fix: docker mount / feat: add docker build test (#41)

* fix: docker mount paths should by default point to the test data

* add docker test and push

* add docker test and push

* add docker test and push

.github/workflows/docker-build-test.yml

@@ -0,0 +1,51 @@
+name: Docker Build and Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/download/1.29.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+          sudo chmod +x /usr/local/bin/docker-compose
+          docker-compose --version
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build and test Docker image
+        run: docker-compose --env-file docker-compose.env up --build --exit-code-from sr2silo
+
+      - name: Push to DockerHub
+        if: github.ref == 'refs/heads/main'
+        run: |
+          docker-compose push

docker-compose.env

@@ -1,7 +1,7 @@
-SAMPLE_DIR=../../../data/sr2silo/daemon_test/samples/A1_05_2024_10_08/20241024_2411515907/alignments/
+SAMPLE_DIR=./tests/data/samples/A1_05_2024_10_08/20241024_2411515907/alignments
 SAMPLE_ID=A1_05_2024_10_08
 BATCH_ID=20241024_2411515907
-TIMELINE_FILE=../../../data/sr2silo/daemon_test/timeline.tsv
+TIMELINE_FILE=./tests/data/samples/timeline_A1_05_2024_10_08.tsv
 PRIMER_FILE=./tests/data/samples/primers.yaml
 NEXTCLADE_REFERENCE=sars-cov2
 RESULTS_DIR=./results