gsmo 0.0.13

Commonsense Jupyter/Docker/Git integrations.

gsmo

Commonsense Jupyter/Docker/Git integrations.

gsmo streamlines mounting and working with Git repositories in Docker containers.

A purpose-built Docker image+container are created (see gsmo.yml for configuration options), and Git configs are embedded so that commits inside the Docker container exist outside it (with correct permissions, authorship info, etc.).

Local notebooks or scripts can be executed non-interactively (with results automatically committed to Git), or a Jupyter server or Bash shell can be booted for interactive work.

Usage

gsmo run: execute notebooks non-interactively

gsmo helps run notebooks and scripts in a reproducible fashion (inside Docker containers), and pass-through changes (especially Git commits) to the host machine:

Running:

gsmo run

in a project directory will:

• load configs (gsmo.yml)
• build a Docker image
• run a container from that image
• run the project's run.ipynb notebook inside that container
• Git-commit results

Interactive

Jupyter Server

Build a Docker image from the current directory, and launch a Jupyter server with the current directory mounted (and various Git- and OS-level configs set, so that changes/commits are reflected on the host machine):

gsmo jupyter  # or: gsmo j

• runs at a "random" but stable port (derived from a hash of the module name)
• easily configure Python/Linux environment using gsmo.yml

Bash shell

Build a Docker image from the current directory, and launch a Bash shell with it mounted (and various Git- and OS-level configs set, so that changes/commits are reflected on the host machine):

gsmo sh

Module configuration:

gsmo.yml

When you run gsmo in a directory, it will look for a gsmo.yml file in the current directory with any of the following fields and build a corresponding Docker image:

Docker configs

• name (str; default: project directory's basename): module name; also used as repository for built Docker image
• pip (str or List[str]): pip libraries to install
• apt (str or List[str]): apt libraries to install
• env (str or List[str]): environment variables to set
• env_file (str): file with environment variables
• group (str or List[str]): OS groups to add to the user inside the container
  • paths are accepted, in which case the group that owns that path will be used
• tag (str or List[str]): additional Docker tags within name repository
• mount (str or List[str]): Docker mounts, in several convenient formats:
  • <path>: equivalent to <path>:/<path>; easily pass local project subdirectories into Docker container, e.g. home/.bashrc, etc/pip.conf, etc.
  • standard Docker <src>:<dst> syntax is also supported
  • in all cases, ~ and env vars are expanded
• image (str; default: runsascoded/gsmo:<gsmo version>): base Docker image to build from; <gsmo version> will be the pip version of gsmo that was installed
• root (bool; default False)
  • when set, run as root inside container
  • by default, host-machine uid+gid are used
• dst (str: default /src): path inside container to mount current directory to

gsmo run configs

These configs are passed into the Docker container / pertain to the running of a script or notebook inside the container (see non-interactive mode):

• run (str; default: run.ipynb): notebook to run
• dir (str; default: current directory): resolve paths (incl. mounts) relative to this directory
• yaml (str or List[str]): YAML string(s) with configuration settings for the module being run
• yaml_path (str or List[str]): YAML file(s) with configuration settings for the module being run
• commit (str or List[str]; default: out config dir): paths to Git commit after a run (in non-interactive mode)
• out (str; default nbs): directory to write executed notebooks to

gsmo jupyter configs

Dockerfile

When building the Docker image (in any of the above modes), if a Dockerfile is present in the repository, it will be built and used as the base image (and any gsmo.yml configs applied on top of it).