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Scientific tools for Python

Project description

Welcome to Sciris

What is Sciris?

Glad you asked! Sciris is a flexible open source framework for building scientific web applications using Python and JavaScript. It comes in two parts: sciris is a collection of tools that should make scientific Python coding a more pleasant experience, while scirisweb is a collection of tools that allow you to easily build Python webapps. Sciris is built on Numpy and Matplotlib, while ScirisWeb is built on Vue.js, Flask, Twisted, Redis, and mpld3.

Some highlights of sciris:

  • odict and objdict -- like an OrderedDict, but allows reference by position like a list, as well as many powerful methods (such as casting to array, sorting and enumeration functions, etc.). For example, instead of my_plain_dict[list(my_plain_dict.keys())[0]]['value'], you can use my_obj_dict[0].value.
  • promotetoarray -- standardizes any kind of numeric input to a Numpy array, so e.g. 1, [1], (1,) etc. are all converted to array([1])
  • checktype -- quickly determine the type of the input, e.g. checktype([1,2,3], 'arraylike', subtype='number') # returns True
  • findnearest -- find the element of an array closest to the input value
  • loadobj, saveobj -- flexible methods to save/load arbitrary Python objects
  • vectocolor -- map a given vector into a set of colors
  • gridcolors -- pick a set of colors from maximally distant parts of color-space (e.g. for plots with large numbers of lines)
  • smoothinterp -- linear interpolation with smoothing
  • asd -- adaptive stochastic descent, an algorithm for optimizing functions as few function evaluations as possible

Some highlights of scirisweb:

  • ScirisApp -- a fully featured server that can be created as simply as app = ScirisApp(config) and run with app.run()
  • RPC -- a simple function for defining links between the frontend (web interface) and the backend (server)
  • Datastore -- user and data management based on Redis

I'm not convinced.

That's OK. Perhaps you'd be interested in seeing what a script that performs tasks like parallelization, saving and loading files, and 3D plotting looks like when written in vanilla Python compared to using Sciris.

Is Sciris ready yet?

Yes. Sciris is available for use, but is still undergoing rapid development. We expect an official launch some time during 2020. If you would like us to let you know when this happens, please email info@sciris.org.

Installation and run instructions

5-second quick start guide

  1. Install Sciris: pip install sciris

  2. Use Sciris: import sciris as sc

20-second quick start guide

  1. Download ScirisWeb (e.g. git clone http://github.com/sciris/scirisweb)

  2. Install ScirisWeb (which will install Sciris as well): cd scirisweb; python setup.py develop

  3. Change to the Hello World folder: cd examples/helloworld

  4. Run the app: python app.py

  5. Go to localhost:8080 in your browser

  6. Have fun!

Medium-quick start guide

Note: if you're a developer, you'll likely already have some/all of these packages installed.

  1. Install NodeJS (JavaScript manager)

  2. Install Redis (database)

  3. Install Anaconda Python (scientific Python environment)

  4. Clone and install Sciris: git clone http://github.com/sciris/sciris

  5. Clone ScirisWeb: git clone http://github.com/sciris/scirisweb

  6. Once you've done all that, to install, simply run python setup.py develop in the root folders of sciris and scirisweb. This should install Sciris and ScirisWeb as importable Python modules.

To test, open up a new Python window and type import sciris (and/or import scirisweb)

If you have problems, please email info@sciris.org, or consult the rest of this guide for more information.

Installing on Linux

The easiest way to install Sciris is by using pip: pip install scirisweb (which will also automatically install sciris). If you want to install from source, follow these steps:

  1. Install Git: sudo apt install git

  2. Install NodeJS: sudo apt install nodejs

  3. Install Redis: https://redis.io/topics/quickstart

  4. (Optional) Install Anaconda Python (as of version 0.15, Sciris is only compatible with Python 3), and make sure it's the default Python, e.g.

your_computer:~> python
Python 3.7.4 (default, Aug 13 2019, 20:35:49)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
  1. Clone the Sciris repositories: git clone http://github.com/sciris/sciris.git and git clone http://github.com/sciris/scirisweb.git.

  2. Run python setup.py develop in each of the two Sciris folders.

  3. To test, open up a new Python window and type import sciris and import scirisweb. You should see something like:

>>> import sciris
>>> import scirisweb
>>>

Installing on Windows

Package and library dependencies

Make sure that you have npm (included in Node.js installation) and git installed on your machine.
First, install Anaconda Python. In your Python setup, you also need to have the following packages (instructions in parentheses show how to install with Anaconda Python environment already installed). Note, these should all be installed automatically when you type python setup.py develop and python setup-web.py develop.

Database dependencies

If you use Redis as your DataStore mode, you will need to have Redis installed on your computer (as a service). Redis does not directly support Windows, but there is a MicrosoftArchive page on GitHub where you may go for installation directions on your Windows machine. (For example, it can be installed at this site , downloading a .msi file). It ends up being installed as a service which you can navigate to by going the Windows Task Manager and going to the Services tab. Make sure the Redis service is in the Running state.

Most likely, the directory for your Redis executables will be installed at C:\Program Files\Redis. In that directory, you can double-click the icon for redis-cli.exe to start the redis database command line interface at the default Redis database (#0). You can do keys * to look at all of the store key / value pairs in the database, and exit exits the interface.
Most likely, you will want to use a non-default (i.e. N is not 0) database. To investigate what keys are in, for example, database #2, while you are within redis-cli, you can type select 2 to switch to that database.

Installing on Mac

  1. Install Git. This can be done by installing Xcode commandline tools.

         xcode-select --install
    
  2. Install NodeJS. Visit https://nodejs.org/en/download/ and download the Mac version and install.

  3. Install Redis: https://redis.io/topics/quickstart or run (Assumming brew is installed)

         brew install redis
    
  4. Install Anaconda Python 3, and make sure it's the default Python, e.g.

your_computer:~> python
Python 3.7.4 (default, Aug 13 2019, 20:35:49)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
  1. Create a directory that will hold Sciris. For reference purposes we will create and refer to that directory as pyenv.

  2. Clone the Sciris repository into pyenv: git clone http://github.com/sciris/sciris.git

  3. Create a Python virtual environment (venv) inside the directory of your choice. This will be the parent of the Sciris folder.

     `virtualenv venv`
    

    More information about python virtual environments can be found here The project structure should be as follows;

             -pyenv
                 -venv
                 -sciris
    
  4. Get into the virtual environment. While inside the pyenv folder, to activate the virtual environment, type:

         ./venv/bin/activate
    
  5. Change to the Sciris root folder and type:

    python setup.py develop
    
  6. Repeat in the ScirisWeb root folder:

python setup.py develop
  1. To test if the if everything is working accordingly, open Python window within the virtual environment and type import sciris and import scirisweb. If no errors occur, then the import worked.

Multhreaded deployment

The problem with the simple deployment method described above is that requests are single-threaded. If this is an issue, recommended deployment is using nginx to serve the static files, and gunicorn to run the Flask app. Note that it is common for an application to call several RPCs with each page load. This means that the multithreaded deployment can result in improved site performance even for a single user.

Requirements

You must have nginx (sudo apt install nginx) and gunicorn (pip install gunicorn) installed.

Set up nginx

  1. Copy examples/gunicorn/example_nginx_config to e.g. /etc/nginx/sites-enabled/my_app (can change filename if desired)
  2. Edit the copied file to specify
    • The hostname/URL for the site e.g. my_app.com
    • The full path to the directory containing index.html on the system running nginx
    • Change the port in proxy_pass line if desired - it must match the port in launch_gunicorn
  3. Reload or restart nginx e.g. sudo service nginx reload

For example, this will start it running at localhost:8188:

server {
    listen 8188;
    server_name localhost;
    location / {
        root /home/my_username/my_sciris_app;
    }
    location /api {
        proxy_pass http://127.0.0.1:8097/;
    }
}

Run gunicorn

  1. Copy examples/gunicorn/example_launch_gunicorn to the folder with your app (e.g. launch_my_app_gunicorn), and set the number of workers as desired - usual recommendation is twice the number of CPUs but for applications that are CPU bound (e.g., an RPC call runs a model) then it may be better to reduce it to just the number of CPUs.
  2. The example script references the Flask app using name_of_your_app:flask_app. The name_of_your_app should be importable in Python (either via running Python in the current directory, or installing as a package via pip) and flask_app is the name of a variable containing the Flask application. So for example, you might have a file foo.py containing
app = sw.ScirisApp(__name__, name="My App")
the_app = app.flask_app

in which case the launch_my_app_gunicorn script should contain foo:the_app instead of name_of_your_app:flask_app.

  1. Run launch_my_app_gunicorn. This will need to be kept running to support the site (so run via nohup or screen etc.).

For example:

cd my_app
screen -S my_app_session
./launch_my_app_gunicorn
<you can now close the terminal>

...

<coming back later, you can restart it with>
screen -R my_app_session

Note that for local development, you can add the --reload flag to the gunicorn command to automatically reload the site. This can be helpful if using the nginx+gunicorn setup for local development.

Examples

In the examples and vue_proto_webapps directories are contained a number of working examples of web applications combining Vue, Flask, and Twisted. These are being used as stepping stones for developing the main framework based in user_interface, session_manager, model_code, and bin.

Hello World

A very simple test case of Sciris. In the examples/helloworld folder, type python app.py. If you go to localhost:8080 in your browser, it should be running a simple Python webapp.

See the directions here on how to install and run this example.

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