From e51da6bce141023562f00611de68e6d118cd865d Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 13:59:21 +0200
Subject: [PATCH 1/8] upgrade peter-evans/create-or-update-comment to v4

---
 .github/workflows/ci.yaml           | 4 ++--
 .github/workflows/workflow_test.yml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5b705a647..ee9b89f90 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -27,7 +27,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -201,7 +201,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-workflow-tests' }}
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 99918de07..caa474b84 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -160,7 +160,7 @@ jobs:
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}

From be7be774c57b5ab1655dd508225c8534110a0339 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:00:24 +0200
Subject: [PATCH 2/8] upgrade actions/setup-python@v4 to v5

---
 .github/workflows/ci.yaml            | 8 ++++----
 .github/workflows/setup.yml          | 2 +-
 .github/workflows/test_workflows.yml | 2 +-
 .github/workflows/workflow_test.yml  | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index ee9b89f90..fd08bdec3 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -43,7 +43,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -88,7 +88,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -132,7 +132,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -175,7 +175,7 @@ jobs:
     - uses: actions/download-artifact@v3
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index 3b0968249..df3d4fcc5 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -60,7 +60,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ inputs.galaxy-fork }}/galaxy refs/heads/${{ inputs.galaxy-branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml
index 073e37fc5..91d28247c 100644
--- a/.github/workflows/test_workflows.yml
+++ b/.github/workflows/test_workflows.yml
@@ -63,7 +63,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index caa474b84..88c11e157 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -27,7 +27,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -72,7 +72,7 @@ jobs:
     - uses: actions/download-artifact@v3
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -117,7 +117,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip

From 71dfa092a89e18a536fc5b9355f1230d5ded8b0f Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:01:47 +0200
Subject: [PATCH 3/8] upgrade actions/cache@v3 to v4

---
 .github/workflows/ci.yaml                         | 8 ++++----
 .github/workflows/setup.yml                       | 4 ++--
 .github/workflows/test_workflows.yml              | 2 +-
 .github/workflows/usegalaxy-star-installation.yml | 2 +-
 .github/workflows/workflow_test.yml               | 6 +++---
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index fd08bdec3..d057caabc 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -47,7 +47,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -92,7 +92,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -136,7 +136,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -179,7 +179,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index df3d4fcc5..a1c25541d 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -64,13 +64,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml
index 91d28247c..e04b2526b 100644
--- a/.github/workflows/test_workflows.yml
+++ b/.github/workflows/test_workflows.yml
@@ -67,7 +67,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
diff --git a/.github/workflows/usegalaxy-star-installation.yml b/.github/workflows/usegalaxy-star-installation.yml
index d6fbf8770..7dbd21f46 100644
--- a/.github/workflows/usegalaxy-star-installation.yml
+++ b/.github/workflows/usegalaxy-star-installation.yml
@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Cache downloads
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/pip
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 88c11e157..f16082538 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -31,7 +31,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -76,7 +76,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -121,7 +121,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip

From 9e88e82e1239ae022f1e8eacaa5bf46a14d34d7b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:02:25 +0200
Subject: [PATCH 4/8] upgrade actions/checkout@v3 to v4

---
 .github/workflows/ci.yaml                         | 6 +++---
 .github/workflows/enable_ci_workflows.yml         | 2 +-
 .github/workflows/setup.yml                       | 2 +-
 .github/workflows/test_workflows.yml              | 2 +-
 .github/workflows/usegalaxy-star-installation.yml | 2 +-
 .github/workflows/workflow_test.yml               | 4 ++--
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index d057caabc..24a3dfc39 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -56,7 +56,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -85,7 +85,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
@@ -129,7 +129,7 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
diff --git a/.github/workflows/enable_ci_workflows.yml b/.github/workflows/enable_ci_workflows.yml
index b7a1999c7..875dfe950 100644
--- a/.github/workflows/enable_ci_workflows.yml
+++ b/.github/workflows/enable_ci_workflows.yml
@@ -8,7 +8,7 @@ jobs:
     name: Enable CI workflows
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - name: run Python script
diff --git a/.github/workflows/setup.yml b/.github/workflows/setup.yml
index a1c25541d..d27bb5919 100644
--- a/.github/workflows/setup.yml
+++ b/.github/workflows/setup.yml
@@ -79,7 +79,7 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml
index e04b2526b..f961e24a4 100644
--- a/.github/workflows/test_workflows.yml
+++ b/.github/workflows/test_workflows.yml
@@ -60,7 +60,7 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
diff --git a/.github/workflows/usegalaxy-star-installation.yml b/.github/workflows/usegalaxy-star-installation.yml
index 7dbd21f46..ea78b5f81 100644
--- a/.github/workflows/usegalaxy-star-installation.yml
+++ b/.github/workflows/usegalaxy-star-installation.yml
@@ -9,7 +9,7 @@ jobs:
   workflow-install:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Cache downloads
         uses: actions/cache@v4
         with:
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index f16082538..32bfdb095 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -24,7 +24,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5
@@ -114,7 +114,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
     - uses: actions/setup-python@v5

From 542a84d91c27fc47028cb0fa9983d96d7170ad16 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:03:50 +0200
Subject: [PATCH 5/8] upgrade actions/upload-artifact@v3 to v4

---
 .github/workflows/ci.yaml            | 4 ++--
 .github/workflows/test_workflows.yml | 2 +-
 .github/workflows/workflow_test.yml  | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 24a3dfc39..c72a14a5c 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -153,7 +153,7 @@ jobs:
         galaxy-branch: ${{ needs.setup.outputs.branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Workflow test output ${{ matrix.chunk }}'
         path: upload
@@ -190,7 +190,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All workflow test results'
         path: upload
diff --git a/.github/workflows/test_workflows.yml b/.github/workflows/test_workflows.yml
index f961e24a4..e205e7804 100644
--- a/.github/workflows/test_workflows.yml
+++ b/.github/workflows/test_workflows.yml
@@ -84,7 +84,7 @@ jobs:
         galaxy-branch: ${{ inputs.galaxy-branch }}
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ inputs.chunk-count }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Workflow test output ${{ matrix.chunk }}'
         path: upload
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 32bfdb095..1d142a6e0 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -94,7 +94,7 @@ jobs:
     - name: Debug PR number
       run: |
           cat ./upload/NR
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload

From fca4a472479070eda253c1aab28eab7062adbdc8 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:04:29 +0200
Subject: [PATCH 6/8] upgrade actions/download-artifact@v3 to v4

---
 .github/workflows/ci.yaml           | 2 +-
 .github/workflows/workflow_test.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index c72a14a5c..2f2f8bf92 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -172,7 +172,7 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
     - uses: actions/setup-python@v5
diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 1d142a6e0..907dded48 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -69,7 +69,7 @@ jobs:
         python-version: ['3.11']
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
     - uses: actions/setup-python@v5

From fc9ca112115bf017a394072ff68f9e5b1c343b97 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:05:55 +0200
Subject: [PATCH 7/8] upgrade peter-evans/slash-command-dispatch v3 to v4

---
 .github/workflows/slash.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
index 8f9e2b2fe..1ffa52169 100644
--- a/.github/workflows/slash.yaml
+++ b/.github/workflows/slash.yaml
@@ -8,7 +8,7 @@ jobs:
     steps:
       - name: Slash Command Dispatch
         if: github.repository_owner == 'galaxyproject'
-        uses: peter-evans/slash-command-dispatch@v3
+        uses: peter-evans/slash-command-dispatch@v4
         with:
           token: ${{ secrets.PAT }}
           commands: |

From 806b58dc27ad5ef7f63b658b2d0f034c2efec87e Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 24 Sep 2024 14:08:04 +0200
Subject: [PATCH 8/8] upgrade 8BitJonny/gh-get-current-pr to 3.0.0

---
 .github/workflows/workflow_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml
index 907dded48..a2e3037fc 100644
--- a/.github/workflows/workflow_test.yml
+++ b/.github/workflows/workflow_test.yml
@@ -155,7 +155,7 @@ jobs:
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
-      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      uses: 8BitJonny/gh-get-current-pr@3.0.0
       id: getpr
       with:
         sha: ${{ github.event.after }}