python publish update

Author: kbestak

.github/workflows/python-publish.yml

@@ -0,0 +1,69 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cozipy/
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

README.md

@@ -1,7 +1,7 @@
 # COZIpy - Neighbor preference analysis with a conditional z-score
 ![License](https://img.shields.io/badge/license-MIT-green)
 
-COZI is a python package for neighbor preference (NEP) analysis of cell type labelled spatial data. As described in [Schiller *et al.* bioRxiv 2025](https://doi.org/10.1101/2025.03.31.646289), COZI is one optimized flavor of neighbor preference analysis and infers directinoal neighbor preferences based on label permutations.
+COZI is a python package for neighbor preference (NEP) analysis of cell type labelled spatial data. As described in [Schiller *et al.* bioRxiv 2025](https://doi.org/10.1101/2025.03.31.646289), COZI is one optimized flavor of neighbor preference analysis and infers directional neighbor preferences based on label permutations.
 
 ## Installation
 
@@ -33,7 +33,7 @@ COZI requires x and y-coordinates and cell type label information as input. The
 
 ### Tutorial
 
-Check the [Tutorial](tutorial/script/cozipy_tutorial.ipynb) for a code example.
+Check the [Tutorial](https://github.com/SchapiroLabor/COZIpy/blob/main/tutorial/cozipy_tutorial.ipynb) for a code example.
 
 ## Contributing
 Contributions, issues, and feature requests are welcome!  

pyproject.toml

@@ -4,10 +4,26 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cozipy"
-version = "0.0.1"
+dynamic = ["version"]
 description = "COZI neighbor preference analysis package"
+readme = "README.md"
+license = { file = "LICENSE" }
 authors = [
     {name="Chiara Schiller", email="chiara.schiller@uni-heidelberg.de"}
 ]
+keywords = ["neighborhood", "spatial", "directionality"]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License"
+]
+
 requires-python = ">=3.9"
 dependencies = ["numpy", "scipy", "pandas", "scikit-learn"]
+
+[project.urls]
+Homepage = "https://github.com/schapirolabor/cozipy"
+Issues = "https://github.com/schapirolabor/cozipy/issues"
+
+[tool.setuptools.dynamic]
+version = {attr = "cozipy.__version__"}

src/cozipy/__init__.py

@@ -1,4 +1,5 @@
 from cozipy.nep_cozi import nep_analysis, run_cozi
 from cozipy.neighbors import knn_graph, radius_graph, delaunay_graph
 
+__version__ = "0.1.0"
 __all__ = ["nep_analysis", "run_cozi", "knn_graph", "radius_graph", "delaunay_graph"]