Merge with master

Author: marghe-molaro

.github/workflows/checks.yml

@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           lfs: false
       - name: Cache tox

.github/workflows/docs.yml

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           lfs: true
       - name: Cache tox

.github/workflows/run-on-comment.yml

@@ -115,7 +115,7 @@ jobs:
           return pr.head.sha;
 
     - name: Checkout SHA
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         lfs: true
         ref: ${{ steps.sha.outputs.result }}
@@ -194,7 +194,7 @@ jobs:
 
     - name: Upload artifact if requested
       if: "${{ inputs.artifact-path != '' }}"
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v5
       with:
         name: ${{ inputs.artifact-name }}
         path: ${{ inputs.artifact-path }}

.github/workflows/run-profiling.yaml

@@ -112,7 +112,7 @@ jobs:
     timeout-minutes: 8640
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.sha }}
           lfs: true
@@ -132,7 +132,7 @@ jobs:
 
       ## Upload the output as an artifact so we can push it to the profiling repository
       - name: Save results as artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: ${{ needs.set-variables.outputs.artifact-name }}
           path: ${{ needs.set-variables.outputs.profiling-output-dir }}
@@ -155,7 +155,7 @@ jobs:
       )
     steps:
       - name: Download the profiling results
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           name: ${{ needs.set-variables.outputs.artifact-name }}
           path: ${{ needs.set-variables.outputs.profiling-output-dir }}
@@ -177,7 +177,7 @@ jobs:
           user_name:  rc-softdev-admin
 
       - name: Trigger website rebuild
-        uses: peter-evans/repository-dispatch@v3
+        uses: peter-evans/repository-dispatch@v4
         with:
           token: ${{ secrets.PROFILING_REPO_ACCESS }}
           repository: UCL/TLOmodel-profiling

.github/workflows/tests-unpinned.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           lfs: true
       - name: Cache tox

.github/workflows/tests.yml

@@ -38,7 +38,7 @@ jobs:
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           # No tests should be under LFS so no need to fetch LFS files
           lfs: false
@@ -64,7 +64,7 @@ jobs:
       fail-fast: false
       matrix: ${{ fromJson(needs.gen-test-matrix.outputs.matrix) }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           lfs: true
       - name: System info

pyproject.toml

@@ -126,8 +126,8 @@ line-length = 120
 exclude = ['src/tlo/_version.py']
 
 [tool.ruff.lint]
-select = ["E", "F", "I", "W"]
-per-file-ignores = {"src/scripts/**" = ["E501", "W"]}
+select = ["E", "F", "I"]
+per-file-ignores = {"src/scripts/**" = ["E501"]}
 
 [tool.setuptools.packages.find]
 where = ["src"]