Merge branch 'main' into graph_provenance

Author: calvinp0

.github/dependabot.yml

@@ -0,0 +1,22 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+
+    groups:
+      core-actions:
+        patterns:
+          - "actions/*"
+
+      third-party-actions:
+        patterns:
+          - "*"
+        exclude-patterns:
+          - "actions/*"

.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
 
@@ -33,7 +33,7 @@ jobs:
           swap-storage: true
 
       - name: Set up micromamba (arc_env)
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: arc_env
           environment-file: ARC/environment.yml
@@ -116,7 +116,7 @@ jobs:
           pytest functional/ --cov --cov-append --cov-report=xml -ra -vv -n auto
 
       - name: Upload coverage data
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ARC/coverage.xml

.github/workflows/codeql.yml

@@ -24,18 +24,18 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v3
+        uses: github/codeql-action/autobuild@v4
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v4
         with:
           category: "/language:${{ matrix.language }}"

.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@v7.1.0
         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@v7.1.0
         with:
           context: .
           file: ./Dockerfile
@@ -80,14 +80,14 @@ jobs:
 
       - name: Login to Docker Hub
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        uses: docker/login-action@v3.5.0
+        uses: docker/login-action@v4.1.0
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - 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@v7.1.0
         with:
           context: .
           file: ./Dockerfile

.github/workflows/gh-pages.yml

@@ -14,15 +14,15 @@ jobs:
     steps:
       # ── clone ARC repo ───────────────────────────────────────────
       - name: Checkout ARC
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ReactionMechanismGenerator/ARC
           path: ARC
           fetch-depth: 1
 
       # ── rmg_env for Arkane/database availability ───────────────
       - name: Set up micromamba (rmg_env)
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: rmg_env
           create-args: >-
@@ -33,7 +33,7 @@ jobs:
 
       # ── docs env (wrapper shell) ────────────────────────────────
       - name: Set up micromamba (arc_env)
-        uses: mamba-org/setup-micromamba@v2
+        uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: arc_env
           environment-file: ARC/environment.yml

.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