From c66139ef7fd03f1830c7cb8f4d51b07ce0cb2894 Mon Sep 17 00:00:00 2001
From: Jennings Zhang <dev@sl.jennin.xyz>
Date: Sat, 27 Jul 2024 00:23:34 -0400
Subject: [PATCH] GHA testing

---
 .github/workflows/test.yml | 35 +++++++++++++++++++++++++++++++++++
 README.md                  |  6 ------
 docker-compose.yml         |  2 +-
 3 files changed, 36 insertions(+), 7 deletions(-)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..86eddc3
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,35 @@
+name: Test
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - '.github/workflows/test.yml'
+      - '**.py'
+  pull_request:
+
+jobs:
+  test:
+    name: Tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Spin up ChRIS
+        uses: FNNDSC/miniChRIS-docker@master
+        with:
+          # for testing, we need to create plugin instances, but we don't need the plugins to actually run.
+          services: chris oxidicom graphql-engine
+      - name: Build
+        run: docker compose build test
+      - name: Test
+        id: test
+        continue-on-error: true  # we want to upload coverage, even on failure
+        run: docker compose run -T --use-aliases test
+      - name: Copy coverage.xml from container
+        run: docker cp "$(docker compose ps -a test -q | tail -n 1):/app/coverage.xml" coverage.xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/README.md b/README.md
index 7257193..98f10a9 100644
--- a/README.md
+++ b/README.md
@@ -55,12 +55,6 @@ so we need to run them with Docker Compose:
 docker compose run test
 ```
 
-Coverage data can be obtained from the stopped test container:
-
-```shell
-docker cp "$(docker compose ps -a test -q | tail -n 1):/app/coverage.xml" coverage.xml
-```
-
 ### Deployment
 
 See https://github.com/FNNDSC/charts
diff --git a/docker-compose.yml b/docker-compose.yml
index e27f979..b81a50e 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -19,7 +19,7 @@ services:
       context: .
       args:
         REQUIREMENTS_FILE: requirements-dev.lock
-    command: pytest --run-e2e --cov=serie --cov-report=xml
+    command: pytest --color=yes --run-e2e --cov=serie --cov-report=xml
     working_dir: /app
     volumes:
       # /app is a volume and the source code files are binded as subdirectories