Merge branch 'develop' into issue-2358-add-temperature-to-experiment

Author: Scottmar93

.all-contributorsrc

@@ -529,7 +529,8 @@
       "profile": "https://github.com/agriyakhetarpal",
       "contributions": [
         "infra",
-        "code"
+        "code",
+        "doc"
       ]
     },
     {
@@ -542,6 +543,15 @@
         "test",
         "doc"
       ]
+    },
+    {
+      "login": "iatzak",
+      "name": "iatzak",
+      "avatar_url": "https://avatars.githubusercontent.com/u/112731474?v=4",
+      "profile": "https://github.com/iatzak",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/periodic_benchmarks.yml

@@ -25,7 +25,7 @@ jobs:
         with:
           python-version: 3.8
       - name: Install tox and asv
-        run: pip install -U pip tox asv
+        run: pip install -U pip "tox<4" asv
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"

.github/workflows/publish_pypi.yml

@@ -79,6 +79,10 @@ jobs:
         if: matrix.os == 'macos-latest'
         run: |
           # https://github.com/actions/virtual-environments/issues/1280
+          rm -f /usr/local/bin/2to3*
+          rm -f /usr/local/bin/idle3*
+          rm -f /usr/local/bin/pydoc3*
+          rm -f /usr/local/bin/python3*
           brew update
           brew reinstall gcc
           python -m pip install cmake wget

.github/workflows/run_benchmarks_over_history.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: 3.8
       - name: Install tox and asv
-        run: pip install -U pip tox asv
+        run: pip install -U pip "tox<4" asv
       - name: Fetch develop branch
         # Not required when worklow trigerred
         # on develop, but useful when

.github/workflows/test_on_push.yml

@@ -36,7 +36,7 @@ jobs:
 
       - name: Check style
         run: |
-          python -m pip install tox
+          python -m pip install "tox<4"
           tox -e flake8
 
   build:
@@ -68,7 +68,10 @@ jobs:
       - name: Install MacOS system dependencies
         if: matrix.os == 'macos-latest'
         run: |
-          rm -f /usr/local/bin/2to3
+          rm -f /usr/local/bin/2to3*
+          rm -f /usr/local/bin/idle3*
+          rm -f /usr/local/bin/pydoc3*
+          rm -f /usr/local/bin/python3*
           brew update
           brew install graphviz
           brew install openblas
@@ -80,7 +83,7 @@ jobs:
       - name: Install standard python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools
-          python -m pip install tox
+          python -m pip install "tox<4"
 
       - name: Install SuiteSparse and Sundials
         if: matrix.os == 'ubuntu-latest'

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
         exclude: assets/js/webapp\.js
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 22.12.0
     hooks:
       - id: black
 

CHANGELOG.md

@@ -1,9 +1,45 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+## Features
+
+- 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)).
+
+# [v22.12](https://github.com/pybamm-team/PyBaMM/tree/v22.12) - 2022-12-31
+
+## Features
+
+- Added functionality to create `pybamm.ParameterValues` from a [BPX standard](https://github.com/pybamm-team/BPX) JSON file ([#2555](https://github.com/pybamm-team/PyBaMM/pull/2555)).
+- Allow the option "surface form" to be "differential" in the `MPM` ([#2533](https://github.com/pybamm-team/PyBaMM/pull/2533))
+- Added variables "Loss of lithium due to loss of active material in negative/positive electrode [mol]". These should be included in the calculation of "total lithium in system" to make sure that lithium is truly conserved. ([#2529](https://github.com/pybamm-team/PyBaMM/pull/2529))
+- `initial_soc` can now be a string "x V", in which case the simulation is initialized to start from that voltage ([#2508](https://github.com/pybamm-team/PyBaMM/pull/2508))
+- The `ElectrodeSOH` solver can now calculate electrode balance based on a target "cell capacity" (requires cell capacity "Q" as input), as well as the default "cyclable cell capacity" (requires cyclable lithium capacity "Q_Li" as input). Use the keyword argument `known_value` to control which is used. ([#2508](https://github.com/pybamm-team/PyBaMM/pull/2508))
+
+## Bug fixes
+
+- Allow models that subclass `BaseBatteryModel` to use custom options classes ([#2571](https://github.com/pybamm-team/PyBaMM/pull/2571))
+- Fixed bug with `EntryPoints` in Spyder IDE ([#2584](https://github.com/pybamm-team/PyBaMM/pull/2584))
+- Fixed electrolyte conservation when options {"surface form": "algebraic"} are used
+- Fixed "constant concentration" electrolyte model so that "porosity times concentration" is conserved when porosity changes ([#2529](https://github.com/pybamm-team/PyBaMM/pull/2529))
+- Fix installation on `Google Colab` (`pybtex` and `Colab` issue) ([#2526](https://github.com/pybamm-team/PyBaMM/pull/2526))
+
+## Breaking changes
+
+- Renamed "Negative/Positive electrode SOC" to "Negative/Positive electrode stoichiometry" to avoid confusion with cell SOC ([#2529](https://github.com/pybamm-team/PyBaMM/pull/2529))
+- Removed external variables and submodels. InputParameter should now be used in all cases ([#2502](https://github.com/pybamm-team/PyBaMM/pull/2502))
+- Trying to use a solver to solve multiple models results in a RuntimeError exception ([#2481](https://github.com/pybamm-team/PyBaMM/pull/2481))
+- Inputs for the `ElectrodeSOH` solver are now (i) "Q_Li", the total cyclable capacity of lithium in the electrodes (previously "n_Li", the total number of moles, n_Li = 3600/F \* Q_Li) (ii) "Q_n", the capacity of the negative electrode (previously "C_n"), and "Q_p", the capacity of the positive electrode (previously "C_p") ([#2508](https://github.com/pybamm-team/PyBaMM/pull/2508))
+
+# [v22.11.1](https://github.com/pybamm-team/PyBaMM/tree/v22.11.1) - 2022-12-13
+
+## Bug fixes
+
+- Fixed installation on Google Colab (`pybtex` issues) ([#2547](https://github.com/pybamm-team/PyBaMM/pull/2547/files))
+
 # [v22.11](https://github.com/pybamm-team/PyBaMM/tree/v22.11) - 2022-11-30
 
 ## Features
 
+- Updated parameter sets so that interpolants are created explicitly in the parameter set python file. This does not change functionality but allows finer control, e.g. specifying a "cubic" interpolator instead of the default "linear" ([#2510](https://github.com/pybamm-team/PyBaMM/pull/2510))
 - Equivalent circuit models ([#2478](https://github.com/pybamm-team/PyBaMM/pull/2478))
 - New Idaklu solver options for jacobian type and linear solver, support Sundials v6 ([#2444](https://github.com/pybamm-team/PyBaMM/pull/2444))
 - Added `scale` and `reference` attributes to `Variable` objects, which can be use to make the ODE/DAE solver better conditioned ([#2440](https://github.com/pybamm-team/PyBaMM/pull/2440))

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "22.11"
+version: "22.12"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

CONTRIBUTING.md

@@ -61,7 +61,7 @@ Finally, if you really, really, _really_ love developing PyBaMM, have a look at
 
 ## Coding style guidelines
 
-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.
+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
 
@@ -85,7 +85,7 @@ We use [black](https://black.readthedocs.io/en/stable/) to automatically configu
 black {source_file_or_directory}
 ```
 
-2. Editor: black can be [configured](https://test-black.readthedocs.io/en/latest/editor_integration.html) to automatically reformat a python script each time the script is saved in an editor.
+2. Editor: black can be [configured](https://test-black.readthedocs.io/en/latest/editor_integration.html) to automatically reformat a Python script each time the script is saved in an editor.
 
 If you want to use black in your editor, you may need to change the max line length in your editor settings.
 
@@ -194,67 +194,76 @@ This also means that, if you can't fix the bug yourself, it will be much easier
 
 1. Run individual test scripts instead of the whole test suite:
 
-```bash
-python tests/unit/path/to/test
-```
+   ```bash
+   python tests/unit/path/to/test
+   ```
 
-You can also run an individual test from a particular script, e.g.
+   You can also run an individual test from a particular script, e.g.
 
-```bash
-python tests/unit/test_quick_plot.py TestQuickPlot.test_failure
-```
+   ```bash
+   python tests/unit/test_quick_plot.py TestQuickPlot.test_failure
+   ```
 
-If you want to run several, but not all, the tests from a script, you can restrict which tests are run from a particular script by using the skipping decorator:
+   If you want to run several, but not all, the tests from a script, you can restrict which tests are run from a particular script by using the skipping decorator:
 
-```python
-@unittest.skip("")
-def test_bit_of_code(self):
-    ...
-```
+   ```python
+   @unittest.skip("")
+   def test_bit_of_code(self):
+       ...
+   ```
 
-or by just commenting out all the tests you don't want to run 2. Set break points, either in your IDE or using the python debugging module. To use the latter, add the following line where you want to set the break point
+   or by just commenting out all the tests you don't want to run.
 
-```python
-import ipdb; ipdb.set_trace()
-```
+2. Set break points, either in your IDE or using the Python debugging module. To use the latter, add the following line where you want to set the break point
 
-This will start the [Python interactive debugger](https://gist.github.com/mono0926/6326015). If you want to be able to use magic commands from `ipython`, such as `%timeit`, then set
+   ```python
+   import ipdb; ipdb.set_trace()
+   ```
 
-```python
-from IPython import embed; embed(); import ipdb; ipdb.set_trace()
-```
+   This will start the [Python interactive debugger](https://gist.github.com/mono0926/6326015). If you want to be able to use magic commands from `ipython`, such as `%timeit`, then set
 
-at the break point instead.
-Figuring out where to start the debugger is the real challenge. Some good ways to set debugging break points are:
-a. Try-except blocks. Suppose the line `do_something_complicated()` is raising a `ValueError`. Then you can put a try-except block around that line as:
+   ```python
+   from IPython import embed; embed(); import ipdb; ipdb.set_trace()
+   ```
 
-```python
-try:
-    do_something_complicated()
-except ValueError:
-    import ipdb; ipdb.set_trace()
-```
+   at the break point instead.
+   Figuring out where to start the debugger is the real challenge. Some good ways to set debugging break points are:
 
-This will start the debugger at the point where the `ValueError` was raised, and allow you to investigate further. Sometimes, it is more informative to put the try-except block further up the call stack than exactly where the error is raised.
-b. Warnings. If functions are raising warnings instead of errors, it can be hard to pinpoint where this is coming from. Here, you can use the `warnings` module to convert warnings to errors:
+   1. Try-except blocks. Suppose the line `do_something_complicated()` is raising a `ValueError`. Then you can put a try-except block around that line as:
 
-```python
-import warnings
-warnings.simplefilter("error")
-```
+      ```python
+      try:
+          do_something_complicated()
+      except ValueError:
+          import ipdb; ipdb.set_trace()
+      ```
 
-Then you can use a try-except block, as in a., but with, for example, `RuntimeWarning` instead of `ValueError`.
-c. Stepping through the expression tree. Most calls in PyBaMM are operations on [expression trees](https://github.com/pybamm-team/PyBaMM/blob/develop/examples/notebooks/expression_tree/expression-tree.ipynb). To view an expression tree in ipython, you can use the `render` command:
+      This will start the debugger at the point where the `ValueError` was raised, and allow you to investigate further. Sometimes, it is more informative to put the try-except block further up the call stack than exactly where the error is raised.
 
-```python
-expression_tree.render()
-```
+   2. Warnings. If functions are raising warnings instead of errors, it can be hard to pinpoint where this is coming from. Here, you can use the `warnings` module to convert warnings to errors:
 
-You can then step through the expression tree, using the `children` attribute, to pinpoint exactly where a bug is coming from. For example, if `expression_tree.jac(y)` is failing, you can check `expression_tree.children[0].jac(y)`, then `expression_tree.children[0].children[0].jac(y)`, etc. 3. To isolate whether a bug is in a model, its jacobian or its simplified version, you can set the `use_jacobian` and/or `use_simplify` attributes of the model to `False` (they are both `True` by default for most models). 4. If a model isn't giving the answer you expect, you can try comparing it to other models. For example, you can investigate parameter limits in which two models should give the same answer by setting some parameters to be small or zero. The `StandardOutputComparison` class can be used to compare some standard outputs from battery models. 5. To get more information about what is going on under the hood, and hence understand what is causing the bug, you can set the [logging](https://realpython.com/python-logging/) level to `DEBUG` by adding the following line to your test or script:
+      ```python
+      import warnings
+      warnings.simplefilter("error")
+      ```
 
-```python3
-pybamm.set_logging_level("DEBUG")
-```
+      Then you can use a try-except block, as in a., but with, for example, `RuntimeWarning` instead of `ValueError`.
+
+   3. Stepping through the expression tree. Most calls in PyBaMM are operations on [expression trees](https://github.com/pybamm-team/PyBaMM/blob/develop/examples/notebooks/expression_tree/expression-tree.ipynb). To view an expression tree in ipython, you can use the `render` command:
+
+      ```python
+      expression_tree.render()
+      ```
+
+      You can then step through the expression tree, using the `children` attribute, to pinpoint exactly where a bug is coming from. For example, if `expression_tree.jac(y)` is failing, you can check `expression_tree.children[0].jac(y)`, then `expression_tree.children[0].children[0].jac(y)`, etc.
+
+3. To isolate whether a bug is in a model, its Jacobian or its simplified version, you can set the `use_jacobian` and/or `use_simplify` attributes of the model to `False` (they are both `True` by default for most models).
+4. If a model isn't giving the answer you expect, you can try comparing it to other models. For example, you can investigate parameter limits in which two models should give the same answer by setting some parameters to be small or zero. The `StandardOutputComparison` class can be used to compare some standard outputs from battery models.
+5. To get more information about what is going on under the hood, and hence understand what is causing the bug, you can set the [logging](https://realpython.com/python-logging/) level to `DEBUG` by adding the following line to your test or script:
+
+   ```python3
+   pybamm.set_logging_level("DEBUG")
+   ```
 
 6. In models that inherit from `pybamm.BaseBatteryModel` (i.e. any battery model), you can use `self.process_parameters_and_discretise` to process a symbol and see what it will look like.
 
@@ -270,24 +279,26 @@ as above, and then use some of the profiling tools. In order of increasing detai
 
 1. Simple timer. In ipython, the command
 
-```
-%time command_to_time()
-```
+   ```
+   %time command_to_time()
+   ```
 
-tells you how long the line `command_to_time()` takes. You can use `%timeit` instead to run the command several times and obtain more accurate timings. 2. Simple profiler. Using `%prun` instead of `%time` will give a brief profiling report 3. Detailed profiler. You can install the detailed profiler `snakeviz` through pip:
+   tells you how long the line `command_to_time()` takes. You can use `%timeit` instead to run the command several times and obtain more accurate timings.
 
-```bash
-pip install snakeviz
-```
+2. Simple profiler. Using `%prun` instead of `%time` will give a brief profiling report 3. Detailed profiler. You can install the detailed profiler `snakeviz` through pip:
 
-and then, in ipython, run
+   ```bash
+   pip install snakeviz
+   ```
 
-```
-%load_ext snakeviz
-%snakeviz command_to_time()
-```
+   and then, in ipython, run
+
+   ```
+   %load_ext snakeviz
+   %snakeviz command_to_time()
+   ```
 
-This will open a window in your browser with detailed profiling information.
+   This will open a window in your browser with detailed profiling information.
 
 ## Documentation
 
@@ -329,9 +340,9 @@ Adding the command
 pybamm.print_citations()
 ```
 
-to the end of a script will print all citations that were used by that script. This will print bibtex information to the terminal; passing a filename to `print_citations` will print the bibtex information to the specified file instead.
+to the end of a script will print all citations that were used by that script. This will print BibTeX information to the terminal; passing a filename to `print_citations` will print the BibTeX information to the specified file instead.
 
-When you contribute code to PyBaMM, you can add your own papers that you would like to be cited if that code is used. First, add the bibtex for your paper to [CITATIONS.txt](pybamm/CITATIONS.txt). Then, add the line
+When you contribute code to PyBaMM, you can add your own papers that you would like to be cited if that code is used. First, add the BibTeX for your paper to [CITATIONS.txt](pybamm/CITATIONS.txt). Then, add the line
 
 ```python3
 pybamm.citations.register("your_paper_bibtex_identifier")
@@ -357,7 +368,7 @@ Note that this file must be kept in sync with the version number in [pybamm/**in
 
 Each change pushed to the PyBaMM GitHub repository will trigger the test and benchmark suites to be run, using [GitHub actions](https://github.com/features/actions).
 
-Tests are run for different operating systems, and for all python versions officially supported by PyBaMM. If you opened a Pull Request, feedback is directly available on the corresponding page. If all tests pass, a green tick will be displayed next to the corresponding test run. If one or more test(s) fail, a red cross will be displayed instead.
+Tests are run for different operating systems, and for all Python versions officially supported by PyBaMM. If you opened a Pull Request, feedback is directly available on the corresponding page. If all tests pass, a green tick will be displayed next to the corresponding test run. If one or more test(s) fail, a red cross will be displayed instead.
 
 Similarly, the benchmark suite is automatically run for the most recently pushed commit. Benchmark results are compared to the results available for the latest commit on the `develop` branch. Should any significant performance regression be found, a red cross will be displayed next to the benchmark run.
 

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2018-2022, the PyBaMM team.
+Copyright (c) 2018-2023, the PyBaMM team.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without