merge develop

Author: valentinsulzer

.all-contributorsrc

@@ -550,7 +550,18 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/112731474?v=4",
       "profile": "https://github.com/iatzak",
       "contributions": [
-        "doc"
+        "doc",
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "ayeankit",
+      "name": "Ankit Kumar",
+      "avatar_url": "https://avatars.githubusercontent.com/u/72691866?v=4",
+      "profile": "https://github.com/ayeankit",
+      "contributions": [
+        "code"
       ]
     }
   ],

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,7 +14,7 @@ Please add a line in the relevant section of [CHANGELOG.md](https://github.com/p
 
 # Key checklist:
 
-- [ ] No style issues: `$ flake8`
+- [ ] No style issues: `$ pre-commit run`
 - [ ] All tests pass: `$ python run-tests.py --unit`
 - [ ] The documentation builds: `$ cd docs` and then `$ make clean; make html`
 

.github/workflows/benchmark_on_push.yml

@@ -11,8 +11,15 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: Install asv
-        run: pip install -U pip virtualenv asv
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt 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
+        run: python scripts/install_KLU_Sundials.py
       - name: Fetch base branch
         run: |
           # This workflow also runs for merge commits
@@ -22,6 +29,7 @@ jobs:
           if [ $current_branch != "develop" ]; then
               git fetch origin develop:develop
           fi
+
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
@@ -30,7 +38,7 @@ jobs:
           HEAD_COMMIT=$(git rev-parse HEAD)
           echo $BASE_COMMIT | tee commits_to_compare.txt
           echo $HEAD_COMMIT | tee -a commits_to_compare.txt
-          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr
+          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr -v
       - name: Compare commits' benchmark results
         run: |
           BASE_COMMIT=$(head -1 commits_to_compare.txt)

.github/workflows/test_on_push.yml

@@ -36,8 +36,8 @@ jobs:
 
       - name: Check style
         run: |
-          python -m pip install "tox<4"
-          tox -e flake8
+          python -m pip install pre-commit
+          pre-commit run ruff
 
   build:
     needs: style

.github/workflows/url_checker.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
       - name: URLs-checker
-        uses: urlstechie/urlchecker-action@0.0.31
+        uses: urlstechie/urlchecker-action@master
         with:
           # A comma-separated list of file types to cover in the URL checks
           file_types: .rst,.md,.py,.ipynb

.gitignore

@@ -6,6 +6,7 @@
 *.DS_Store
 *.mat
 *.csv
+*.hidden
 
 # don't ignore important .txt and .csv files
 !requirements*
@@ -61,9 +62,6 @@ dist/
 coverage.xml
 htmlcov/
 
-# black setup file seems to make Travis CI fail
-pyproject.toml
-
 # virtual enviroment
 env/
 venv/

.pre-commit-config.yaml

@@ -10,11 +10,12 @@ repos:
         exclude: assets/js/webapp\.js
 
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
       - id: black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.246"
     hooks:
-      - id: flake8
+      - id: ruff
+        args: [--ignore=E741, --exclude=__init__.py]

CHANGELOG.md

@@ -3,8 +3,26 @@
 ## Features
 
 - Added temperature control to experiment class. ([#2518])(https://github.com/pybamm-team/PyBaMM/pull/2518)
+- The "particle size" option can now be a tuple to allow different behaviour in each electrode([#2672](https://github.com/pybamm-team/PyBaMM/pull/2672)).
+
+## Bug fixes
+
+- Fixed the length scaling for the first dimension of r-R plots ([#2663](https://github.com/pybamm-team/PyBaMM/pull/2663)).
+
+# [v23.1](https://github.com/pybamm-team/PyBaMM/tree/v23.1) - 2023-01-31
+
+## Features
+
+- Changed linting from `flake8` to `ruff` ([#2630](https://github.com/pybamm-team/PyBaMM/pull/2630)).
+- Changed docs theme to pydata theme and start to improve docs in general ([#2618](https://github.com/pybamm-team/PyBaMM/pull/2618)).
+- New `contact resistance` option, new parameter `Contact resistance [Ohm]` and new variable `Contact overpotential [V]` ([#2598](https://github.com/pybamm-team/PyBaMM/pull/2598)).
 - Steps in `Experiment` can now be tagged and cycle numbers be searched based on those tags ([#2593](https://github.com/pybamm-team/PyBaMM/pull/2593)).
 
+## Bug fixes
+
+- Fixed a bug where the solid phase conductivity was double-corrected for tortuosity when loading parameters from a BPX file ([#2638](https://github.com/pybamm-team/PyBaMM/pull/2638)).
+- Changed termination from "success" to "final time" for algebraic solvers to match ODE/DAE solvers ([#2613](https://github.com/pybamm-team/PyBaMM/pull/2613)).
+
 # [v22.12](https://github.com/pybamm-team/PyBaMM/tree/v22.12) - 2022-12-31
 
 ## Features

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "22.12"
+version: "23.1"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

CONTRIBUTING.md

@@ -63,17 +63,18 @@ Finally, if you really, really, _really_ love developing PyBaMM, have a look at
 
 PyBaMM follows the [PEP8 recommendations](https://www.python.org/dev/peps/pep-0008/) for coding style. These are very common guidelines, and community tools have been developed to check how well projects implement them. We recommend using pre-commit hooks to check your code before committing it. See [installing and using pre-commit](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) section for more details.
 
-### Flake8
+### Ruff
 
-We use [flake8](http://flake8.pycqa.org/en/latest/) to check our PEP8 adherence. To try this on your system, navigate to the PyBaMM directory in a console and type
+We use [ruff](https://github.com/charliermarsh/ruff) to check our PEP8 adherence. To try this on your system, navigate to the PyBaMM directory in a console and type
 
 ```bash
-flake8
+python -m pip install pre-commit
+pre-commit run ruff
 ```
 
-Flake8 is configured inside the file `tox.ini`, under the section `[flake8]`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](#issues)
+ruff is configured inside the file `pre-commit-config.yaml`, allowing us to ignore some errors. If you think this should be added or removed, please submit an [issue](#issues)
 
-When you commit your changes they will be checked against flake8 automatically (see [infrastructure](#infrastructure)).
+When you commit your changes they will be checked against ruff automatically (see [infrastructure](#infrastructure)).
 
 ### Black
 
@@ -89,7 +90,7 @@ black {source_file_or_directory}
 
 If you want to use black in your editor, you may need to change the max line length in your editor settings.
 
-Even when code has been formatted by black, you should still make sure that it adheres to the PEP8 standard set by [Flake8](#flake8).
+Even when code has been formatted by black, you should still make sure that it adheres to the PEP8 standard set by [ruff](#ruff).
 
 ### Naming
 
@@ -111,7 +112,7 @@ On the other hand... We _do_ want to compare several tools, to generate document
 1. Core PyBaMM: A minimal set, including things like NumPy, SciPy, etc. All infrastructure should run against this set of dependencies, as well as any numerical methods we implement ourselves.
 2. Extras: Other inference packages and their dependencies. Methods we don't want to implement ourselves, but do want to provide an interface to can have their dependencies added here.
 3. Documentation generating code: Everything you need to generate and work on the docs.
-4. Development code: Everything you need to do PyBaMM development (so all of the above packages, plus flake8 and other testing tools).
+4. Development code: Everything you need to do PyBaMM development (so all of the above packages, plus ruff and other testing tools).
 
 Only 'core pybamm' is installed by default. The others have to be specified explicitly when running the installation command.