bblean 0.6.0b1__tar.gz

bblean-0.6.0b1/.cruft.json

@@ -0,0 +1,20 @@
+{
+  "template": "git@github.com:IgnacioJPickering/cookiecutter-pycargo",
+  "commit": "5d9ffa2461db9a78fcbab0194efefb7000d85d4e",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "access": "private",
+      "repo_name": "bbtools",
+      "package_name": "bbtools",
+      "command": "bbtools",
+      "author_name": "Ignacio Pickering",
+      "author_git_profile": "IgnacioJPickering",
+      "author_email": "ign.pickering@gmail.com",
+      "python_version_minor": "10",
+      "_template": "git@github.com:IgnacioJPickering/cookiecutter-pycargo",
+      "_commit": "5d9ffa2461db9a78fcbab0194efefb7000d85d4e"
+    }
+  },
+  "directory": null
+}

bblean-0.6.0b1/.flake8

@@ -0,0 +1,11 @@
+[flake8]
+ignore = W503,E203,E731
+max-line-length = 88
+exclude =
+    .git,
+    __pycache__,
+    build,
+    .eggs,
+    bblean.egg-info,
+    bblean/_legacy/*.py,
+    docs,

bblean-0.6.0b1/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @IgnacioJPickering

bblean-0.6.0b1/.github/workflows/ci-cpp.yaml

@@ -0,0 +1,63 @@
+name: ci-cpp
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  cpp-tests:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-repo
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-subtests inline-snapshot
+          BITBIRCH_BUILD_NATIVE=1 BITBIRCH_BUILD_CPP=1 pip install --verbose .
+
+      - name: run-pytest
+        run: BITBIRCH_CANT_SKIP_CPP_TESTS=1 pytest -s ./tests/test_similarity.py
+
+
+  # Ubuntu 24.04 for reproducibility in regression tests only
+  # coverage makes tests slightly slower, so regression tests should not run with
+  # coverage
+  # skip these for pushes to main since they are slower
+  cpp-regression-tests:
+    runs-on: ubuntu-24.04
+    if: github.ref != 'refs/heads/main'
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-repo
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-subtests inline-snapshot
+          BITBIRCH_BUILD_NATIVE=1 BITBIRCH_BUILD_CPP=1 pip install --verbose .
+
+      - name: run-pytest
+        run: BITBIRCH_CANT_SKIP_CPP_TESTS=1 pytest -s ./tests/test_regression.py

bblean-0.6.0b1/.github/workflows/ci.yaml

@@ -0,0 +1,155 @@
+name: ci
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 0 * * *'
+
+env:
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  flake8:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+
+      - name: run-flake8
+        run: flake8 .
+
+  tests:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-repo-and-test-deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-subtests pytest-cov coverage inline-snapshot
+          pip install --verbose --editable .
+
+      - name: run-pytest
+        run: |
+          pytest --cov=bblean --cov-report=json -s -k 'not regression' ./tests
+          coverage report
+
+      - name: upload-badge-artifact
+        if: ${{ runner.os == 'Linux' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage.json
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-repo-and-docs-deps
+        run: |
+          sudo apt-get install -y pandoc
+          python -m pip install --upgrade pip
+          pip install sphinx sphinx-design pydata-sphinx-theme nbsphinx
+          pip install --verbose --editable .
+
+      - name: build-docs
+        run: BITBIRCH_NO_EXTENSIONS=1 sphinx-build docs/src docs/build 
+
+      - name: upload-docs-artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs
+          path: docs/build
+
+  upload-docs-and-badges-to-gh-pages:
+    runs-on: ubuntu-latest
+    needs: [tests, docs]
+    if: github.ref == 'refs/heads/main'
+    permissions:
+      contents: write
+    steps:
+      - name: create-site-dirs
+        run:  |
+          mkdir -p site/coverage
+          mkdir -p site/devdocs
+          mkdir -p site/docs/stable
+
+      # TODO: releases to docs/stable
+      - name: fetch-docs
+        uses: actions/download-artifact@v4
+        with:
+          name: docs
+          path: './site/devdocs'
+
+      - name: fetch-coverage-report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-report
+          path: ./site/coverage/
+
+      - name: generate-coverage-badge
+        run: |
+          COVERAGE=$(jq -r '.totals.percent_covered_display' site/coverage/coverage.json)
+          echo "{\"schemaVersion\":1,\"label\":\"coverage\",\"message\":\"${COVERAGE}%\",\"color\":\"green\"}" > site/coverage/coverage-badge.json
+
+      - name: deploy-to-gh-pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site
+          publish_branch: gh-pages
+
+  # Ubuntu 24.04 for reproducibility in regression tests only
+  # coverage makes tests slightly slower, so regression tests should not run with
+  # coverage
+  # skip these for pushes to main since they are slower
+  regression-tests:
+    runs-on: ubuntu-24.04
+    if: github.ref != 'refs/heads/main'
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-repo
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest pytest-subtests inline-snapshot
+          pip install --verbose .
+
+      - name: run-pytest
+        run: pytest -s ./tests/test_regression.py

bblean-0.6.0b1/.github/workflows/upload-to-pypi.yaml

@@ -0,0 +1,134 @@
+name: upload-to-pypi
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Force version
+      upload-pypi:
+        description: Upload to pypi
+        required: false
+        default: false
+        type: boolean
+      upload-testpypi:
+        description: Upload to test-pypi
+        required: false
+        default: false
+        type: boolean
+
+env:
+  PYTHON_VERSION: '3.11'
+  SETUPTOOLS_SCM_PRETEND_VERSION: ${{ github.event.inputs.version }}
+  # cibuildwheel configuration:
+  # Skip py 3.14, 32 bit and musllinux (Alpine) wheels
+  CIBW_SKIP: "cp314-* cp314t-* *-manylinux_i686 *-win32 *-musllinux_*"
+  CIBW_TEST_REQUIRES: pytest pytest-subtests inline-snapshot
+  CIBW_TEST_COMMAND: pytest -k 'not regression' {project}/tests
+  CIBW_PRERELEASE_PYTHONS: False
+  CIBW_ENVIRONMENT: "SETUPTOOLS_SCM_PRETEND_VERSION=${{ github.event.inputs.version }} BITBIRCH_BUILD_CPP=1"
+  # Build wheels that support both aarch64 and x86_64 on macOS
+  CIBW_ARCHS_MACOS: "universal2"
+  CIBW_BUILD_VERBOSITY: 3
+
+jobs:
+  make_sdist:
+    name: make-source-distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-sdist-deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: build-sdist
+        run: python -m build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+      - name: validate-sdist-metadata
+        run: twine check dist/*
+
+  build_wheels:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    name: build-${{ matrix.os }}-wheels
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: checkout-repo
+        uses: actions/checkout@v5
+        with:
+          persist-credentials: false
+
+      - name: setup-python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: install-wheel-deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install cibuildwheel
+
+      - name: build-wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  publish_to_testpypi:
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    if: ${{ github.event.inputs.upload-testpypi == 'true' }}
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/bblean
+    permissions:
+      id-token: write 
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+      - name: publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          repository-url: https://test.pypi.org/legacy/
+
+  publish_to_pypi:
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    if: ${{ github.event.inputs.upload-pypi == 'true' }}
+    environment:
+      name: pypi
+      url: https://pypi.org/p/bblean
+    permissions:
+      id-token: write 
+
+    steps:
+      - uses: actions/download-artifact@v5
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+      - name: publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

bblean-0.6.0b1/.gitignore

@@ -0,0 +1,95 @@
+# Byte-compiled / optimized
+__pycache__/
+*.py[cod]
+
+# Setuptools-scm file
+_version.py
+
+# C extensions and binaries
+*.so
+*.o
+
+# Compressed files
+*.tar
+*.tar.gz
+*.zip
+
+# Distribution / packaging
+build/
+dist/
+sdist/
+eggs/
+.eggs/
+*.egg-info/
+*.egg
+wheels/
+wheelhouse/
+share/python-wheels/
+
+# Coverage
+htmlcov/
+.coverage
+.coverage.*
+coverage.xml
+coverage.json
+.hypothesis
+.pytest_cache/
+
+# Sphinx documentation
+docs/build
+docs/src/_api_autogen/
+
+# Mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Vim swap files
+*.swo
+*.swp
+
+# nohup
+nohup.out
+
+# vscode
+.vscode
+
+# language server
+.ccls-cache
+
+# memray memory profile files
+*.bin
+*-flamegraph-memray.html
+
+# py-spy profile files
+profile.svg
+profile_output*
+
+# Outputs / inputs
+*.npy
+monitor-rss*.csv
+peak-rss*.json
+cluster-mol-ids*.json
+config*.json
+timings*.json
+max-rss.txt
+
+# Pickle
+*.pkl
+*.pickle
+
+# Shell and python scripts
+*.script.sh
+*.script.bash
+*.script.py
+script.py
+script.sh
+
+# Jupyter checkpoints
+.ipynb_checkpoints/
+
+# Outputs from examples
+examples/*.png
+examples/*.csv
+!examples/biogen_logS.csv
+*.pdf

bblean-0.6.0b1/.pre-commit-config.yaml

@@ -0,0 +1,71 @@
+# Configuration file that stores all hooks that pre-commit runs
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: no-commit-to-branch  # disallow commiting to master / main directly
+        args: ['--branch', 'main', '--branch', 'master']
+        stages: [pre-commit]
+      - id: check-yaml  # check yaml files for parsable syntax
+        stages: [pre-push]
+      - id: check-toml  # checks toml files for parsable syntax
+        stages: [pre-push]
+      - id: check-json  # checks json files for parsable syntax
+        stages: [pre-push]
+      - id: check-added-large-files  # prevent large files from commit
+        stages: [pre-push]
+      - id: check-merge-conflict  # checks for merge conflict strings
+        stages: [pre-push]
+      - id: debug-statements  # checks for "breakpoint()" and debugger imports
+        stages: [pre-push]
+
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+        files: \.py$
+        stages: [pre-push]
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        stages: [pre-push]
+
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        files: \.py$
+        exclude: bblean/bitbirch\.py$|bblean/_legacy/bb_uint8\.py$|bblean/_legacy/bb_int64\.py$
+        stages: [pre-push]
+
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: "mypy --ignore-missing ."
+        # Don't generate a venv for the exe
+        language: system
+        types: [python]
+        # Pass no files but run regardless
+        files: $^
+        always_run: true
+        # Print output on success
+        verbose: true
+        stages: [pre-push]
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: "pytest ./tests -k 'not regression and not tsne'"
+        # Don't generate a venv for the exe
+        language: system
+        types: [python]
+        # Pass no files but run regardless
+        files: $^
+        always_run: true
+        # Print output on success
+        verbose: true
+        stages: [pre-push]

bblean-0.6.0b1/LICENSE

@@ -0,0 +1,48 @@
+BitBIRCH-Lean Python Package: An open-source clustering module based on iSIM.
+
+If you find this software useful please cite the following articles:
+- BitBIRCH: efficient clustering of large molecular libraries:
+    https://doi.org/10.1039/D5DD00030K
+- BitBIRCH Clustering Refinement Strategies:
+    https://doi.org/10.1021/acs.jcim.5c00627
+- BitBIRCH-Lean:
+    (preprint) https://www.biorxiv.org/content/10.1101/2025.10.22.684015v1
+
+Copyright (C) 2025  The Miranda-Quintana Lab and other BitBirch developers, comprised
+exclusively by:
+- 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 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>.

bblean-0.6.0b1/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.