Merge remote-tracking branch 'origin/master' into upgrade-wdl-1.1

Author: dpark01

.github/workflows/build.yml

@@ -48,9 +48,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags      
       - name: Programmatic environment setup
@@ -80,7 +80,7 @@ jobs:
         run: |
           env
       - name: install python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.10'
       - name: install system dependencies
@@ -103,9 +103,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -131,7 +131,7 @@ jobs:
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
       - name: install java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           distribution: 'temurin'
           java-version: '17'
@@ -155,9 +155,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -183,7 +183,7 @@ jobs:
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
       - name: install python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with: 
           python-version: '3.10'
       - name: install docs dependencies
@@ -202,9 +202,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -237,7 +237,7 @@ jobs:
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: install java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           distribution: 'temurin'
           java-version: '17'
@@ -259,9 +259,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -294,7 +294,7 @@ jobs:
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
       - name: install python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.10'
       - name: install system dependencies
@@ -305,7 +305,7 @@ jobs:
         run: |
           pip3 install miniwdl docker[tls] six
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
       - name: test with miniwdl
         shell: bash
         run: |
@@ -330,9 +330,9 @@ jobs:
       DX_PROJECT: project-F8PQ6380xf5bK0Qk0YPjB17P
     steps:
       - name: checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v6 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -363,11 +363,11 @@ jobs:
           echo "${{ github.event.action }}"
           echo "${{ github.event.pull_request.merged }}"
       - name: install python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with: 
           python-version: '3.10'
       - name: install java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           distribution: 'temurin'
           java-version: '17'