multiscoresplot 1.0.0__tar.gz

multiscoresplot-1.0.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uv run --group dev ruff check src/ tests/
+      - run: uv run --group dev ruff format --check src/ tests/
+
+  typecheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uv run --group type mypy src/
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: uv run --group test pytest --cov --cov-report=xml
+      - if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml

multiscoresplot-1.0.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uv build
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

multiscoresplot-1.0.0/.gitignore

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+CLAUDE.md
+.claude
+
+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.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/
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+Pipfile.lock
+
+# PEP 582
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+
+# IDE
+.vscode/
+*.swp
+*.swo
+*~
+.DS_Store

multiscoresplot-1.0.0/.pre-commit-config.yaml

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+exclude: '\.ipynb$'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+        args: ["--maxkb=500"]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.9
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

multiscoresplot-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Andre Macedo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

multiscoresplot-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: multiscoresplot
+Version: 1.0.0
+Summary: Multi-dimensional gene set scoring and visualization for single-cell transcriptomics
+Project-URL: Homepage, https://github.com/andrecmacedo/multiscoresplot
+Project-URL: Repository, https://github.com/andrecmacedo/multiscoresplot
+Project-URL: Issues, https://github.com/andrecmacedo/multiscoresplot/issues
+Author: Andre Macedo
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: anndata>=0.10
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.24
+Requires-Dist: pyucell>=0.5
+Requires-Dist: scanpy>=1.9
+Requires-Dist: scikit-learn>=1.3
+Provides-Extra: interactive
+Requires-Dist: plotly>=5.0; extra == 'interactive'
+Description-Content-Type: text/markdown
+
+# multiscoresplot
+
+[![CI](https://github.com/andrecmacedo/multiscoresplot/actions/workflows/ci.yml/badge.svg)](https://github.com/andrecmacedo/multiscoresplot/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Multi-dimensional gene set scoring and visualization for single-cell transcriptomics.
+
+Color dimensionality reduction plots (UMAP, PCA, etc.) using a multi-dimensional color space derived from gene set scores.
+
+## Installation
+
+```bash
+pip install multiscoresplot
+```
+
+## Quick Start
+
+```python
+import multiscoresplot  # more to come!
+```
+
+## Pipeline
+
+1. **Score** -- Calculate gene set scores per cell
+2. **Color space** -- Build a color space where each axis/vertex maps to a gene set
+3. **Project** -- Map each cell into the color space based on its scores
+4. **Plot** -- Color dimensionality reduction coordinates using the projected colors
+5. **Legend** -- Render a simplex/ternary plot as the colorbar
+
+## Development
+
+```bash
+# Install in editable mode with all dev dependencies
+pip install -e ".[dev,test,type]"
+
+# Run tests
+pytest
+
+# Lint & format
+ruff check src/ tests/
+ruff format src/ tests/
+
+# Type check
+mypy src/
+
+# Set up pre-commit hooks
+pre-commit install
+```
+
+## License
+
+[MIT](LICENSE)

multiscoresplot-1.0.0/README.md

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+# multiscoresplot
+
+[![CI](https://github.com/andrecmacedo/multiscoresplot/actions/workflows/ci.yml/badge.svg)](https://github.com/andrecmacedo/multiscoresplot/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/multiscoresplot)](https://pypi.org/project/multiscoresplot/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Multi-dimensional gene set scoring and visualization for single-cell transcriptomics.
+
+Color dimensionality reduction plots (UMAP, PCA, etc.) using a multi-dimensional color space derived from gene set scores.
+
+## Installation
+
+```bash
+pip install multiscoresplot
+```
+
+## Quick Start
+
+```python
+import multiscoresplot  # more to come!
+```
+
+## Pipeline
+
+1. **Score** -- Calculate gene set scores per cell
+2. **Color space** -- Build a color space where each axis/vertex maps to a gene set
+3. **Project** -- Map each cell into the color space based on its scores
+4. **Plot** -- Color dimensionality reduction coordinates using the projected colors
+5. **Legend** -- Render a simplex/ternary plot as the colorbar
+
+## Development
+
+```bash
+# Install in editable mode with all dev dependencies
+pip install -e ".[dev,test,type]"
+
+# Run tests
+pytest
+
+# Lint & format
+ruff check src/ tests/
+ruff format src/ tests/
+
+# Type check
+mypy src/
+
+# Set up pre-commit hooks
+pre-commit install
+```
+
+## License
+
+[MIT](LICENSE)

multiscoresplot-1.0.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "multiscoresplot"
+version = "1.0.0"
+description = "Multi-dimensional gene set scoring and visualization for single-cell transcriptomics"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.10"
+authors = [{ name = "Andre Macedo" }]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+    "Typing :: Typed",
+]
+dependencies = [
+    "anndata>=0.10",
+    "matplotlib>=3.7",
+    "numpy>=1.24",
+    "pyucell>=0.5",
+    "scanpy>=1.9",
+    "scikit-learn>=1.3",
+]
+
+[project.optional-dependencies]
+interactive = ["plotly>=5.0"]
+
+[project.urls]
+Homepage = "https://github.com/andrecmacedo/multiscoresplot"
+Repository = "https://github.com/andrecmacedo/multiscoresplot"
+Issues = "https://github.com/andrecmacedo/multiscoresplot/issues"
+
+[tool.hatch.build.targets.sdist]
+exclude = ["tests/"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/multiscoresplot"]
+
+[dependency-groups]
+dev = ["pre-commit>=3.6", "ruff>=0.9"]
+test = ["pytest>=8.0", "pytest-cov>=6.0"]
+type = ["mypy>=1.13"]
+
+# ---------------------------------------------------------------------------
+# Tool configuration
+# ---------------------------------------------------------------------------
+
+[tool.ruff]
+src = ["src"]
+target-version = "py310"
+line-length = 99
+extend-exclude = ["*.ipynb"]
+
+[tool.ruff.lint]
+select = ["F", "E", "W", "I", "UP", "B", "SIM", "TCH", "RUF"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["multiscoresplot"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+strict = true
+markers = []
+
+[tool.mypy]
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+
+[[tool.mypy.overrides]]
+module = ["pyucell", "pyucell.*", "anndata", "anndata.*", "scanpy", "scanpy.*", "pandas", "pandas.*", "sklearn", "sklearn.*", "plotly", "plotly.*"]
+ignore_missing_imports = true
+disable_error_code = ["import-untyped"]
+
+[tool.coverage.run]
+source = ["multiscoresplot"]
+
+[tool.coverage.report]
+fail_under = 0
+show_missing = true

multiscoresplot-1.0.0/src/multiscoresplot/__init__.py

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+"""multiscoresplot -- multi-dimensional gene set scoring visualization."""
+
+from multiscoresplot._colorspace import (
+    blend_to_rgb,
+    get_component_labels,
+    project_direct,
+    project_pca,
+    reduce_to_rgb,
+    register_reducer,
+)
+from multiscoresplot._interactive import plot_embedding_interactive
+from multiscoresplot._legend import render_legend
+from multiscoresplot._plotting import plot_embedding
+from multiscoresplot._scoring import score_gene_sets
+
+__all__ = [
+    "blend_to_rgb",
+    "get_component_labels",
+    "plot_embedding",
+    "plot_embedding_interactive",
+    "project_direct",
+    "project_pca",
+    "reduce_to_rgb",
+    "register_reducer",
+    "render_legend",
+    "score_gene_sets",
+]
+__version__ = "1.0.0"