From abc195e975c9b903330dc5d9382e694505d52be5 Mon Sep 17 00:00:00 2001
From: Ryan McGinty <rpmcginty@users.noreply.github.com>
Date: Fri, 20 Dec 2024 22:48:54 -0800
Subject: [PATCH] Add Codecov integration and update GitHub Actions workflow

---
 .github/workflows/build.yml | 18 ++++++++++++++++++
 README.md                   |  1 +
 codecov.yml                 | 34 ++++++++++++++++++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 codecov.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 417f5ac..51458dc 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -9,6 +9,8 @@ on:
     branches: [ main ]
     paths-ignore:
       - '**/_version.py'
+  workflow_dispatch:
+
 
 jobs:
   test:
@@ -35,3 +37,19 @@ jobs:
         run: |
           make release
         shell: bash
+      - name: Upload coverage reports
+        if: |
+          ${{ 
+            success() 
+            && (
+              (github.event_name == 'pull_request' && github.base_ref == 'main')
+              || (github.event_name == 'push' && github.ref_name == 'main')
+              || github.event_name == 'workflow_dispatch'
+            )
+            && matrix.python-version == '3.11'
+          }}
+        uses: codecov/codecov-action@v5
+        with:
+          # https://github.com/codecov/codecov-action#arguments
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: PYTHON_VERSION
diff --git a/README.md b/README.md
index d8753a3..395895b 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 # AIBS Informatics Core
 
 [![Build Status](https://github.com/AllenInstitute/aibs-informatics-core/actions/workflows/build.yml/badge.svg)](https://github.com/AllenInstitute/aibs-informatics-core/actions/workflows/build.yml)
+[![codecov](https://codecov.io/gh/AllenInstitute/aibs-informatics-core/graph/badge.svg?token=X66KBYWELP)](https://codecov.io/gh/AllenInstitute/aibs-informatics-core)
 
 ---
 
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..a6bc968
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,34 @@
+codecov:
+  bot: aibsgithub
+
+coverage:
+  range: 0..100
+  status:
+    project: 
+      default:
+        target: auto  # auto compares coverage to the previous base commit
+        informational: true
+    patch:
+      default:
+        informational: true
+
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default
+  require_changes: false  # if true: only post the comment if coverage changes
+  require_head: yes       # [yes :: must have a head report to post]
+  require_base: no        # default yes
+
+github_checks:
+  # set to true in future perhaps?
+  annotations: false
+
+flag_management:
+  default_rules: # the rules that will be followed for any flag added, generally
+    carryforward: true
+    statuses:
+      - type: project
+        target: auto
+        threshold: 1%
+      - type: patch
+        target: 90%
\ No newline at end of file