Merge pull request #680 from pybamm-team/issue-646-install

Issue 646 install

.travis.yml

@@ -62,6 +62,7 @@ matrix:
           env:
             - PYTHON=3.7.4
             - PYBAMM_UNIT=true
+            - PYBAMM_KLU=true
           if: type != cron
         - python: "3.7"
           addons:
@@ -177,6 +178,8 @@ before_install: |
     brew update;
     # Per the `pyenv homebrew recommendations <https://github.com/yyuu/pyenv/wiki#suggested-build-environment>`_.
     brew install graphviz openssl readline;
+    # Other brew packages
+    brew install gcc cmake openblas suitesparse;
     # See https://docs.travis-ci.com/user/osx-ci-environment/#A-note-on-upgrading-packages.
     brew outdated pyenv || brew upgrade pyenv
     # virtualenv doesn't work without pyenv knowledge. venv in Python 3.3

CHANGELOG.md

@@ -62,6 +62,7 @@
 -   Added missing temperature dependence in electrolyte and interface submodels ([#698](https://github.com/pybamm-team/PyBaMM/pull/698))
 -   Fixed differentiation of functions that have more than one argument ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
 -   Added warning if `ProcessedVariable` is called outside its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
+-   Updated installation instructions for Mac OS ([#680](https://github.com/pybamm-team/PyBaMM/pull/680))
 -   Improved the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
 
 ## Breaking changes

INSTALL-LINUX.md → INSTALL-LINUX-MAC.md

@@ -1,6 +1,7 @@
 ## Prerequisites
 
-To use and/or contribute to PyBaMM, you must have Python 3.6 or above installed.
+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).
+
 To install Python 3 on Debian-based distribution (Debian, Ubuntu, Linux mint), open a terminal and run
 ```bash
 sudo apt update
@@ -10,6 +11,18 @@ On Fedora or CentOS, you can use DNF or Yum. For example
 ```bash
 sudo dnf install python3
 ```
+On Mac OS distributions, you can use `homebrew`. 
+First [install `brew`](https://docs.python-guide.org/starting/install3/osx/):
+
+```bash
+ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+```
+
+then follow instructions in link on adding brew to path, and run
+
+```bash
+brew install python3
+```
 
 ## Install PyBaMM
 
@@ -46,11 +59,19 @@ For an introduction to virtual environments, see (https://realpython.com/python-
 ### Developer install
 
 If you wish to contribute to PyBaMM, you should get the latest version from the GitHub repository.
-To do so, you must have Git installed. For instance run
+To do so, you must have Git and graphviz installed. For instance run
+
 ```bash
-sudo apt install git
+sudo apt install git graphviz
 ```
-on Debian-based distributions.
+
+on Debian-based distributions, or
+
+```bash
+brew install git graphviz
+```
+
+on Mac OS.
 
 To install PyBaMM, the first step is to get the code by cloning this repository
 

INSTALL-WINDOWS.md

@@ -18,7 +18,7 @@ To download the PyBaMM source code, you first need to install git, which you can
 typing
 
 ```bash 
-$ sudo apt install git-core
+sudo apt install git-core
 ```
 
 For easier integration with WSL, we recommend that you install PyBaMM in your *Windows* 
@@ -31,21 +31,21 @@ $ 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
+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 
+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.md).
+[here](INSTALL-LINUX-MAC.md).
 
 ## Use Visual Studio Code to run PyBaMM 
 

README.md

@@ -35,7 +35,11 @@ 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.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)
 
 ### Windows
 

scripts/install_scikits_odes.sh

@@ -16,7 +16,8 @@ cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DBUILD_ARKODE:BOOL=OFF -
 make install
 cd $CURRENT_DIR
 rm -rf $TMP_DIR
-export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH # For Linux
+export DYLD_LIBRARY_PATH=$INSTALL_DIR/lib:$DYLD_LIBRARY_PATH # For Mac
 export SUNDIALS_INST=$INSTALL_DIR
 pip install scikits.odes
 

scripts/install_sundials_4.1.0.sh

@@ -32,14 +32,20 @@ cmake -DBLAS_ENABLE=ON\
       -DKLU_ENABLE=ON\
       ../sundials-4.1.0
 
-
-NUM_OF_CORES=$(cat /proc/cpuinfo | grep processor | wc -l)
+if [ "$(uname)" == "Darwin" ]; then
+    # Mac OS X platform        
+    NUM_OF_CORES=$(sysctl -n hw.cpu)
+elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
+    # GNU/Linux platform
+    NUM_OF_CORES=$(cat /proc/cpuinfo | grep processor | wc -l)
+fi
 make clean
 make -j$NUM_OF_CORES install
 cd $CURRENT_DIR
 rm -rf build-sundials-4.1.0
 rm -rf sundials-4.1.0
-export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH # For Linux
+export DYLD_LIBRARY_PATH=$INSTALL_DIR/lib:$DYLD_LIBRARY_PATH # For Mac
 export SUNDIALS_INST=$INSTALL_DIR
 
 # get pybind11