From 06d68e4b94cdfbdaf3986860b32cfd65ebd98ec2 Mon Sep 17 00:00:00 2001
From: John Bradley <johnbradley2008@gmail.com>
Date: Tue, 20 Aug 2024 10:10:04 -0400
Subject: [PATCH 1/2] Adds Dockerfile to build a container

Command to build the container for pybioclip:
```
docker build --platform=linux/amd64 --build-arg="PYBIOCLIP_VERSION=1.0.0" -t pybioclip .
```

Adds GitHub action config to build the docker container and
apptainer container on release.
---
 .github/workflows/deploy-image.yml | 58 ++++++++++++++++++++++++++++++
 Dockerfile                         |  7 ++++
 2 files changed, 65 insertions(+)
 create mode 100644 .github/workflows/deploy-image.yml
 create mode 100644 Dockerfile

diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml
new file mode 100644
index 0000000..098602e
--- /dev/null
+++ b/.github/workflows/deploy-image.yml
@@ -0,0 +1,58 @@
+name: Create and publish a Docker image
+
+on:
+  release:
+    types: [published]
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      # Step below from https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
+      - name: Delete unnecessary tools folder to avoid running out of space
+        run: rm -rf /opt/hostedtoolcache
+
+      - 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 metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=semver,pattern={{major}}.{{minor}}.{{patch}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          build-args: "PYBIOCLIP_VERSION=${{ steps.meta.outputs.version }}"
+      - uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.3
+      - name: print stuff
+        run: echo "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}"
+      - name: pull an apptainer container
+        run: apptainer pull apptainer.sif docker://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
+      - name: push the apptainer container
+        run: apptainer push apptainer.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..892a764
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,7 @@
+FROM condaforge/miniforge3:24.3.0-0
+
+ARG PYBIOCLIP_VERSION
+
+# Install pybioclip from the release archive because pypi can take a while to start working.
+RUN pip install "https://github.com/Imageomics/pybioclip/archive/refs/tags/${PYBIOCLIP_VERSION}.tar.gz" && \
+    pip cache purge

From 7e7ada106ce6c5f23002a6aa795d38c0d4f48e90 Mon Sep 17 00:00:00 2001
From: John Bradley <johnbradley2008@gmail.com>
Date: Tue, 27 Aug 2024 15:02:29 -0400
Subject: [PATCH 2/2] Fix sif container name

---
 .github/workflows/deploy-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml
index 098602e..51b2d81 100644
--- a/.github/workflows/deploy-image.yml
+++ b/.github/workflows/deploy-image.yml
@@ -55,4 +55,4 @@ jobs:
       - name: pull an apptainer container
         run: apptainer pull apptainer.sif docker://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
       - name: push the apptainer container
-        run: apptainer push apptainer.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
+        run: apptainer push apptainer.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-sif:${{ steps.meta.outputs.version }}