From c011f658cff9b1c79b4cd3f3728286551d102d7a Mon Sep 17 00:00:00 2001
From: Bo Peng <bo.peng@bcm.edu>
Date: Wed, 9 Sep 2026 13:30:28 -0500
Subject: [PATCH] Publish to PyPI via trusted publishing

Replace the token-based python-publish.yml with release.yml, which builds
the sdist and wheel in one job and uploads them from a separate job that
holds the OIDC id-token permission and is gated on the `pypi` environment.

Triggers on `release: published` (so drafts do not publish) and on manual
workflow_dispatch. Removes the need for the PYPI_USERNAME/PYPI_PASSWORD
secrets.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_011tke9h11djfduXhZ3MsYre
---
 .github/workflows/python-publish.yml | 31 -------------
 .github/workflows/release.yml        | 67 ++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+), 31 deletions(-)
 delete mode 100644 .github/workflows/python-publish.yml
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
deleted file mode 100644
index 94c0016e7..000000000
--- a/.github/workflows/python-publish.yml
+++ /dev/null
@@ -1,31 +0,0 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: Upload Python Package
-
-on:
-  release:
-    types: [created]
-
-jobs:
-  deploy:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python -m build
-        twine upload dist/*
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 000000000..e0f3a4fdf
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,67 @@
+# Publish sos to PyPI using PyPI Trusted Publishing (OIDC), no API token needed.
+#
+# PyPI trusted publisher settings for this workflow:
+#   PyPI Project Name: sos
+#   Owner:             vatlab
+#   Repository name:   SoS
+#   Workflow name:     release.yml
+#   Environment name:  pypi
+#
+# https://docs.pypi.org/trusted-publishers/
+
+name: Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Build sdist and wheel
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build
+
+      - name: Check distributions
+        run: |
+          python -m pip install --upgrade twine
+          twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sos
+    permissions:
+      id-token: write  # required for trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1