fix: explicit set workflow permission and move secrets to necessary

.github/workflows/base.yml

@@ -15,6 +15,9 @@ on:
       - '.github/workflows/base.yml'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   build-base:
     if: ${{ github.repository_owner == 'axolotl-ai-cloud' && (github.event_name != 'pull_request' || !github.event.pull_request.draft) }}
@@ -124,15 +127,15 @@ jobs:
           images: |
             axolotlai/axolotl-base
       - name: Login to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         if: ${{ github.event_name != 'pull_request' && env.HAS_DOCKERHUB_CREDS == 'true' }}
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: ./docker/${{ matrix.dockerfile }}
@@ -239,15 +242,15 @@ jobs:
           images: |
             axolotlai/axolotl-base-uv
       - name: Login to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         if: ${{ github.event_name != 'pull_request' && env.HAS_DOCKERHUB_CREDS == 'true' }}
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
       - name: Build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: ./docker/${{ matrix.dockerfile }}

.github/workflows/lint.yml

@@ -13,6 +13,9 @@ on:
        - ".pre-commit-config.yaml"
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   pre-commit:
     name: pre-commit

.github/workflows/main.yml

@@ -8,6 +8,9 @@ on:
       - "v*"
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   build-axolotl:
     if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}

.github/workflows/multi-gpu-e2e.yml

@@ -20,6 +20,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
+permissions:
+  contents: read
+
 env:
   MODAL_IMAGE_BUILDER_VERSION: "2025.06"
 
@@ -78,8 +81,9 @@ jobs:
           echo "AXOLOTL_EXTRAS=${{ matrix.axolotl_extras}}" >> $GITHUB_ENV
           echo "CUDA=${{ matrix.cuda }}" >> $GITHUB_ENV
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
           echo "E2E_DOCKERFILE=${{ matrix.dockerfile || 'Dockerfile.jinja'}}" >> $GITHUB_ENV
       - name: Run tests job on Modal
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           modal run -m cicd.multigpu

.github/workflows/nightlies.yml

@@ -5,6 +5,9 @@ on:
   schedule:
     - cron: '0 0 * * *'  # Runs at 00:00 UTC every day
 
+permissions:
+  contents: read
+
 jobs:
   build-axolotl:
     if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}

.github/workflows/precommit-autoupdate.yml

@@ -5,6 +5,8 @@ on:
     - cron: '0 0 1 * *'  # Run monthly
   workflow_dispatch:  # Manual kickoff
 
+permissions: {}
+
 jobs:
   auto-update:
     runs-on: ubuntu-latest

.github/workflows/pypi.yml

@@ -3,9 +3,11 @@ name: publish pypi
 on:
   push:
     tags:
-      - 'v*'
+      - "v*"
   workflow_dispatch:
 
+permissions: {}
+
 jobs:
   setup_release:
     name: Create Release
@@ -28,7 +30,8 @@ jobs:
       name: pypi
       url: https://pypi.org/p/axolotl
     permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      contents: read
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
@@ -46,7 +49,7 @@ jobs:
 
       - name: Extract tag name
         id: tag
-        run: echo ::set-output name=TAG_NAME::$(echo $GITHUB_REF | cut -d / -f 3)
+        run: echo "TAG_NAME=$(echo $GITHUB_REF | cut -d / -f 3)" >> "$GITHUB_OUTPUT"
 
       - name: Update version in VERSION file
         run: |

.github/workflows/tests-nightly.yml

@@ -8,6 +8,9 @@ on:
     paths:
       - '.github/workflows/tests-nightly.yml'
 
+permissions:
+  contents: read
+
 jobs:
   pre-commit:
     name: pre-commit
@@ -156,8 +159,9 @@ jobs:
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
           echo "E2E_DOCKERFILE=${{ matrix.dockerfile || 'Dockerfile.jinja'}}" >> $GITHUB_ENV
           echo "NIGHTLY_BUILD=${{ matrix.nightly_build }}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
       - name: Run tests job on Modal
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           modal run cicd.e2e_tests
   docker-e2e-multigpu-tests:
@@ -198,7 +202,8 @@ jobs:
           echo "CUDA=${{ matrix.cuda }}" >> $GITHUB_ENV
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
           echo "NIGHTLY_BUILD=${{ matrix.nightly_build }}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
       - name: Run tests job on Modal
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           modal run cicd.multigpu

.github/workflows/tests.yml

@@ -28,6 +28,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 
+permissions:
+  contents: read
+
 env:
   TRANSFORMERS_IS_CI: "yes"
 
@@ -303,9 +306,10 @@ jobs:
           echo "CUDA=${{ matrix.cuda }}" >> $GITHUB_ENV
           echo "MODAL_IMAGE_BUILDER_VERSION=2024.10" >> $GITHUB_ENV
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
           echo "E2E_DOCKERFILE=${{ matrix.dockerfile || 'Dockerfile.jinja'}}" >> $GITHUB_ENV
       - name: Run tests job on Modal
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           modal run cicd.e2e_tests
 
@@ -371,9 +375,10 @@ jobs:
           echo "MODAL_IMAGE_BUILDER_VERSION=2024.10" >> $GITHUB_ENV
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
           echo "GPU_TYPE=${{ matrix.gpu_type || 'L40S'}}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
           echo "E2E_DOCKERFILE=${{ matrix.dockerfile || 'Dockerfile.jinja'}}" >> $GITHUB_ENV
       - name: Run tests job on Modal
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         run: |
           modal run cicd.e2e_tests
 
@@ -413,7 +418,6 @@ jobs:
           echo "CUDA=${{ matrix.cuda }}" >> $GITHUB_ENV
           echo "MODAL_IMAGE_BUILDER_VERSION=2024.10" >> $GITHUB_ENV
           echo "N_GPUS=${{ matrix.num_gpus }}" >> $GITHUB_ENV
-          echo "CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }}" >> $GITHUB_ENV
       - name: Run tests job on Modal
         run: |
           modal run cicd.cleanup