Merge branch 'pybamm-team:develop' into jax_gpu

.all-contributorsrc

@@ -442,7 +442,7 @@
       "login": "wigging",
       "name": "Gavin Wiggins",
       "avatar_url": "https://avatars.githubusercontent.com/u/6828967?v=4",
-      "profile": "https://wigging.me",
+      "profile": "https://gavinw.me",
       "contributions": [
         "bug",
         "code"
@@ -531,7 +531,8 @@
       "contributions": [
         "infra",
         "code",
-        "doc"
+        "doc",
+        "review"
       ]
     },
     {
@@ -613,7 +614,8 @@
       "contributions": [
         "infra",
         "code",
-        "doc"
+        "doc",
+        "review"
       ]
     },
     {
@@ -697,7 +699,25 @@
         "code",
         "test"
       ]
-    }
+    },
+    {
+      "login": "aitorres",
+      "name": "Andrés Ignacio Torres",
+      "avatar_url": "https://avatars.githubusercontent.com/u/26191851?v=4",
+      "profile": "https://aitorres.com",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "Agnik7",
+      "name": "Agnik Bakshi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/77234005?v=4",
+      "profile": "https://github.com/Agnik7",
+      "contributions": [
+        "doc"
+      ]
+    },
   ],
   "contributorsPerLine": 7,
   "projectName": "PyBaMM",

.github/release_reminder.md

@@ -6,4 +6,4 @@ Quarterly reminder to create a -
 1. pre-release if the month has just started.
 2. non-pre-release if the month is about to end (**before the end of the month**).
 
-See [Release Workflow](./release_workflow.md) for more information.
+See [Release Workflow](https://github.com/pybamm-team/PyBaMM/blob/develop/.github/release_workflow.md) for more information.

.github/release_workflow.md

@@ -4,7 +4,7 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub an
 
 ## rc0 releases (automated)
 
-1. The `update_version.yml` workflow will run on every 1st of January, May and September, updating incrementing the version to `YY.MMrc0` by running `scripts/update_version.py` in the following files -
+1. The `update_version.yml` workflow will run on every 1st of January, May and September, updating incrementing the version to `vYY.MMrc0` by running `scripts/update_version.py` in the following files -
 
    - `pybamm/version.py`
    - `docs/conf.py`
@@ -13,21 +13,21 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub an
    - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to a new branch `YY.MM`.
+      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).
 
-2. Create a new GitHub _pre-release_ with the tag `YY.MMrc0` from the `YY.MM` branch and a description copied from `CHANGELOG.md`.
+2. Create a new GitHub _pre-release_ with the tag `vYY.MMrc0` from the `vYY.MM` branch and a description copied from `CHANGELOG.md`.
 
 3. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
 
 ## rcX releases (manual)
 
 If a new release candidate is required after the release of `rc0` -
 
-1. Fix a bug in `YY.MM` (no new features should be added to `YY.MM` once `rc0` is released) and `develop` individually.
+1. Fix a bug in `vYY.MM` (no new features should be added to `vYY.MM` once `rc0` is released) and `develop` individually.
 
 2. Run `update_version.yml` manually while using `append_to_tag` to specify the release candidate version number (`rc1`, `rc2`, ...).
 
-3. This will increment the version to `YY.MMrcX` by running `scripts/update_version.py` in the following files -
+3. This will increment the version to `vYY.MMrcX` by running `scripts/update_version.py` in the following files -
 
    - `pybamm/version.py`
    - `docs/conf.py`
@@ -36,9 +36,9 @@ If a new release candidate is required after the release of `rc0` -
    - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing branch `YY.MM`.
+      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).
 
-4. Create a new GitHub _pre-release_ with the same tag (`YY.MMrcX`) from the `YY.MM` branch and a description copied from `CHANGELOG.md`.
+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`.
 
 5. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
 
@@ -48,7 +48,7 @@ Once satisfied with the release candidates -
 
 1. Run `update_version.yml` manually, leaving the `append_to_tag` field blank ("") for an actual release.
 
-2. This will increment the version to `YY.MMrcX` by running `scripts/update_version.py` in the following files -
+2. This will increment the version to `vYY.MMrcX` by running `scripts/update_version.py` in the following files -
 
    - `pybamm/version.py`
    - `docs/conf.py`
@@ -57,9 +57,9 @@ Once satisfied with the release candidates -
    - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing branch `YY.MM`.
+      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).
 
-3. Next, a PR from `YY.MM` to `main` will be generated that should be merged once all the tests pass.
+3. Next, a PR from `vYY.MM` to `main` will be generated that should be merged once all the tests pass.
 
 4. Create a new GitHub _release_ with the same tag from the `main` branch and a description copied from `CHANGELOG.md`.
 
@@ -72,3 +72,8 @@ 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
+- 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 origin <tag_name>  # can only be carried out by the maintainers
+  ```

.github/workflows/benchmark_on_push.yml

@@ -18,16 +18,20 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
+
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
           sudo apt install gfortran gcc libopenblas-dev
+
       - name: Install python dependencies
-      # Pin asv==0.5.1 to fix failing benchmarks. Related to https://github.com/airspeed-velocity/asv/issues/1323
         run: |
-          python -m pip install --upgrade pip wheel setuptools virtualenv asv==0.5.1 wget cmake casadi numpy
-      - name: Install SuiteSparse and Sundials
+          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install asv[virtualenv]
+
+      - name: Install SuiteSparse and SUNDIALS
         run: python scripts/install_KLU_Sundials.py
+
       - name: Fetch base branch
         run: |
           # This workflow also runs for merge commits
@@ -49,7 +53,8 @@ jobs:
           HEAD_COMMIT=$(git rev-parse HEAD)
           echo $BASE_COMMIT | tee commits_to_compare.txt
           echo $HEAD_COMMIT | tee -a commits_to_compare.txt
-          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr --strict -v
+          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr -v
+
       - name: Compare commits' benchmark results
         run: |
           BASE_COMMIT=$(head -1 commits_to_compare.txt)

.github/workflows/docker.yml

@@ -0,0 +1,75 @@
+name: Build & Push Docker Images
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - develop
+
+jobs:
+  pre_job:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+            username: ${{ secrets.DOCKERHUB_USERNAME }}
+            password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: List built images
+        run: docker images
+
+      - name: Build and Push Docker Image (Without Solvers)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:latest
+          push: true
+
+      - name: Build and Push Docker Image (With JAX Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:jax
+          push: true
+          build-args: |
+            JAX=true
+
+      - name: Build and Push Docker Image (With ODES & DAE Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:odes
+          push: true
+          build-args: |
+            ODES=true
+
+      - name: Build and Push Docker Image (With IDAKLU Solver)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:idaklu
+          push: true
+          build-args: |
+            IDAKLU=true
+
+      - name: Build and Push Docker Image (With All Solvers)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: scripts/Dockerfile
+          tags: pybamm/pybamm:latest
+          push: true
+          build-args: |
+            ALL=true

.github/workflows/periodic_benchmarks.yml

@@ -20,26 +20,33 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
+
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install gfortran gcc libopenblas-dev
+
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy
-      - name: Install SuiteSparse and Sundials
+          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install asv[virtualenv]
+
+      - name: Install SuiteSparse and SUNDIALS
         run: python scripts/install_KLU_Sundials.py
+
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
-          asv run --machine "GitHubRunner" NEW --show-stderr --strict -v
+          asv run --machine "GitHubRunner" NEW --show-stderr -v
         env:
           SUNDIALS_INST: $HOME/.local
           LD_LIBRARY_PATH: $HOME/.local/lib
+
       - name: Upload results as artifact
         uses: actions/upload-artifact@v3
         with:
@@ -55,18 +62,22 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
+
       - name: Install asv
         run: pip install asv
+
       - name: Checkout pybamm-bench repo
         uses: actions/checkout@v4
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
+
       - name: Download results artifact
         uses: actions/download-artifact@v3
         with:
           name: asv_new_results
           path: new_results
+
       - name: Copy new results and push to pybamm-bench repo
         env:
           PUSH_BENCH_EMAIL: ${{ secrets.PUSH_BENCH_EMAIL }}
@@ -78,6 +89,7 @@ jobs:
           git add results
           git commit -am "Add new results"
           git push
+
       - name: Publish results
         run: |
           asv publish

.github/workflows/publish_pypi.yml

@@ -102,10 +102,10 @@ jobs:
       - name: Build wheels on Linux and MacOS
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          # TODO: openblas no longer available on centos 7 i686 image, use blas instead for now
+          CIBW_ARCHS_LINUX: x86_64
           CIBW_BEFORE_ALL_LINUX: >
-            yum -y install blas-devel lapack-devel &&
-            bash build_manylinux_wheels/install_sundials.sh 5.8.1 6.5.0
+            yum -y install openblas-devel lapack-devel &&
+            bash build_manylinux_wheels/install_sundials.sh 6.0.3 6.5.0
 
           CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake casadi numpy"
           CIBW_BEFORE_BUILD_MACOS: >
@@ -135,13 +135,13 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install dependencies
-        run: pip install wheel
+        run: pip install --upgrade pip setuptools wheel build
 
       - name: Build sdist
-        run: python setup.py sdist --formats=gztar
+        run: python -m build --sdist
 
       - name: Upload sdist
         uses: actions/upload-artifact@v3
@@ -171,13 +171,13 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-          packages_dir: files/
+          packages-dir: files/
 
       - name: Publish on TestPyPI
         if: github.event.inputs.target == 'testpypi'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TESTPYPI_TOKEN }}
-          packages_dir: files/
-          repository_url: https://test.pypi.org/legacy/
+          packages-dir: files/
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/release_reminder.yml

@@ -13,7 +13,7 @@ jobs:
   remind:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: JasonEtco/create-an-issue@v2
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/run_periodic_tests.yml

@@ -111,6 +111,10 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s doctests
 
+      - name: Check if the documentation can be built
+        if: matrix.os == 'ubuntu-latest'
+        run: nox -s docs
+
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
         run: nox -s examples