_fn, MergeAcceptFunction
+from bblean.merges import get_merge_accept_fn, MergeAcceptFunction
 
 
 # For backwards compatibility with the global "set_merge", keep weak references to all

bbtools/cli.py → bblean/cli.py

@@ -17,10 +17,10 @@
 import typer
 from typer import Typer, Argument, Option, Abort, Context
 
-from bbtools.memory import monitor_rss_daemon, get_peak_memory
-from bbtools.config import DEFAULTS, collect_system_specs_and_dump_config
-from bbtools.packing import pack_fingerprints
-from bbtools.utils import _import_bitbirch_variant, batched
+from bblean.memory import monitor_rss_daemon, get_peak_memory
+from bblean.config import DEFAULTS, collect_system_specs_and_dump_config
+from bblean.packing import pack_fingerprints
+from bblean.utils import _import_bitbirch_variant, batched
 
 app = Typer(
     rich_markup_mode="markdown",
@@ -32,15 +32,15 @@
         [https://doi.org/10.1039/D5DD00030K](https://doi.org/10.1039/D5DD00030K)
     - BitBirch refinement strategies:
         (TODO)
-    - BitBirch-Lean and BB-Tools:
+    - BitBirch-Lean:
         (TODO)
     """,  # noqa
 )
 
 
 def _print_help_banner(ctx: Context, value: bool) -> None:
     if value:
-        from bbtools._console import get_console
+        from bblean._console import get_console
 
         console = get_console()
         console.print_banner()
@@ -146,7 +146,7 @@ def _fps_from_smiles(
     """
     import numpy as np
     from rdkit.Chem import rdFingerprintGenerator, DataStructs, MolFromSmiles
-    from bbtools._console import get_console
+    from bblean._console import get_console
 
     console = get_console(silent=not verbose)
 
@@ -320,7 +320,7 @@ def _run(
 ) -> None:
     r"""Run standard BitBirch clustering"""
     import numpy as np
-    from bbtools._console import get_console
+    from bblean._console import get_console
 
     console = get_console(silent=not verbose)
 
@@ -527,8 +527,8 @@ def _multiround(
     ] = True,
 ) -> None:
     r"""Run multi-round BitBirch clustering, with the option to parallelize"""
-    from bbtools._console import get_console
-    from bbtools.multiround import run_multiround_bitbirch
+    from bblean._console import get_console
+    from bblean.multiround import run_multiround_bitbirch
 
     console = get_console(silent=not verbose)
 

bbtools/config.py → bblean/config.py

@@ -4,13 +4,13 @@
 import json
 import sys
 import dataclasses
-from bbtools.memory import system_mem_gib
+from bblean.memory import system_mem_gib
 import multiprocessing as mp
 import os
 
 import numpy as np
 
-from bbtools.utils import cpu_name
+from bblean.utils import cpu_name
 
 
 @dataclasses.dataclass(slots=True)

bbtools/merges.py → bblean/merges.py

@@ -2,7 +2,7 @@
 import numpy as np
 import warnings
 
-from bbtools.utils import calc_centroid
+from bblean.utils import calc_centroid
 
 
 def jt_isim(c_total: NDArray[np.integer], n_objects: int) -> float:

bbtools/multiround.py → bblean/multiround.py

@@ -1,3 +1,45 @@
+# BitBirch-Lean Python Package: An open-source clustering module based on iSIM.
+#
+# If you find this code useful, please cite the BitBirch paper:
+# https://doi.org/10.1039/D5DD00030K
+#
+# Copyright (C) 2025  The Miranda-Quintana Lab and other BitBirch developers, including:
+# - 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>
+#
+# Authors of this file are:
+# - Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+# - Ignacio Pickering <ipickering@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 ./bblean/bitbirch.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
+# ./bblean/bitbirch.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.
+#
+# Portions of ./bblean/bitbirch.py were previously licensed under the LGPL 3.0
+# license (SPDX-License-Identifier: LGPL-3.0-only), they are relicensed in this program
+# as GPL-3.0, with permission of all original copyright holders:
+# - Ramon Alain Miranda Quintana <ramirandaq@gmail.com>, <quintana@chem.ufl.edu>
+# - Vicky (Vic) Jung <jungvicky@ufl.edu>
+# - Kenneth Lopez Perez <klopezperez@chem.ufl.edu>
+# - Kate Huddleston <kdavis2@chem.ufl.edu>
+#
+# 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>.
 import functools
 import pickle
 import gc
@@ -10,9 +52,9 @@
 import numpy as np
 from numpy.typing import NDArray
 
-from bbtools._console import get_console
-from bbtools.utils import numpy_streaming_save, batched, _import_bitbirch_variant
-from bbtools.config import DEFAULTS
+from bblean._console import get_console
+from bblean.utils import numpy_streaming_save, batched, _import_bitbirch_variant
+from bblean.config import DEFAULTS
 
 
 def _glob_and_sort_by_uint_bits(path: Path | str, glob_expr: str) -> list[Path]:

bbtools/utils.py → bblean/utils.py

@@ -20,13 +20,13 @@ def _import_bitbirch_variant(
         raise ValueError(f"Unknown variant {variant}")
         # Most up-to-date bb varaint
     if variant in ["lean", "lean_dense"]:
-        module = importlib.import_module("bbtools.bb_lean")
+        module = importlib.import_module("bblean.bitbirch")
         # Legacy variant of bb that uses uint8 and supports packing, but no extra optim
     elif variant in ["uint8", "uint8_dense"]:
-        module = importlib.import_module("bbtools.legacy.bb_uint8")
+        module = importlib.import_module("bblean.legacy.bb_uint8")
         # Legacy variant of bb that uses dense int64 fps
     elif variant == "int64_dense":
-        module = importlib.import_module("bbtools.legacy.bb_int64_dense")
+        module = importlib.import_module("bblean.legacy.bb_int64_dense")
 
     Cls = getattr(module, "BitBirch")
     fn = getattr(module, "set_merge")

environment.yaml

@@ -1,4 +1,4 @@
-name: bbtools
+name: bblean
 channels:
   - nodefaults
   - https://conda.anaconda.org/conda-forge