Merge branch 'develop' into GSoC

Author: valentinsulzer

.github/workflows/benchmark_on_push.yml

@@ -20,7 +20,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Set up Python 3.12

.github/workflows/docker.yml

@@ -18,7 +18,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 

.github/workflows/lychee_url_checker.yml

@@ -23,20 +23,20 @@ jobs:
 
       # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@82202e5e9c2f4ef1a55a3d02563e1cb6041e5332 # v2.4.1
+        uses: lycheeverse/lychee-action@5c4ee84814c983aa7164eaee476f014e53ff3963 # v2.5.0
         with:
           # arguments with file types to check
           args: >-

.github/workflows/periodic_benchmarks.yml

@@ -28,7 +28,7 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -78,14 +78,14 @@ jobs:
         run: pip install asv
 
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
           persist-credentials: false
 
       - name: Download results artifact(s)
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           path: results
           merge-multiple: true

.github/workflows/publish_pypi.yml

@@ -13,7 +13,7 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: true
       - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
@@ -39,7 +39,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           path: deploy
           merge-multiple: true

.github/workflows/run_benchmarks_over_history.yml

@@ -37,7 +37,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Set up Python 3.12
@@ -140,14 +140,14 @@ jobs:
         run: pip install asv
 
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
           persist-credentials: false
 
       - name: Download results artifact(s)
-        uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.6.2
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v4.6.2
         with:
           name: asv_over_history_results
           path: results

.github/workflows/run_periodic_tests.yml

@@ -36,7 +36,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -103,7 +103,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -141,7 +141,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -175,7 +175,7 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 

.github/workflows/scorecard.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
@@ -65,6 +65,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@51f77329afa6477de8c49fc9c7046c15b9a4e79d # v3.29.5
+        uses: github/codeql-action/upload-sarif@96f518a34f7a870018057716cc4d7a5c014bd61c # v3.29.5
         with:
           sarif_file: results.sarif

.github/workflows/test_on_push.yml

@@ -24,7 +24,7 @@ jobs:
     permissions:
       contents: read
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Setup Python
@@ -54,12 +54,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -132,13 +132,13 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: graphviz pandoc
           execute_install_scripts: true
@@ -179,12 +179,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -222,12 +222,12 @@ jobs:
 
     steps:
       - name: Check out PyBaMM repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
 
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@4c82c3ccdc1344ee11e9775dbdbdf43aa8a5614e # v1.5.1
+        uses: awalsh128/cache-apt-pkgs-action@2c09a5e66da6c8016428a2172bd76e5e4f14bb17 # v1.5.3
         with:
           packages: gfortran gcc graphviz
           execute_install_scripts: true

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.8"
+    rev: "v0.12.9"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -44,6 +44,6 @@ repos:
         - id: sp-repo-review
 
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.11.0
+    rev: v1.12.1
     hooks:
       - id: zizmor