incorporate latest changes

from

- galaxyproject#4850
- galaxyproject#4892

and fix fork (use IUC master for called WFs, instead of my fork)

.github/workflows/pr.yaml

@@ -17,7 +17,7 @@ jobs:
     name: Setup cache and determine changed repositories
     # adapt the owner name
     if: ${{ github.repository_owner == 'galaxyproject' }}
-    uses: bernt-matthias/tools-iuc/.github/workflows/wf_setup.yaml@topic/reusable-workflows
+    uses: galaxyproject/tools-iuc/.github/workflows/wf_setup.yaml@master
     with:
       fetch-depth: 0
       # set these variables if you want to update independent of the IUC repo
@@ -32,7 +32,7 @@ jobs:
   lint:
     name: Lint
     needs: setup
-    uses: bernt-matthias/tools-iuc/.github/workflows/wf_lint.yaml@topic/reusable-workflows
+    uses: galaxyproject/tools-iuc/.github/workflows/wf_lint.yaml@master
     with:
       repository-list: ${{ needs.setup.outputs.repository-list }}
       tool-list: ${{ needs.setup.outputs.tool-list }}
@@ -48,7 +48,7 @@ jobs:
   test:
     name: Test tools
     needs: setup
-    uses: bernt-matthias/tools-iuc/.github/workflows/wf_test.yaml@topic/reusable-workflows
+    uses: galaxyproject/tools-iuc/.github/workflows/wf_test.yaml@master
     with:
       galaxy-fork: ${{ needs.setup.outputs.galaxy-fork }}
       galaxy-branch: ${{ needs.setup.outputs.galaxy-branch }}
@@ -65,7 +65,7 @@ jobs:
     name: Deploy
     if: ${{ github.repository_owner == 'galaxyproject' }}
     needs: [setup, lint, test]
-    uses: bernt-matthias/tools-iuc/.github/workflows/wf_deploy.yaml@topic/reusable-workflows
+    uses: galaxyproject/tools-iuc/.github/workflows/wf_deploy.yaml@master
     with:
       repository-list: ${{ needs.setup.outputs.repository-list }}
       galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }}

.github/workflows/wf_lint.yaml

@@ -43,7 +43,7 @@ on:
         type: string
       r-version-list:
         description: 'stringified JSON array of R versions'
-        default: "[\"4.0.1\"]"
+        default: "[\"release\"]"
         required: false
         type: string
       os-version-list:
@@ -136,7 +136,7 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: r-lib/actions/setup-r@master
+    - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages

.github/workflows/wf_setup.yaml

@@ -73,7 +73,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v2
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -84,13 +84,13 @@ jobs:
       run: |
         SLASH_FORK="${{ github.event.client_payload.slash_command.args.named.fork }}"
         DEFAULT_FORK="${{ inputs.default-galaxy-fork }}"
-        echo "::set-output name=fork::${SLASH_FORK:-$DEFAULT_FORK}"
+        echo "fork=${SLASH_FORK:-$DEFAULT_FORK}" >> $GITHUB_OUTPUT
         SLASH_BRANCH="${{ github.event.client_payload.slash_command.args.named.branch }}"
         DEFAULT_BRANCH="${{ inputs.default-galaxy-branch }}"
-        echo "::set-output name=branch::${SLASH_BRANCH:-$DEFAULT_BRANCH}"
+        echo "branch=${SLASH_BRANCH:-$DEFAULT_BRANCH}" >> $GITHUB_OUTPUT
         SLASH_PLANEMO="${{ github.event.client_payload.slash_command.args.named.planemo-version }}"
         DEFAULT_PLANEMO="${{ inputs.default-planemo-version }}"
-        echo "::set-output name=planemo-version::${SLASH_PLANEMO:-$DEFAULT_PLANEMO}"
+        echo "planemo-version=${SLASH_PLANEMO:-$DEFAULT_PLANEMO}" >> $GITHUB_OUTPUT
     - name: Print used Galaxy for and branch
       run: |
         echo 'fork: ${{ steps.get-fork-branch.outputs.fork }}'
@@ -121,7 +121,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ needs.fork-branch.outputs.galaxy-fork }}/galaxy refs/heads/${{ needs.fork-branch.outputs.galaxy-branch }} | cut -f1)"
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ needs.fork-branch.outputs.galaxy-fork }}/galaxy refs/heads/${{ needs.fork-branch.outputs.galaxy-branch }} | cut -f1)" >> $GITHUB_OUTPUT
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}