Installation

MSNoise is a python package that uses a database (sqlite or MySQL) for storing station and files metadata together with jobs. When installed, it provides a top level command msnoise in the console.

To run MSNoise, you need:

  • A recent version of Python (3.x recommended). We suggest using Anaconda with a few extra modules. MSNoise is tested “continuously” by automatic build systems (TravisCI and Appeveyor) for Python 2.7 and Python 3.5, on Windows, Linux and MacOSX 64 bits systems!
    • Those modules are already distributed with Anaconda:
      • setuptools
      • numpy
      • scipy
      • pandas
      • matplotlib
      • statsmodels
      • sqlalchemy
      • click
      • flask
      • pymysql
      • wtforms
    • Not shipped with Anaconda:
      • obspy
      • flask-admin
      • markdown
      • folium
      • flask-wtf
  • MySQL: if you want to use MySQL, you need to install and configure a MySQL Server beforehand. This is not needed for sqlite. Read About Databases and Performances for more information. We recommend using MySQL.

Full Installation

  1. Download and install Anaconda for your machine, make sure Anaconda’s Python is the default python for your user

  2. Execute the following command to install the missing packages:

    pip install flask-admin flask-wtf markdown folium
    conda install -c conda-forge obspy
    
  3. Install a MySQL server and MySQL Workbench:

    Download and install MySQL Community Server (MySQLs ) and MySQL Workbench (MySQLw ) ; On Windows one can also use the MySQL installer (MySQLi ).

    On Linux, the MySQL server can also be installed using the following command:

    sudo apt-get install mysql-server
    
  4. Create a privileged user and a database:

    • Start MySQL Workbench and connect to the local database
    • Click on “Privileges” and create a new user, with all privileges (Select all). Ideally, create user “msnoise” with password “msnoise”.
  5. Install the latest release version of MSNoise:

    pip install msnoise
    

    Power user could install the development version too, but it is not recommended.

  6. Check which required packages you are still missing by executing the msnoise bugreport command. (See Testing the Dependencies)

  7. To be sure all is running OK, one could start the msnoise test command in an empty directory. This will start the standard MSNoise test suite, which should end with a “Ran xx tests in yy seconds : OK”.

  8. Proceed to the Workflow description to start MSNoise!

Done !

MySQL Server and Workbench

Using the MySQL Server and Workbench is fairly easy and lots of tutorials are available online as text or videos.

Once both are installed, start Workbench and you should see the local MySQL server automatically identified:

_images/workbench_1.png

And by clicking on “Local Instance ...” another tab should open, connected to the local database.

Create a msnoise user

Select “Users and Privileges” in the left sidebar, then “Add Account”. Define the username and the password (msnoise:msnoise could do, although “weak”):

_images/workbench_2.png

Then, under “Administrative Roles”, grant this user the DBA mode (user can perform all tasks on the database server) and click “Apply”.

_images/workbench_3.png

Create an empty database

Each “project” needs a database. That is, if one has two different volcanoes and wants to run MSNoise the two datasets, one needs to create two empty databases.

Click on the “Create new schema” button in the taskbar:

_images/workbench_4.png

and give the database a name (for example msnoise; or msnoise_project1, or project1, or else, you choose) ; and click “Apply”:

_images/workbench_5.png

and click “Apply” again and it should state all is OK:

_images/workbench_6.png _images/workbench_7.png

When done, the database we created is present in the left sidebar:

_images/workbench_8.png

And you’re ready to start your first project: Workflow.

When moving your project to a larger server, HPC or else, just add the connection to this server in Workbench and you’re good to go with the very same interface/tool !

Database Structure –- Tables

MSNoise will create the tables automatically upon running the installer script (see Workflow).

Building this documentation

To build this documentation, some modules are required:

pip install sphinx
pip install sphinx_bootstrap_theme

Then, this should simply work:

make html

it will create a .build folder containing the documentation.

You can also build the doc to Latex and then use your favorite Latex-to-PDF tool.

Using the development version

This is not recommended, but users willing to test the latest development (hopefully stable) version of MSNoise can:

pip uninstall msnoise
pip install http://msnoise.org/master.zip

Please note this version most probably uses the very latest version of every package: Release versions of numpy, scipy, etc obtained from conda-forge and “master” version of obspy. The development version (master) of obspy can be installed from github:

pip uninstall obspy
pip install https://github.com/obspy/obspy/archive/master.zip

If you are using the master version, please use the issue tracker of github to communicate about bugs and not the mailing list, preferably used for Releases.