ci: add GitHub Actions (tests, docs deploy, PyPI release) and release metadata

Author: aivuk

.github/workflows/ci.yml

@@ -0,0 +1,52 @@
+name: CI
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Run tests
+        run: uv run pytest -v --tb=short
+
+  docs:
+    runs-on: ubuntu-latest
+    needs: test
+    if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+
+      - name: Deploy docs
+        run: uv run mkdocs gh-deploy --force

.github/workflows/release.yml

@@ -0,0 +1,28 @@
+name: Release to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write  # trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Fuzue Tech
+
+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.

docs/CNAME

@@ -0,0 +1 @@
+densitree.fuzue.tech

mkdocs.yml

@@ -1,6 +1,6 @@
 site_name: densitree
 site_description: "SPADE clustering for high-dimensional cytometry data in Python"
-site_url: https://densitree.readthedocs.io
+site_url: https://densitree.fuzue.tech
 repo_url: https://github.com/fuzue/densitree
 repo_name: fuzue/densitree
 

pyproject.toml

@@ -5,7 +5,34 @@ build-backend = "hatchling.build"
 [project]
 name = "densitree"
 version = "0.1.0"
+description = "Density-normalized clustering with minimum spanning tree construction for high-dimensional data"
+readme = "README.md"
+license = "MIT"
 requires-python = ">=3.10"
+authors = [
+    { name = "Edgar Zanella Alvarenga", email = "edgar@fuzue.tech" },
+]
+keywords = [
+    "clustering",
+    "spade",
+    "cytometry",
+    "single-cell",
+    "density",
+    "spanning-tree",
+    "machine-learning",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "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 :: Artificial Intelligence",
+]
 dependencies = [
     "numpy>=1.24",
     "scipy>=1.10",
@@ -16,6 +43,12 @@ dependencies = [
     "pandas>=2.0",
 ]
 
+[project.urls]
+Homepage = "https://densitree.fuzue.tech"
+Documentation = "https://densitree.fuzue.tech"
+Repository = "https://github.com/fuzue/densitree"
+Issues = "https://github.com/fuzue/densitree/issues"
+
 [project.optional-dependencies]
 dev = ["pytest>=7.4", "pytest-cov"]
 bench = ["readfcs>=2.0", "flowsom>=0.2", "leidenalg>=0.10", "igraph>=1.0", "tabulate"]