Skip to content

Develop

Included with the codebase is the recommended development environment configured using DevContainer.

Launch Environment

Here are some options that provide a great developer experience:

  • Cloud-based IDE: (recommended)
    • Launch using GitHub Codespaces using the option Create codespace on master in the codebase repository on your fork.
    • Build time for a 2-Core codespace is ~6m. This is done infrequently and cached for convenience.
    • Start time for a 2-Core codespace is ~2m. This will pull the built codespace from cache when you need it.
    • Tip: GitHub auto names the codespace but you can rename the codespace so that it is easier to identify later.
  • Local IDE:
    • Ensure you have Git
    • Ensure you have Docker
    • Ensure you have VSCode
    • Install the Dev Containers extension
    • git clone the codebase repository and open it in VSCode
    • Use the Dev Containers extension to Reopen in Container (More info in the Getting started included with the extension)

You will know your environment has finished loading once you see a terminal open related to Running postStartCommand with a final message: Done.

Features

Once you've successfully launched the development environment, you'll be able to take advantage of our developer tooling to help improve productivity and quality.

Syntax Tests

The following will verify that there are no syntax errors.

flake8 datajoint --count --select=E9,F63,F7,F82 --show-source --statistics

Integration Tests

The following will verify there are no regression errors by running our test suite of unit and integration tests.

  • Entire test suite: 
    nosetests -vw tests_old

    Note: We are in the process of upgrading to pytest tests. To run those, use: 

    pytest -sv --cov-report term-missing --cov=datajoint tests

  • A single functional test: 
    nosetests -vs --tests=tests_old.test_external_class:test_insert_and_fetch

    Note: We are in the process of upgrading to pytest tests. To run those, use: 

    pytest -sv tests/test_connection.py::test_dj_conn

  • A single class test: 
    nosetests -vs --tests=tests_old.test_fetch:TestFetch.test_getattribute_for_fetch1

Style Tests

The following will verify that there are no code styling errors.

flake8 --ignore=E203,E722,W503 datajoint --count --max-complexity=62 --max-line-length=127 --statistics

The following will ensure the codebase has been formatted with black.

black datajoint --check -v

The following will ensure the test suite has been formatted with black.

black tests --check -v

Jupyter

Jupyter notebooks are supported in this environment. This means that when you import datajoint, it will use the current state of the source.

Be sure to see the reference documentation if you are new to running Jupyter notebooks w/ VSCode.

Debugger

VSCode Debugger is a powerful tool that can really accelerate fixes.

Try it as follows:

  • Create a python script of your choice
  • import datajoint (This will use the current state of the source)
  • Add breakpoints by adding red dots next to line numbers
  • Select the Run and Debug tab
  • Start by clicking the button Run and Debug

MySQL CLI

It is often useful in development to connect to DataJoint's relational database backend directly using the MySQL CLI.

Connect as follows to the database running within your developer environment:

mysql -hfakeservices.datajoint.io -uroot -psimple

Documentation

Our documentation is built using MkDocs Material. The easiest way to improve the documentation is by using the docs/docker-compose.yaml environment. The source can be modified in docs/src using markdown.

The docs environment can be run using 3 modes:

  • LIVE: (recommended) This serves the docs locally. It supports live reloading on saves to docs/src files but does not support the docs version dropdown. Useful to see changes live. 
    MODE="LIVE" PACKAGE=datajoint UPSTREAM_REPO=https://github.com/datajoint/datajoint-python.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
  • QA: This serves the docs locally. It supports the docs version dropdown but does not support live reloading. Useful as a final check. 
    MODE="QA" PACKAGE=datajoint UPSTREAM_REPO=https://github.com/datajoint/datajoint-python.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
  • BUILD: This compiles the docs. Most useful for the docs deployment automation. Other modes are more useful to new contributors. 
    MODE="BUILD" PACKAGE=datajoint UPSTREAM_REPO=https://github.com/datajoint/datajoint-python.git HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build

When the docs are served locally, use the VSCode PORTS tab (next to TERMINAL) to manage access to the forwarded ports. Docs are served on port 8080.