Resolve merge conflict

.all-contributorsrc

@@ -331,7 +331,8 @@
         "example",
         "doc",
         "test",
-        "tutorial"
+        "tutorial",
+        "review"
       ]
     },
     {
@@ -610,7 +611,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/104268427?v=4",
       "profile": "https://github.com/arjxn-py",
       "contributions": [
-        "infra"
+        "infra",
+        "code",
+        "doc"
       ]
     },
     {
@@ -629,7 +632,8 @@
       "profile": "https://www.aboutenergy.io/",
       "contributions": [
         "code",
-        "bug"
+        "bug",
+        "ideas"
       ]
     },
     {
@@ -660,6 +664,16 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "ejfdickinson",
+      "name": "ejfdickinson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/116663050?v=4",
+      "profile": "https://github.com/ejfdickinson",
+      "contributions": [
+        "ideas",
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.git-blame-ignore-revs

@@ -2,3 +2,5 @@
 0054efe388d2d17301f7e0554449eac9a7d3b7fc
 # activated pre-commit for notebooks - https://github.com/pybamm-team/PyBaMM/pull/3110
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
+# activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
+5273214b585c5a4286609aed40e0b092d0e05f42

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,11 +14,11 @@ Please add a line in the relevant section of [CHANGELOG.md](https://github.com/p
 
 # Key checklist:
 
-- [ ] No style issues: `$ pre-commit run` (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
-- [ ] All tests pass: `$ python run-tests.py --all`
-- [ ] The documentation builds: `$ python run-tests.py --doctest`
+- [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
+- [ ] All tests pass: `$ python run-tests.py --all` (or `$ nox -s tests`)
+- [ ] The documentation builds: `$ python run-tests.py --doctest` (or `$ nox -s doctests`)
 
-You can run unit and doctests together at once, using `$ python run-tests.py --quick`.
+You can run integration tests, unit tests, and doctests together at once, using `$ python run-tests.py --quick` (or `$ nox -s quick`).
 
 ## Further checks:
 

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/benchmark_on_push.yml

@@ -1,8 +1,14 @@
 name: Run benchmarks on push
 on:
   push:
+    branches: [main, develop]
   pull_request:
 
+concurrency:
+  # Cancel intermediate builds always
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   benchmarks:
     runs-on: ubuntu-latest

.github/workflows/create_release.yml

@@ -26,7 +26,7 @@ jobs:
 
       - name: Fail the job if date < 20
         if: env.TODAY < 20
-        uses: actions/github-script@v5
+        uses: actions/github-script@v6
         with:
           script: core.setFailed('This workflow should be triggered only at the end of the month, or else it will create a release for the wrong month.')
 

.github/workflows/lychee_url_checker.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      # cache Lychee results to avoid hitting rate limits  
+      # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
         uses: actions/cache@v3
         with:
@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v1.6.1
+        uses: lycheeverse/lychee-action@v1.8.0
         with:
           # arguments with file types to check
           args: >-
@@ -41,8 +41,9 @@ jobs:
             --exclude-loopback
             --exclude https://twitter.com/pybamm_
             --exclude "https://doi\.org|www.sciencedirect\.com/*"
+            --exclude https://www.rse.ox.ac.uk
             --accept 200,429
-            --exclude-path ./CHANGELOG.md 
+            --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
             './**/*.rst'
             './**/*.md'

.github/workflows/need_reply_remove.yml

@@ -11,7 +11,7 @@ jobs:
     if: |
       github.event.comment.author_association != 'OWNER' &&
       github.event.comment.author_association != 'COLLABORATOR' &&
-      github.repository-owner == 'pybamm-team'
+      github.repository_owner == 'pybamm-team'
     steps:
       - name: Remove needs-reply label
         uses: octokit/[email protected]
@@ -22,4 +22,4 @@ jobs:
           issue: ${{ github.event.issue.number }}
           label: needs-reply
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/needs_reply.yml

@@ -7,10 +7,10 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    if: github.repository-owner == 'pybamm-team'
+    if: github.repository_owner == 'pybamm-team'
     steps:
       - name: Close old issues that need reply
         uses: dwieeb/needs-reply@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-          issue-label: needs-reply
+          issue-label: needs-reply

.github/workflows/periodic_benchmarks.yml

@@ -41,7 +41,7 @@ jobs:
           SUNDIALS_INST: $HOME/.local
           LD_LIBRARY_PATH: $HOME/.local/lib
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: asv_new_results
           path: results
@@ -63,7 +63,7 @@ jobs:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
       - name: Download results artifact
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: asv_new_results
           path: new_results

.github/workflows/run_periodic_tests.yml

@@ -1,11 +1,11 @@
-# Run all unit tests and integration tests for all Python versions 
+# Run all unit tests and integration tests for all Python versions
 # and platforms at 3am UTC every day and on PRs to the main branch
 name: Scheduled
 
 on:
   workflow_dispatch:
   pull_request:
-    branches: 
+    branches:
     - main
 
   # Run everyday at 3 am UTC
@@ -102,7 +102,7 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3.1.4
 
       - name: Run integration tests
         run: nox -s integration
@@ -119,13 +119,13 @@ jobs:
   build-apple-mseries:
     needs: style
     runs-on: [self-hosted, macOS, ARM64]
-    env: 
+    env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        
+
     steps:
       - uses: actions/checkout@v3
       - name: Install python & create virtualenv