Installation

We currently support Linux & Mac OS X. On Windows it is tricky to set up an environment that works reliably with compilers for building some dependencies. From our experience it’s much easier to just install Linux and use the Snap.

Linux

The easiest way to get Mesmerize is through the Snap Store. You can also install from the GitHub repo.

Snap

Command line snap installation:

sudo snap install mesmerize

After installation simply run mesmerize in the terminal and the application will launch in ~10-30 seconds. Make sure your PYTHONPATH environment variable is empty otherwise it might conflict with the snap:

export PYTHONPATH=

You can also open an ipython console in the snap environment:

mesmerize.ipython

Note

You might get the following warnings when you launch the snap, this is normal. Just be patient and wait a few minutes:

warnings.warn(‘%s%s’ % (e, warn))

/snap/mesmerize/x1/lib/python3.6/site-packages/matplotlib/font_manager.py:281: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.

‘Matplotlib is building the font cache using fc-list. ‘

Bokeh could not be loaded. Either it is not installed or you are not running within a notebook

Loading, please wait…

Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed

Requirements

Make sure you have snapd installed, which is required for running snap apps. Ubuntu 16.04 and later usually come pre-installed with snapd.

You should be able to install snapd through apt for most Debian based distros:

sudo apt update
sudo apt install snapd

Installing snapd on Fedora:

sudo dnf install snapd

To install snapd on other distros please see: https://docs.snapcraft.io/installing-snapd

If you have trouble installing Mesmerize via snap you might need to install core18 first:

sudo snap install core18

Limitations

The snap installation has several limitations, most importantly you will not be able to access arbitrary filesystems. If you need this you will have to install directly from the repo (see From GitHub). If you are able to mount your external filesystem in /media (or wherever your distro places removeable media) then you should be able to access these filesystems if you do the following:

sudo snap connect mesmerize:removable-media

Alternatively you can install the snap in devmode (gives that snap broad access to the system):

sudo snap install mesmerize --devmode

Warning

Analysis graphs do not work in the snap version at the moment.

From GitHub

First, make sure you have compilers & python.

For Debian & Ubuntu based distros

Get build tools and other things:

sudo apt-get install build-essential

For other distros look for the equivalent meta-package that contains gcc, glibc, etc.

If you don’t have python3.6:

sudo apt-get install python3.6

For other distros lookup how to install python3.6 through their package manager.

Install dependencies:

sudo apt-get install qt5-default tcl graphviz git

For other distros these packages probably have the same or similar names.

Create a virtual environment & install Mesmerize

1. Create a virtual environment:

   # Choose a path to house the virtual environment
   python3.6 -m venv /path/to/venv
   

2. Activate the virtual environment:

   source /path/to/venv/bin/activate
   

3. Clone the repo:

   git clone https://github.com/kushalkolar/MESmerize.git
   

4. cd & switch to the snap branch:

   cd MESmerize
   git checkout snap
   

5. Install some build dependencies:

   pip install Cython numpy python-dateutil
   

6. Install remaining dependencies:

   pip install -r requirements.txt
   

7. Build some things:

   python setup.py build_ext -i
   

8. Add to PYTHONPATH environment variable. You will always need to add the path to MESmerize to the PYTHONPATH environment varible before launching.:

   export PYTHONPATH=$PWD:$PYTHONPATH
   

9. Launch:

   python ./mesmerize
   

Mac OSX

This requires Anaconda and will install Mesmerize in an Anaconda environment. Tested on macOS Catalina 10.15.1

Download Anaconda for Python 3: https://www.anaconda.com/distribution/

First make sure you have xcode:

xcode-select --install

This might take a while.

Create an environment & install Mesmerize

1. Create a new environment using python 3.6:

   conda create --name mesmerize python=3.6
   

2. Enter the environment:

   source activate mesmerize
   

3. Install cython, numpy and pandas:

   conda install cython numpy pandas
   

4. Clone the mesmerize repo and enter it:

   git clone https://github.com/kushalkolar/MESmerize.git
   cd MESmerize
   

5. Checkout the snap branch:

   git checkout snap
   

6. Install more dependencies:

   pip install -r requirements.txt
   

7. Install Mesmerize:

   CFLAGS='-stdlib=libc++' python setup.py build_ext -i
   

Launching Mesmerize

1. Export the path to the MESmerize repo directory:

   export PYTHONPATH=<path_to_MESmerize_dir>
   

2. Launch. It may take a few minutes the first time:

   python <path_to_MESmerize_dir>/mesmerize
   

You might get a matplotlib error, if so execute the following which appends the default matplotlib backend-option. Note that this will probably affect matplotlib in all your environments:

echo "backend: qt5" >> ~/.matplotlib/matplotlibrc

Customized

Troubleshooting

Qt version

PyPI