eLife python project POC

The purpose of this project is to create a template for other python projects.

The idea is to create a list of guidelines that all projects try should follow. This should help to standardise projects and make them easy to use and contribute to.

Ideally repositories should:

have a basic description about its purpose/function
be easy to run
be easy to test
be easy to debug
be containerised
be tidy (minimal amount of files in project root)

Dependencies

Docker

Getting started

This project provides a Makefile with short commands to run common tasks.

make help

Run this for a full list of commands.

make start

This command will build and/or run the site locally configured for development purposes.

make stop

Use this command to stop containers and clean up any anonymous volumes.

Running the tests

make tests

Use this command to run unit tests.

make checks

Use this command to run static checks such as: mypy, flake8, pylint.

make all-tests

Combines the two commands above by running all checks followed by unit tests

Adding and removing dependencies

The following commands update files that keep track of project dependencies.

make build

Run this if you would like to persist changes to dependencies to your docker container.

make dependency package=<package name>
make dev-dependency package=<package name>

# examples:
make dependency package=flask
make dependency package=flask==1.0.2
make dev-dependency package=pytest

Run either of these commands to add a python package as a project dependency or development dependency alike. You can specify just the package name to get the latest version or specify a specific version number.

make remove-dependency package=<package name>
make remove-dev-dependency package=<package name>

Run either of these commands to remove dependencies accordingly.

Other useful commands

make run

Use this command to only run the python service. It is possible to use pdb breakpoints with this configuration.

make shell

Use this to run the python container that would run the application and enter a bash prompt.

make dependency-tree
# or
make d-tree

Use this to display a dependency tree

make fix-imports