From c92b4e70db4d36f638082a4cd47bf95de1c7e124 Mon Sep 17 00:00:00 2001
From: Martin Chase <outofculture@gmail.com>
Date: Wed, 26 Mar 2025 12:05:05 -0700
Subject: [PATCH 1/3] put badges in readme

---
 .github/workflows/deploy.yml                  | 93 +++++++++++++++++++
 .../{python-package-conda.yml => test.yml}    |  0
 README.md                                     |  4 +
 3 files changed, 97 insertions(+)
 create mode 100644 .github/workflows/deploy.yml
 rename .github/workflows/{python-package-conda.yml => test.yml} (100%)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
new file mode 100644
index 00000000..99da6c4d
--- /dev/null
+++ b/.github/workflows/deploy.yml
@@ -0,0 +1,93 @@
+name: Publish Python 🐍 distribution 📦 to PyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/neuroanalysis
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/test.yml
similarity index 100%
rename from .github/workflows/python-package-conda.yml
rename to .github/workflows/test.yml
diff --git a/README.md b/README.md
index de8f0c65..398c8532 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,10 @@ Neuroanalysis
 Modular and interactive tools for analysis of neurophysiology data, with emphasis on 
 patch-clamp electrophysiology.
 
+
+[![Tests](https://github.com/AllenInstitute/neuroanalysis/actions/workflows/test.yml/badge.svg)](https://github.com/AllenInstitute/neuroanalysis/actions/workflows/test.yml)
+[![PyPI version](https://badge.fury.io/py/neuroanalysis.svg)](https://badge.fury.io/py/neuroanalysis)
+
 * Functions for running common analysis algorithms
     * Synaptic/calcium event detection and characterization
     * Synaptic release modeling

From acf092aa6f153ed9daef94b33eadc7c4ad44a7bb Mon Sep 17 00:00:00 2001
From: "Martin Chase (aider)" <outofculture@gmail.com>
Date: Wed, 26 Mar 2025 12:07:27 -0700
Subject: [PATCH 2/3] ci: Ensure tests run on every push and pull request

---
 .github/workflows/test.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ed732c6c..9b07c24b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,6 +1,10 @@
 name: Python Package using Conda
 
-on: [push]
+on:
+  push:
+    branches: [ "**" ]
+  pull_request:
+    branches: [ "**" ]
 
 jobs:
   build-linux:

From 54f897633031d8c5c1b2efc83534562c5f535d78 Mon Sep 17 00:00:00 2001
From: Martin Chase <outofculture@gmail.com>
Date: Wed, 26 Mar 2025 12:07:36 -0700
Subject: [PATCH 3/3] ignore aider files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 43e3738d..cae51e4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@
 neuroanalysis.egg-info
 build/
 dist/
+.aider*