Completely update the lesson

[ocaisa]

This update is completely disruptive, it's basically an entirely new lesson written for Snakemake 8.x

You can find the rendered version at https://ocaisa.github.io/hpc-workflows/01-introduction.html

There are still a few holes:

• Setup instructions are not complete
• No credit given to the origin lessons for the content
• Questions, objectives and keypoints need work
• Timings need work (though I did manage to fit the lesson in a 4 hour window)
• Requires some learner profiles as motivation

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/carpentries-incubator/hpc-workflows/compare/md-outputs..md-outputs-PR-14

The following changes were observed in the rendered markdown documents:

 01-introduction.md (new)                           | 176 ++++++++
 02-snakemake_on_the_cluster.md (new)               | 248 ++++++++++++
 03-placeholders.md (new)                           |  79 ++++
 04-snakemake_and_mpi.md (new)                      | 442 +++++++++++++++++++++
 05-chaining_rules.md (new)                         | 191 +++++++++
 06-expansion.md (new)                              | 194 +++++++++
 amdahl_foundation.md (gone)                        | 126 ------
 amdahl_snakemake.md (gone)                         |  61 ---
 config.yaml                                        |  20 +-
 files/plot_terse_amdahl_results.py (new)           |  49 +++
 files/snakefiles/Snakefile_ep01 (new)              |   5 +
 files/snakefiles/Snakefile_ep02 (new)              |  13 +
 files/snakefiles/Snakefile_ep04 (new)              |  22 +
 files/snakefiles/Snakefile_ep05 (new)              |  28 ++
 files/snakefiles/Snakefile_ep06 (new)              |  32 ++
 .../cluster_profile_ep02/config.yaml (new)         |   6 +
 .../cluster_profile_ep04/config.yaml (new)         |   7 +
 md5sum.txt                                         |  14 +-
 snakemake_cluster.md (gone)                        |  63 ---
 snakemake_multiple.md (gone)                       |  77 ----
 snakemake_profiles.md (gone)                       |  67 ----
 snakemake_single.md (gone)                         |  69 ----
 22 files changed, 1509 insertions(+), 480 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2024-04-08 13:02:37 +0000

[tkphd]

I changed this to a draft, so that it does not get merged until we address the attribution gap for resources we borrowed material from. Otherwise, we're in violation of the authors' copy-rights.

[tobyhodges]

Regarding attribution of other content, a heads-up that the lesson infrastructure will soon support Citation File Format. In addition to adding attribution to the lesson site itself, you can use the references section of a CFF file to cite other works on which your lesson content is based/inspired by.

[ocaisa]

I changed this to a draft, so that it does not get merged until we address the attribution gap for resources we borrowed material from. Otherwise, we're in violation of the authors' copy-rights.

@tkphd I've added a CITATION.cff which includes references to the main lessons from which I've incorporated content.

[tkphd]

Looks good! Thank you for all the work, @ocaisa!