Add tests

.github/workflows/tests.yml

@@ -0,0 +1,28 @@
+name: tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install uv
+      run: make install-uv
+    - name: Lint and test
+      run: make

Makefile

@@ -0,0 +1,14 @@
+tests: lint install
+	uv run pytest tests
+
+install-uv:
+	curl -LsSf https://astral.sh/uv/0.4.27/install.sh | sh
+
+install:
+	uv sync --all-extras --dev
+
+lint:
+	uvx ruff check src
+	uvx ruff check tests
+
+.PHONY: install-uv install lint tests

pyproject.toml

@@ -17,3 +17,8 @@ scripts.arcmapper = "arcmapper:main"
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3.3",
+]

src/arcmapper/__init__.py

@@ -6,7 +6,6 @@
 import subprocess
 import webbrowser
 
-import pandas as pd
 from waitress import serve
 from .app import app
 from .arc import read_arc_schema

src/arcmapper/app.py

@@ -218,7 +218,9 @@ def upload_data_dictionary(
     col_description,
 ):
     ok = dbc.Alert("Upload successful", color="success")
-    err = lambda msg: dbc.Alert(msg, color="danger")
+
+    def err(msg): return dbc.Alert(msg, color="danger")
+
     if ctx.triggered_id == "upload-btn" and upload_contents is not None:
         try:
             df = read_upload_data(upload_contents, filename)

tests/test_arc.py

@@ -0,0 +1,14 @@
+"Module to read ARC schema"
+
+from pathlib import Path
+
+from arcmapper.arc import arc_schema_url, read_arc_schema
+
+
+def test_arc_schema_url():
+    assert arc_schema_url("1.0.0") == "https://github.com/ISARICResearch/DataPlatform/raw/refs/heads/main/ARCH/ARCH1.0.0/ARCH.csv"
+
+
+def test_read_arc_schema():
+    arc = read_arc_schema(str(Path(__file__).parent / 'data' / 'ARCH.csv'))
+    print(arc)

tests/test_util.py

@@ -0,0 +1,19 @@
+"Utility functions for arcmapper"
+from pathlib import Path
+
+import pandas as pd
+
+from arcmapper.util import read_data, read_csv_with_encoding_detection, parse_redcap_response
+
+def test_read_data():
+    arc_path = str(Path(__file__).parent / 'data' / 'ARCH.csv')
+    assert isinstance(read_data(arc_path), pd.DataFrame)
+
+def test_read_csv_with_encoding_detection():
+    "Reads CSV file with encoding detection"
+
+    arc_path = str(Path(__file__).parent / 'data' / 'ARCH.csv')
+    assert isinstance(read_csv_with_encoding_detection(arc_path), pd.DataFrame)
+
+def test_parse_redcap_response():
+    assert parse_redcap_response("1, male | 2, female") == [("1", "male"), ("2", "female")]