From 4e7aec38ddc839dafc7d3f4c4ae752f8062601a3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 3 Jun 2026 18:10:55 +0000
Subject: [PATCH 1/2] Update singularity deploy actions to Node24-ready
 versions

---
 .github/workflows/singularity-deploy.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/singularity-deploy.yml b/.github/workflows/singularity-deploy.yml
index 4305a174..6a0a20a1 100644
--- a/.github/workflows/singularity-deploy.yml
+++ b/.github/workflows/singularity-deploy.yml
@@ -18,9 +18,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v6
 
-      - uses: chrnorm/deployment-action@releases/v1
+      - uses: chrnorm/deployment-action@v2.0.8
         name: Create GitHub deployment
         id: deployment
         with:
@@ -30,7 +30,7 @@ jobs:
 
       - name: Update deployment status (success)
         if: success()
-        uses: chrnorm/deployment-status@releases/v1
+        uses: chrnorm/deployment-status@v2.0.4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           state: "success"
@@ -38,7 +38,7 @@ jobs:
 
       - name: Update deployment status (failure)
         if: failure()
-        uses: chrnorm/deployment-status@releases/v1
+        uses: chrnorm/deployment-status@v2.0.4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           state: "failure"

From c0dd8a2b2520742621e0d2f47acf37fcab6c93e9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 3 Jun 2026 18:11:28 +0000
Subject: [PATCH 2/2] Modernize Docker and release workflows for current action
 runtimes

---
 .github/workflows/main.yml              | 10 ++++-----
 .github/workflows/python-publish.yml    |  4 ++--
 .github/workflows/release-triggered.yml | 22 ++++++++-----------
 .github/workflows/release.yml           | 29 ++++++++++---------------
 .github/workflows/triggered-build.yml   | 10 ++++-----
 5 files changed, 32 insertions(+), 43 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bd5f23f9..8db86b71 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,21 +21,21 @@ jobs:
     steps:
 
       - name: Check Out Repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v4
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v7
         with:
           context: ./
           file: ./Dockerfile
@@ -46,7 +46,7 @@ jobs:
         run: echo "digest=${{ steps.docker_build.outputs.digest }}" >> $GITHUB_OUTPUT
 
       - name: Repository Dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: nextgenusfs/funannotate
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 94209999..867707f2 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
     - name: Install dependencies
diff --git a/.github/workflows/release-triggered.yml b/.github/workflows/release-triggered.yml
index 4b701439..4eb44f6c 100644
--- a/.github/workflows/release-triggered.yml
+++ b/.github/workflows/release-triggered.yml
@@ -9,6 +9,10 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
+    inputs:
+      release_tag:
+        description: "Release tag to publish when manually triggered"
+        required: true
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -19,34 +23,26 @@ jobs:
 
     steps:
       - name: Check Out Repo
-        uses: actions/checkout@v2
-
-      - name: Get release
-        id: get_release
-        uses: kaliber5/action-get-release@v1
-        with:
-          token: ${{ github.token }}
-          latest: true
+        uses: actions/checkout@v6
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v4
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v7
         with:
           context: ./
           file: ./Dockerfile2
           push: true
-          tags: nextgenusfs/funannotate:${{ steps.get_release.outputs.tag_name }}
+          tags: nextgenusfs/funannotate:${{ inputs.release_tag || github.event.client_payload.tag }}
 
       - name: Image digest
         run: echo "digest=${{ steps.docker_build.outputs.digest }}" >> $GITHUB_OUTPUT
-
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 6b37de6d..5fc12adb 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -9,6 +9,10 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
+    inputs:
+      release_tag:
+        description: "Release tag to publish when manually triggered"
+        required: true
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -19,45 +23,34 @@ jobs:
 
     steps:
       - name: Check Out Repo
-        uses: actions/checkout@v2
-
-      - name: Get release
-        id: get_release
-        uses: kaliber5/action-get-release@v1
-        with:
-          token: ${{ github.token }}
-          latest: true
-
-      - name: Test git release scrapper
-        id: test_release
-        run: echo "tag_name=${{ steps.get_release.outputs.tag_name }}" >> $GITHUB_OUTPUT
+        uses: actions/checkout@v6
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v4
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v7
         with:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: nextgenusfs/funannotate-slim:${{ steps.get_release.outputs.tag_name }}
+          tags: nextgenusfs/funannotate-slim:${{ inputs.release_tag || github.event.release.tag_name }}
 
       - name: Image digest
         run: echo "digest=${{ steps.docker_build.outputs.digest }}" >> $GITHUB_OUTPUT
 
       - name: Repository Dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: nextgenusfs/funannotate
           event-type: docker-hub-release-complete
-          client-payload: '{"ref": "${{ github.ref }}", "sha": "${{ github.sha }}"}'
+          client-payload: '{"ref": "${{ github.ref }}", "sha": "${{ github.sha }}", "tag": "${{ inputs.release_tag || github.event.release.tag_name }}"}'
diff --git a/.github/workflows/triggered-build.yml b/.github/workflows/triggered-build.yml
index 84125399..7dfe7293 100644
--- a/.github/workflows/triggered-build.yml
+++ b/.github/workflows/triggered-build.yml
@@ -20,21 +20,21 @@ jobs:
     steps:
 
       - name: Check Out Repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v4
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v7
         with:
           context: ./
           file: ./Dockerfile2
@@ -45,7 +45,7 @@ jobs:
         run: echo "digest=${{ steps.docker_build.outputs.digest }}" >> $GITHUB_OUTPUT
 
       - name: Repository Dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: nextgenusfs/funannotate