Merge branch 'develop' into issue-2111-custom-transport-efficiency

.all-contributorsrc

@@ -1,6 +1,6 @@
 {
   "files": [
-    "README.md"
+    "all_contributors.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -215,7 +215,8 @@
       "profile": "https://github.com/jonchapman1",
       "contributions": [
         "ideas",
-        "fundingFinding"
+        "fundingFinding",
+        "doc"
       ]
     },
     {
@@ -772,7 +773,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/99216956?v=4",
       "profile": "https://github.com/prady0t",
       "contributions": [
-        "infra"
+        "infra",
+        "code",
+        "test"
       ]
     },
     {
@@ -815,6 +818,44 @@
         "bug",
         "code"
       ]
+    },
+    {
+      "login": "Akhil-Sharma30",
+      "name": "AKHIL SHARMA",
+      "avatar_url": "https://avatars.githubusercontent.com/u/68015525?v=4",
+      "profile": "http://akhilsharma.info",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "HarshvirSandhu",
+      "name": "Harshvir Sandhu",
+      "avatar_url": "https://avatars.githubusercontent.com/u/75773763?v=4",
+      "profile": "https://github.com/HarshvirSandhu",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "lorenzofavaro",
+      "name": "Lorenzo",
+      "avatar_url": "https://avatars.githubusercontent.com/u/44714920?v=4",
+      "profile": "https://github.com/lorenzofavaro",
+      "contributions": [
+        "code",
+        "test",
+        "doc"
+      ]
+    },
+    {
+      "login": "AndyLiuElysia",
+      "name": "AndyLiuElysia",
+      "avatar_url": "https://avatars.githubusercontent.com/u/143705453?v=4",
+      "profile": "https://github.com/AndyLiuElysia",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.git-blame-ignore-revs

@@ -10,3 +10,5 @@ a63e49ece0f9336d1f5c2562f7459e555c6e6693
 ff6d81c01331c7d269303b4a8321d9881bdf98fa
 # migrated to ruff-format - https://github.com/pybamm-team/PyBaMM/pull/3655
 60ebd4148059a95428a496f4f55c1175ead362d3
+# implemented cleaner string formatting via f-strings - https://github.com/pybamm-team/PyBaMM/pull/3890
+f395819d1c874071b7e76e32ec4f0bbe42462b48

.github/codecov.yml

@@ -1,2 +0,0 @@
-ignore:
-  - pybamm/install_odes.py

.github/workflows/benchmark_on_push.yml

@@ -2,7 +2,6 @@ name: Run benchmarks on push
 on:
   push:
     branches: [main, develop]
-  pull_request:
 
 concurrency:
   # Cancel intermediate builds always
@@ -14,10 +13,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install Linux system dependencies
         run: |

.github/workflows/docker.yml

@@ -7,15 +7,11 @@ on:
     - develop
 
 jobs:
-  build_docker_images:
+  build_docker_image:
     # This workflow is only of value to PyBaMM and would always be skipped in forks
     if: github.repository_owner == 'pybamm-team'
-    name: Image (${{ matrix.build-args }})
+    name: Build image
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        build-args: ["No solvers", "JAX", "ODES", "IDAKLU", "ALL"]
-      fail-fast: true
 
     steps:
       - name: Checkout
@@ -33,27 +29,12 @@ jobs:
             username: ${{ secrets.DOCKERHUB_USERNAME }}
             password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-      - name: Create tags for Docker images based on build-time arguments
-        id: tags
-        run: |
-          if [ "${{ matrix.build-args }}" = "No solvers" ]; then
-            echo "tag=latest" >> "$GITHUB_OUTPUT"
-          elif [ "${{ matrix.build-args }}" = "JAX" ]; then
-            echo "tag=jax" >> "$GITHUB_OUTPUT"
-          elif [ "${{ matrix.build-args }}" = "ODES" ]; then
-            echo "tag=odes" >> "$GITHUB_OUTPUT"
-          elif [ "${{ matrix.build-args }}" = "IDAKLU" ]; then
-            echo "tag=idaklu" >> "$GITHUB_OUTPUT"
-          elif [ "${{ matrix.build-args }}" = "ALL" ]; then
-            echo "tag=all" >> "$GITHUB_OUTPUT"
-          fi
-
-      - name: Build and push Docker image to Docker Hub (${{ matrix.build-args }})
+      - name: Build and push Docker image to Docker Hub
         uses: docker/build-push-action@v5
         with:
           context: .
           file: scripts/Dockerfile
-          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
+          tags: pybamm/pybamm:latest
           push: true
           platforms: linux/amd64, linux/arm64
 

.github/workflows/lychee_url_checker.yml

@@ -17,7 +17,7 @@ jobs:
 
       # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v1.9.1
+        uses: lycheeverse/lychee-action@v1.9.3
         with:
           # arguments with file types to check
           args: >-
@@ -47,6 +47,7 @@ jobs:
             --exclude-path ./scripts/update_version.py
             --exclude-path asv.conf.json
             --exclude-path docs/conf.py
+            --exclude-path all_contributors.md
             './**/*.rst'
             './**/*.md'
             './**/*.py'

.github/workflows/need_reply_remove.yml

@@ -1,6 +1,8 @@
 name: Remove needs-reply label
 
 on:
+  schedule:
+      - cron:  '0 3 * * 1'
   issue_comment:
     types:
       - created
@@ -11,7 +13,8 @@ jobs:
     if: |
       github.event.comment.author_association != 'OWNER' &&
       github.event.comment.author_association != 'COLLABORATOR' &&
-      github.repository_owner == 'pybamm-team'
+      github.repository_owner == 'pybamm-team' &&
+      github.event_name != 'pull_request'
     steps:
       - name: Remove needs-reply label
         uses: octokit/request-action@v2.x

.github/workflows/periodic_benchmarks.yml

@@ -8,7 +8,7 @@
 # - Publish website
 name: Benchmarks
 on:
-  # Everyday at 3 am UTC
+  # Every day at 3 am UTC
   schedule:
     - cron: "0 3 * * *"
   # Make it possible to trigger the
@@ -21,10 +21,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install Linux system dependencies
         run: |
@@ -52,16 +52,18 @@ jobs:
         with:
           name: asv_periodic_results
           path: results
+          if-no-files-found: error
 
   publish-results:
+    if: github.repository == 'pybamm-team/PyBaMM'
     name: Push and publish results
     needs: benchmarks
     runs-on: ubuntu-latest
     steps:
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install asv
         run: pip install asv
@@ -72,18 +74,17 @@ jobs:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
 
-      - name: Download results artifact
+      - name: Download results artifact(s)
         uses: actions/download-artifact@v4
         with:
-          name: asv_periodic_results
-          path: new_results
+          path: results
+          merge-multiple: true
 
       - name: Copy new results and push to pybamm-bench repo
         env:
           PUSH_BENCH_EMAIL: ${{ secrets.PUSH_BENCH_EMAIL }}
           PUSH_BENCH_NAME: ${{ secrets.PUSH_BENCH_NAME }}
         run: |
-          cp -vr new_results/* results
           git config --global user.email "$PUSH_BENCH_EMAIL"
           git config --global user.name "$PUSH_BENCH_NAME"
           git add results