From 79e9939a6ba94642f7c917f80589811ba6288828 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Wed, 20 Mar 2024 13:20:08 +0100
Subject: [PATCH] more ci updates

---
 .github/workflows/ci.yaml | 10 +++++-----
 .github/workflows/pr.yaml | 14 +++++++-------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 0682dec1..90e1e49d 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -105,11 +105,11 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
-        path: lint_report.txt
+        path: lint_report.txt1
 
   test:
     name: Test tools
@@ -147,7 +147,7 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -164,7 +164,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -201,7 +201,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index a46588fe..e51125f3 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -143,7 +143,7 @@ jobs:
         fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -176,7 +176,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -235,7 +235,7 @@ jobs:
         }
         quit(status = status)
       shell: Rscript {0}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -262,7 +262,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -309,7 +309,7 @@ jobs:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v1
+      uses: SimenB/github-actions-cpu-cores@v2
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -326,7 +326,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -363,7 +363,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload