SciPost

The complete scientific publication portal

Dependencies

SciPost is written in Python 3.5 using Django and requires PostgreSQL 9.3 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 will take care of frontend dependencies. To install all packages now run:

(scipostenv) $ npm install

Host-specific settings

In this project, host-specific settings are defined in the scipost-host-settings.json file in the directory above the project root. The structure is as follows:

{
    "SECRET_KEY": "<change_me>",
    "CERTFILE": "none",
    "DEBUG": true,
    "ADMINS": "",
    "ALLOWED_HOSTS": ["localhost", "127.0.0.1"],
    "SESSION_COOKIE_SECURE": false,
    "CSRF_COOKIE_SECURE": false,
    "DB_NAME": "scipost",
    "DB_USER": "scipost",
    "DB_PWD": "",
    "MEDIA_ROOT": "<media_dir>",
    "MEDIA_URL": "/media/",
    "STATIC_URL": "/static/",
    "STATIC_ROOT": "<static_dir>",
    "EMAIL_BACKEND": "django.core.mail.backends.filebased.EmailBackend",
    "EMAIL_FILE_PATH": "<email_dir>",
    "EMAIL_HOST": "",
    "EMAIL_HOST_USER": "",
    "EMAIL_HOST_PASSWORD": "",
    "DEFAULT_FROM_EMAIL": "",
    "SERVER_EMAIL": "",
    "JOURNALS_DIR": "<journals_dir>",
    "CROSSREF_LOGIN_ID": "",
    "CROSSREF_LOGIN_PASSWORD": "",
    "HAYSTACK_PATH": "<haystack_dir>"
}

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 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 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.

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

Project documentation can be found in docs and 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. You may probably need to use the fixture list ["permissions", "groups"] in your tests make sure the permissions groups are working properly. It is recommended, when writing tests for new models, to make use of ModelFactories instead of fixtures to prevent issues with altering fields in the model later on.

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


class VetCommentaryRequestsTest(TestCase):
    fixtures = ['groups', 'permissions']

    def setUp(self):
        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