Updated github CI/CD tests

.github/workflows/tests.yml

@@ -4,36 +4,30 @@ on: ["push", "pull_request"]
 
 
 jobs:
-  test-python:
+  test-api-python:
     name: Coverage
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.10, 3.11, 3.12]
         mongodb-version: ["3.6"]
 
     steps:
-
     # Check out Scout code
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # Set up python
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version}}
-
     - name: Production Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -e .
-        pip install pytest-cov
-        pip install coveralls
-    - name: Test with pytest & Coveralls
+        pip install ./api[test]
+    - name: Test API with pytest & coveralls
       run: |
-        pip install -r requirements-dev.txt
-        pytest --cov=./
+        pytest --cov ./api
         coveralls
       env: 
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -49,11 +43,17 @@ jobs:
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v1
+      uses: actions/setup-node@v4
       with:
         node-version: ${{ matrix.node-version }}
-    - run: npm ci
-    - run: npm run build --if-present
-    - run: npm run test
+    - name: Install node packages
+      working-directory: ./api
+      run: npm ci
+    - name: Build packages
+      working-directory: ./api
+      run: npm run build --if-present
+    - name: Run tests
+      working-directory: ./api
+      run: npm run test

api/pyproject.toml

@@ -6,7 +6,6 @@ description = "Gens API"
 dependencies = [
     "setuptools",
     "wheel",
-    "click",
     "requests",
     "fastapi[all]",
     "uvicorn[standard]",
@@ -19,6 +18,16 @@ authors = [
   {name = "Markus Johansson", email = "[email protected]"},
 ]
 
+[project.optional-dependencies]
+test = [
+    "black",
+    "isort",
+    "mypy",
+    "pytest",
+    "pytest-cov",
+    "pytest-flask",
+]
+
 [project.urls]
 Repository = "https://github.com/Clinical-Genomics-Lund/gens.git"
 Issues = "https://github.com/Clinical-Genomics-Lund/gens/issues"

frontend/tests/test_io.py → api/tests/test_io.py

@@ -1,11 +1,8 @@
 """Test IO related functions."""
 
-import os
-from unittest.mock import Mock
-
 import pytest
 
-from gens.io import _get_filepath
+from app.io import _get_filepath
 
 
 def test_get_filepath():

frontend/pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = [
+test = [
     "black",
     "isort",
     "mypy",