From 1909a17b337ba109061ed88bb428d934bb7fb3a8 Mon Sep 17 00:00:00 2001
From: John Bradley <johnbradley2008@gmail.com>
Date: Tue, 3 Sep 2024 14:52:35 -0400
Subject: [PATCH] Add apptainer support

Adds apptainer definition and config to automatically build the
apptainer image on release. The apptainer image is based on the
docker image.

Part of #27

Co-authored-by: Hilmar Lapp <hlapp@drycafe.net>
---
 .github/workflows/deploy-image.yml | 40 ++++++++++++++++++++++++++++--
 apptainer.def                      |  8 ++++++
 2 files changed, 46 insertions(+), 2 deletions(-)
 create mode 100644 apptainer.def

diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml
index 12e2cf1..0467e0d 100644
--- a/.github/workflows/deploy-image.yml
+++ b/.github/workflows/deploy-image.yml
@@ -1,4 +1,5 @@
-name: Create and publish a Docker image
+
+name: Create and publish container images
 
 on:
   release:
@@ -8,7 +9,7 @@ env:
   IMAGE_NAME: ${{ github.repository }}
 
 jobs:
-  build-and-push-image:
+  build-and-push-docker:
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -43,3 +44,38 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           build-args: "PYBIOCLIP_VERSION=${{ steps.meta.outputs.version }}"
+
+  build-and-push-apptainer:
+    runs-on: ubuntu-latest
+    needs: build-and-push-docker
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract version for apptainer build
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Setup apptainer executable
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.3
+
+      - name: Build an apptainer image
+        run: apptainer build --build-arg PYBIOCLIP_VERSION=${{ steps.meta.outputs.version }} apptainer.sif apptainer.def
+
+      - name: Publish apptainer image
+        run: apptainer push apptainer.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-sif:${{ steps.meta.outputs.version }}
diff --git a/apptainer.def b/apptainer.def
new file mode 100644
index 0000000..18aea20
--- /dev/null
+++ b/apptainer.def
@@ -0,0 +1,8 @@
+Bootstrap: docker
+From: ghcr.io/imageomics/pybioclip:{{ PYBIOCLIP_VERSION }}
+
+%arguments
+    PYBIOCLIP_VERSION=
+
+%runscript
+   exec "$@"