chore: update GitHub Actions versions (#1113)

No more EOL 2022 Actions in production

Author: paperbenni

.github/workflows/GithubActionTests.yml

@@ -8,10 +8,10 @@ jobs:
   qc:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/ruff-action@v3
+      - uses: actions/checkout@v6
+      - uses: astral-sh/ruff-action@v4.0.0
         name: ruff check
-      - uses: astral-sh/ruff-action@v3
+      - uses: astral-sh/ruff-action@v4.0.0
         name: ruff format
         with:
           args: "format --check --diff"
@@ -42,7 +42,7 @@ jobs:
           - long_running_2
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -80,7 +80,7 @@ jobs:
     name: OSX tests
     runs-on: macos-15-intel
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -112,7 +112,7 @@ jobs:
     name: autobump test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 

.github/workflows/base-glibc-busybox-bash.yaml

@@ -29,7 +29,7 @@ jobs:
       DEBIAN_VERSION: '12.5'
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up QEMU
       run: |

.github/workflows/base-glibc-debian-bash.yaml

@@ -28,7 +28,7 @@ jobs:
       DEBIAN_VERSION: '12.5'
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up QEMU
       run: |

.github/workflows/bioconda-recipes-issue-responder.yaml

@@ -20,7 +20,7 @@ jobs:
       IMAGE_VERSION: '1.1.1'
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
 
     - name: Build
       id: buildah-build

.github/workflows/bot.yaml

@@ -33,7 +33,7 @@ jobs:
       IMAGE_VERSION: '1.4.1'
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Install Tools
       run: |

.github/workflows/build-image.yml

@@ -24,7 +24,7 @@ jobs:
             image: bioconda-utils-build-env-cos7-x86_64
             base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
 

.github/workflows/changevisibility.yml

@@ -20,7 +20,7 @@ jobs:
           QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_BIOCONTAINERS_TOKEN }}
 
       - name: Upload logs
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: logs
           path: biocontainers-*.txt

.github/workflows/conventional-prs.yml

@@ -11,6 +11,6 @@ jobs:
   title-format:
     runs-on: ubuntu-latest
     steps:
-      - uses: amannn/action-semantic-pull-request@v5
+      - uses: amannn/action-semantic-pull-request@v6
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/create-env.yaml

@@ -25,7 +25,7 @@ jobs:
       IMAGE_NAME: create-env
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up QEMU
       run: |

.github/workflows/release-please.yml

@@ -13,7 +13,7 @@ jobs:
       release_created: ${{ steps.release.outputs.release_created }}
       tag_name: ${{ steps.release.outputs.tag_name }}
     steps:
-      - uses: googleapis/release-please-action@v4
+      - uses: googleapis/release-please-action@v5
         id: release
         with:
           release-type: python