Merge branch 'pybamm-team:develop' into Saswatsusmoy-pybamm-team#3441-…

…Call-processed-variables-with-custom-spatial-coordinates

.all-contributorsrc

@@ -727,6 +727,112 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "chmabaur",
+      "name": "chmabaur",
+      "avatar_url": "https://avatars.githubusercontent.com/u/127507466?v=4",
+      "profile": "https://github.com/chmabaur",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "AbhishekChaudharii",
+      "name": "Abhishek Chaudhari",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91185083?v=4",
+      "profile": "https://github.com/AbhishekChaudharii",
+      "contributions": [
+        "doc",
+        "code"
+      ]
+    },
+    {
+      "login": "shubhambhar007",
+      "name": "Shubham Bhardwaj",
+      "avatar_url": "https://avatars.githubusercontent.com/u/32607282?v=4",
+      "profile": "https://github.com/shubhambhar007",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "jlauber18",
+      "name": "Jonathan Lauber",
+      "avatar_url": "https://avatars.githubusercontent.com/u/28939653?v=4",
+      "profile": "https://github.com/jlauber18",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "prady0t",
+      "name": "Pradyot Ranjan",
+      "avatar_url": "https://avatars.githubusercontent.com/u/99216956?v=4",
+      "profile": "https://github.com/prady0t",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "XuboGU",
+      "name": "XuboGU",
+      "avatar_url": "https://avatars.githubusercontent.com/u/53944452?v=4",
+      "profile": "https://github.com/XuboGU",
+      "contributions": [
+        "code",
+        "bug"
+      ]
+    },
+    {
+      "login": "cringeyburger",
+      "name": "Ankit Meda",
+      "avatar_url": "https://avatars.githubusercontent.com/u/121183876?v=4",
+      "profile": "https://github.com/cringeyburger",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "AlessioBugetti",
+      "name": "Alessio Bugetti",
+      "avatar_url": "https://avatars.githubusercontent.com/u/38499721?v=4",
+      "profile": "https://github.com/AlessioBugetti",
+      "contributions": [
+        "infra",
+        "code",
+        "doc",
+        "test"
+      ]
+    },
+    {
+      "login": "kawaMANMI",
+      "name": "kawaMANMI",
+      "avatar_url": "https://avatars.githubusercontent.com/u/39382602?v=4",
+      "profile": "https://github.com/kawaMANMI",
+      "contributions": [
+        "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"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.git-blame-ignore-revs

@@ -4,3 +4,9 @@
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
 # activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
 5273214b585c5a4286609aed40e0b092d0e05f42
+# migrated config to pyproject.toml - https://github.com/pybamm-team/PyBaMM/pull/3557
+12c5d77203bd93542785d237bac00bad5ed5469a
+# activated pyupgrade - https://github.com/pybamm-team/PyBaMM/pull/3579
+ff6d81c01331c7d269303b4a8321d9881bdf98fa
+# migrated to ruff-format - https://github.com/pybamm-team/PyBaMM/pull/3655
+60ebd4148059a95428a496f4f55c1175ead362d3

.github/CODEOWNERS

@@ -0,0 +1,34 @@
+# Automatically request reviews from maintainers
+
+# Package
+/pybamm/discretisations/ @martinjrobins @rtimms @tinosulzer
+/pybamm/experiment/ @brosaplanella @martinjrobins @rtimms @tinosulzer @TomTranter
+/pybamm/expression_tree/ @martinjrobins @rtimms @tinosulzer
+/pybamm/geometry/ @martinjrobins @rtimms @tinosulzer
+/pybamm/input/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @kratman
+/pybamm/meshes/ @martinjrobins @rtimms @tinosulzer @rtimms
+/pybamm/models/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @rtimms
+/pybamm/parameters/ @brosaplanella @DrSOKane @rtimms @tinosulzer @TomTranter @rtimms  @kratman
+/pybamm/plotting/ @martinjrobins @rtimms @Saransh-cpp @tinosulzer @rtimms  @kratman @agriyakhetarpal
+/pybamm/solvers/ @martinjrobins @rtimms @tinosulzer @TomTranter @rtimms
+/pybamm/spatial_methods/ @martinjrobins @rtimms @tinosulzer @rtimms
+/pybamm/* @pybamm-team/maintainers # the files directly under /pybamm/, will not recurse
+
+# CI/CD workflows
+/.github/ @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
+
+# Benchmarks
+/benchmarks/ @brosaplanella @Saransh-cpp @agriyakhetarpal @arjxn-py
+
+# Documentation
+/docs/ @kratman @arjxn-py @agriyakhetarpal @Saransh-cpp
+
+# Example scripts
+/examples/ @kratman @agriyakhetarpal @Saransh-cpp
+
+# Installation and other scripts
+/scripts/ @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
+
+# Files in the root directory
+/* @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
+/CHANGELOG.md # no owner (almost every PR edits the CHANGELOG)

.github/dependabot.yml

@@ -5,3 +5,8 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    # group updates in a single PR
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/release_reminder.md

@@ -1,6 +1,6 @@
 ---
 title: Create {{ date | date('YY.MM') }} (final or rc0) release
-labels: priority:high
+labels: "priority: high"
 ---
 Quarterly reminder to create a -
 

.github/release_workflow.md

@@ -1,6 +1,6 @@
 # Release workflow
 
-This file contains the workflow required to make a `PyBaMM` release on GitHub and PyPI by the maintainers.
+This file contains the workflow required to make a `PyBaMM` release on GitHub, PyPI, and conda-forge by the maintainers.
 
 ## rc0 releases (automated)
 
@@ -9,8 +9,8 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub an
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
       These changes will be automatically pushed to a new branch `vYY.MM` and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
@@ -21,9 +21,9 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub an
 
 ## rcX releases (manual)
 
-If a new release candidate is required after the release of `rc0` -
+If a new release candidate is required after the release of `rc{X-1}` -
 
-1. Fix a bug in `vYY.MM` (no new features should be added to `vYY.MM` once `rc0` is released) and `develop` individually.
+1. Cherry-pick the bug fix (no new features should be added to `vYY.MM` once `rc{X-1}` is released) commit to `vYY.MM` branch once the fix is merged into `develop`. The CHANGELOG entry for such fixes should go under the `rc{X-1}` heading in `CHANGELOG.md`
 
 2. Run `update_version.yml` manually while using `append_to_tag` to specify the release candidate version number (`rc1`, `rc2`, ...).
 
@@ -32,11 +32,11 @@ If a new release candidate is required after the release of `rc0` -
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
 
 4. Create a new GitHub _pre-release_ with the same tag (`vYY.MMrcX`) from the `vYY.MM` branch and a description copied from `CHANGELOG.md`.
 
@@ -53,11 +53,11 @@ Once satisfied with the release candidates -
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
 
 3. Next, a PR from `vYY.MM` to `main` will be generated that should be merged once all the tests pass.
 
@@ -70,10 +70,11 @@ Once satisfied with the release candidates -
 Some other essential things to check throughout the release process -
 
 - If updating our custom vcpkg registory entries [pybamm-team/sundials-vcpkg-registry](https://github.com/pybamm-team/sundials-vcpkg-registry) or [pybamm-team/casadi-vcpkg-registry](https://github.com/pybamm-team/casadi-vcpkg-registry) (used to build Windows wheels), make sure to update the baseline of the registories in vcpkg-configuration.json to the latest commit id.
-- Update jax and jaxlib to the latest version in `pybamm.util` and `setup.py`, fixing any bugs that arise
-- Make sure the URLs in `docs/_static/versions.json` are valid
+- Update jax and jaxlib to the latest version in `pybamm.util` and `pyproject.toml`, fixing any bugs that arise
 - As the release workflow is initiated by the `release` event, it's important to note that the default `GITHUB_REF` used by `actions/checkout` during the checkout process will correspond to the tag created during the release process. Consequently, the workflows will consistently build PyBaMM based on the commit associated with this tag. Should new commits be introduced to the `vYY.MM` branch, such as those addressing build issues, it becomes necessary to manually update this tag to point to the most recent commit -
   ```
   git tag -f <tag_name> <commit_hash>
   git push -f <pybamm-team/PyBaMM_remote_name> <tag_name>  # can only be carried out by the maintainers
   ```
+- If changes are made to the API, console scripts, entry points, new optional dependencies are added, support for major Python versions is dropped or added, or core project information and metadata are modified at the time of the release, make sure to update the `meta.yaml` file in the `recipe/` folder of the [conda-forge/pybamm-feedstock](https://github.com/conda-forge/pybamm-feedstock) repository accordingly by following the instructions in the [conda-forge documentation](https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-feedstock-repository) and re-rendering the recipe
+- The conda-forge release workflow will automatically be triggered following a stable PyPI release, and the aforementioned updates should be carried out directly in the main repository by pushing changes to the automated PR created by the conda-forge-bot. A manual PR can also be created if the updates are not included in the automated PR for some reason. This manual PR **must** bump the build number in `meta.yaml` and **must** be from a personal fork of the repository.

.github/wheel_failure.md

@@ -1,6 +1,6 @@
 ---
 title: Fortnightly build for wheels failed
-labels: priority:high, bug
+labels: "priority: high, bug"
 ---
 
 The build is failing with the following logs - {{ env.LOGS }}

.github/workflows/benchmark_on_push.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/docker.yml

@@ -48,8 +48,7 @@ jobs:
             echo "tag=all" >> "$GITHUB_OUTPUT"
           fi
 
-      - name: Build and push Docker image to Docker Hub (no solvers)
-        if: matrix.build-args == 'No solvers'
+      - name: Build and push Docker image to Docker Hub (${{ matrix.build-args }})
         uses: docker/build-push-action@v5
         with:
           context: .
@@ -58,29 +57,5 @@ jobs:
           push: true
           platforms: linux/amd64, linux/arm64
 
-      - name: Build and push Docker image to Docker Hub (with ODES and IDAKLU solvers)
-        if: matrix.build-args == 'ODES' || matrix.build-args == 'IDAKLU'
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
-          push: true
-          build-args: ${{ matrix.build-args }}=true
-          platforms: linux/amd64, linux/arm64
-
-      - name: Build and push Docker image to Docker Hub (with ALL and JAX solvers)
-        if: matrix.build-args == 'ALL' || matrix.build-args == 'JAX'
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: scripts/Dockerfile
-          tags: pybamm/pybamm:${{ steps.tags.outputs.tag }}
-          push: true
-          build-args: ${{ matrix.build-args }}=true
-          # exclude arm64 for JAX and ALL builds for now, see
-          # https://github.com/google/jax/issues/13608
-          platforms: linux/amd64
-
       - name: List built image(s)
         run: docker images

.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@v1.8.0
+        uses: lycheeverse/lychee-action@v1.9.1
         with:
           # arguments with file types to check
           args: >-
@@ -45,13 +45,18 @@ jobs:
             --accept 200,429
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
+            --exclude-path asv.conf.json
             --exclude-path docs/conf.py
             './**/*.rst'
             './**/*.md'
             './**/*.py'
             './**/*.ipynb'
+            './**/*.json'
+            './**/*.toml'
           # fail the action on broken links
           fail: true
+          jobSummary: true
+          format: markdown
         env:
           # to be used in case rate limits are surpassed
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/periodic_benchmarks.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -48,9 +48,9 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_periodic_results
           path: results
 
   publish-results:
@@ -59,7 +59,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -73,9 +73,9 @@ jobs:
           token: ${{ secrets.BENCH_PAT }}
 
       - name: Download results artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: asv_new_results
+          name: asv_periodic_results
           path: new_results
 
       - name: Copy new results and push to pybamm-bench repo