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pybamm-team · Mar 30, 2020 · 6f454f2 · 6f454f2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,16 +8,17 @@
 -   Added functionality to broadcast to edges ([#891](https://github.com/pybamm-team/PyBaMM/pull/891))
 -   Reformatted and cleaned up `QuickPlot` ([#886](https://github.com/pybamm-team/PyBaMM/pull/886))
 -   Added thermal effects to lead-acid models ([#885](https://github.com/pybamm-team/PyBaMM/pull/885))
--   Add new symbols `VariableDot`, representing the derivative of a variable wrt time, 
-    and `StateVectorDot`, representing the derivative of a state vector wrt time 
-    ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
+-   Added a helper function for info on function parameters ([#881](https://github.com/pybamm-team/PyBaMM/pull/881))
 -   Added additional notebooks showing how to create and compare models ([#877](https://github.com/pybamm-team/PyBaMM/pull/877))
 -   Added `Minimum`, `Maximum` and `Sign` operators
     ([#876](https://github.com/pybamm-team/PyBaMM/pull/876))
 -   Added a search feature to `FuzzyDict` ([#875](https://github.com/pybamm-team/PyBaMM/pull/875))
 -   Add ambient temperature as a function of time ([#872](https://github.com/pybamm-team/PyBaMM/pull/872))
 -   Added `CasadiAlgebraicSolver` for solving algebraic systems with CasADi ([#868](https://github.com/pybamm-team/PyBaMM/pull/868))
 -   Added electrolyte functions from Landesfeind ([#860](https://github.com/pybamm-team/PyBaMM/pull/860))
+-   Add new symbols `VariableDot`, representing the derivative of a variable wrt time,
+    and `StateVectorDot`, representing the derivative of a state vector wrt time
+    ([#858](https://github.com/pybamm-team/PyBaMM/issues/858))
 
 ## Optimizations
 

diff --git a/INSTALL-WINDOWS-WSL.md b/INSTALL-WINDOWS-WSL.md
@@ -0,0 +1,89 @@
+We recommend the use of Windows Subsystem for Linux (WSL) to install PyBaMM, see the
+instructions below to get PyBaMM working using Windows, WSL and VSCode.
+
+## Install WSL
+
+Follow the instructions from Microsoft
+[here](https://docs.microsoft.com/en-us/windows/wsl/install-win10). When given the
+option, choose the Ubuntu 18.04 LTS distribution to install. Don't forget to initialise
+the Ubuntu installation using the instructions given
+[here](https://docs.microsoft.com/en-us/windows/wsl/initialize-distro).
+
+## Install PyBaMM
+
+Open a terminal window in your installed Ubuntu distribution by selecting "Ubuntu" from
+the start menu. This should give you a bash prompt in your home directory. 
+
+To download the PyBaMM source code, you first need to install git, which you can do by
+typing
+
+```bash 
+sudo apt install git-core
+```
+
+For easier integration with WSL, we recommend that you install PyBaMM in your *Windows* 
+Documents folder, for example by first navigating to
+
+```bash
+$ cd /mnt/c/Users/USER_NAME/Documents
+```
+
+where USER_NAME is your username. Exact path to Windows documents may vary. Now use git to clone the PyBaMM repository:
+
+```bash
+git clone https://github.com/pybamm-team/PyBaMM.git
+```
+
+This will create a new directly called `PyBaMM`, you can move to this directory in bash
+using the `cd` command:
+
+```bash 
+cd PyBaMM 
+```
+
+If you are unfamiliar with the linux command line, you might find it useful to work through this
+[tutorial](https://tutorials.ubuntu.com/tutorial/command-line-for-beginners) provided by Ubuntu.
+
+Now head over and follow the installation instructions for PyBaMM for linux
+[here](INSTALL-LINUX-MAC.md).
+
+## Use Visual Studio Code to run PyBaMM 
+
+You will probably want to use a native Windows IDE such as Visual Studio Code or the
+full Microsoft Visual Studio IDE. Both of these packages can connect to WSL so that you
+can write python code in a native windows environment, while at the same time using WSL
+to run the code using your installed Ubuntu distribution. The following instructions
+assume that you are using Visual Studio Code.
+
+First, setup VSCode to run within the `PyBaMM` directory that you created above, using
+the instructions provided [here](https://code.visualstudio.com/docs/remote/wsl). 
+
+Once you have opened the `PyBaMM` folder in vscode, use the `Extensions` panel to
+install the `Python` extension from Microsoft. Note that extensions are either installed
+on the Windows (Local) or on in WSL (WSL:Ubuntu), so even if you have used VSCode
+previously with the Python extension, you probably haven't installed it in WSL. Make
+sure to reload after installing the Python extension so that it is available.
+
+If you have installed PyBaMM into the virtual environment `env` as in the PyBaMM linux
+install guide, then VSCode should automatically start using this environment and you
+should see something similar to "Python 3.6.8 64-bit ('env': venv)" in the bottom bar.
+
+To test that vscode can run a PyBaMM script, navigate to the `examples/scripts` folder
+and right click on the `create-model.py` script. Select "Run current file in Python
+Interactive Window". This should run the script, which sets up and solves a model of SEI
+thickness using PyBaMM. You should see a plot of SEI thickness versus time pop up in the
+interactive window.
+
+The Python Interactive Window in VSCode can be used to view plots, but is restricted in 
+functionality and cannot, for example, launch separate windows to show plot. To setup an 
+xserver on windows and use this to launch windows for plotting, follow these 
+instructions:
+
+1. Install VcXsrv from [here](https://sourceforge.net/projects/vcxsrv/).
+1. Set the display port in the WSL command-line: `echo "export DISPLAY=localhost:0.0" >> 
+   ~/.bashrc`
+1. Install python3-tk in WSL: `sudo apt-get install python3-tk`
+1. Set the matplotlib backend to TKAgg in WSL: `echo "backend : TKAgg" >> 
+   ~/.config/matplotlib/matplotlibrc`
+1. Before running the code, just launch XLaunch (with the default settings) from within 
+   Windows. Then the code works as usual.
diff --git a/INSTALL-WINDOWS.md b/INSTALL-WINDOWS.md
@@ -1,89 +1,54 @@
-We recommend the use of Windows Subsystem for Linux (WSL) to install PyBaMM, see the
-instructions below to get PyBaMM working using Windows, WSL and VSCode.
+## Prerequisites
 
-## Install WSL
+To use and/or contribute to PyBaMM, you must have Python 3.6 or 3.7 installed (note that 3.8 is not yet supported).
 
-Follow the instructions from Microsoft
-[here](https://docs.microsoft.com/en-us/windows/wsl/install-win10). When given the
-option, choose the Ubuntu 18.04 LTS distribution to install. Don't forget to initialise
-the Ubuntu installation using the instructions given
-[here](https://docs.microsoft.com/en-us/windows/wsl/initialize-distro).
+To install Python 3 download the installation files from [Python's website](https://www.python.org/downloads/windows/). Make sure
+to tick the box on `Add Python 3.X to PATH`. For more detailed instructions please see the 
+[official Python on Windows guide](https://docs.python.org/3.7/using/windows.html).
 
 ## Install PyBaMM
 
-Open a terminal window in your installed Ubuntu distribution by selecting "Ubuntu" from
-the start menu. This should give you a bash prompt in your home directory. 
+### User install
+Launch the Command Prompt and go to the directory where you want to install PyBaMM. You can find a reminder of how to
+navigate the terminal [here](http://www.cs.columbia.edu/~sedwards/classes/2015/1102-fall/Command%20Prompt%20Cheatsheet.pdf).
 
-To download the PyBaMM source code, you first need to install git, which you can do by
-typing
+We recommend to install PyBaMM within a virtual environment, in order not
+to alter any distribution python files.
 
-```bash 
-sudo apt install git-core
-```
-
-For easier integration with WSL, we recommend that you install PyBaMM in your *Windows* 
-Documents folder, for example by first navigating to
+To create a virtual environment `env` within your current directory type:
 
 ```bash
-$ cd /mnt/c/Users/USER_NAME/Documents
+python -m venv env
 ```
-
-where USER_NAME is your username. Exact path to Windows documents may vary. Now use git to clone the PyBaMM repository:
+You can then "activate" the environment using:
 
 ```bash
-git clone https://github.com/pybamm-team/PyBaMM.git
+env\Scripts\activate.bat
 ```
+Now all the calls to pip described below will install PyBaMM and its dependencies into
+the environment `env`. When you are ready to exit the environment and go back to your
+original system, just type:
 
-This will create a new directly called `PyBaMM`, you can move to this directory in bash
-using the `cd` command:
-
-```bash 
-cd PyBaMM 
+```bash
+deactivate
 ```
 
-If you are unfamiliar with the linux command line, you might find it useful to work through this
-[tutorial](https://tutorials.ubuntu.com/tutorial/command-line-for-beginners) provided by Ubuntu.
-
-Now head over and follow the installation instructions for PyBaMM for linux
-[here](INSTALL-LINUX-MAC.md).
-
-## Use Visual Studio Code to run PyBaMM 
-
-You will probably want to use a native Windows IDE such as Visual Studio Code or the
-full Microsoft Visual Studio IDE. Both of these packages can connect to WSL so that you
-can write python code in a native windows environment, while at the same time using WSL
-to run the code using your installed Ubuntu distribution. The following instructions
-assume that you are using Visual Studio Code.
-
-First, setup VSCode to run within the `PyBaMM` directory that you created above, using
-the instructions provided [here](https://code.visualstudio.com/docs/remote/wsl). 
-
-Once you have opened the `PyBaMM` folder in vscode, use the `Extensions` panel to
-install the `Python` extension from Microsoft. Note that extensions are either installed
-on the Windows (Local) or on in WSL (WSL:Ubuntu), so even if you have used VSCode
-previously with the Python extension, you probably haven't installed it in WSL. Make
-sure to reload after installing the Python extension so that it is available.
+PyBaMM can be installed via pip:
+```bash
+pip install pybamm
+```
 
-If you have installed PyBaMM into the virtual environment `env` as in the PyBaMM linux
-install guide, then VSCode should automatically start using this environment and you
-should see something similar to "Python 3.6.8 64-bit ('env': venv)" in the bottom bar.
+PyBaMM's dependencies (such as `numpy`, `scipy`, etc) will be installed automatically when you install PyBaMM using `pip`.
 
-To test that vscode can run a PyBaMM script, navigate to the `examples/scripts` folder
-and right click on the `create-model.py` script. Select "Run current file in Python
-Interactive Window". This should run the script, which sets up and solves a model of SEI
-thickness using PyBaMM. You should see a plot of SEI thickness versus time pop up in the
-interactive window.
+For an introduction to virtual environments, see (https://realpython.com/python-virtual-environments-a-primer/).
 
-The Python Interactive Window in VSCode can be used to view plots, but is restricted in 
-functionality and cannot, for example, launch separate windows to show plot. To setup an 
-xserver on windows and use this to launch windows for plotting, follow these 
-instructions:
+## Uninstall PyBaMM
+PyBaMM can be uninstalled by running
+```bash
+pip uninstall pybamm
+```
+in your virtual environment.
 
-1. Install VcXsrv from [here](https://sourceforge.net/projects/vcxsrv/).
-1. Set the display port in the WSL command-line: `echo "export DISPLAY=localhost:0.0" >> 
-   ~/.bashrc`
-1. Install python3-tk in WSL: `sudo apt-get install python3-tk`
-1. Set the matplotlib backend to TKAgg in WSL: `echo "backend : TKAgg" >> 
-   ~/.config/matplotlib/matplotlibrc`
-1. Before running the code, just launch XLaunch (with the default settings) from within 
-   Windows. Then the code works as usual.
+## Installation using WSL
+If you want to install the optional PyBaMM solvers, you have to use the Windows Subsystem for Linux (WSL). You can find
+the installation instructions [here](INSTALL-WINDOWS-WSL.md).
diff --git a/README.md b/README.md
@@ -53,16 +53,15 @@ For further examples, see the list of repositories that use PyBaMM [here](https:
 
 ### Linux
 
-For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX-MAC.md)
+For instructions on installing PyBaMM on Debian-based distributions, please see [here](INSTALL-LINUX-MAC.md).
 
 ### Mac OS
 
-For instructions on installing PyBaMM on Mac OS distributions, please see [here](INSTALL-LINUX-MAC.md)
+For instructions on installing PyBaMM on Mac OS distributions, please see [here](INSTALL-LINUX-MAC.md).
 
 ### Windows
 
-We recommend using Windows Subsystem for Linux to install PyBaMM on a Windows OS, for
-instructions please see [here](INSTALL-WINDOWS.md)
+For instructions on installing PyBaMM on Windows distributions, please see [here](INSTALL-WINDOWS.md). If you want to install the optional solvers (such as scikits-odes and KLU solvers), install PyBaMM on the Windows Subsystem for Linux following the instructions [here](INSTALL-WINDOWS-WSL.md) 
 
 ## Citing PyBaMM
 

diff --git a/examples/notebooks/Creating Models/1-an-ode-model.ipynb b/examples/notebooks/Creating Models/1-an-ode-model.ipynb
@@ -271,7 +271,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/2-a-pde-model.ipynb b/examples/notebooks/Creating Models/2-a-pde-model.ipynb
@@ -298,7 +298,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb b/examples/notebooks/Creating Models/3-negative-particle-problem.ipynb
@@ -316,7 +316,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb b/examples/notebooks/Creating Models/4-comparing-full-and-reduced-order-models.ipynb
@@ -375,7 +375,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb b/examples/notebooks/Creating Models/5-a-simple-SEI-model.ipynb
@@ -249,7 +249,7 @@
     "c_inf_dim = pybamm.Parameter(\"Bulk electrolyte solvent concentration\")\n",
     "\n",
     "def D_dim(cc):\n",
-    "    return pybamm.FunctionParameter(\"Diffusivity\", cc)\n",
+    "    return pybamm.FunctionParameter(\"Diffusivity\", {\"Solvent concentration [mol.m-3]\": cc})\n",
     "\n",
     "# dimensionless parameters\n",
     "k = k_dim * L_0_dim / D_dim(c_inf_dim)\n",
@@ -591,7 +591,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b2a5f649a3b64685ad9510649f130829",
+       "model_id": "efe1fe18458a42d88056baf689f6da80",
        "version_major": 2,
        "version_minor": 0
       },
@@ -653,7 +653,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.9"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,

diff --git a/examples/notebooks/parameter-values.ipynb b/examples/notebooks/parameter-values.ipynb
diff --git a/examples/scripts/create-model.py b/examples/scripts/create-model.py
@@ -18,7 +18,7 @@
 
 
 def D_dim(cc):
-    return pybamm.FunctionParameter("Diffusivity", cc)
+    return pybamm.FunctionParameter("Diffusivity", {"Concentration [mol.m-3]": cc})
 
 
 # dimensionless parameters