Bump actions/cache from 4 to 5

.github/labeler.yml

@@ -1,63 +1,104 @@
 repo:
-  - ./*
-
+  - changed-files:
+    - any-glob-to-any-file:
+      - './*'
+
 examples:
-  - examples/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'examples/**/*'
 
 tests:
-  - arc/**/*Tests.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/**/*Tests.py'
 
 'Module: Conformers':
-  - arc/species/conformers.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/species/conformers.py'
 
 'Module: Mapping':
-  - arc/mapping/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/mapping/*'
 
 'Module: Converter':
-  - arc/species/converter.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/species/converter.py'
 
 'Module: Job':
-  - arc/job/job.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/job/job.py'
 
 'Module: Local':
-  - arc/job/local.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/job/local.py'
 
 'Module: Main':
-  - arc/main.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/main.py'
 
 'Module: Parser':
-  - arc/parser.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/parser.py'
 
 'Module: Plotter':
-  - arc/plotter.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/plotter.py'
 
 'Module: Processor':
-  - arc/processor.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/processor.py'
 
 'Module: Reaction':
-  - arc/reaction.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/reaction.py'
 
 'Module: rmgdb':
-  - arc/rmgdb.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/rmgdb.py'
 
 'Module: Scheduler':
-  - arc/scheduler.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/scheduler.py'
 
 'Module: Species':
-  - arc/species/species.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/species/species.py'
 
 'Module: SSH':
-  - arc/job/ssh.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/job/ssh.py'
 
 'Module: trsh':
-  - arc/job/trsh.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/job/trsh.py'
 
 'Module: Utils':
-  - arc/job/utils/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/job/utils/**/*'
 
 'Module docs':
-  - arc/docs/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'arc/docs/**/*'
 
 'Module Functional':
-  - functional/*
-
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'functional/*'

.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/labeler.yml

@@ -11,6 +11,6 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/labeler@v2
+    - uses: actions/labeler@v6
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"

.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

Dockerfile

@@ -2,7 +2,7 @@
 # The parent image is the base image that the Dockerfile builds upon.
 # The RMG installation instructions suggest Anaconda for installation by source, however, we use micromamba for the Docker image due to its smaller size and less overhead.
 # Installation of ARC will also be done in this stage.
 FROM --platform=linux/amd64 mambaorg/micromamba:2.2-ubuntu24.04 AS builder
 
 # Set ARGS
 ARG RMG_PY_BRANCH=main
@@ -35,32 +35,38 @@
 
 # Switch directory to Code and RMG clone
 WORKDIR /home/mambauser/Code
-RUN git clone --branch ${RMG_PY_BRANCH} https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
-    git clone --branch ${RMG_DATABASE_BRANCH} https://github.com/ReactionMechanismGenerator/RMG-database.git && \
-    git clone --branch ${ARC_BRANCH} https://github.com/ReactionMechanismGenerator/ARC.git
-
-# Create RMG-Py environment
-RUN micromamba create -y -n rmg_env -f /home/mambauser/Code/RMG-Py/environment.yml && \
-    micromamba run -n rmg_env micromamba install -y -c conda-forge pyjuliacall conda && \
-    micromamba clean --all --yes && \
-    micromamba run -n rmg_env make -C /home/mambauser/Code/RMG-Py -j"$(nproc)" && \
-    micromamba run -n rmg_env bash -c "\
+RUN git clone --depth 1 --branch ${RMG_PY_BRANCH} https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
+    git clone --depth 1 --branch ${RMG_DATABASE_BRANCH} https://github.com/ReactionMechanismGenerator/RMG-database.git && \
+    git clone --depth 1 --branch ${ARC_BRANCH} https://github.com/ReactionMechanismGenerator/ARC.git
+
+# Create RMG-Py environment (split into separate layers for GHA cache)
+# Pin python=3.9 to drastically reduce solver search space
+RUN micromamba create -y -v -n rmg_env python=3.9 -f /home/mambauser/Code/RMG-Py/environment.yml && \
+    micromamba run -n rmg_env micromamba install -y -v -c conda-forge pyjuliacall conda && \
+    micromamba clean --all --yes
+
+RUN micromamba run -n rmg_env make -C /home/mambauser/Code/RMG-Py -j"$(nproc)"
+
+RUN micromamba run -n rmg_env bash -c "\
       cd /home/mambauser/Code/RMG-Py && \
+      export RMS_INSTALLER=continuous && \
+      export RMS_BRANCH=for_rmg && \
       source install_rms.sh \
     "
 
 WORKDIR /home/mambauser/Code/ARC
-RUN micromamba create -y -n arc_env -f environment.yml --channel-priority flexible && \
-    micromamba install -y -n arc_env -c conda-forge pytest && \
-    micromamba clean --all -f -y && \
-    micromamba run -n arc_env bash -euxo pipefail -c \
+RUN micromamba create -y -v -n arc_env python=3.12 -f environment.yml && \
+    micromamba install -y -v -n arc_env -c conda-forge pytest && \
+    micromamba clean --all -f -y
+
+RUN micromamba run -n arc_env bash -euxo pipefail -c \
       "make compile && bash ./devtools/install_pyrdl.sh" && \
     micromamba clean --all --yes
 
 # Stage 2: Final image
 # The final image is based on the same micromamba image, but we copy over the installed RMG and ARC from the builder stage.
 # This keeps the final image size smaller and avoids unnecessary layers.
 FROM --platform=linux/amd64 mambaorg/micromamba:2.2-ubuntu24.04
 
 ENV MAMBA_ROOT_PREFIX=/opt/conda
 ENV PATH=$MAMBA_ROOT_PREFIX/bin:/home/mambauser/.juliaup/bin:/home/mambauser/Code/RMG-Py:/home/mambauser/Code/ARC:$PATH