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This repository contains basic tools that are useful for every IMP tutorial. It is intended to be included in each IMP tutorial repository as a submodule.

Setup of a new tutorial

Make a GitHub repository for your tutorial. Then run in the top level tutorial directory:

mkdir support
(cd support && git submodule add https://github.com/salilab/tutorial_tools)

Make a metadata.yaml file in the support directory to describe the tutorial, with contents similar to:

title: My tutorial
description: >
    Longer description of the tutorial, which
    can span multiple lines.
depends: [foo, bar]
show_in_index: false

This metadata is used on the IMP tutorial index.

  • title provides a short name for the tutorial.
  • description gives a longer text.
  • depends, if given, lists other tutorials that are recommended for the user before this one. GitHub repo names can be used here (e.g. imp_coding_tutorial) although the imp_ prefix or _tutorial suffix are optional (e.g. coding would be equivalent). This controls the ordering of the tutorial list on the website.
  • show_in_index: false prevents the tutorial from showing up in the index. Remove this line once the tutorial is ready for public consumption.

Choose a suitable license for the tutorial and put it in a file LICENSE. We recommend the CC BY-SA license. One way to do this is to simply copy this LICENSE file.

Make a simple README.md file. Generally a brief description of the tutorial and a link to the website (see below) is sufficient content.

Branches

  • The main branch of your tutorial should work with both the latest stable IMP release and the nightly build.
  • The develop branch of your tutorial (if present) only needs to work with the IMP nightly build - this is for developing new tutorials.
  • Other branches (if present) are treated like develop.

Testing

Make a support/test directory and put one or more Python test scripts there. These should run the tutorial scripts and check that everything worked correctly. Note that there is a 20 minute time limit for tests, so you may need to run shorter simulations (perhaps with a --test flag). Each file should be executable (with a #!/usr/bin/env python first line), and use the Python unittest module.

Then copy a GitHub Actions configuration file to the .github/workflows/ subdirectory under the top level directory of your tutorial. For the main branch of your tutorial, use cp support/tutorial_tools/github-main.yml .github/workflows/build.yml. For other branches such as develop, use github-develop.yml instead.

The build.yml config file will ensure the tutorial tests get run every time the tutorial is changed (pushed to GitHub) for the current IMP nightly build and also the latest stable release (if applicable).

Tutorial text

The actual text of the tutorial should be written using one or more files in the doc directory. Each should have a .md file extension, and use doxygen markdown. Give each file a label, using mainpage for the main page, as described in the doxygen docs.

See the existing IMP coding or PMI2 tutorials for examples.

Any references to IMP classes in the text will be automatically linked by doxygen to the IMP manual (the main branch of the tutorial to the most recent IMP release, and other branches to the IMP nightly build). To add explicit links to IMP objects or to sections in the IMP manual, use the @ref notation as described in the doxygen manual. (To prevent a word from being automatically linked, prefix it with the % character. This is often used for "IMP" which otherwise is linked to the documentation for the IMP (kernel) namespace.)

To include images in the tutorial, put them in an images subdirectory and use the \image command.

To put example code (e.g. C++, Python, or shell) directly in the text, use the \code and \endcode commands. To include all or part of a file in the repository, use the \include or \snippet commands, respectively. In all cases the code will be syntax highlighted and any IMP classes or functions will be automatically linked to the IMP manual. (For \include or \snippet use the full path to the file, relative to the top of the repository.)

To format the text, run ../support/tutorial_tools/doxygen/make-docs.py (it requires network access and that you have doxygen installed) then open html/index.html in a web browser.

The formatted tutorial text for the main branch will also be deployed automatically to https://integrativemodeling.org/tutorials/<name> on each push to GitHub. (<name> is the name of the tutorial GitHub repository, with any imp_ prefix or _tutorial suffix removed). Non-main branches of the tutorial will be found under a subdirectory named for the branch, e.g. https://integrativemodeling.org/tutorials/<name>/develop/.

Generation from Jupyter Notebook templates (experimental)

Tutorials can also be generated using a slightly-modified Jupyter Notebook as the input. (This is still in development.)

Given a template notebook, .template.foo.ipynb, running the script notebook/process_notebook.py foo will generate:

  • foo.ipynb, a standard Jupyter notebook, suitable for general use
  • foo-colab.ipynb, a Jupyter notebook suitable for running on Google Colaboratory, if any %%nbexclude, %%nbonly, %%colabexclude, %%colabonly directives are present (see below).
  • foo.py or foo.sh, a simple Python or shell script that can be run standalone (to generate a Bash script, install and use a Jupyter Bash kernel such as Calysto Bash)
  • foo.md, markdown which is further processed using doxygen to generate HTML files in the html subdirectory

The template notebook allows for additional functionality not present in regular Jupyter notebooks:

  • doxygen-style links of the form [foo](@ref bar) can be used. @ref bar will be replaced with the full URL for the identifier bar. bar can be any IMP class, method or module name (e.g. IMP.atom.Selection, IMP::pmi), an IMP header (e.g. IMP/Restraint.h, IMP/core/Harmonic.h), or any identifier read with %intersphinx (see below).
  • The ``foo`` syntax is shorthand for [foo](@ref foo).
  • The ``~x.y.z.foo`` syntax is shorthand for [foo](@ref x.y.z.foo).
  • A line of the form %intersphinx url acts like the Sphinx intersphinx extension. It fetches a Python inventory file from url so that @ref can also be used to refer to Python objects from that URL. For example, after using %intersphinx https://docs.python.org/3 links can be made to Python standard library objects, e.g. @ref itertools.
  • The special command %%include foo will be replaced with the contents of the file foo.
  • The special command [TOC] will generate a table of contents.
  • Custom anchors can be added to headings, of the form # Heading {#anchor}.
  • A cell starting with %%nbexclude will be excluded from the notebook output (#%%nbexclude can also be used, which prevents Jupyter from complaining about a magic it doesn't understand in a code cell).
  • A cell starting with %%htmlexclude (or #%%htmlexclude) will be excluded from the HTML output.
  • A cell starting with %%colabexclude (or #%%colabexclude) will be excluded from the Google Colaboratory output.
  • Similarly, cells marked with %%nbonly, %%htmlonly, or %%colabonly will be included only in the given output (a # prefix can also be used here).

The notebook should start with a title and #mainpage anchor of the form

My title {#mainpage}
========

To include images, put them in an images subdirectory. It's recommended to use HTML syntax rather than Markdown so that the size and caption can be precisely controlled in the HTML output, e.g.:

<img src="images/links.png" width="700px" title="Nup84 file linkage" />

All cell outputs in the template notebook should be cleared. If you want to include pregenerated outputs in the notebook and HTML output, use the %gencelloutputs magic in any markdown cell in your template notebook. This will run all of the cells in order and add stdout or matplotlib plots. See the cross-linking tutorial for an example.

Otherwise, normal Jupyter notebook syntax can be used.

A tutorial can consist of multiple notebooks (see the FoXS tutorial for an example). In this case

  • All the notebooks should be in the same directory.
  • Each notebook should start with a title (as above). Exactly one notebook should use the #mainpage anchor; every other notebook should use a different anchor (usually the name of the file).
  • Anchors should be unique across all notebooks.
  • To link to the notebook foo, use the link syntax [link text](@file foo).
  • Outputs are generated using the process_notebook.py script as above; simply list all notebooks on the command line. For example, given notebooks .template.foo.ipynb and .template.bar.ipynb, running the script process_notebook.py foo bar will generate all outputs.