SciPost

The complete scientific publication portal

Dependencies

SciPost is written in Python 3.5 using Django and requires PostgreSQL 9.4 or higher. Python dependencies are listed in requirements.txt. Frontend dependencies are managed by NPM in package.json.

Getting started

Database

Make sure that Postgres is installed and running, and that a database and user are set up for it. A good guide how to do this can be found here (NOTE: stop before the 'Update settings' part).

Python version

Make sure you're using Python 3.5. If you need to use multiple versions of Python, use pyenv.

Python dependencies

Setup a virtual environment using(py)venv, and activate it:

$ pyvenv scipostenv
$ source scipostenv/bin/activate

Now install dependencies:

(scipostenv) $ pip install -r requirements.txt

Frontend dependencies

NPM (version 4.0 or higher; tested on v4.1.2) will take care of frontend dependencies. To install all packages now run:

(scipostenv) $ npm install

Settings

In this project, most settings are tracked using Git. Some settings however, are still secret are and should stay that way. These settings may be saved into the secrets.json file in the root of the project. The minimum required structure is as follows, please mind the non-empty, but still invalid SECRET_KEY:

{
  "SECRET_KEY": "<key>",
  "DB_NAME": "",
  "DB_USER": "",
  "DB_PWD": ""
}

The settings files itself are saved into SciPost_v1/settings/local_<name>.py. Be sure to wildcard import the base.py file in the top of your settings file. To run the server, one can do it two ways. Either:

(scipostenv) $ ./manage.py runserver --settings=SciPost_v1.settings.local_<name>

...or for convenience export the same settingsfile path to the DJANGO_SETTINGS_MODULE variable, so that one can run the django commands are default:

(scipostenv) $ export DJANGO_SETTINGS_MODULE="SciPost_v1.settings.local_<name>"

One can of course also add the variable to the ~/.bash_profile for convenience.

Check, double check

To make sure everything is setup and configured well, run:

(scipostenv) $ ./manage.py check

Module bundler

Webpack takes care of assets in the scipost/static/scipost/assets folder. To (re)compile all assets into the static_bundles folder, simply run:

(scipostenv) $ npm run webpack

While editing assets, it is helpful to put Webpack in watch mode. This will recompile your assets every time you edit them. To do so, instead of the above command, run:

(scipostenv) $ npm run webpack-live

Sass and bootstrap

Styling will mainly be configured using .scss files in the scipost/static/scipost/scss/preconfig.scss file, relying on Bootstrap 4.0.0-beta.6. A full list of variables available by default can be found here. All modules are configured in the .bootstraprc file. Most modules are disabled by default.

Collectstatic

In order to collect static files from all INSTALLED_APPS, i.e. the assets managed by Webpack, run:

(scipostenv) $ ./manage.py collectstatic

This will put all static files in the STATIC_ROOT folder defined in your settings file. It's a good idea to use the clear option in order to remove stale static files:

(scipostenv) $ ./manage.py collectstatic --clear

Create and run migrations

Now that everything is setup, we can setup the datastructures.

(scipostenv) $ ./manage.py migrate

Create a superuser

In order to use the admin site, you'll need a superuser.

(scipostenv) $ ./manage.py createsuperuser

Create groups and permissions

Groups and their respective permissions are created using the management command.

(scipostenv) $ ./manage.py add_groups_and_permissions

Run development server

You are now ready to run the development server:

(scipostenv) $ ./manage.py runserver

Contributors

Users of the portal are known as Contributors and are created through the registration form accessible from the home page.

You can create a number of users, and use the admin site to give them various permissions through memberships of certain groups. For example, you'll want members of the SciPost Administrators and Editorial Administrators groups in order to access the internal management and editorial tools.

Initial data

If you're working on a (almost) empty database, one can easily fill its test database using one of the built-in commands. To create few instances for each available object, simply run:

(scipostenv) $ ./manage.py populate_db --all

Run the help argument to find arguments to create instances for individual models.

(scipostenv) $ ./manage.py populate_db --help

Maintaining database migratons

Every time fields in any of the models change, a database migration needs to be created and applied. The first documents a database change and its inverse, the second actually changes the database.

Make sure to commit the migration to GIT after applying it, so other developers can use them.

(scipostenv) $ ./manage.py makemigration
(scipostenv) $ ./manage.py migrate

Documentation

All project documentation is gathered from .rst files and code-embedded docstrings. The documentation itself can be found in docs.

Sphinxdoc

The documentation is saved in the local database as a Project with name SciPost (this project should be manually created in the admin under the Sphinxdoc app).

To update the docs, simply run

(scipostenv) $ python3 ../manage.py updatedoc -b scipost

The documentation is then viewable by navigating to docs/.

Locally-served

The documentation can be rendered using Sphinx. Note that rendering documentation is only available from the virtual environment - and only when the host settings have been configured.

To build the documentation, run:

(scipostenv) $ cd docs
(scipostenv) $ make html

After this, generated documentation should be available in docs/_build/html.

Writing tests

It is recommended, when writing tests, to use the ContributorFactory located in scipost.factories. This will automatically generate a related user with Registered Contributor membership. Using the Contributor model in tests requires loading the permissions and groups. Previously, this was done by including fixtures = ["permissions", "groups"] at the top of the TestCase, but since these fixtures behave unpredictable and are a nuisance to keep up to date with the actual groups and permissions, it is much better to call add_groups_and_permissions, located in common.helpers.test, in a function named setUp, which runs before each test. add_groups_and_permissions wraps the management command of the same name.

It is recommended, when writing tests for new models, to make use of ModelFactory instead of fixtures for the same reason.

A basic example of a test might look like:

from django.contrib.auth.models import Group
from django.test import TestCase

from scipost.factories import ContributorFactory
from common.helpers.test import add_groups_and_permissions


class VetCommentaryRequestsTest(TestCase):
    def setUp(self):
        add_groups_and_permissions()
        self.contributor = ContributorFactory(user__password='test123')  # The default password is `adm1n`

    def test_example_test(self):
        group = Group.objects.get(name="Vetting Editors")
        self.contributor.user.groups.add(group)  # Assign user membership to an extra group
        self.client.login(username=self.contributor.user.username, password='test123')

        # Write your tests here

Django-extensions

django-extensions provide added commands like ./manage.py shell_plus, which preloads all models in a shell session. Additional imports may be specified in settings.py as follows:

SHELL_PLUS_POST_IMPORTS = (
    ('theses.factories', ('ThesisLinkFactory')),
    ('comments.factories', ('CommentFactory')),
)