Developer Note Guide

Overview
Using Curvenote Preview to view a DevNote
Setting up your DevNote
Connecting a Jupyer Notebook to a DevNote
Reference figures in main.md

Overview

This guide will introduce you to Developer Notes (DevNotes) as a way to quickly share ideas and results with the developer community. This guide assumes that you have familiarized yourself with Nucleus Hub (see Nucleus Hub Guide for more information).

Using Curvenote Preview to view a DevNote

From the Launcher window, select the icon for Curvenote Preview.

You will see a window that says ‘Please set your Curvenote token:

Create a Curvenote account

Create a new blank project and click ‘NEXT’

Go to personal settings:

Select ‘API Access’ and click ‘Generate New Token’.

Give the token a useful descrption and select Expiry for the maximum time allowed.

Open a terminal window from the Launcher window and run the command curvenote token set [my-token]

You should see a message that says: Token set for "[curvenote-username]" <curvenote-email-account> at https://api.curvenote.com/login”

You should now be able to view a DevNote by clicking Curvenote Preview from the Launcher window. Note: it may take up to a minute to populate the following viewer window if this is the first time you using the Preview feature.

click the template/ directory.

Congratulations! You should now see a rendered DevNote file:

Setting up your DevNote

In the File Directory (left panel), navigate to the /devnotes/ directory and make a copy of the /template/ directory and rename it. Note: we recommend that you always work off of a copy of the template file and never edit the template file itself so that it can serve as a working reference.

Inspect the output of the directory. In the Launcher Window (Main Panel), click Curvenote Preview and then select your renamed template file.

Change the title and author of your DevNote by opening the file curvenote.yml from the File Directory and modify the corresponding fields:

# Ensure your title is the same as in your `main.md`
  title: "An Unexpected Enzyme in PURE"  
  subtitle: "The enzyme MTHFS is needed for 36 pot PURE"
  description:  
# Add any supporting files to the toc, but ensure that your main manuscript
# is first is the list. The title field is optional.
# Authors should have affiliations, emails and ORCIDs if available
  authors:
    - name: Sam Cell
      email: samcell@bnext.bio
      orcid: 0000-0001-1234-1234
      affiliations:
        - b.next

Connecting a Jupyer Notebook to a DevNote

Navigate to your DevNote’s experimental directory devnotes/my-devnote/experiments/

In your current directory, open a Launcher Window by creating a new tab (”+” button) from the main panel. Click the Template icon, select /analysis/platereader.ipynb, and click GO. Note: there is a working analysis notebook already in the directory to serve as a reference: 20250220-analysis.ipynb.

Link this notebook to your DevNote by including a reference to it in your curvenote.yml file as follows:

# Add any supporting files to the toc, but ensure that your main manuscript
# is first is the list. The title field is optional.
  toc:
    - file: main.md
    - file: ./experiments/experiment-01/my-platereader.ipynb
      title: Analysis Notebook

In the newly created Jupyter Notebook, adjust the paths to your platemap and data file respectively.

Run the notebook cells.

The figure output of a cell can be referenced in two ways. We recommend using both.

Option 1: save the output of a cell to the /analysis/ directory by adding the following code to the end of the cell:

plt.savefig(./analysis/my-fig.png)

Option 2: label the cell by adding the following syntax to the top of the cell:

#| label: fig:name-of-figure

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Note: complete documentation of MyST Markdown is available online

If the output of a cell is a table rather than a figure , it can be referenced as follows:

Label the cell by adding the following syntax to the top of the cell:

#| label: tbl:name-of-table

Reference figures in `main.md`

A figure can be generated in two ways depending on how you want to reference it:

Option 1: reference the saved file:

:::{figure} ./experiments/experiment-01/my-fig.png
:name: name-of-fig
:align: center
:width: 50%

My caption
:::

Option 2: reference the output of a labelled jupyter cell:

:::{figure} #fig:name-of-figure
:kind: table
:name: name-of-fig
:width: 50%

My caption
:::

Multiple figures can be handled elegently by using tabs:

:::::{tab-set}

::::{tab-item} Tab Title 1
:sync: tab1
:::{figure} #fig:name-of-figure-1
:name: name-of-fig-1
:align: center
:width: 50%

My caption 1
:::
::::

::::{tab-item} Tab Title 2
:sync: tab2
:::{figure} ./experiments/experiment-01/my-fig-2.png
:name: name-of-fig-2
:align: center
:width: 50%

My caption 2
:::
::::

:::::

A table output can be included from a labelled jupyter cell as follows:

:::{figure} #tbl:name-of-table
:kind: table
:name: name-of-table

My caption
:::

Figures and tables can be referenced in documents using the following syntax:

This point is illustrated in {ref}`name-of-fig`.

Verify that the changes have been made by clicking Curvenote Preview.

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Note: a complete Curvenote writing guide is available online