notebook

This repository provides the framework for creating a digital notebook based on a jekyll blog. My intention is for this notebook to be run as a local server, with each jekyll post corresponding to a traditional notebook entry. The notebook is fully searchable, using the client-side search library lunr.js.

Set up

Install jekyll and git then clone this repository:

$ git clone https://github.com/niklasbt/notebook

Then simply navigate to the folder where the local version of this repo is and run jekyll serve to launch the server, which is found at http://127.0.0.1:4000.

Organization

The landing page of the notebook at index.html serves as a brief table of contents, displaying the most recent five notebook entries. The full table of contents can be accessed on the TOC page at contents.html. Additionally, entries can be grouped into projects, which are listed at projects.html.

Creating projects and entries

At the moment, I envision a workflow based around projects, where each entry is assigned to a particular project. Project and entry creation is centralized in the helper script note.py, which calls upon the content creation scripts in the lib folder.

When you create a project, the program will ask for a project name (name), a project nickname (short_name; which is the tag used to label entries as belonging to the project), and a short project description. This will create a project file _projects/short_name.md, which will be listed under the Projects page in the notebook.

Alternatively, when creating a new entry, you can choose option 0: New project to create a new project along with its first entry. New entries assigned to existing projects as well. When creating an entry, the program will ask for a long and a short title for the entry (title and short_title), and will automatically create the markdown file _posts/YYYY-MM-DD-short_title.md.

Templates

You can also create custom entry templates, if you plan on creating cookiecutter-type entries. Simply write a markdown file with the desired boilerplate and then select 2: New template, from note.py, which will create a template script in lib/templates that will be appended to the list of available templates when creating entries.

Alternatively, you can create your own template manually and save it in the lib/templates folder. The template must be a python script containing the get_body() function (which is called by lib/entry.py):

def get_body():
    body = []
    ### Customization here #####################################################
    # body must be a list of strings, to be written to the output file

    ### Customization end ######################################################
    return(body)

An example of a more complex template file is provided in lib/templates/reaction.py, which is a use case I find typical in my synthetic chemistry workflow. You can, of course, create templates for whatever use case, as long as the template returns in body a list of strings to be appended to the entry file.