Merge pull request #67 from paulsengroup/update-ci

Update build-dockerfile workflow to test image after build

.github/workflows/build-dockerfile.yml

@@ -149,14 +149,15 @@ jobs:
         with:
           platforms: arm64
 
-      - name: Build Docker image and push to registries
+      - name: Build Docker image
         uses: docker/build-push-action@v5
         with:
           context: ${{ github.workspace }}
-          push: ${{ github.event_name != 'pull_request' }}
+          load: true
+          push: false
           cache-from: type=gha,scope=build-dockerfile
           cache-to: type=gha,mode=min,scope=build-dockerfile
-          tags: ${{ steps.meta.outputs.tags }}
+          tags: hictk:test
           platforms: ${{ steps.build-args.outputs.PLATFORMS }}
           build-args: |
             C_COMPILER=${{ steps.build-args.outputs.C_COMPILER }}
@@ -173,33 +174,35 @@ jobs:
             GIT_IS_DIRTY=false
             VERSION=${{ steps.build-args.outputs.VERSION }}
 
-
-  test-docker-image:
-    name: Test Docker image
-    needs: build-dockerfile
-    runs-on: ubuntu-latest
-    permissions:
-      packages: 'read'
-
-    if: github.event_name != 'pull_request'
-
-    container:
-      image: ghcr.io/${{ github.repository }}:latest
-      options: '--entrypoint /bin/bash'
-      credentials:
-        username: ${{ github.actor }}
-        password: ${{ secrets.github_token }}
-
-    steps:
-      - name: Test hictk
+      - name: Test Docker image
         run: |
-          set -o pipefail
+          utils/devel/test_docker_image.sh hictk:test
 
-          whereis -b hictk
-          ls -lah "$(whereis -b hictk | cut -d$' ' -f 2)"
+      - name: Push image to registries
+        if: github.event_name != 'pull_request'
+        uses: docker/build-push-action@v5
+        with:
+          context: ${{ github.workspace }}
+          push: true
+          cache-from: type=gha,scope=build-dockerfile
+          cache-to: type=gha,mode=min,scope=build-dockerfile
+          tags: ${{ steps.meta.outputs.tags }}
+          platforms: ${{ steps.build-args.outputs.PLATFORMS }}
+          build-args: |
+            C_COMPILER=${{ steps.build-args.outputs.C_COMPILER }}
+            CXX_COMPILER=${{ steps.build-args.outputs.CXX_COMPILER }}
+            BUILD_BASE_IMAGE=${{ steps.build-args.outputs.BUILD_BASE_IMAGE }}
+            TEST_BASE_IMAGE=${{ steps.build-args.outputs.TEST_BASE_IMAGE }}
+            FINAL_BASE_IMAGE=${{ steps.build-args.outputs.FINAL_BASE_IMAGE }}
+            FINAL_BASE_IMAGE_TAG=${{ steps.build-args.outputs.FINAL_BASE_IMAGE_TAG }}
+            FINAL_BASE_IMAGE_DIGEST=${{ steps.build-args.outputs.FINAL_BASE_IMAGE_DIGEST }}
+            GIT_HASH=${{ steps.build-args.outputs.GIT_HASH }}
+            GIT_SHORT_HASH=${{ steps.build-args.outputs.GIT_SHORT_HASH }}
+            CREATION_DATE=${{ steps.build-args.outputs.CREATION_DATE }}
+            GIT_TAG=${{ steps.build-args.outputs.GIT_TAG }}
+            GIT_IS_DIRTY=false
+            VERSION=${{ steps.build-args.outputs.VERSION }}
 
-          hictk --help
-          hictk --version
 
 
   build-dockerfile-status-check:
@@ -208,12 +211,9 @@ jobs:
     runs-on: ubuntu-latest
     needs:
       - build-dockerfile
-      - test-docker-image
 
     steps:
       - name: Collect job results
         if: |
-          needs.build-dockerfile.result != 'success'  ||
-          (needs.test-docker-image.result != 'success'  &&
-           needs.test-docker-image.result != 'skipped')
+          needs.build-dockerfile.result != 'success'
         run: exit 1

utils/devel/test_docker_image.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+# Copyright (c) 2023 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+set -eu
+set -o pipefail
+
+if [ $# -ne 1 ]; then
+  2>&1 echo "Usage: $0 hictk:latest"
+  status=1
+fi
+
+IMG="$1"
+
+tmpdir="$(mktemp -d)"
+trap "rm -rf '$tmpdir'" EXIT
+
+cat > "$tmpdir/runme.sh" <<- 'EOM'
+
+set -eu
+cd /tmp/hictk
+
+apt-get update
+apt-get install -y --no-install-recommends \
+  curl \
+  python3 \
+  xz-utils
+
+tar -xf test/data/hictk_test_data.tar.xz
+
+tmpdir="$(mktemp -d)"
+trap "rm -rf '$tmpdir'" EXIT
+
+hic_tools_url='https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar'
+curl -L "$hic_tools_url" -o "$tmpdir/hic_tools.jar"
+
+whereis -b hictk
+
+test/scripts/hictk_convert_hic2cool.sh "$(which hictk)"
+test/scripts/hictk_convert_cool2hic.sh "$(which hictk)" "$tmpdir/hic_tools.jar"
+
+EOM
+
+chmod 755 "$tmpdir/runme.sh"
+
+sudo docker run --rm --entrypoint=/bin/bash \
+  -v "$tmpdir/runme.sh:/tmp/runme.sh:ro" \
+  -v "$PWD/test/scripts:/tmp/hictk/test/scripts:ro" \
+  -v "$PWD/test/data/hictk_test_data.tar.xz:/tmp/hictk/test/data/hictk_test_data.tar.xz:ro" \
+  "$IMG" \
+  /tmp/runme.sh