From cd896da3b981ea40cc4b7c386d9d3a56b6e30988 Mon Sep 17 00:00:00 2001
From: Joshua Allen <jallen17@illinois.edu>
Date: Sun, 3 May 2026 07:59:38 -0500
Subject: [PATCH 1/2] Update Python publish workflow to use Poetry

---
 .github/workflows/python-publish.yml | 70 ++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 .github/workflows/python-publish.yml

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
new file mode 100644
index 00000000..772fa6a4
--- /dev/null
+++ b/.github/workflows/python-publish.yml
@@ -0,0 +1,70 @@
+# 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.
+          pip install poetry
+          poetry 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
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      url: https://pypi.org/p/neat-genreads
+      #
+      # 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/

From f1c887c446f15a7c26d8cd104d05464a3879ac1d Mon Sep 17 00:00:00 2001
From: Joshua Allen <jallen17@illinois.edu>
Date: Sun, 3 May 2026 08:10:48 -0500
Subject: [PATCH 2/2] Patching workflow on github

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 239e751f..37749f5e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,6 +4,7 @@ version = "4.3.6"
 description = "NGS Simulation toolkit"
 authors = ["Joshua Allen <jallen17@illinois.edu>"]
 license = "BSD 3-Clause License"
+packages = [{include = "neat"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"