RTN-045: Guidelines for User Tutorials

  • The Rubin Observatory Community Science Team

Latest Revision: 2023-09-27

1 Abstract

This document provides guidelines for anyone creating or updating the tutorials produced and maintained by the Vera C. Rubin Observatory Community Science Team (CST). This includes all community-facing demonstrations made by CST members of how to use the Rubin Science Platform (RSP) or how to analyze Legacy Survey of Space and Time (LSST) data. Formatting, editorial standards, workflow, and review policies are provided.

The CST uses these guidelines in the Documentation for Data Preview 0.2 (DP0.2), the Documentation for Data Preview 0.3 (DP0.3), and GitHub tutorial-notebooks repository. Members of the Rubin Observatory staff, as well as the broad community, are encouraged to contribute to the tutorial documentation.

2 Pedagogical principles

All tutorials should have the following attributes.

2.1 Inclusive

Follow the best practices described under Accessibility considerations.

Offensive or exclusionary language is never permitted (e.g., violent or ableist terms). Ensure jargon and acronyms are defined, regardless of target audience.

See the Rubin Observatory Communications Code of Conduct for additional guidance.

2.2 Level-appropriate

Tutorials should clearly identify and teach to their target audience: beginner, intermediate, or advanced.

2.3 Skill-focused

Tutorials should focus on teaching one or a few new skills or techniques, or providing one scientific demonstration.

2.4 Consumable

The user should be able to work through the core contents of a tutorial within about 30 minutes (i.e., not including any additional suggested “Exercises for the learner”).

2.5 Well-documented

High-quality documentation should be provided with the tutorial, including narrative descriptions, citations, references, and external links to, e.g., package documentation.

2.6 Clearly-written

Tutorials should write in short, clear statements describing the actions a user should take and the expected results. Aside from introductory or background information, instructional text should be written in the imperative mood, as is commonly adopted for technical writing.

2.7 Cross-referenced

Tutorials should reference any precursor or advanced tutorials that users should consider as prerequisites or follow-up resources.

2.8 Proper credits

Appropriate acknowledgments should be provided to credit individuals whose notebooks were used as examples, and to set a precedent of prioritizing credits in an openly collaborative environment. Authors should cite other scientists or papers within the text of the tutorial where appropriate.

3 Jupyter notebook format, style, and code standards

3.1 Template

As a starting point, use the template Jupyter notebook in the cet-dev repository, which is part of the rubin-dp0 GitHub Organization. The template contains an example of the header and the mandatory first section described below.

3.1.2 First section

The structure of the first section is mandatory, and all of the following is already set up in the template.

Provide a brief narrative about this notebook, e.g., “This notebook will teach the user…”. Cite or link to any external information or documentation, and cross-reference to other notebooks.

The first subsection should always be 1.1 Import packages. It should have a markdown cell that provides explanations and/or links to external package documentation, as appropriate. All package imports must be done in the first code cell.

The second subsection should always be 1.2 Define functions and parameters. Globally defined utility functions, classes, plotting defaults, or constants should be here. (Single-use functions or classes can be defined immediately before they are used; see the section on functions and classes below).

If a notebook has no functions or parameters to define, it is preferred to leave this subsection header in the document and state that no additional functions and parameters are used.

If a notebook has many such things to define, it is acceptable to rename the subsection to be more specific to the notebook, and/or to use sub-subsections like 1.2.1 Define global cosmological parameter values or 1.2.2 Define a function to make an image cutout.

3.1.3 Section structure

For all sections after the first, use numbers for sections, subsections, and sub-subsections to enable referencing in support requests, e.g., “I’m having trouble with the second code cell in Section 2.3.”

Use section titles that actively describe what is being done, e.g., 2.2 Create a color-magnitude diagram instead of 2.2 Plot, so that the auto-generated table of contents is easy to navigate.

Do not use title case for section headings; use sentence case.

It is very common, but not mandatory, to end all notebook tutorials with a section called Exercises for the learner with suggestions of how the user can make changes to the tutorial test options and examples, or guide them on the next step forward on their own.

3.2 Tables and plots

3.2.1 Table data format

Results from a Table Access Protocol (TAP) service search are best displayed as an astropy table using .to_table(), or as a pandas dataframe using .to_table().to_pandas().

Do not use the .to_table().show_in_notebook() method. This can cause issues in the RSP JupyterLab environment that cause the notebook to hang indefinitely.

3.2.2 Plot format and style

Plots should be large enough such that the details in the data are easily discerned, but small enough to fit within a small browser window (e.g., a laptop screen). Typically, a statement such as fig = plt.figure(figsize=(6, 4)) is sufficient (or (6, 6) for square plots).

Axes labels with units are mandatory. A legend must be included if multiple types of data are co-plotted. A descriptive title is encouraged but not mandatory.

In general, the default matplotlib style is sufficient and should be adopted for plot attributes such as line thickness, tick labels, fontsize, and so on. However, the default matplotlib color palette is not sufficient, and the recommendations under Accessibility considerations should be adopted to create colorblind-friendly plots.

Error bars should be included wherever possible, and especially in cases where analyses such as line fitting is being performed on the data in the plot, to help the user understand data quality.

A markdown cell underneath the figure should provide a caption that adequately explains what the main attributes of the plot. This caption should serve as alt-text (as described under Accessibility considerations) and also as a way for the user to confirm the plot appears as expected.

3.2.3 Image orientation

When using a World Coordinate System (WCS), display East left, North up. If only using pixels, (0,0) should be the lower-left, which is the default for awfDisplay.

When using other plotting packages, transformations might be needed in order to match the afwDisplay default. See the LSST Science Pipelines documentation about Image Indexing.

Since use of “extent” is necessary for displaying a WCS overlay for deepCoadds, use it all the time:

deepCoadd = butler.get('deepCoadd', dataId=dataId)
deepCoadd_bbox = butler.get('deepCoadd_calexp.bbox', dataId=dataId)
deepCoadd_wcs = butler.get('deepCoadd_calexp.wcs', dataId=dataId)
deepCoadd_WCSfMd = WCS(deepCoadd_wcs.getFitsMetadata())
deepCoadd_extent = (deepCoadd_bbox.beginX, deepCoadd_bbox.endX, deepCoadd_bbox.beginY, deepCoadd_bbox.endY)
plt.subplot(projection=deepCoadd_WCSfMd)
plt.imshow(deepCoadd.image.array, cmap='gray', vmin=0, vmax=2, extent=deepCoadd_extent, origin='lower')

3.3 Functions and classes

While globally defined functions or classes which are used more than once in a notebook should be defined in section 1.2 Define Functions and Parameters, single-use functions or classes can be defined immediately before they are used.

Functions or classes that are particularly long blocks of code (e.g., >20 lines) can be hidden by going to the “View” menu item and choosing “Collapse Selected Code”, or by clicking on the blue bar that appears to the left of a selected cell. Hidden cells should be described in the preceding markdown cell with text like “the following hidden cell contains code that defines the make_cmd_plot function”. The first hidden cell in a notebook should include instructions for displaying the cell, such as “to see the contents of the hidden cell, select View from the menu bar and then Expand Selected Code or click on the vertical next to the cell or on the three dots that denote that the cell is hidden”.

3.4 Clearing memory

These are optional methods for keeping memory use manageable in notebooks which may be computationally restrictive, e.g., demonstrating data visualization techniques with big datasets.

To reduce the memory footprint of a notebook, remove figures once they’re no longer needed. See the remove_figure function defined in the DP0 notebook 03_Image_Display_and_Manipulation.ipynb in the tutorial-notebooks repository.

Better ways to clear the memory of, for example, large arrays that are not going to be used further on in the notebook is in development as mentioned under Stretch goals.

3.5 Assert statements

It is not mandatory nor expected for assert statements to be included in python scripts or notebooks, but tutorial developers should consider the following guidance.

Where essential, or where a very specific value is expected, the assert command can be used to demonstrate to users that a condition is true. For example, assert statements can be used to confirm that service objects like TAP are not None or null before moving on and using that instance, or to check that values meet expectations (e.g., total rows returned from a query).

However, take care not to use assert statements when, e.g., querying dynamic (prompt) datasets, which could return different results and cause the assert statement to fail. Consider more pedagogical alternatives when possible (e.g., printing schema columns would also fail if the TAP service was not instantiated).

3.6 Known warnings

If a code cell produces a warning which is known and it should be ignored, the preferred method is to add a markdown cell before the code cell which produces the warning, to tell the user it is acceptable to ignore.

Guidelines about the options to ignore categories of warnings are under consideration, and will be added here in the future. Until then, use of, e.g., warnings.simplefilter("ignore", category=UserWarning) is not preferred because ignoring categories of warnings can allow real issues to go unnoticed.

3.7 Markdown style

Any references to variables used in code cells or any code commands should be in monospaced font.

Use of indented text should be limited to warnings and notices, e.g., > **Warning:** the following cell....

3.8 Code cell comments

Markdown cells are the preferred way to provide descriptive text. Avoid using comments within a code cell as documentation.

3.9 Code cell style standard PEP8

PEP8 is the style guide for Python code that comprises the standard library of the distribution, and flake8 is a tool to ensure compliance with these standards.

Use flake8 to ensure notebook code conforms to PEP 8 – Style Guide for Python Code, with a few exceptions.

Notebook tutorial developers must install the following packages locally in their home directory:

pip install --user flake8-nb
pip install --user pycodestyle_magic

It is known that the most up-to-date version of flake8 has some issues. If errors are encountered such as AttributeError: '_io.StringIO' object has no attribute 'buffer', force-downgrade flake8 from version 4.0.1 to 3.9.2 with pip install flake8==3.9.2.

3.9.1 The flake8 config file

Create a configuration file for flake8. For example, from the command line in the home directory, execute the following. These instructions use emacs, but it doesn’t matter so long as the end result is a correctly-named file with the right contents.

touch .config/flake8
emacs .config/flake8

Then copy-paste the following into the opened config file.

[flake8]
max-line-length = 99
ignore = E133, E226, E228, E266, N802, N803, N806, N812, N813, N815, N816, W503

Use x-s then x-c to save and exit emacs.

3.9.2 While developing a notebook

While developing a notebook, have the following “magic” commands as the first code cell:

%load_ext pycodestyle_magic
%flake8_on
import logging
logging.getLogger("flake8").setLevel(logging.FATAL)

Whenever a cell is executed, it will use flake8 to check for adherence to the PEP8 coding style guide, and report violations which can be fixed immediately. When the notebook is ready to be merged, the cell with the magic commands must be removed.

3.9.3 When the notebook is complete

When the notebook is complete, execute the following from the command line in the notebook’s directory:

flake8-nb notebook_name.ipynb

This will do a final check of any violations with PEP8. This will catch things that can be missed line-by-line, such as packages that are imported but never used.

4 Git branch, merge, and review policy for the tutorial-notebooks repository

The following applies when creating or updating notebooks in the tutorial-notebooks repository, which is part of the rubin-dp0 GitHub Organization. The main branch is where changes are collected before pushing prod branch. The prod branch is the version available in the RSP.

4.1 Branch

Develop new notebooks, or update existing ones, in a new branch. This branch should be named for the corresponding Jira ticket (e.g., “tickets/PREOPS-12345”). The new branch should be created from main, not from prod.

Only update one notebook per ticket branch, unless the ticket is to make similar updates to all notebooks (e.g., when bumping the RSP’s recommended image).

Update the repository’s README.md file in the branch when appropriate.

4.2 Commit and push

Always restart the Jupyter Notebook kernel and clear all outputs before saving, committing, and pushing changes to the branch.

4.3 Pull request

When the notebook is complete open a pull request (PR) to merge the ticket branch into the main branch (again, not to prod).

4.4 Review

Contact one or more Rubin Observatory staff members with the appropriate expertise and ask them to review the tutorial. Reviewers do not need to be members of the CST. If they agree, assign them as a reviewer on the pull request. If there is uncertainty about whom to assign as a reviewer, ask the Lead Community Scientist to help identify someone.

If the reviewer requests changes, ensure that all of the reviewers’ comments are addressed. Make changes and new commits to the branch, and respond to all of their comments with either a confirmation a change was made, or an explanation of why the request was not implemented. Contact the reviewers to let them know the pull request now awaits their approval.

4.5 Merge

After the reviewers have approved the pull request, rebase and merge the ticket branch into the main branch (again, not to prod). Resolve all conflicts, if there are any. After the successful merge, delete the ticket branch.

4.6 Release to prod branch

To “release” the new version of main to prod branch (i.e., to update all RSP users’ tutorial notebooks), delete the current prod-prior-to-rebranch branch, rename prod as prod-prior-to-rebranch, then create a new prod branch from main. Doing this way avoids weird history-based git issues that cause conflicts in main to prod merges. There is no need to track the history between main and prod.

The number of pushes to the prod branch should be minimized. For example, if there are a few tickets being completed within a week, coordinate with other notebook developers to collect all changes in the main branch, and then do a single “release” to prod.

4.7 Jira tickets

Remember to make comments in the associated Jira tickets about the major updates as work progresses.

After the PR is merged, request a review on the ticket (usually from the CST team lead). After the ticket has been reviewed, the ticket status can be set as done.

4.9 Major updates log

All new tutorials or significant changes should be documented for users in the logs of major tutorial updates for DP0.2 and DP0.3.

5 Portal tutorial format and style

The portal tutorials are written in reStructuredText (RST) format and are kept within the data release documentation at DP0.2 Tutorials and DP0.3 Tutorials.

All portal tutorials should have a descriptive title, list the contact authors, the date last verified to run, and the targeted learning level. A brief narrative introduction to the tutorial should be provided at the top of the page.

The rest of the portal tutorial should be divided into sequentially numbered steps and substeps.

It is very common, but not mandatory, to end all portal tutorials with a section called Exercises for the learner with suggestions of how the user can make changes to the tutorial test options and examples, or guide them on the next step forward on their own.

5.1 Code blocks

Ensure that any Astronomical Data Query Language (ADQL) is put into code boxes in RST so that users may copy-paste whenever possible. In RST, this is done as in the following example.

.. code-block:: SQL

  SELECT e, q, incl
  FROM dp03_catalogs_10yr.MPCORB
  WHERE ssObjectId > 9000000000000000000

5.2 Figures

Use descriptive text and screenshots to demonstrate the steps of the tutorial, to show the user what to do, and to show the expected results for comparison.

Augment screenshots with indicators (e.g., arrows or circles) to guide the users attention as needed.

Include a caption that describes the figure (see example below, with alt-text and a caption).

For plots made in the Portal results view, the recommendations under Accessibility considerations should be adopted to create colorblind-friendly plots.

5.2.1 Alternate-Text (alt-text)

All figures in Portal tutorials should have an alt-text statement. The motivation and guidance for writing alt-text is provided under Accessibility considerations.

To add alt-text to an image in the reStructured text environment, use the :alt: command. In RST, this is done as in the following example.

.. figure:: /_static/figure_filename.png
  :name: name_of_figure
  :alt: Descriptive text of image (use tab to indent second line of text)

  The caption goes here, indented the same way, but with an empty line between code and caption text.

6 Git branch, merge, and review policy for portal tutorials

The following applies when creating or updating tutorials in the dp0-2_lsst_io repository, which is part of the lsst GitHub Organization.

Develop new tutorials, or update existing ones, in a new branch. This branch should be named for the corresponding Jira ticket (e.g., “tickets/PREOPS-12345”). The new branch should be created from main. Typically, only one tutorial is updated per ticket branch.

Make commits and push changes to the branch in the dp0-2_lsst_io (or dp0-3_lsst_io) repository until work is complete, then open a pull request to main.

Contact one or more Rubin Observatory staff members with the appropriate expertise and ask them to review the tutorial. At least one reviewer should be a member of the CST. If they agree, assign them as a reviewer on the pull request.

If the reviewer requests changes, ensure that all of the reviewers’ comments are addressed. Make changes and new commits to the branch, and respond to all of their comments with either a confirmation a change was made, or an explanation of why the request was not implemented. Contact the reviewers to let them know the pull request now awaits their approval.

After the reviewers have approved the pull request, rebase and merge the ticket branch into the main branch. Resolve all conflicts, if there are any. After the successful merge, delete the ticket branch.

Remember to make comments in the associated Jira tickets about the major updates as work progresses.

After the PR is merged, request a review on the ticket (usually from the CST team lead). After the ticket has been reviewed, the ticket status can be set as done.

All new tutorials or significant changes should be documented for users in the logs of major tutorial updates for DP0.2 and DP0.3.

7 Accessibility considerations

The following set of best practices to be implemented for Rubin tutorials is a work in progress. Individual components have been incorporated into the sections above, but are collected here for reference.

7.1 Vision-impaired astronomers

7.1.1 Colorblind-friendly plots

The most common form of colorblindness is being unable to differentiate red and green. Guidelines for colorblind-friendly plots includes the following.

  • Do not use red and green together.

  • Use color combinations that are high contrast.

  • Do not use color alone, but with different symbol and line styles.

In Jupyter Notebooks, in order to be accessible to those with Color Vision Deficiency (CVD or colorblind), plots color tables with matplotlib should be either a greyscale, a preceptually uniform sequential colormap like viridis or cividis, or tableau-colorblind10.

The tableau-colorblind10 color table can be loaded with the following python code.

import matplotlib.pyplot as plt
plt.style.use('tableau-colorblind10')

For the LSST filter set ugrizy, adopt the same colors as Dark Energy Survey (DES), which were chosen to be colorblind-friendly. The following python code can be used to create a dictionary that assigns colors by filter name.

plot_filter_colors = {'u': '#56b4e9', 'g': '#008060', 'r': '#ff4000', 'i': '#850000', 'z': '#6600cc', 'y': '#000000'}

7.1.2 Alternative-Text (alt-text)

Alt-text is added to figures, images, and graphics in the documentation and documentation-based tutorials (but not notebooks, where figures are typically dynamically generated) to ensure that visually impaired individuals, who use screen readers, are given sufficient information to understand what is displayed.

In general, alt-text descriptions can be written as either a literal description of the figure or image, or a more creative description. In CST tutorials, most figures display screen shots of the RSP portal interface and should describe the information in a practical way versus a creative way.

Guidelines for writing alt-text:

  • Be brief, if possible. Write in short, succinct sentences.

  • Spell out acronyms (e.g. Right Ascension versus RA).

  • Avoid jargon or undefined terms.

  • Symbols and equations should be expressed in words (e.g. use “equals” rather than “=”).

  • Write for the text to be read aloud. Written visual cues (e.g. quotation marks or dashes) are not necessary.

  • Pictures should be described in terms of what the listener needs to know (e.g., a large galaxy in the center).

  • For RSP screenshots, state which interface is being shown and describe the actions the user should take and the expected results, or the main functionality of the interface (as appropriate).

  • Where possible, use consistent terms such as the JupyterLab User Interface Naming Conventions.

  • Limit the use of visual cues, such as colors or shapes, or visual-centric language (e.g., “as you can see”).

  • If color is a useful attribute to distinguish items in a figure, then describe the attribute rather than the color (e.g. a blue star versus a red star could be described as a hotter star and a cooler star).

  • For plots, include type of plot (e.g., bar, scatter), titles and labels, and a general explanation of the data and what it means.

7.1.3 Converted notebooks

For offline viewing, create html versions of executed notebooks and not pdf versions, as the latter are typically less compatible with screen readers.

At this time it is not necessary to use, e.g., nbconvert, but a customized application might be considered in the future (and is included under Stretch goals).

7.2 Neurodivergent astronomers

Use fonts that work well for people with dyslexia, such as sans serif, monospaced, and roman font types such as Helvetica, Courier, Arial, Verdana and CMU (Computer Modern Unicode), OpenDyslexic.

Italic fonts decrease readability and should be used sparingly.

Avoid text crowding and long paragraphs. Use short sentences and, where possible, arrange text in shorter paragraphs.

7.3 Resources

A few useful resources for accessibility include:

8 Stretch goals

Work is on-going in these areas, and in time they will become part of the guidelines above.

8.1 Notebook metadata

Embed notebook metadata (e.g., version, skills, packages) in a way that can be scraped and used to auto-generate the README.md file or a Table of Contents, to enable users to browse notebook contents.

8.2 Accessibility

Continue to improve tutorials’ accessibility to people with disabilities by finding and implementing, e.g., screen reader compatibility software, data sonification packages, customized use of nbconvert, additional policies for supporting neurodivergent users, and other jupyter notebook accessibility techniques.

8.3 Translations

At minimum, translate any undergraduate-level tutorials into Spanish.

Additionally, improve tutorials’ accessibility to non-English speakers by finding and implementing automatic translation and localization software.

8.4 Purge extraneous items in notebooks

Develop a best practice for how to keep notebook memory usage in check, in addition to deleting figures. E.g., whether or not the del command is sufficient for this.

8.5 Recipe functions

Create recipes for common user activities. These could be, e.g., ADQL searches for the portal, code snippets for the command line, or python modules that can be imported.

When these are used in the advanced notebooks, also demonstrate use of the inspect.getsource functionality for users to display function code.