From aae47f93178df4045bcd0e128cb3ab8eb29e859c Mon Sep 17 00:00:00 2001
From: Jennings Zhang <dev@sl.jennin.xyz>
Date: Sat, 27 Jul 2024 01:56:16 -0400
Subject: [PATCH] Run tests in GHA

---
 .github/workflows/test.yml  | 55 +++++++++++++++++++++++++++++++++++++
 docker-compose.yml          |  2 +-
 pyproject.toml              |  5 ++--
 requirements-dev.lock       |  4 +++
 src/chrisomatic/__init__.py |  2 +-
 5 files changed, 64 insertions(+), 4 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..5099ece
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,55 @@
+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
+      - name: Build
+        run: docker compose build
+      - name: Test
+        id: test
+        continue-on-error: true  # we want to upload coverage, even on failure
+        run: docker compose run -T test pytest --color=yes --cov=chrisomatic --cov-report=xml
+      - 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 test coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Run example
+        run: |
+          set +e
+          docker compose run -T test sh -c '
+          export PYTHONPATH=$PWD
+          /app/scripts/create_example.py | coverage run python -m chrisomatic.cli -
+          '
+          if [ "$?" = '0' ]; then
+            echo "::error::Expected run to fail, but it did not.
+            exit 1
+          fi
+          docker compose run -T test coverage xml -o - > simulation_coverage.xml
+      - name: Upload simulation coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./simulation_coverage.xml
+          flags: simulation
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/docker-compose.yml b/docker-compose.yml
index a54bb3a..3b9fba1 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,5 +1,5 @@
 services:
-  dev:
+  test:
     build:
       context: .
       dockerfile: dev.Dockerfile
diff --git a/pyproject.toml b/pyproject.toml
index 1aa467e..2fa9830 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,8 +21,8 @@ requires-python = "== 3.12.3"
 chrisomatic = "chrisomatic.cli.typer:app"
 
 [tool.rye.scripts]
-test = "docker compose run --rm --build dev"
-simulate = "docker compose run --rm --build dev /app/scripts/simulation.sh"
+test = "docker compose run --rm --build test"
+simulate = "docker compose run --rm --build test /app/scripts/simulation.sh"
 
 [build-system]
 requires = ["hatchling"]
@@ -33,6 +33,7 @@ managed = true
 dev-dependencies = [
     "pytest>=8.3.2",
     "pytest-asyncio>=0.23.8",
+    "pytest-cov>=5.0.0",
 ]
 
 [tool.hatch.metadata]
diff --git a/requirements-dev.lock b/requirements-dev.lock
index 3403589..cd174be 100644
--- a/requirements-dev.lock
+++ b/requirements-dev.lock
@@ -31,6 +31,8 @@ casefy==0.1.7
     # via pyserde
 click==8.1.7
     # via typer
+coverage==7.6.0
+    # via pytest-cov
 frozenlist==1.4.1
     # via aiohttp
     # via aiosignal
@@ -64,7 +66,9 @@ pyserde==0.19.3
     # via chrisomatic
 pytest==8.3.2
     # via pytest-asyncio
+    # via pytest-cov
 pytest-asyncio==0.23.8
+pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
     # via strictyaml
 rich==13.7.1
diff --git a/src/chrisomatic/__init__.py b/src/chrisomatic/__init__.py
index 70cd492..b8df28b 100644
--- a/src/chrisomatic/__init__.py
+++ b/src/chrisomatic/__init__.py
@@ -1 +1 @@
-from __version__ import __version__
+from chrisomatic.__version__ import __version__