Maximum likelihood dating and ancestral sequence inference

This is an experimental merge and remix of

• neherlab/treetime
• neherlab/treetime_web
• neherlab/treetime_examples

built with containerized miniservice architecture in mind.

• Table of contents
• Getting started
  • TL;DR
  • Architecture
  • Directory structure
    • Legend
  • Development setup
    • 0. Clone git repository
    • 1. Install requirements
    • 2. Setup the environment
    • 3. Launch
    • 4. Testing
    • 5. Linting (static analysis)
    • 6. Code style
• Production setup
• Release setup
• Continuous integration, deployment
• Code of conduct
• Contributing
• License

If you share Kevin's "Small talk" philosophy

then just copy this into your terminal window:

git clone --recursive https://github.com/ivan-aksamentov/treetime-monorepo
cd treetime-monorepo
tools/ubuntu-install-docker # if you don't have docker installed yet
cp .env{.example,}
yarn dev

otherwise, follow the Development setup section.

You can read about the architecture of the application, as well as about included services and their functions here: docs/architecture

Take a quick look if you are a new developer!

This section describes what you can find in the repository and where.

As a user you don't really need to worry about this repository, but you may find examples/ (📘) and docs/ (📘) directories useful.

As a developer you are most likely interested in the actual source code (⭐) or configuration files (🛠️).

• ⭐ - source code (start browsing here!)
• ☁️ - implements a service
• ⚙️ - contains configuration or infrastructure setup
• ⏰ - temporary
• 📘 - contains learning materials
• 📚 - implements a library
• ♻️ - safe to delete
• 🛠️ - useful tools

This section describes how to run the application in development mode. You need this as a developer, in order to develop and test new features and bug fixes.

git clone --recursive https://github.com/ivan-aksamentov/treetime-monorepo

Currently, the following are required to be installed on host machine:

• docker version 19 or higher
• docker-compose version 1.24 or higher
• Node.js version 10 or higher (nvm installer is recommended)
• yarn

The recommended developer tools also include:

• lazydocker - to manage containers from a terminal-based UI
• ctop - to monitor performance characteristics of running containers

ℹ️ As of right now, the only supported host OS is Ubuntu 18.04 LTS.

ℹ️ Directory tools/ contains, among others, the following utility scripts:

• tools/ubuntu-install-docker - installs docker and docker-compose, adds current user to docker group.

  ⚠️ This script requires superuser privileges.

  ⚠️ This script modifies the system. Make sure you understand what it does before running it!

• tools/ubuntu-install-node - installs nvm, Node.js and yarn

• tools/ubuntu-install-lazydocker - installs lazydocker

• tools/ubuntu-install-ctop - installs ctop

ℹ️ Node.js and yarn are currently only used to run npm scripts, which further run services through docker-compose. Yarn scripts are likely to be replaced (probably with a Makefile), then the dependency on Node.js can be dropped.

Create a .env file with desired environment configuration. If not sure, just copy the example one:

cp .env.example .env

it contains sane defaults which should be good enough to kick-start local development. Modify as needed.

ℹ️ Don't forget to update .env file every time you pull changes to the .env.example

⚠️ .env file may contain passwords, API keys and other secrets, especially in production environment. Keep these in a safe place!

⛔ Never commit your .env file into source control! Instead, modify .env.example file as a reference for other developers and for production environment.

From project root run:

yarn dev

This will bring up a set of services in development mode, as described in docker-compose file at docker/docker-compose.dev.yml. In development mode this will ensure that the necessary container images are built or pulled from Docker Hub and that all containers are started, and their corresponding services are built and ran.

Watch for treetime-web build, as it is the one that takes the longest. Once the build is done, web client will be listening on http://localhost:8080 (by default, can be modified in .env file).

On code changes, most of the services will either be automatically restarted or will have relevant modules hot reloaded. It is almost never necessary to restart any of the services. If you find yourself in need to selectively restart a particular service, use docker-compose CLI. Or, even better, lazydocker.

Press Ctrl+C to bring all the running services down.

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