From e84d190864f406cf993a7df417a7332158dbee9f Mon Sep 17 00:00:00 2001
From: themattinthehatt <themattinthehatt@gmail.com>
Date: Fri, 3 Oct 2025 16:53:23 -0400
Subject: [PATCH 1/2] publish workflow

---
 .github/workflows/publish.yaml | 72 ++++++++++++++++++++++++++++++++++
 README.md                      | 13 +++++-
 2 files changed, 83 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/publish.yaml

diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
new file mode 100644
index 0000000..813cb31
--- /dev/null
+++ b/.github/workflows/publish.yaml
@@ -0,0 +1,72 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        version: latest
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+
+    - name: Extract version from pyproject.toml
+      id: get_version
+      run: |
+        # Extract version from [project] section
+        VERSION=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")
+        echo "project_version=$VERSION" >> $GITHUB_OUTPUT
+        echo "Project version: $VERSION"
+
+    - name: Extract tag version
+      id: get_tag
+      run: |
+        # Remove 'refs/tags/' prefix and optional 'v' prefix
+        TAG_VERSION=${GITHUB_REF#refs/tags/}
+        TAG_VERSION=${TAG_VERSION#v}
+        echo "tag_version=$TAG_VERSION" >> $GITHUB_OUTPUT
+        echo "Tag version: $TAG_VERSION"
+
+    - name: Verify version matches tag
+      run: |
+        if [ "${{ steps.get_version.outputs.project_version }}" != "${{ steps.get_tag.outputs.tag_version }}" ]; then
+          echo "ERROR: Tag version (${{ steps.get_tag.outputs.tag_version }}) doesn't match project version (${{ steps.get_version.outputs.project_version }})"
+          echo "Please ensure your git tag matches the version in pyproject.toml [project] section"
+          exit 1
+        fi
+        echo "Version verification passed"
+
+    - name: Install dependencies
+      run: poetry install --only-root
+
+    - name: Build package
+      run: poetry build
+
+    - name: Verify build contents
+      run: |
+        echo "Built packages:"
+        ls -la dist/
+        echo "Checking wheel contents:"
+        python -m zipfile -l dist/*.whl | head -20
+
+    - name: Publish to PyPI
+      run: poetry publish --username __token__ --password ${{ secrets.PYPI_API_TOKEN }}
+
+    - name: Verify publication
+      run: |
+        echo "🎉 Successfully published beast v${{ steps.get_version.outputs.project_version }} to PyPI!"
+        echo "Package should be available at: https://pypi.org/project/beast-backbones/${{ steps.get_version.outputs.project_version }}/"
\ No newline at end of file
diff --git a/README.md b/README.md
index 04771de..c7e06a7 100644
--- a/README.md
+++ b/README.md
@@ -34,8 +34,10 @@ conda create --yes --name beast python=3.10
 conda activate beast
 ```
 
-### Step 3: Download the repo from github and install
-Move to your home directory (or wherever you would like to download the code) and install:
+### Step 3: Download and install
+Move to your home directory (or wherever you would like to download the code) and install via Github clone or through PyPI.
+
+For Github cloning:
 
 ```commandline
 cd ~
@@ -44,6 +46,13 @@ cd beast
 pip install -e .
 ```
 
+For installation through PyPI:
+
+```commandline
+cd ~
+pip install beast-backbones
+```
+
 ## Usage
 
 `beast` comes with a simple command line interface. To get more information, run

From bf0a56439eda9390f39ee81aeba2596f32e85a3c Mon Sep 17 00:00:00 2001
From: themattinthehatt <themattinthehatt@gmail.com>
Date: Fri, 3 Oct 2025 16:59:39 -0400
Subject: [PATCH 2/2] clean up README

---
 README.md | 2 --
 1 file changed, 2 deletions(-)

diff --git a/README.md b/README.md
index c7e06a7..1b09f4d 100644
--- a/README.md
+++ b/README.md
@@ -40,7 +40,6 @@ Move to your home directory (or wherever you would like to download the code) an
 For Github cloning:
 
 ```commandline
-cd ~
 git clone https://github.com/paninski-lab/beast
 cd beast
 pip install -e .
@@ -49,7 +48,6 @@ pip install -e .
 For installation through PyPI:
 
 ```commandline
-cd ~
 pip install beast-backbones
 ```