diff options
Diffstat (limited to 'topics')
| -rw-r--r-- | topics/notebooks/binding-lite.gmi | 77 |
1 files changed, 77 insertions, 0 deletions
diff --git a/topics/notebooks/binding-lite.gmi b/topics/notebooks/binding-lite.gmi index 04e4726..6b55cf2 100644 --- a/topics/notebooks/binding-lite.gmi +++ b/topics/notebooks/binding-lite.gmi @@ -16,3 +16,80 @@ We should create this separately from genenetwork because all we want to do is r binding-lite will be packaged in GNU Guix. GeneNetwork will essentially be a 'rebranding' of binding-lite. Later we'll add an API to create notebooks on the fly. That is a separate topic. + +## Background + +The current way of using guix-jupyter is to create a guix environment that contains the guix-jupyter kernel and jupyter. + +The user can then run the `jupyter notebook` command which prints a url to the terminal for the user to copy/paste into the browser. + +Once the url is opened in the browser, a user has to select the guix kernel and choose the notebook from the file manager menu. + +## Initial Design Ideas + +The first goal is to fire up a jupyter notebook from a local git repository. + +Afterwards, this would be implemented with a remote git repository. + +We need a command line interface/tool and guile library to automate the process of opening a jupyter notebook from a local git repository. + +I am tentatively calling this tool `repo2guix`. + +Some of the tasks that `repo2guix` will need to automate is preselecting the guix kernel and opening the browser to the notebook view +of the given url. + +Here is an example of how the command line interface would be used: + +``` +$ repo2guix file:///path/to/<git-repository> + +To access the notebook, open this file in a browser: + file:///path/to/<git-repository> + or copy and paste one of these URLs: + http://localhost:8890/?token=fc21c17b9ec31eddbea28c06ce086cf71b5605a09610439b + or http://127.0.0.1:8890/?token=fc21c17b9ec31eddbea28c06ce086cf71b5605a09610439b +``` + +## Managing Jupyter Notebook Dependencies + +We'll need a manifest.scm file that will specify the dependencies needed by the guix-jupyter notebook. + +Below is an example of the contents of a guix-jupyter notebook repository that can be given to `repo2guix`: + +``` +$ tree <git-repository> +. +├── LICENSE +├── README.md +├── index.ipynb +└── manifest.scm +``` + +An example of the contents of manifest.scm: + +``` +(specifications->manifest + '("python-numpy" + "python-pandas" + "python-matplotlib")) +``` + +## Additional Features and Ideas + +One possibility for easing the creation of a manifest.scm in the notebook repository is to parse the requirements.txt/setup.py, +in the case of a python notebook, and generate the manifest.scm file for the notebook user. + +We would have to write similar manifest generators for Julia and R project dependencies in order to support this feature. + +I will ask on the guix mailing lists for feedback on this idea. + +Once we have this library we can start building binder-lite on top of it. + +## Use Cases + +The use cases for `repo2guix` are driven by the following design decisions: + +1. Automated guix container building guile library to be used by binder-lite. + +2. Manual guix container building and running the container from the command line, + `repo2guix`, by users on their workstations. |