nextstrain-cli

This is the Nextstrain command-line tool. It aims to provide access to Nextstrain components in a local environment with a minimum of fuss.

You can use it to run a pathogen build which makes use of components like sacra, fauna, and augur or view the results of such a build in our standard viewer, auspice.

If you're unfamiliar with Nextstrain builds, you may want to follow our quickstart guide first and then come back here.

Usage

This package provides a nextstrain program which provides access to a few commands. If you've installed this package (nextstrain-cli), you can just run nextstrain. Otherwise, you can run ./bin/nextstrain from a copy of the source code.

usage: nextstrain [-h]
                  {build,view,deploy,remote,shell,update,check-setup,version}
                  ...

Nextstrain command-line tool

optional arguments:
  -h, --help            show this help message and exit

commands:
  {build,view,deploy,remote,shell,update,check-setup,version}
    build               Run pathogen build
    view                View pathogen build
    deploy              Deploy pathogen build
    remote              Upload, download, and manage Nextstrain files on
                        remote sources.
    shell               Start a new shell in the build environment
    update              Update your local image copy
    check-setup         Test your local setup
    version             Show version information

For more information on a specific command, you can run it with the --help option, for example, nextstrain build --help.

Installation

Python 3.5 or newer

This tool is written in Python 3 and requires at least Python 3.5. There are many ways to install Python 3 on Windows, macOS, or Linux, including the official packages, Homebrew for macOS, and the Anaconda Distribution. Details are beyond the scope of this guide, but make sure you install Python 3.5 or higher. You may already have Python 3 installed, especially if you're on Linux. Check by running python --version or python3 --version.

nextstrain-cli

With Python 3 installed, you can use pip to install the nextstrain-cli package:

$ python3 -m pip install nextstrain-cli
Collecting nextstrain-cli
[…a lot of output…]
Successfully installed nextstrain-cli-1.6.1

After installation, make sure the nextstrain command works by running nextstrain version:

$ nextstrain version
nextstrain.cli 1.6.1

The version you get will probably be different than the one shown in the example above.

Docker

This tool also currently requires Docker, which is freely available. On Windows or a Mac you should download and install Docker Desktop (also known as "Docker for Mac" and "Docker for Windows"). On Linux, your package manager should include a Docker package.

After installing Docker, run nextstrain check-setup to ensure it works:

$ nextstrain check-setup
nextstrain-cli is up to date!

Testing your setup…

✔ docker is installed
✔ docker run works

All good!

If the final message doesn't indicate success (as with "All good!" in the example above), something may be wrong with your Docker installation.

Big picture

The Nextstrain CLI glues together many different components with an easy-to-use interface that doesn't require a lot of fussing. Below is a brief overview of the big picture:

Development

Development of nextstrain-cli happens at https://github.com/nextstrain/cli.

We currently target compatibility with Python 3.5 and higher. This may be increased to 3.6 in the future.

Versions for this project follow the Semantic Versioning rules.

Running with local changes

From within a clone of the git repository you can run ./bin/nextstrain to test your local changes without installing them. (Note that ./bin/nextstrain is not the script that gets installed by pip as nextstrain; that script is generated by the entry_points configuration in setup.py.)

Releasing

New releases are made frequently and tagged in git using a signed tag. The source and wheel (binary) distributions are uploaded to the nextstrain-cli project on PyPi.

There is a ./devel/release script which will prepare a new release from your local repository. It ends with instructions for you on how to push the release commit/tag and how to upload the built distributions to PyPi. You'll need a PyPi account and twine installed.

Type annotations and static analysis

Our goal is to gradually add type annotations to our code so that we can catch errors earlier and be explicit about the interfaces expected and provided. Annotation pairs well with the functional approach taken by the package.

During development you can run static type checks using mypy:

$ mypy nextstrain
# No output is good!

There are also many editor integrations for mypy.

Note that our goal of compatibility with Python 3.5 means that type comments are necessary to annotate variable declarations:

# Not available in Python 3.5:
foo: int = 3

# Instead, use trailing type hint comments:
foo = 3  # type: int

The typing_extensions module should be used for features added to the standard typings module after 3.5. (Currently this isn't necessary since we don't use those features.)

We also use Flake8 for some static analysis checks focusing on runtime safety and correctness. You can run them like this:

$ flake8
# No output is good!