buscar 0.1.0__tar.gz

buscar-0.1.0/.github/dependabot.yml

@@ -0,0 +1,40 @@
+# GitHub Dependabot configuration
+# Note: this configuration controls Dependabot version updates. Dependabot security
+# updates are configured separately in the repository security settings.
+# See:
+# https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/about-dependabot-security-updates
+
+version: 2
+updates:
+  # GitHub Actions workflow dependencies under .github/workflows.
+  # See:
+  # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for GitHub Actions updates every week.
+      interval: "monthly"
+
+  # Python project dependencies managed by uv.
+  # Dependabot's uv ecosystem updates uv.lock for projects using uv.
+  # See:
+  # https://docs.github.com/en/code-security/dependabot/ecosystems-supported-by-dependabot/supported-ecosystems-and-repositories
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      # Check for project dependency updates every month.
+      interval: "monthly"
+    groups:
+      python-packages:
+        patterns:
+          - "*"
+        update-types:
+          - "minor"
+          - "patch"
+
+  # Pre-commit hook revisions in .pre-commit-config.yaml.
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      # Check for pre-commit hook updates every week.
+      interval: "weekly"

buscar-0.1.0/.github/release-drafter.yml

@@ -0,0 +1,18 @@
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+version-resolver:
+  major:
+    labels:
+      - release-major
+  minor:
+    labels:
+      - release-minor
+  patch:
+    labels:
+      - release-patch
+  default: patch
+change-template: '- $TITLE (@$AUTHOR via #$NUMBER)'
+template: |
+  ## Changes
+
+  $CHANGES

buscar-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v7
+
+      - name: Run pre-commit (required)
+        uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files --show-diff-on-failure
+
+  test:
+    needs: pre-commit
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v7
+      - name: Set up Python
+        uses: actions/setup-python@v7.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+
+      - name: Install dependencies
+        run: uv sync --group dev --frozen
+
+      - name: Run tests with coverage (Ubuntu 3.12)
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        run: uv run --frozen pytest --cov=buscar --cov-report=term-missing --cov-report=xml --cov-report=html
+
+      - name: Upload coverage artifact
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+      - name: Upload HTML coverage artifact
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: coverage-html
+          path: htmlcov
+
+      - name: Run tests
+        if: matrix.os != 'ubuntu-latest' || matrix.python-version != '3.12'
+        run: uv run --frozen pytest
+
+  build:
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v7
+
+      - name: Set up Python
+        uses: actions/setup-python@v7.0.0
+        with:
+          python-version: "3.12"
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+
+      - name: Install dependencies
+        run: uv sync --group dev --frozen
+
+      - name: Build package
+        run: uv build
+
+      - name: Validate wheel import
+        shell: bash
+        run: |
+          uv run --isolated --no-project --with ./dist/buscar-*.whl -- \
+            python -c "import buscar; print(buscar.__name__, buscar.__version__)"

buscar-0.1.0/.github/workflows/draft-release.yml

@@ -0,0 +1,16 @@
+name: Draft release
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  draft-release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: read
+    steps:
+      - uses: release-drafter/release-drafter@34d80673e067bdc0c24568d3af899c216adcfaa9
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

buscar-0.1.0/.github/workflows/publish-pypi.yml

@@ -0,0 +1,70 @@
+name: Publish PyPI release
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout release tag and history
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v7.0.0
+        with:
+          python-version: "3.12"
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v10.2.0
+        with:
+          enable-cache: false
+
+      - name: Build package
+        run: uv build
+
+      - name: Validate wheel import
+        shell: bash
+        run: |
+          uv run --isolated --no-project --with ./dist/buscar-*.whl -- \
+            python -c "import buscar; print(buscar.__name__, buscar.__version__)"
+
+      # Jobs run on separate runners, so pass the validated distributions to
+      # the publish job as an artifact instead of rebuilding them there.
+      - name: Upload package distributions
+        uses: actions/upload-artifact@v7.0.1
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+
+  pypi-publish:
+    name: Upload release to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+      url: https://pypi.org/project/buscar/
+    # PyPI verifies this workflow run through OpenID Connect.
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      # Retrieve the exact distributions built and validated by the build job.
+      - name: Download package distributions
+        uses: actions/download-artifact@v8.0.1
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.14.2

buscar-0.1.0/.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# prevent storing large datasets
+data/
+
+# ignoring prototype files
+_*
+!**/__init__.py
+!**/__main__.py
+
+# ignoring results files as they are generated when running the notebooks
+# also to prevent storing large datasets
+results/
+
+# remove background jobs
+*nohup.out
+
+# ignore .vscode settings
+.vscode/
+
+# ignore ruff catch
+.ruff_cache/
+
+# ignore for now
+recipe/metal.yaml
+
+#ignore prototype files
+_*

buscar-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,83 @@
+# Pre-commit configuration file
+# Documentation: https://pre-commit.com/
+
+repos:
+    # Basic file checks first (fast and foundational)
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-yaml
+        exclude: ^recipe/meta\.yaml$
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: check-added-large-files
+        args: ["--maxkb=102400"]
+
+      # Format TOML files early (before other tools might read config)
+-   repo: https://github.com/pappasam/toml-sort
+    rev: v0.25.0
+    hooks:
+    -   id: toml-sort
+        args: ["--in-place"]
+
+      # Python syntax upgrades (should run before linting/formatting)
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.2
+    hooks:
+    -   id: pyupgrade
+        args: ["--py311-plus"]
+
+      # Import sorting (should run before Ruff to avoid conflicts)
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.10.1
+    hooks:
+    -   id: isort
+        args: ["--profile", "black"]
+
+      # Ruff for linting and formatting Python files
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.9
+    hooks:
+    -   id: ruff-check
+        args: ["--fix"]
+    -   id: ruff-format     # Add Ruff formatter
+
+      # nbQA to run Ruff on Jupyter Notebooks (after Python tools)
+-   repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+    -   id: nbqa-ruff
+        name: nbQA-Ruff
+        args: ["--fix"]
+        additional_dependencies: ["ruff"]
+
+      # validates CITATION.cff file formatting expectations
+-   repo: https://github.com/citation-file-format/cffconvert
+    rev: b6045d78aac9e02b039703b030588d54d53262ac
+    hooks:
+    -   id: validate-cff
+
+      # Final cleanup (whitespace and newlines)
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+      # Keep pre-commit itself up to date (run last)
+-   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update
+    rev: v0.9.0
+    hooks:
+    -   id: pre-commit-update
+        args: ["--verbose", "--exclude", "cffconvert"]
+
+-   repo: local
+    hooks:
+    -   id: shellcheck
+        name: ShellCheck
+        description: Test shell scripts with ShellCheck
+        entry: shellcheck
+        language: system
+        types: [shell]
+        args: ["--exclude=SC1091"]
+        require_serial: true

buscar-0.1.0/CITATION.cff

@@ -0,0 +1,24 @@
+cff-version: 1.2.0
+message: If you use Buscar, please cite it using the metadata from the CITATION.cff file.
+title: Single-cell hit calling in high-content imaging screens with Buscar
+date-released: 2026-05-09
+authors:
+  - family-names: Serrano
+    given-names: Erik
+    orcid: https://orcid.org/0000-0003-4188-9080
+    email: erik.serrano@cuanschutz.com
+  - family-names: Weishan
+    given-names: Li
+    orcid: https://orcid.org/0009-0001-4643-9372
+  - family-names: Bunten
+    given-names: Dave
+    orcid: https://orcid.org/0000-0001-6041-3665
+  - family-names: Way
+    given-names: Gregory
+    orcid: https://orcid.org/0000-0002-0503-9348
+license: BSD-3-Clause
+identifiers:
+  - type: doi
+    value: 10.64898/2026.04.15.718737
+repository-code: https://github.com/WayScience/buscar
+abstract: Buscar is a Python framework for prioritizing compounds in high-content imaging drug screening using single-cell profiles.

buscar-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,109 @@
+# Contributing
+
+Thanks for your interest in improving Buscar. Contributions that fix bugs, improve
+documentation, add tests, or make the package easier to install and maintain are
+welcome.
+
+## Development Setup
+
+Buscar uses [uv](https://docs.astral.sh/uv/) for environment and package
+management.
+
+```bash
+git clone https://github.com/WayScience/buscar.git
+cd buscar
+uv sync --frozen --group dev
+```
+
+Install the pre-commit hooks before making changes:
+
+```bash
+uv tool install pre-commit
+pre-commit install
+```
+
+## Checks
+
+Run the test suite:
+
+```bash
+uv run --frozen pytest
+```
+
+Run tests with coverage:
+
+```bash
+uv run --frozen pytest --cov=buscar --cov-report=term-missing --cov-report=xml --cov-report=html
+```
+
+The coverage run creates `coverage.xml` and an `htmlcov/` directory. CI uploads
+these files from the Ubuntu Python 3.12 test job so maintainers can download the
+machine-readable coverage report or inspect the browsable HTML coverage report
+when reviewing pull requests.
+
+Run linting and formatting checks:
+
+```bash
+pre-commit run --all-files
+```
+
+Build the package:
+
+```bash
+uv build
+uv run --frozen twine check dist/*
+```
+
+## Pull Requests
+
+Before opening a pull request:
+
+- Keep changes focused on one bug fix, feature, or documentation update.
+- Add or update tests when behavior changes.
+- Update documentation when user-facing behavior changes.
+- Run `uv run --frozen pytest` and `pre-commit run --all-files`.
+- Make sure generated files and large local artifacts are not committed.
+
+CI runs pre-commit checks, the test matrix across supported Python versions, and
+package build validation.
+
+Dependabot checks GitHub Actions and pre-commit hooks weekly, and uv-managed
+Python dependencies monthly. Review dependency update pull requests like any
+other change and make sure CI passes before merging.
+
+## Releases
+
+A push to `main` runs `.github/workflows/draft-release.yml`.
+Release Drafter updates a draft GitHub release with merged pull requests.
+Use the `release-major`, `release-minor`, or `release-patch` label to choose the version bump; the default is a patch bump.
+
+Before the first release, a maintainer must:
+
+1. Create the `release` environment in the `WayScience/buscar` GitHub repository.
+   Add required reviewers if the release needs approval.
+2. Create the `release-major`, `release-minor`, and `release-patch` labels if they do not exist.
+   Apply them to pull requests that need a specific version bump.
+3. In their PyPI account's Publishing settings, add a pending trusted publisher for the `buscar` project.
+   Set the owner to `WayScience`, repository to `buscar`, workflow filename to `publish-pypi.yml`, and environment to `release`.
+   The pending publisher does not reserve the project name until the first upload.
+
+To release, make sure CI passes on `main`.
+Review the draft release and its `vX.Y.Z` tag, then publish it from GitHub Releases.
+Publishing the GitHub release runs `.github/workflows/publish-pypi.yml`.
+That workflow builds a wheel and source distribution from the release tag, checks the wheel import, and uploads both files to PyPI with Trusted Publishing.
+No PyPI API token is needed.
+Check the new version on PyPI after the workflow finishes.
+
+## Reporting Issues
+
+When reporting a bug, include:
+
+- The Buscar version or commit you are using.
+- Your Python version and operating system.
+- A minimal example or traceback that reproduces the issue.
+- Any relevant input data shape, schema, or metadata column names.
+
+## License
+
+By contributing, you agree that your contribution will be licensed under the
+BSD 3-Clause license used by this project.

buscar-0.1.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2026 Erik Serrano
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. 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.
+
+3. 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.

buscar-0.1.0/MANIFEST.in

@@ -0,0 +1,4 @@
+# Keep non-package assets and the development lockfile out of the sdist.
+prune media
+prune logo
+exclude uv.lock