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‎AUTHORS‎

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lesson-template was written by:
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Aaron O'Leary <aaron.oleary@gmail.com>
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Abigail Cabunoc <abigail.cabunoc@oicr.on.ca>
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Andy Boughton <abought@gmail.com>
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Bill Mills <mills.wj@gmail.com>
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Francois Michonneau <francois.michonneau@gmail.com>
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Greg Wilson <gvwilson@software-carpentry.org>
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James Allen <jamesallen0108@gmail.com>
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John Blischak <jdblischak@gmail.com>
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Jon Pipitone <jon.pipitone@utoronto.ca>
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Michael Hansen <hansen.mike@gmail.com>
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Piotr Banaszkiewicz <piotr@banaszkiewicz.org>
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Raniere Silva <raniere@ime.unicamp.br>
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Rémi Emonet <remi.emonet@reverse--com.heeere>
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Timothée Poisot <tim@poisotlab.io>
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Trevor Bekolay <tbekolay@gmail.com>
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W. Trevor King <wking@tremily.us>

‎CONDUCT.md‎

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---
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layout: page
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title: "Contributor Code of Conduct"
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permalink: /conduct/
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---
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As contributors and maintainers of this project,
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we pledge to respect all people who contribute through reporting issues,
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posting feature requests,
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updating documentation,
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submitting pull requests or patches,
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and other activities.
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We are committed to making participation in this project a harassment-free experience for everyone,
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regardless of level of experience,
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gender,
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gender identity and expression,
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sexual orientation,
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disability,
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personal appearance,
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body size,
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race,
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ethnicity,
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age,
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or religion.
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Examples of unacceptable behavior by participants include the use of sexual language or imagery,
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derogatory comments or personal attacks,
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trolling,
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public or private harassment,
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insults,
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or other unprofessional conduct.
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Project maintainers have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct.
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Project maintainers who do not follow the Code of Conduct may be removed from the project team.
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Instances of abusive, harassing, or otherwise unacceptable behavior
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may be reported by opening an issue or contacting one or more of the project maintainers.
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This Code of Conduct is adapted from
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the [Contributor Covenant][contrib-covenant] Version 1.0.0.
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[contrib-covenant]: http://contributor-covenant.org/

‎CONTRIBUTING.md‎

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Software Carpentry is an open source project,
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and we welcome contributions of all kinds:
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new lessons,
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fixes to existing material,
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bug reports,
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and reviews of proposed changes are all equally welcome.
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By contributing,
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you are agreeing that Software Carpentry may redistribute your work under
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[these licenses][license].
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You also agree to abide by our
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[contributor code of conduct][conduct].
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## Getting Started
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1. We use GitHub flow to manage changes,
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which is explained in the chapter [Contributing to a Project][pro-git-chapter]
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in Scott Chacon's book *Pro Git*.
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2. For our lessons,
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you should branch from and submit pull requests against the `gh-pages` branch.
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3. When editing lesson pages, you need only commit changes to the Markdown source files.
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4. If you're looking for things to work on,
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please see [the list of issues for this repository][issues],
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or for [our other lessons][swc-lessons].
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Comments on issues and reviews of pull requests are equally welcome.
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## Other Resources
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1. This lesson is based on the template found at
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[https://github.com/swcarpentry/lesson-template](https://github.com/swcarpentry/lesson-template).
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That repository has instructions on formatting and previewing lessons.
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2. For a list of helpful commands run `make` in this directory.
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[conduct]: CONDUCT.md
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[issues]: https://github.com/swcarpentry/lesson-template/issues
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[license]: LICENSE.md
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[pro-git-chapter]: http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project
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[swc-lessons]: http://software-carpentry.org/lessons.html

‎LICENSE.md‎

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---
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layout: page
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title: "Licenses"
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permalink: /license/
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---
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## Instructional Material
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All Software Carpentry and Data Carpentry instructional material is
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made available under the [Creative Commons Attribution
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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
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license terms.
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Under the following terms:
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* **Attribution**---You must give appropriate credit (mentioning that
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your work is derived from work that is Copyright © Software
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Carpentry and, where practical, linking to
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http://software-carpentry.org/), provide a [link to the
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license][cc-by-human], and indicate if changes were made. You may do
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so in any reasonable manner, but not in any way that suggests the
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licensor endorses 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
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anything the 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
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material in the public domain or where your use is permitted by an
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applicable exception or limitation.
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* No warranties are given. The license may not give you all of the
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permissions necessary for your intended use. For example, other
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rights such as publicity, privacy, or moral rights may limit how you
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use the material.
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## Software
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Except where otherwise noted, the example programs and other software
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provided by Software Carpentry and Data Carpentry are made available under the
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[OSI][osi]-approved
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[MIT license][mit-license].
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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## Trademark
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"Software Carpentry" and "Data Carpentry" and their respective logos
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are registered trademarks of [NumFOCUS][numfocus].
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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]: http://opensource.org/licenses/mit-license.html
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[numfocus]: http://numfocus.org/
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[osi]: http://opensource.org

‎Makefile‎

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## ========================================
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## Commands for both workshop and lesson websites.
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# Settings
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MAKEFILES=Makefile $(wildcard *.mk)
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JEKYLL=jekyll
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PARSER=bin/markdown_ast.rb
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DST=_site
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# Controls
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.PHONY : commands clean files
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.NOTPARALLEL:
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all : commands
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## commands : show all commands.
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commands :
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@grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g'
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## serve : run a local server.
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serve : lesson-md
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${JEKYLL} serve
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## site : build files but do not run a server.
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site : lesson-md
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${JEKYLL} build
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# repo-check : check repository settings.
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repo-check :
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@bin/repo_check.py -s .
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## clean : clean up junk files.
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clean :
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@rm -rf ${DST}
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@rm -rf .sass-cache
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@rm -rf bin/__pycache__
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@find . -name .DS_Store -exec rm {} \;
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@find . -name '*~' -exec rm {} \;
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@find . -name '*.pyc' -exec rm {} \;
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## clean-rmd : clean intermediate R files (that need to be committed to the repo).
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clear-rmd :
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@rm -rf ${RMD_DST}
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@rm -rf fig/rmd-*
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## ----------------------------------------
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## Commands specific to workshop websites.
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.PHONY : workshop-check
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## workshop-check : check workshop homepage.
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workshop-check :
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@bin/workshop_check.py .
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## ----------------------------------------
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## Commands specific to lesson websites.
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.PHONY : lesson-check lesson-md lesson-files lesson-fixme
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# RMarkdown files
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RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
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RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC))
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# Lesson source files in the order they appear in the navigation menu.
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MARKDOWN_SRC = \
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index.md \
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CONDUCT.md \
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setup.md \
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$(wildcard _episodes/*.md) \
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reference.md \
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$(wildcard _extras/*.md) \
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LICENSE.md
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# Generated lesson files in the order they appear in the navigation menu.
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HTML_DST = \
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${DST}/index.html \
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${DST}/conduct/index.html \
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${DST}/setup/index.html \
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$(patsubst _episodes/%.md,${DST}/%/index.html,$(wildcard _episodes/*.md)) \
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${DST}/reference/index.html \
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$(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \
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${DST}/license/index.html
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## lesson-md : convert Rmarkdown files to markdown
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lesson-md : ${RMD_DST}
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# Use of .NOTPARALLEL makes rule execute only once
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${RMD_DST} : ${RMD_SRC}
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@bin/knit_lessons.sh ${RMD_SRC}
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## lesson-check : validate lesson Markdown.
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lesson-check :
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@bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md
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## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace.
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lesson-check-all :
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@bin/lesson_check.py -s . -p ${PARSER} -l -w
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## lesson-figures : re-generate inclusion displaying all figures.
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lesson-figures :
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@bin/extract_figures.py -p ${PARSER} ${MARKDOWN_SRC} > _includes/all_figures.html
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## unittest : run unit tests on checking tools.
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unittest :
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python bin/test_lesson_check.py
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## lesson-files : show expected names of generated files for debugging.
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lesson-files :
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@echo 'RMD_SRC:' ${RMD_SRC}
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@echo 'RMD_DST:' ${RMD_DST}
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@echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC}
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@echo 'HTML_DST:' ${HTML_DST}
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## lesson-fixme : show FIXME markers embedded in source files.
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lesson-fixme :
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@fgrep -i -n FIXME ${MARKDOWN_SRC} || true
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#-------------------------------------------------------------------------------
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# Include extra commands if available.
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#-------------------------------------------------------------------------------
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-include commands.mk

‎README.md‎

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# hpc-parallel-novice
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Introductory material on parallelization using python with a focus on HPC platforms
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# HPC-in-a-day [![DOI](https://zenodo.org/badge/83803821.svg)](https://zenodo.org/badge/latestdoi/83803821)
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Novice introduction to high performance computing. This material was conceived as a sandbox project for [swcarpentry/hpc-novice](https://github.com/psteinb/hpc-in-a-day). Parts of it will be contributed to [swcarpentry/hpc-novice](https://github.com/psteinb/hpc-in-a-day) in due course.
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## Material
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The material can be viewed [here](https://psteinb.github.io/hpc-in-a-day)!
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## Audience
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The material as such targets future users of a HPC infrastructure of any discipline. The learners are expected to have an introductory level of programming skills and should know their way around the UNIX command line on a beginners level as well.
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## Scheduler
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hpc-in-a-day is scheduler agnostic. Currently, it supports LSF and SLURM. The job scheduler type can be set with the `workshop_scheduler` variable in [_config.yaml](https://github.com/psteinb/hpc-in-a-day/blob/711cf3f309a04d4a6e955e39c701444733194fed/_config.yml#L40).
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# How to build
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## Dependencies
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The material is based on the [software carpentry lesson template](https://github.com/swcarpentry/styles). It hence depends on a fairly recent version of [jekyll](jekyllrb.org). Just give building it with `make site` in the root directory a try. If you find any problems, please open an issue.

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