From b299daac0fca22fd3fd1519337aee3db6827c452 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 11:46:08 -0600
Subject: [PATCH 01/15] Create GitHub Actions workflow to build and push Docker
 Images

---
 .github/workflows/docker.yaml | 48 +++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 .github/workflows/docker.yaml

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
new file mode 100644
index 00000000..1e634c9a
--- /dev/null
+++ b/.github/workflows/docker.yaml
@@ -0,0 +1,48 @@
+name: Build and Push Docker Images
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        image:
+          - name: base
+            dockerfile: ./images/Dockerfile
+          - name: matlab
+            dockerfile: ./images/Dockerfile.matlab
+          - name: gpu
+            dockerfile: ./images/Dockerfile
+          - name: gpu-matlab
+            dockerfile: ./images/Dockerfile
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push Docker Image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: |
+            ${{ vars.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file

From 88544673e8f998173204070f746c013f18c625af Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 11:52:25 -0600
Subject: [PATCH 02/15] Update username

---
 .github/workflows/docker.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 1e634c9a..4ca037cd 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -29,7 +29,7 @@ jobs:
       - name: Log in to Docker Hub
         uses: docker/login-action@v3
         with:
-          username: ${{ vars.DOCKER_USERNAME }}
+          username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up QEMU
@@ -45,4 +45,4 @@ jobs:
           file: ${{ matrix.dockerfile }}
           push: true
           tags: |
-            ${{ vars.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file
+            ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file

From ac0918f75a4e034a6043c2008c5f01077482949c Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 11:54:29 -0600
Subject: [PATCH 03/15] Fix filenames

---
 .github/workflows/docker.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 4ca037cd..5b8867c7 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -19,9 +19,9 @@ jobs:
           - name: matlab
             dockerfile: ./images/Dockerfile.matlab
           - name: gpu
-            dockerfile: ./images/Dockerfile
+            dockerfile: ./images/Dockerfile.gpu
           - name: gpu-matlab
-            dockerfile: ./images/Dockerfile
+            dockerfile: ./images/Dockerfile.gpu.matlab
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4

From 14fa34f74a4fb8248618c2131bec6c0a22a1a88d Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 11:57:48 -0600
Subject: [PATCH 04/15] Update filepath

---
 .github/workflows/docker.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 5b8867c7..7f0dc789 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -15,13 +15,13 @@ jobs:
       matrix:
         image:
           - name: base
-            dockerfile: ./images/Dockerfile
+            dockerfile: Dockerfile
           - name: matlab
-            dockerfile: ./images/Dockerfile.matlab
+            dockerfile: Dockerfile.matlab
           - name: gpu
-            dockerfile: ./images/Dockerfile.gpu
+            dockerfile: Dockerfile.gpu
           - name: gpu-matlab
-            dockerfile: ./images/Dockerfile.gpu.matlab
+            dockerfile: Dockerfile.gpu.matlab
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
@@ -42,7 +42,7 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          file: ${{ matrix.dockerfile }}
+          file: ./images/${{ matrix.dockerfile }}
           push: true
           tags: |
             ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file

From 80e8dc3179ce3ce883b9f70540b4924e1eccf3ae Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 12:00:41 -0600
Subject: [PATCH 05/15] Update context

---
 .github/workflows/docker.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 7f0dc789..2db1c50a 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -41,8 +41,8 @@ jobs:
       - name: Build and push Docker Image
         uses: docker/build-push-action@v6
         with:
-          context: .
-          file: ./images/${{ matrix.dockerfile }}
+          context: images
+          file: images/${{ matrix.dockerfile }}
           push: true
           tags: |
             ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file

From 0214e3c297b01b9595350ec404a5eb5a5bee7b99 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 12:05:17 -0600
Subject: [PATCH 06/15] Update context

---
 .github/workflows/docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 2db1c50a..40be6c1c 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -42,7 +42,7 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: images
-          file: images/${{ matrix.dockerfile }}
+          file: ${{ matrix.dockerfile }}
           push: true
           tags: |
             ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file

From 5c36dacbc33b17e7356fe9e12298d8308d493283 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 12:27:56 -0600
Subject: [PATCH 07/15] Fix tag

---
 .github/workflows/docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 40be6c1c..981f54d0 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -45,4 +45,4 @@ jobs:
           file: ${{ matrix.dockerfile }}
           push: true
           tags: |
-            ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.name }}
\ No newline at end of file
+            ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
\ No newline at end of file

From 9b37357e0e63ce320ca7db2a1fed65e3ef377a46 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 13:00:57 -0600
Subject: [PATCH 08/15] Update image tags to use `base` suffix

---
 envs/shared/jupyterhub.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/envs/shared/jupyterhub.yaml b/envs/shared/jupyterhub.yaml
index 5a3e3ed9..a114f5cf 100755
--- a/envs/shared/jupyterhub.yaml
+++ b/envs/shared/jupyterhub.yaml
@@ -50,7 +50,7 @@ singleuser:
               display_name: "Standard"
               default: true
               kubespawner_override:
-                image: "${singleuser_image_repo}:${singleuser_image_tag}"
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-base"
       kubespawner_override:
         image_pull_policy: Always
         cpu_limit: 2
@@ -69,7 +69,7 @@ singleuser:
     #           display_name: "Standard"
     #           default: true
     #           kubespawner_override:
-    #             image: "${singleuser_image_repo}:${singleuser_image_tag}"
+    #             image: "${singleuser_image_repo}:${singleuser_image_tag}-base"
     #         matlab:
     #           display_name: "MATLAB (must provide your own license)"
     #           kubespawner_override:
@@ -93,7 +93,7 @@ singleuser:
               display_name: "Standard"
               default: true
               kubespawner_override:
-                image: "${singleuser_image_repo}:${singleuser_image_tag}"
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-base"
             matlab:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:
@@ -118,7 +118,7 @@ singleuser:
               display_name: "Standard"
               default: true
               kubespawner_override:
-                image: "${singleuser_image_repo}:${singleuser_image_tag}"
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-base"
             matlab:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:
@@ -141,7 +141,7 @@ singleuser:
               display_name: "Standard"
               default: true
               kubespawner_override:
-                image: "${singleuser_image_repo}:${singleuser_image_tag}"
+                image: "${singleuser_image_repo}:${singleuser_image_tag}-base"
             matlab:
               display_name: "MATLAB (must provide your own license)"
               kubespawner_override:

From 677e40821c1650aabacfadfedff863cca118a069 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 14:16:40 -0600
Subject: [PATCH 09/15] Use token

---
 .github/workflows/docker.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 981f54d0..391f04ad 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -30,7 +30,7 @@ jobs:
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
+          password: ${{ secrets.DOCKER_TOKEN }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3

From 7e05432cf8c502a8cdf55eeccdd540c26c0d0dcf Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 14:31:18 -0600
Subject: [PATCH 10/15] Update secret names

---
 .github/workflows/docker.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
index 391f04ad..c48f451b 100644
--- a/.github/workflows/docker.yaml
+++ b/.github/workflows/docker.yaml
@@ -29,8 +29,8 @@ jobs:
       - name: Log in to Docker Hub
         uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_TOKEN }}
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
@@ -45,4 +45,4 @@ jobs:
           file: ${{ matrix.dockerfile }}
           push: true
           tags: |
-            ${{ secrets.DOCKER_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
\ No newline at end of file
+            ${{ secrets.DOCKERHUB_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
\ No newline at end of file

From 8fc30b20bbafede8ca2c65108d83e59c5cd75f7d Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 14:42:10 -0600
Subject: [PATCH 11/15] Rename file

---
 .github/workflows/{docker.yaml => docker-push.yaml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{docker.yaml => docker-push.yaml} (100%)

diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker-push.yaml
similarity index 100%
rename from .github/workflows/docker.yaml
rename to .github/workflows/docker-push.yaml

From 98d7bb14dd4c9124a9c21b82ce0b5213da01187d Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 14:46:14 -0600
Subject: [PATCH 12/15] Add workflow for testing

---
 .github/workflows/docker-push.yaml |  3 +--
 .github/workflows/docker-test.yaml | 37 ++++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/docker-test.yaml

diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml
index c48f451b..4b03ae6e 100644
--- a/.github/workflows/docker-push.yaml
+++ b/.github/workflows/docker-push.yaml
@@ -1,14 +1,13 @@
 name: Build and Push Docker Images
 
 on:
-  pull_request:
   push:
     branches:
       - main
   workflow_dispatch:
 
 jobs:
-  docker:
+  docker-push:
     runs-on: ubuntu-latest
 
     strategy:
diff --git a/.github/workflows/docker-test.yaml b/.github/workflows/docker-test.yaml
new file mode 100644
index 00000000..339e7ba8
--- /dev/null
+++ b/.github/workflows/docker-test.yaml
@@ -0,0 +1,37 @@
+name: Build Docker Images
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  docker-test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        image:
+          - name: base
+            dockerfile: Dockerfile
+          - name: matlab
+            dockerfile: Dockerfile.matlab
+          - name: gpu
+            dockerfile: Dockerfile.gpu
+          - name: gpu-matlab
+            dockerfile: Dockerfile.gpu.matlab
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Docker Image
+        uses: docker/build-push-action@v6
+        with:
+          context: images
+          file: ${{ matrix.dockerfile }}
+          push: false
\ No newline at end of file

From 2ee929aa92645ef25a9698b4511b964de22c47cf Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 21:58:42 -0600
Subject: [PATCH 13/15] Add caching mechanism

---
 .github/workflows/docker-push.yaml | 4 +++-
 .github/workflows/docker-test.yaml | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml
index 4b03ae6e..29505ed9 100644
--- a/.github/workflows/docker-push.yaml
+++ b/.github/workflows/docker-push.yaml
@@ -44,4 +44,6 @@ jobs:
           file: ${{ matrix.dockerfile }}
           push: true
           tags: |
-            ${{ secrets.DOCKERHUB_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
\ No newline at end of file
+            ${{ secrets.DOCKERHUB_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
+          cache-from: type=registry,ref=${{ secrets.DOCKERHUB_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
+          cache-to: type=inline
\ No newline at end of file
diff --git a/.github/workflows/docker-test.yaml b/.github/workflows/docker-test.yaml
index 339e7ba8..59ccdc3e 100644
--- a/.github/workflows/docker-test.yaml
+++ b/.github/workflows/docker-test.yaml
@@ -34,4 +34,6 @@ jobs:
         with:
           context: images
           file: ${{ matrix.dockerfile }}
-          push: false
\ No newline at end of file
+          push: false
+          cache-from: type=registry,ref=${{ secrets.DOCKERHUB_USERNAME }}/dandihub:latest-${{ matrix.image.name }}
+          cache-to: type=inline
\ No newline at end of file

From 1db250aa4118fb20a49f57eebc2af54276f4c29e Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 22:15:01 -0600
Subject: [PATCH 14/15] Add path filtering

---
 .github/workflows/docker-push.yaml | 2 ++
 .github/workflows/docker-test.yaml | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/.github/workflows/docker-push.yaml b/.github/workflows/docker-push.yaml
index 29505ed9..b0632695 100644
--- a/.github/workflows/docker-push.yaml
+++ b/.github/workflows/docker-push.yaml
@@ -4,6 +4,8 @@ on:
   push:
     branches:
       - main
+    paths:
+      - 'Dockerfile*'
   workflow_dispatch:
 
 jobs:
diff --git a/.github/workflows/docker-test.yaml b/.github/workflows/docker-test.yaml
index 59ccdc3e..51cb69c5 100644
--- a/.github/workflows/docker-test.yaml
+++ b/.github/workflows/docker-test.yaml
@@ -2,6 +2,8 @@ name: Build Docker Images
 
 on:
   pull_request:
+  paths:
+    - 'Dockerfile*'
   workflow_dispatch:
 
 jobs:

From 409599e66372d32905feb3d6b965b888e9492f23 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 11 Dec 2024 22:16:15 -0600
Subject: [PATCH 15/15] Fix syntax

---
 .github/workflows/docker-test.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-test.yaml b/.github/workflows/docker-test.yaml
index 51cb69c5..81f1a694 100644
--- a/.github/workflows/docker-test.yaml
+++ b/.github/workflows/docker-test.yaml
@@ -2,8 +2,8 @@ name: Build Docker Images
 
 on:
   pull_request:
-  paths:
-    - 'Dockerfile*'
+    paths:
+      - 'Dockerfile*'
   workflow_dispatch:
 
 jobs: