[CI] Switch to codecov

.github/workflows/test.yaml

@@ -5,7 +5,6 @@ on:
     branches:
       - main
   pull_request:
-  workflow_dispatch:
 
 jobs:
   test:
@@ -47,12 +46,15 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --per-file-ignores=./app/api/models.py:F722
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
+    
     - name: Test with pytest
       run: |
         coverage run -m pytest -m "integration or not integration"
         coverage lcov -o ./coverage/lcov.info
-    - name: Coveralls GitHub Action
-      uses: coverallsapp/[email protected]
+
+    - name: Upload results to Codecov
+      uses: codecov/codecov-action@v5
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+

README.md

@@ -2,10 +2,12 @@
 
 # Neurobagel API
 
-[![Tests](https://img.shields.io/github/actions/workflow/status/neurobagel/api/test.yaml?color=BDB76B&label=test&style=flat-square)](https://github.com/neurobagel/api/actions/workflows/test.yaml)
-[![Coverage](https://img.shields.io/coverallsCoverage/github/neurobagel/api?style=flat-square&color=8FBC8F)](https://coveralls.io/github/neurobagel/api)
-[![Python](https://img.shields.io/badge/python-3.10-4682B4?style=flat-square)](https://www.python.org/)
-[![License](https://img.shields.io/github/license/neurobagel/api?color=CD5C5C&style=flat-square)](LICENSE)
+[![Tests](https://img.shields.io/github/actions/workflow/status/neurobagel/api/test.yaml?color=BDB76B&label=test&style=flat)](https://github.com/neurobagel/api/actions/workflows/test.yaml)
+[![codecov](https://codecov.io/gh/neurobagel/api/graph/badge.svg?token=ZEOGQFFZMJ)](https://codecov.io/gh/neurobagel/api)
+[![Python](https://img.shields.io/badge/python-3.10-4682B4?style=flat)](https://www.python.org/)
+[![License](https://img.shields.io/github/license/neurobagel/api?color=CD5C5C&style=flat)](LICENSE)
+![Docker Image Version (tag)](https://img.shields.io/docker/v/neurobagel/api/latest?logo=docker)
+
 
 </div>
 
@@ -15,9 +17,17 @@ Please refer to our [**official documentation**](https://neurobagel.org/api/) fo
 
 - [Quickstart](#quickstart)
 - [Local installation](#local-installation)
-    - [Environment variables](#set-the-environment-variables)
-    - [Docker (recommended)](#docker)
-    - [Python](#python)
+  - [Clone the repo](#clone-the-repo)
+  - [Set the environment variables](#set-the-environment-variables)
+  - [Docker](#docker)
+    - [Option 1 (RECOMMENDED): Use the Neurobagel Docker Compose recipe](#option-1-recommended-use-the-neurobagel-docker-compose-recipe)
+    - [Option 2: Use the latest image from Docker Hub](#option-2-use-the-latest-image-from-docker-hub)
+    - [Option 3: Build the image using the Dockerfile](#option-3-build-the-image-using-the-dockerfile)
+    - [Send a test query to the API](#send-a-test-query-to-the-api)
+  - [Python](#python)
+    - [Install dependencies](#install-dependencies)
+    - [Launch the API](#launch-the-api)
+  - [Troubleshooting](#troubleshooting)
 - [Testing](#testing)
 - [The default Neurobagel SPARQL query](#the-default-neurobagel-sparql-query)
 - [License](#license)