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‎CODE_OF_CONDUCT.md

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---
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title: "Contributor Code of Conduct"
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---
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As contributors and maintainers of this project,
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we pledge to follow the [The Carpentries Code of Conduct][coc].
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Instances of abusive, harassing, or otherwise unacceptable behavior
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may be reported by following our [reporting guidelines][coc-reporting].
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[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
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[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html

‎LICENSE.md

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---
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title: "Licenses"
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---
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## Instructional Material
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All Carpentries (Software Carpentry, Data Carpentry, and Library Carpentry)
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instructional material is made available under the [Creative Commons
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Attribution license][cc-by-human]. The following is a human-readable summary of
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(and not a substitute for) the [full legal text of the CC BY 4.0
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license][cc-by-legal].
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You are free:
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- to **Share**---copy and redistribute the material in any medium or format
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- to **Adapt**---remix, transform, and build upon the material
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for any purpose, even commercially.
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The licensor cannot revoke these freedoms as long as you follow the license
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terms.
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Under the following terms:
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- **Attribution**---You must give appropriate credit (mentioning that your work
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is derived from work that is Copyright (c) The Carpentries and, where
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practical, linking to <https://carpentries.org/>), provide a [link to the
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license][cc-by-human], and indicate if changes were made. You may do so in
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any reasonable manner, but not in any way that suggests the licensor endorses
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you or your use.
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- **No additional restrictions**---You may not apply legal terms or
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technological measures that legally restrict others from doing anything the
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license permits. With the understanding that:
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Notices:
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* You do not have to comply with the license for elements of the material in
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the public domain or where your use is permitted by an applicable exception
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or limitation.
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* No warranties are given. The license may not give you all of the permissions
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necessary for your intended use. For example, other rights such as publicity,
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privacy, or moral rights may limit how you use the material.
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## Software
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Except where otherwise noted, the example programs and other software provided
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by The Carpentries are made available under the [OSI][osi]-approved [MIT
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license][mit-license].
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
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of the Software, and to permit persons to whom the Software is furnished to do
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so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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## Trademark
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"The Carpentries", "Software Carpentry", "Data Carpentry", and "Library
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Carpentry" and their respective logos are registered trademarks of [The Carpentries Inc][the-carpentries].
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[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
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[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
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[mit-license]: https://opensource.org/licenses/mit-license.html
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[ci]: https://communityin.org/
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[osi]: https://opensource.org
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[the-carpentries]: https://carpentries.org

‎config.yaml

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#------------------------------------------------------------
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# Values for this lesson.
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#------------------------------------------------------------
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# Which carpentry is this (swc, dc, lc, or cp)?
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# swc: Software Carpentry
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# dc: Data Carpentry
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# lc: Library Carpentry
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# cp: Carpentries (to use for instructor training for instance)
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# incubator: The Carpentries Incubator
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#
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# This option supports custom types so lessons can be branded
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# and themed with your own logo and alt-text (see `carpentry_description`)
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# See https://carpentries.github.io/sandpaper-docs/editing.html#adding-a-custom-logo
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carpentry: 'incubator'
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# Alt-text description of the lesson.
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carpentry_description: 'Lesson Description'
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# c.f. https://carpentries.github.io/sandpaper-docs/introduction.html
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# Overall title for pages.
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title: 'Reproducible Machine Learning Workflows for Scientists'
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# Date the lesson was created (YYYY-MM-DD, this is empty by default)
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created: 2025-03-16
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# Comma-separated list of keywords for the lesson
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keywords: 'software, lesson, The Carpentries, machine learning, CUDA, hardware acceleration, reproducible'
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# Life cycle stage of the lesson
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# possible values: pre-alpha, alpha, beta, stable
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life_cycle: 'pre-alpha'
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# License of the lesson
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license: 'CC-BY 4.0'
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# Link to the source repository for this lesson
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source: 'https://github.com/carpentries-incubator/reproducible-ml-workflows'
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# Default branch of your lesson
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branch: 'main'
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# Who to contact if there are any issues
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contact: '[email protected]'
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# Navigation ------------------------------------------------
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#
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# Use the following menu items to specify the order of
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# individual pages in each dropdown section. Leave blank to
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# include all pages in the folder.
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#
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# Example -------------
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#
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# episodes:
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# - introduction.md
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# - first-steps.md
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#
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# learners:
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# - setup.md
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#
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# instructors:
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# - instructor-notes.md
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#
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# profiles:
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# - one-learner.md
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# - another-learner.md
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# Order of episodes in your lesson
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episodes:
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- introduction.md
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# Information for Learners
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learners:
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# Information for Instructors
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instructors:
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# Learner Profiles
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profiles:
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# Customisation ---------------------------------------------
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#
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# This space below is where custom yaml items (e.g. pinning
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# sandpaper and varnish versions) should live
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‎index.md

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---
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site: sandpaper::sandpaper_site
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---
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This is a new lesson built with [The Carpentries Workbench][workbench].
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[workbench]: https://carpentries.github.io/sandpaper-docs
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‎instructor-notes.md

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---
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title: 'Instructor Notes'
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---
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This is a placeholder file. Please add content here.

‎introduction.md

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---
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title: "Using Markdown"
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teaching: 10
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exercises: 2
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---
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:::::::::::::::::::::::::::::::::::::: questions
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- How do you write a lesson using Markdown and `{sandpaper}`?
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::::::::::::::::::::::::::::::::::::::::::::::::
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::::::::::::::::::::::::::::::::::::: objectives
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- Explain how to use markdown with The Carpentries Workbench
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- Demonstrate how to include pieces of code, figures, and nested challenge blocks
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::::::::::::::::::::::::::::::::::::::::::::::::
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## Introduction
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This is a lesson created via The Carpentries Workbench. It is written in
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[Pandoc-flavored Markdown](https://pandoc.org/MANUAL.html) for static files and
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[R Markdown][r-markdown] for dynamic files that can render code into output.
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Please refer to the [Introduction to The Carpentries
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Workbench](https://carpentries.github.io/sandpaper-docs/) for full documentation.
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What you need to know is that there are three sections required for a valid
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Carpentries lesson:
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1. `questions` are displayed at the beginning of the episode to prime the
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learner for the content.
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2. `objectives` are the learning objectives for an episode displayed with
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the questions.
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3. `keypoints` are displayed at the end of the episode to reinforce the
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objectives.
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:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: instructor
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Inline instructor notes can help inform instructors of timing challenges
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associated with the lessons. They appear in the "Instructor View"
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::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
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::::::::::::::::::::::::::::::::::::: challenge
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## Challenge 1: Can you do it?
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What is the output of this command?
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```r
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paste("This", "new", "lesson", "looks", "good")
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```
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:::::::::::::::::::::::: solution
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## Output
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```output
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[1] "This new lesson looks good"
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```
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:::::::::::::::::::::::::::::::::
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## Challenge 2: how do you nest solutions within challenge blocks?
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:::::::::::::::::::::::: solution
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You can add a line with at least three colons and a `solution` tag.
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:::::::::::::::::::::::::::::::::
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::::::::::::::::::::::::::::::::::::::::::::::::
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## Figures
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You can use standard markdown for static figures with the following syntax:
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`![optional caption that appears below the figure](figure url){alt='alt text for
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accessibility purposes'}`
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![You belong in The Carpentries!](https://raw.githubusercontent.com/carpentries/logo/master/Badge_Carpentries.svg){alt='Blue Carpentries hex person logo with no text.'}
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::::::::::::::::::::::::::::::::::::: callout
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Callout sections can highlight information.
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They are sometimes used to emphasise particularly important points
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but are also used in some lessons to present "asides":
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content that is not central to the narrative of the lesson,
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e.g. by providing the answer to a commonly-asked question.
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::::::::::::::::::::::::::::::::::::::::::::::::
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## Math
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One of our episodes contains $\LaTeX$ equations when describing how to create
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dynamic reports with {knitr}, so we now use mathjax to describe this:
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`$\alpha = \dfrac{1}{(1 - \beta)^2}$` becomes: $\alpha = \dfrac{1}{(1 - \beta)^2}$
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Cool, right?
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::::::::::::::::::::::::::::::::::::: keypoints
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- Use `.md` files for episodes when you want static content
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- Use `.Rmd` files for episodes when you need to generate output
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- Run `sandpaper::check_lesson()` to identify any issues with your lesson
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- Run `sandpaper::build_lesson()` to preview your lesson locally
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::::::::::::::::::::::::::::::::::::::::::::::::
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[r-markdown]: https://rmarkdown.rstudio.com/

‎learner-profiles.md

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---
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title: FIXME
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---
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This is a placeholder file. Please add content here.

‎links.md

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<!--
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Place links that you need to refer to multiple times across pages here. Delete
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any links that you are not going to use.
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-->
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[pandoc]: https://pandoc.org/MANUAL.html
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[r-markdown]: https://rmarkdown.rstudio.com/
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[rstudio]: https://www.rstudio.com/
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[carpentries-workbench]: https://carpentries.github.io/sandpaper-docs/
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‎md5sum.txt

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"file" "checksum" "built" "date"
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"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2025-04-16"
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"LICENSE.md" "16e8eaad880865bc4a41811b3e8fa945" "site/built/LICENSE.md" "2025-04-16"
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"config.yaml" "3d2ac02f5410e0aa29b7c999d5098b95" "site/built/config.yaml" "2025-04-29"
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"index.md" "a02c9c785ed98ddd84fe3d34ddb12fcd" "site/built/index.md" "2025-04-16"
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"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2025-04-16"
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"pixi.lock" "49230335af6ae57457fbf81456984e37" "site/built/pixi.lock" "2025-04-29"
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"episodes/introduction.md" "083b4b050f08100db65af47082e12105" "site/built/introduction.md" "2025-04-16"
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"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2025-04-16"
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"learners/reference.md" "ee8aac2b5f1e80b406154ad56a7b6803" "site/built/reference.md" "2025-04-29"
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"learners/setup.md" "725894174d3e70dbae791c7301038970" "site/built/setup.md" "2025-04-29"
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"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2025-04-16"

‎reference.md

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---
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title: 'Reference'
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---
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## Glossary
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[Pixi](https://pixi.sh/)
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: A package and software environment management tool that allows for fully reproducible multi-platform software environments.
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Pixi currently supports management of conda packages from conda package indexes (e.g. [conda-forge](https://conda-forge.org/), [S3 buckets](https://pixi.sh/latest/deployment/s3/)) and Python packages from Python package indexes (e.g. [PyPI](https://pypi.org/)).

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