Bump actions/cache from 4 to 5

Bumps [actions/cache](https://github.com/actions/cache) from 4 to 5.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v4...v5)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bump actions/checkout from 3 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bump docker/setup-buildx-action from 3.11.1 to 4.0.0

Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.11.1 to 4.0.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](docker/setup-buildx-action@v3.11.1...v4.0.0)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-version: 4.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bump docker/build-push-action from 6.18.0 to 7.0.0

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.18.0 to 7.0.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@v6.18.0...v7.0.0)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Verbosity

Change it so we always docker build for main branch when PR merges

Author: dependabot[bot]

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
       - name: Checkout ARC
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           path: ARC
 

.github/workflows/codeql.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v3

.github/workflows/docker_build.yml

@@ -6,9 +6,6 @@ on:
   push:
     branches:
       - main
-    paths:
-      - "Dockerfile"
-      - ".github/workflows/docker_build.yml"
   pull_request:
     branches:
       - main
@@ -18,6 +15,9 @@ on:
     types: [opened, synchronize, reopened, ready_for_review]
   #workflow_dispatch: # Add this line to enable manual trigger
 
+env:
+  BUILDKIT_PROGRESS: plain
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -34,16 +34,16 @@ jobs:
           swap-storage: true
 
       - name: Checkout
-        uses: actions/checkout@v5.0.0
+        uses: actions/checkout@v6
 
       - name: Set up Buildx
-        uses: docker/setup-buildx-action@v3.11.1
+        uses: docker/setup-buildx-action@v4.0.0
 
       # ----- PR and non-main branch steps -----
       # For PRs: Build image but do not push and run smoke tests
       - name: Build Docker Image (No Push)
         if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.ref != 'refs/heads/main')
-        uses: docker/build-push-action@v6.18.0
+        uses: docker/build-push-action@v7.0.0
         with:
           context: .
           file: ./Dockerfile
@@ -63,7 +63,7 @@ jobs:
       # For pushes to main: Build, run smoke tests, and push to Docker Hub
       - name: Build test stage (main)
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/build-push-action@v6.18.0
+        uses: docker/build-push-action@v7.0.0
         with:
           context: .
           file: ./Dockerfile
@@ -87,7 +87,7 @@ jobs:
 
       - name: Build final and push (main)
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/build-push-action@v6.18.0
+        uses: docker/build-push-action@v7.0.0
         with:
           context: .
           file: ./Dockerfile

.github/workflows/gh-pages.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       # ── clone ARC repo ───────────────────────────────────────────
       - name: Checkout ARC
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/ARC
           path: ARC

.github/workflows/update-cache.yml

@@ -19,20 +19,20 @@ jobs:
     steps:
       # ────────── source repo ──────────
       - name: Checkout ARC
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       # ────────── AutoTST ──────────
       - name: Cache AutoTST
         id: cache-autotst
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: AutoTST
           key: ${{ runner.os }}-autotst-main
           restore-keys: |
             ${{ runner.os }}-autotst-
       - name: Checkout AutoTST
         if: steps.cache-autotst.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/AutoTST
           path: AutoTST
@@ -42,15 +42,15 @@ jobs:
       # ────────── TS‑GCN ──────────
       - name: Cache TS-GCN
         id: cache-tsgcn
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: TS-GCN
           key: ${{ runner.os }}-tsgcn-main
           restore-keys: |
             ${{ runner.os }}-tsgcn-
       - name: Checkout TS-GCN
         if: steps.cache-tsgcn.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/TS-GCN
           path: TS-GCN
@@ -60,15 +60,15 @@ jobs:
       # ────────── KinBot ──────────
       - name: Cache KinBot
         id: cache-kinbot
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: KinBot
           key: ${{ runner.os }}-kinbot-2.0.6
           restore-keys: |
             ${{ runner.os }}-kinbot-
       - name: Checkout KinBot 2.0.6
         if: steps.cache-kinbot.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: zadorlab/KinBot
           path: KinBot