Merge pull request #1139 from pybamm-team/develop

Release 0.2.4

.github/workflows/build_wheels_and_publish.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
         include:
           - os: ubuntu-latest
             python-version: 3.8

.github/workflows/test_on_push.yml

@@ -15,18 +15,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - name: Check style
+    - name: Setup python
       uses: actions/setup-python@v1
       with:
         python-version: 3.7
 
-    - name: Install package
-      run: |
-        python -m pip install --upgrade pip wheel setuptools
-        pip install -e .[dev]
-
     - name: Check style
-      run: python -m flake8
+      run: |
+        python -m pip install tox
+        tox -e flake8
 
   build:
     needs: style
@@ -35,7 +32,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -47,7 +44,7 @@ jobs:
     - name: Install Linux system dependencies
       if: matrix.os == 'ubuntu-latest'
       run: |
-        sudo apt install gfortran gcc libopenblas-dev liblapack-dev graphviz
+        sudo apt install gfortran gcc libopenblas-dev graphviz
         sudo apt install python${{ matrix.python-version }}.dev
     
     - name: Install MacOS system dependencies
@@ -64,51 +61,33 @@ jobs:
     - name: Install standard python dependencies
       run: |
         python -m pip install --upgrade pip wheel setuptools
-        pip install -e .
+        python -m pip install tox
 
-    - name: Install SUNDIALS and SuiteSparse
+    - name: Install SuiteSparse and Sundials
       if: matrix.os != 'windows-latest'
-      run: |
-        pip install wget
-        git clone https://github.com/pybind/pybind11.git
-        python scripts/setup_KLU_module_build.py
-        export SUNDIALS_INST=$HOME/.local
-        pip install scikits.odes
-        pip install -e .
+      run: tox -e pybamm-requires
 
-    - name: Run unit tests Windows
-      if: matrix.os == 'windows-latest'
-      run: |
-        python run-tests.py --unit --folder all
-
-    - name: Run unit tests
+    - name: Run unit tests for GNU/Linux and MacOS
       if: matrix.os != 'windows-latest'
-      run: |
-        export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
-        python run-tests.py --unit --folder all
+      run: python -m tox -e tests
+
+    - name: Run unit tests for Windows
+      if: matrix.os == 'windows-latest'
+      run: python -m tox -e windows-tests
 
     - name: Install docs dependencies and run doctests
       if: matrix.os != 'windows-latest'
-      run: |
-        export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
-        pip install -e .[docs]
-        python run-tests.py --doctest
-
+      run: tox -e doctests
+
     - name: Install dev dependencies and run example tests
       if: matrix.os != 'windows-latest'
-      run: |
-        export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
-        pip install -e .[dev]
-        python run-tests.py --examples
-
-    - name: Install and run coverage
-      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7)
-      run: |
-        pip install coverage
-        export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
-        coverage run run-tests.py --nosub
-        coverage xml
+      run: tox -e examples
+
+    - name: Instal and run coverage
+      if: success() && (matrix.os == 'unbuntu-latest' && matrix.python-version == 3.7)
+      run: tox -e coverage
 
     - name: Upload coverage report
       if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
       uses: codecov/codecov-action@v1
+

.gitignore

@@ -95,11 +95,15 @@ cmake_install.cmake
 *.so
 *.json
 
-
 third-party/pybind11
 pybind11/
 
-setup.log
+# Build dependencies/
+KLU_module_deps
 
+# setup
+setup.log
 
+# tox
+.tox/
 

CHANGELOG.md

@@ -1,9 +1,46 @@
+# [v0.2.4](https://github.com/pybamm-team/PyBaMM/tree/v0.2.4) - 2020-09-07
+
+This release adds new operators for more complex models, some basic sensitivity analysis, and a spectral volumes spatial method, as well as some small bug fixes.
+
+## Features
+
+-   Added variables which track the total amount of lithium in the system ([#1136](https://github.com/pybamm-team/PyBaMM/pull/1136))
+-   Added `Upwind` and `Downwind` operators for convection ([#1134](https://github.com/pybamm-team/PyBaMM/pull/1134))
+-   Added Getting Started notebook on solver options and changing the mesh. Also added a notebook detailing the different thermal options, and a notebook explaining the steps that occur behind the scenes in the `Simulation` class ([#1131](https://github.com/pybamm-team/PyBaMM/pull/1131))
+-   Added particle submodel that use a polynomial approximation to the concentration within the electrode particles ([#1130](https://github.com/pybamm-team/PyBaMM/pull/1130))
+-   Added `Modulo`, `Floor` and `Ceiling` operators ([#1121](https://github.com/pybamm-team/PyBaMM/pull/1121))
+-   Added DFN model for a half cell ([#1121](https://github.com/pybamm-team/PyBaMM/pull/1121))
+-   Automatically compute surface area per unit volume based on particle shape for li-ion models ([#1120](https://github.com/pybamm-team/PyBaMM/pull/1120))
+-   Added "R-averaged particle concentration" variables ([#1118](https://github.com/pybamm-team/PyBaMM/pull/1118))
+-   Added support for sensitivity calculations to the casadi solver ([#1109](https://github.com/pybamm-team/PyBaMM/pull/1109))
+-   Added support for index 1 semi-explicit dae equations and sensitivity calculations to JAX BDF solver ([#1107](https://github.com/pybamm-team/PyBaMM/pull/1107))
+-   Allowed keyword arguments to be passed to `Simulation.plot()` ([#1099](https://github.com/pybamm-team/PyBaMM/pull/1099))
+-   Added the Spectral Volumes spatial method and the submesh that it works with ([#900](https://github.com/pybamm-team/PyBaMM/pull/900))
+
+## Bug fixes
+
+-   Fixed bug where some parameters were not being set by the `EcReactionLimited` SEI model ([#1136](https://github.com/pybamm-team/PyBaMM/pull/1136))
+-   Fixed bug on electrolyte potential for `BasicDFNHalfCell` ([#1133](https://github.com/pybamm-team/PyBaMM/pull/1133))
+-   Fixed `r_average` to work with `SecondaryBroadcast` ([#1118](https://github.com/pybamm-team/PyBaMM/pull/1118))
+-   Fixed finite volume discretisation of spherical integrals ([#1118](https://github.com/pybamm-team/PyBaMM/pull/1118))
+-   `t_eval` now gets changed to a `linspace` if a list of length 2 is passed ([#1113](https://github.com/pybamm-team/PyBaMM/pull/1113))
+-   Fixed bug when setting a function with an `InputParameter` ([#1111](https://github.com/pybamm-team/PyBaMM/pull/1111))
+
+## Breaking changes
+
+-   The "fast diffusion" particle option has been renamed "uniform profile" ([#1130](https://github.com/pybamm-team/PyBaMM/pull/1130))
+-   The modules containing standard parameters are now classes so they can take options
+(e.g. `standard_parameters_lithium_ion` is now `LithiumIonParameters`) ([#1120](https://github.com/pybamm-team/PyBaMM/pull/1120))
+-   Renamed `quick_plot_vars` to `output_variables` in `Simulation` to be consistent with `QuickPlot`. Passing `quick_plot_vars` to `Simulation.plot()` has been deprecated and `output_variables` should be passed instead ([#1099](https://github.com/pybamm-team/PyBaMM/pull/1099))
+
+
 # [v0.2.3](https://github.com/pybamm-team/PyBaMM/tree/v0.2.3) - 2020-07-01
 
 This release enables the use of [Google Colab](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/master/) for running example notebooks, and adds some small new features and bug fixes.
 
 ## Features
 
+-   Added JAX evaluator, and ODE solver ([#1038](https://github.com/pybamm-team/PyBaMM/pull/1038))
 -   Reformatted Getting Started notebooks ([#1083](https://github.com/pybamm-team/PyBaMM/pull/1083))
 -   Reformatted Landesfeind electrolytes ([#1064](https://github.com/pybamm-team/PyBaMM/pull/1064))
 -   Adapted examples to be run in Google Colab ([#1061](https://github.com/pybamm-team/PyBaMM/pull/1061))
@@ -32,7 +69,7 @@ This release enables the use of [Google Colab](https://colab.research.google.com
 ## Breaking changes
 
 -   `Simulation.specs` and `Simulation.set_defaults` have been deprecated. Users should create a new `Simulation` object for each different case instead ([#1090](https://github.com/pybamm-team/PyBaMM/pull/1090))
--  The solution times `t_eval` must now be provided to `Simulation.solve()` when not using an experiment or prescribing the current using drive cycle data ([#1086](https://github.com/pybamm-team/PyBaMM/pull/1086))
+-   The solution times `t_eval` must now be provided to `Simulation.solve()` when not using an experiment or prescribing the current using drive cycle data ([#1086](https://github.com/pybamm-team/PyBaMM/pull/1086))
 
 # [v0.2.2](https://github.com/pybamm-team/PyBaMM/tree/v0.2.2) - 2020-06-01
 

CONTRIBUTING.md

@@ -9,11 +9,8 @@ If you're already familiar with our workflow, maybe have a quick look at the [pr
 Before you commit any code, please perform the following checks:
 
 - [No style issues](#coding-style-guidelines): `$ flake8`
-- [All tests pass](#testing): `$ python run-tests.py --unit`
-- [The documentation builds](#building-the-documentation): `$ cd docs` and then `$ make clean; make html`
-
-You can even run all three at once, using `$ python run-tests.py --quick`.
-
+- [All tests pass](#testing): `$ tox -e quick` (GNU/Linux and MacOS), `$ python -m tox -e windows-quick` (Windows)
+- [The documentation builds](#building-the-documentation): `$ python -m tox -e docs`
 
 ## Workflow
 
@@ -52,13 +49,26 @@ Finally, if you really, really, _really_ love developing PyBaMM, have a look at
 To install PyBaMM with all developer options, type:
 
 ```bash
-pip install -e .[dev,docs]
+tox -e dev # (GNU/Linux and MacOS)
+#
+python -m tox -e windows-dev # (Windows)
 ```
 
 This will
 
-1. Install all the dependencies for PyBaMM, including the ones for documentation (docs) and development (dev).
-2. Tell Python to use your local pybamm files when you use `import pybamm` anywhere on your system.
+1. Create a virtual environment located at `.tox/dev`.
+2. Install all the dependencies for PyBaMM, including the ones for documentation and development.
+3. Tell Python to use your local pybamm files when you use `import pybamm` anywhere on your system.
+
+Finally, activate your environment.
+
+
+```bash
+source .tox/dev/bin/activate # (GNU/Linux and MacOS)
+#
+.tox\dev\Scripts\activate.bat # (Windows)
+```
+
 
 ## Coding style guidelines
 
@@ -71,11 +81,7 @@ We use [flake8](http://flake8.pycqa.org/en/latest/) to check our PEP8 adherence.
 ```bash
 flake8
 ```
-The configuration file
-```
-.flake8
-```
-allows us to ignore some errors. If you think this should be added or removed, please submit an [issue](#issues)
+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)
 
 When you commit your changes they will be checked against flake8 automatically (see [infrastructure](#infrastructure)).
 
@@ -145,7 +151,9 @@ All code requires testing. We use the [unittest](https://docs.python.org/3.3/lib
 To run quick tests, type
 
 ```bash
-python run-tests.py --unit
+tox -e quick # (GNU/Linux and MacOS)
+#
+python -m tox -e windows-quick (Windows)
 ```
 
 ### Writing tests
@@ -160,7 +168,9 @@ The tests are divided into `unit` tests, whose aim is to check individual bits o
 If you want to check integration tests as well as unit tests, type
 
 ```bash
-python run-tests.py --unit --folder all
+tox -e tests # (GNU/Linux and MacOS)
+#
+python -m tox -e windows-tests (Windows)
 ```
 
 When you commit anything to PyBaMM, these checks will also be run automatically (see [infrastructure](#infrastructure)).
@@ -170,7 +180,9 @@ When you commit anything to PyBaMM, these checks will also be run automatically
 To test all example scripts and notebooks, type
 
 ```bash
-python run-tests.py --examples
+tox -e examples # (GNU/Linux and MacOS)
+#
+python -m tox -e windows-examples (Windows)
 ```
 
 If notebooks fail because of changes to pybamm, it can be a bit of a hassle to debug. In these cases, you can create a temporary export of a notebook's Python content using
@@ -277,16 +289,12 @@ Using [Sphinx](http://www.sphinx-doc.org/en/stable/) the documentation in `docs`
 
 ### Building the documentation
 
-To test and debug the documentation, it's best to build it locally. To do this, make sure you have the relevant dependencies installed (see [installation](#installation)), navigate to your PyBaMM directory in a console, and then type:
+To test and debug the documentation, it's best to build it locally. To do this, navigate to your PyBaMM directory in a console, and then type:
 
 ```
-cd docs
-make clean
-make html
+python -m tox -e docs (GNU/Linux, MacOS and Windows)
 ```
-
-Next, open a browser, and navigate to your local PyBaMM directory (by typing the path, or part of the path into your location bar). Then have a look at `<your pybamm path>/docs/build/html/index.html`.
-
+And then visit the webpage served at http://127.0.0.1:8000. Each time a change to the documentation source is detected, the HTML is rebuilt and the browser automatically reloaded.
 
 ### Example notebooks
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2018-2020, University of Oxford (University of Oxford means the Chancellor, Masters and Scholars of the University of Oxford, having an administrative office at Wellington Square, Oxford OX1 2JD, UK).
+Copyright (c) 2018-2020, the PyBaMM team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -84,3 +84,4 @@ include pybamm/input/parameters/lithium-ion/separators/separator_Chen2020/README
 include pybamm/input/parameters/lithium-ion/separators/separator_Marquis2019/README.md
 include pybamm/version
 include pybamm/CITATIONS.txt
+include CMakeBuild.py

README.md

@@ -36,9 +36,9 @@ sim = pybamm.Simulation(model, experiment=experiment, solver=pybamm.CasadiSolver
 sim.solve()
 sim.plot()
 ```
-However, much greater customisation is available. It is possible to change the physics, parameter values, geometry, submesh type,  number of submesh points, methods for spatial discretisation and solver for integration (see DFN [script](examples/scripts/DFN.py) or [notebook](examples/notebooks/models/dfn.ipynb)).
+However, much greater customisation is available. It is possible to change the physics, parameter values, geometry, submesh type,  number of submesh points, methods for spatial discretisation and solver for integration (see DFN [script](examples/scripts/DFN.py) or [notebook](examples/notebooks/models/DFN.ipynb)).
 
-For new users we recommend the [Getting Started](examples/notebooks/Getting%20Started/) guides. These are intended to be very simple step-by-step guides to show the basic functionality of PyBaMM.
+For new users we recommend the [Getting Started](examples/notebooks/Getting%20Started/) guides. These are intended to be very simple step-by-step guides to show the basic functionality of PyBaMM, and can either be downloaded and used locally, or used online through [Google Colab](https://colab.research.google.com/github/pybamm-team/PyBaMM/blob/master/).
 
 Further details can be found in a number of [detailed examples](examples/notebooks/README.md), hosted here on
 github. In addition, there is a [full API documentation](http://pybamm.readthedocs.io/),

docs/conf.py

@@ -22,13 +22,13 @@
 # -- Project information -----------------------------------------------------
 
 project = "PyBaMM"
-copyright = "2020, Valentin Sulzer"
+copyright = "2020, The PyBaMM Team"
 author = "The PyBaMM Team"
 
 # The short X.Y version
 version = "0.2"
 # The full version, including alpha/beta/rc tags
-release = "0.2.3"
+release = "0.2.4"
 
 
 # -- General configuration ---------------------------------------------------