Contributing to CATMAID

CATMAID is open source software and welcomes contributions. This document provides a brief overview of the structure of CATMAID and guidelines contributing developers follow to help keep the codebase easy to understand and easy to extend.

If you are considering contributing a feature to CATMAID, you can get guidance from other active developers through the CATMAID mailing list and GitHub repository. Always check the list of open issues as there may be valuable discussion relevant to your plans.

Before developing any features you should follow the basic installation instructions to set up your development environment.

Architecture Overview

CATMAID is a distributed client-server application. The backend HTTP API, hosted by the server, retrieves and stores information about projects, image stacks, and annotations. The client frontend, which runs in the browser, provides an interface and suite of analysis tools which interact with the backend’s HTTP API. The frontend also has its own APIs which allow new tools to be quickly constructed or expert users to perform novel analysis using the browser console.

The backend is written primarily in Python 2.7 using the Django web framework. Annotations and metadata about stacks are stored in a PostgreSQL database. Most endpoints in the backend API expect and return JSON.

The frontend is written primarily in Javascript and makes use of a several external libraries. Most interfaces are built dynamically through Javascript; few HTML templates are used.

_images/architecture.svg

A core philosophy of this architecture is to keep the backend API fast and minimal. The primary purpose of the backend is to mediate the database. Complex analysis and data processing is performed on the client whenever possible. This allows large scale collaboration with constrained server resources. Distributing computation this way also exploits CATMAID’s implementation choices, as modern Javascript VMs are typically much faster than Python.

CATMAID is not an image host. Rather, the CATMAID backend provides resource, spatial, and semantic metadata about image stacks hosted elsewhere, while the CATMAID frontend is capable of rendering and navigating these image stacks. More information about the types of image hosts CATMAID supports is available in the tile source conventions documentation.

Project Organization

Code you are likely to be interested in is under the django folder in the repository root. The sections below outline basic folder, file, and module structure for the backend and frontend, as well as primers on a few common data structures.

Backend

All of the relevant backend code is in the django/applications/catmaid folder. Within this folder, models.py defines the database schema and logical objects on which the back API operates, while urls.py maps URI endpoints in the API to Python methods. Both are useful starting points when locating particular functionality or determining where to add new functionality. In case an endpoint changes data, a transaction log entry is added. This way semantic information can be linked to individual database changes.

Most of the API routes to the catmaid.control module and folder. Within this module API functions are organized into logical units like skeleton or connector, which are grouped into corresponding Python modules. These often contain utility functions not exposed by the API that may be useful, so when developing a new API endpoint be sure to check related modules for reusable utilities.

Back-end errors should always be signaled to the front-end with the help of Exceptions. Regardless whether an argument is missing, permissions are lacking or something went wrong otherwise. A dedicated middleware will catch them and return them in an expected format to the front-end.

Frontend

If developing frontend functionality, a good strategy is to start by running scripts in the browser console to quickly prototype and become familiar with client APIs. The scripting wiki provides an introduction to these APIs and snippets for common scripting tasks.

Javascript source files should be placed in the django/applications/catmaid/static/js folder. External libraries are located in the django/applications/catmaid/static/libs folder, although there is also a special CATMAID library for shared, stable components. Javascript and CSS assets from these locations are managed by django-pipeline. When you add a Javascript file to the static/js folder and then run:

./manage.py collectstatic -l

from the project folder, pipeline detects these assets, compiles and compresses them (if configured to do so), then passes them to Django to be linked from the configured static server directory. Assets for this pipeline are configured in django/projects/mysite/pipelinefiles.py. Source files placed in static/js will be detected automatically, but any external libraries added to the static/libs folder must also be added to pipelinefiles.py.

Within the static/js folder and within the CATMAID frontend there is a distinction between tools and widgets. A tool contains a suite of annotations, interfaces and analyses. A widget, meanwhile, provides a single specific interface. Most likely you are familiar with a single tool in CATMAID, the tracing tool, but many widgets within the tracing tool, such as the 3D viewer, connectivity widget, and selection table.

Widgets are generally prototyped objects that extend InstanceRegistry, which provides an easy means to track open instances of a particular widget. Rather than construct their own DOM, most widgets’ DOM is built by a corresponding method in WindowMaker. WindowMaker binds events from the DOM it constructs to relevant handlers in the widget object.

Code Style and Conventions

Over the history of its development, CATMAID has accumulated a mixture of many coding styles. To improve the consistency and clarity of code going forward, as well as to prevent some common technical pitfalls, the core developers now follow some simple guidelines for new code. These guidelines are relaxed and permissive.

If modifying existing code, feel free to imitate the style of the surrounding code if it conflicts with these guidelines.

Python

CATMAID does not currently adhere to a specific Python style convention like PEP8. However, code should still follow common Python conventions and idioms including:

  • 4 spaces (not tabs) for indentation
  • Maximum line length of 79 characters for comments
  • Maximum line length of 120 characters for code
  • PEP8 naming conventions

All new code should include docstrings that follow PEP257 and use Google’s argument formatting.

HTTP API

Documentation for endpoints exposed by the HTTP API is available from the CATMAID server itself via the /apis/ page:

http://localhost:8000/apis/

... or, for custom configurations:

http://<catmaid_servername>/<catmaid_subdirectory>/apis/

Functions that are exposed as HTTP API endpoints should declare what HTTP methods they accept using the @api_view decorator. Endpoints’ docstrings should define what parameters they accept and the strucuture of their response in Swagger spec using django-rest-swagger’s YAML hooks:

@api_view(['GET', 'POST'])
def api_endpoint(request):
    """Short endpoint description.

    Longer description of the endpoint's purpose, expectations and behavior.

    This endpoint returns an array of objects, so the model of the objects
    in the array must be specified in a separate ``model`` stanza.
    ---
    parameters:
        - name: resource_id
          description: ID of a resource.
          required: true
          type: integer
          paramType: form
    models:
      api_endpoint_inner_type:
        id: api_endpoint_inner_type
        properties:
          name:
            description: Name of some example type that this endpoint
            type: string
            required: true
    type:
    - type: array
      items:
        $ref: api_endpoint_inner_type
      required: true
    """
    #...

API URLs should prefer plural resource names and use hyphens rather than underscores. Non-terminal endpoint paths that represent resources should have a trailing slash, e.g., GET http://localhost/{project_id}/skeletons/, but not terminal operations on that resource collection like GET http://localhost/{project_id}/skeletons/review-status.

Parameters that are not resource identifiers should be passed as query or form parameters, not in the URL path. If an endpoint accepts an array of parameters, it should support receiving the array encoded as JSON; form array parameters may be accepted, but a JSON array in a single form parameter must be accepted for ease of use.

Prefer descriptive, consistent names for parameters. For example, an endpoint receiving a list of skeleton identifiers should prefer a parameter named skeleton_ids over skids or ids; a few bytes in the header are not going to have a performance impact relative to the packaging of HTTP and transport, much less when HTTP/2 and modern compression-aware browsers are involved. However, abbreviated property names or array-packed values are acceptable for the responses of performance-critical endpoints.

Date and time response values should be in UTC and formatted as ISO 8601.

Endpoints containing write operations should be decorated with a record_view decorator in urls.py, which expects a label as argument. This label should follow the pattern resource.action and just like URI itself, the resource is expected to be in its plural form. Make sure to follow this convention for new endpoints.

Javascript

New code in CATMAID is styled similar to the Google Javascript style guide, with notable exceptions that:

  • CATMAID does not use any Google libraries
  • CATMAID does not use any requirements/dependency libraries
  • CATMAID uses CamelCase namespace naming

New javascript files should place all code inside an IIFE to namespace it inside the CATMAID object and use ES5 strict mode:

(function (CATMAID) {

  "use strict";

  var variableNotExposedOutsideFile;

  var ClassExposedOutsideFile = function () {
    //...
  };

  CATMAID.ClassExposedOutsideFile = ClassExposedOutsideFile;

})(CATMAID);

This prevents unintentional leaking of variables into the global scope and possible naming conflicts with other libraries.

CATMAID makes full use of ES5 language features and allows the following ES6 features:

  • Promises
  • Maps and Sets (IE11-supported get, has, set, delete and forEach only)
  • const and let declarations (in strict mode contexts only)

All features must work correctly in recent versions of Chrome and Firefox, while core browsing features must work in IE11. Requiring polyfills for IE is acceptable.

Git

Try to follow the seven rules of great git commit messages:

  1. Separate subject from body with a blank line
  2. Limit the subject line to 50 characters
  3. Capitalize the subject line
  4. Do not end the subject line with a period
  5. Use the imperative mood in the subject line
  6. Wrap the body at 72 characters
  7. Use the body to explain what and why vs. how

That said, always prefer clarity over dogma. The core CATMAID contributors break #2 frequently to keep messages descriptive (apologies to our VAX users). If a commit focuses on a particular component or widget, prefix the commit message with its name, such as “Selection table:” or “SVG overlay:”.

Granular commits are preferred. Squashes and rollups are avoided, and rebasing branches then fast-forwarding is preferred over merge commits when merging, except for large feature branches.

Development occurs on the dev branch, which is merged to master when a release is made. It is usually best to develop new features by branching from dev, although critical fixes or extensions to particular releases can be based on master or the appropriate release tag.

Never rewrite history of master, dev, or any other branch used by others.

Linting and Testing

As part of the continuous integration build, several automated processes are performed to help verify the correctness and quality of CATMAID:

If you enable Travis-CI for your fork of CATMAID on GitHub, Travis will run all of these checks automatically. However, Travis builds take a long time, and you may want feedback before committing and pushing changes. Luckily all of these checks are easy to run locally.

Django tests are run through Django’s admin commands:

cd /<path_to_catmaid_install>/django/projects
./manage.py test catmaid.tests

JSHint can be installed from NPM or your platform’s package manager and should use CATMAID’s config settings:

cd /<path_to_catmaid_install>
jshint --config=.travis.jshintrc --exclude-path=.travis.jshintignore django/applications

If you do not want to configure your own JSHint settings, you can set these as defaults:

ln -s .travis.jshintrc .jshintrc
ln -s .travis.jshintignore .jshintignore
jshint django/applications

CSS linting is performed by running csslint from the static CSS directory:

cd django/applications/catmaid/static/css
csslint .

QUnit tests can be run from the browser while your Django server is running. For example, with the default configuration this would be:

http://localhost:8000/tests

... or, for custom configurations:

http://<catmaid_servername>/<catmaid_subdirectory>/tests

Documentation

In addition to the backend, HTTP API, and frontend documentation mentioned above, CATMAID provides a general documentation manual for users, administrators, and developers (including this page) and in-client documentation for keyboard shortcuts and widget help.

General Documentation

General documentation is part of the CATMAID repository under the sphinx-doc folder. This documentation is written in Sphinx ReStructured Text. Documentation from commits pushed to the official CATMAID repository are built by Read the Docs and hosted at catmaid.org.

To build the general documentation from within your pip virtualenv, run:

cd sphinx-doc
make html

The built documentation is now in sphinx-doc/build/html/index.html.

In-Client Documentation

Documentation is provided from within the web client through tool-scoped mouse and keyboard shortcut documentation (accessed by pressing F1) and per-widget help accessible through the question mark icon in the title bar of some widgets.

If you find that widget help documentation is missing, incomplete, confusing, or incorrect, you can contribute better documentation by creating an issue on GitHub or editing the helpText property of the widget and creating a pull request.

Other Policies

Security

The disclosure policy of the CATMAID developers for vulnerabilities is that arbitrary SQL execution by anonymous users or users with “browse” permissions must be notified to the mailing list simultaneous with patch publication. Vulnerabilities only exploitable by users with “annotate” permissions will be noted in the release changelog but will not be sent to the mailing list.