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MyST Libre

PyPI - Version

Following the REES, myst-libre streamlines building ✨MyST articles✨ in containers.

  • A repository containing MyST sources
  • A Docker image (built by binderhub) in a public (or private) registry, including:
    • Dependencies to execute notebooks/markdown files in the MyST repository
    • JupyterHub (typically part of images built by binderhub)
  • Input data required by the executable content (optional)

Given these resources, myst-libre starts a Docker container, mounts the MyST repository and data (if available), and builds a MyST publication.

Note

This project was started to support publishing MyST articles as living preprints on NeuroLibre.

Installation

External dependencies

Important

Ensure the following prerequisites are installed:

Install myst-libre

pip install myst-libre

Set up environment variables:

If you are using a private image registry, create a .env file in the project root and add the following:

DOCKER_PRIVATE_REGISTRY_USERNAME=your_username
DOCKER_PRIVATE_REGISTRY_PASSWORD=your_password

Quick Start

Import libraries and define REES resources

from myst_libre.tools import JupyterHubLocalSpawner, MystMD
from myst_libre.rees import REES
from myst_libre.builders import MystBuilder

rees_resources = REES(dict(
                  registry_url="https://your-registry.io",
                  gh_user_repo_name = "owner/repository",
                  gh_repo_commit_hash = "full_SHA_commit_A",
                  binder_image_tag = "full_SHA_commit_A_or_B",
                  dotenv = '/path/to/dotenv'))

Note

Currently, the assumption is that the Docker image was built by binderhub from a REES-compliant repository that also includes the MyST content. Therefore, binder_image_tag and gh_repo_commit_hash are simply two different commits in the same (gh_repo_user_name) repository. However, binder_image_tag is not allowed to be ahead of gh_repo_commit_hash.

Fetch resources and spawn JupyterHub in the respective container

hub = JupyterHubLocalSpawner(rees_resources,
                             host_build_source_parent_dir = '/tmp/myst_repos',
                             container_build_source_mount_dir = '/home/jovyan', #default
                             host_data_parent_dir = "/tmp/myst_data", #optional
                             container_data_mount_dir = '/home/jovyan/data', #optional
                             )
hub.spawn_jupyter_hub()
  • MyST repository will be cloned at:
tmp/
└── myst_repos/
    └── owner/
        └── repository/
            └── full_commit_SHA_A/
                ├── myst.yml
                ├── _toc.yml
                ├── binder/
                │   ├── requirements.txt (or other REES dependencies)
                │   └── data_requirement.json (optional)
                ├── content/
                │   ├── my_notebook.ipynb
                │   └── my_myst_markdown.md
                ├── paper.md
                └── paper.bib

Repository will be mounted to the container as /tmp/myst_repos/owner/repository/full_commit_SHA_A:/home/jovyan.

  • If a repo2data manifest is found in the repository, the data will be downloaded to and cached at:
tmp/
└── myst_data/
    └── my-dataset

otherwise, it can be manually defined for an existing data under /tmp/myst_data as follows:

rees_resources.dataset_name = "my-dataset"

In either case, data will be mounted as /tmp/myst_data/my-dataset:/home/jovyan/data/my-dataset. If no data is provided, this step will be skipped.

Build your MyST article

MystBuilder(hub).build()

Check out the built document

In your terminal:

npx serve /tmp/myst_repos/owner/repository/full_commit_SHA_A/_build/html

Visit ✨http://localhost:3000✨.

Table of Contents

Usage

Authentication

The Authenticator class handles loading authentication credentials from environment variables.

from myst_libre.tools.authenticator import Authenticator

auth = Authenticator()
print(auth._auth)

Docker Registry Client

The DockerRegistryClient class provides methods to interact with a Docker registry.

from myst_libre.tools.docker_registry_client import DockerRegistryClient

client = DockerRegistryClient(registry_url='https://my-registry.example.com', gh_user_repo_name='user/repo')
token = client.get_token()
print(token)

Build Source Manager

The BuildSourceManager class manages source code repositories.

from myst_libre.tools.build_source_manager import BuildSourceManager

manager = BuildSourceManager(gh_user_repo_name='user/repo', gh_repo_commit_hash='commit_hash')
manager.git_clone_repo('/path/to/clone')
project_name = manager.get_project_name()
print(project_name)

Module and Class Descriptions

AbstractClass

Description: Provides basic logging functionality and colored printing capabilities.

Authenticator

Description: Handles authentication by loading credentials from environment variables.
Inherited from: AbstractClass
Inputs: Environment variables DOCKER_PRIVATE_REGISTRY_USERNAME and DOCKER_PRIVATE_REGISTRY_PASSWORD

RestClient

Description: Provides a client for making REST API calls.
Inherited from: Authenticator

DockerRegistryClient

Description: Manages interactions with a Docker registry.
Inherited from: Authenticator
Inputs:

  • registry_url: URL of the Docker registry
  • gh_user_repo_name: GitHub user/repository name
  • auth: Authentication credentials

BuildSourceManager

Description: Manages source code repositories.
Inherited from: AbstractClass
Inputs:

  • gh_user_repo_name: GitHub user/repository name
  • gh_repo_commit_hash: Commit hash of the repository

JupyterHubLocalSpawner

Description: Manages JupyterHub instances locally.
Inherited from: AbstractClass
Inputs:

  • rees: Instance of the REES class
  • registry_url: URL of the Docker registry
  • gh_user_repo_name: GitHub user/repository name
  • auth: Authentication credentials
  • binder_image_tag: Docker image tag
  • build_src_commit_hash: Commit hash of the repository
  • container_data_mount_dir: Directory to mount data in the container
  • container_build_source_mount_dir: Directory to mount build source in the container
  • host_data_parent_dir: Host directory for data
  • host_build_source_parent_dir: Host directory for build source

MystMD

Description: Manages MyST markdown operations such as building and converting files.
Inherited from: AbstractClass
Inputs:

  • build_dir: Directory where the build will take place
  • env_vars: Environment variables needed for the build process
  • executable: Name of the MyST executable (default is 'myst')