Verified Commit c8a0458d authored by Toby Hodges's avatar Toby Hodges
Browse files

initialise lesson

parent b7c23add
# Travis CI is only used to check the lesson and is not involved in its deployment
dist: xenial # Ubuntu 16.04 (required for python 3.7)
language: python
python: 3.7
branches:
only:
- gh-pages
- /.*/
before_install:
- sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
- echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" | sudo tee -a /etc/apt/sources.list
- sudo apt-get update -y
- sudo apt-get install -y r-base
- sudo Rscript -e "install.packages('knitr', repos = 'https://', dependencies = TRUE)"
- sudo Rscript -e "install.packages('stringr', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
- sudo Rscript -e "install.packages('checkpoint', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
- sudo Rscript -e "install.packages('ggplot2', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
- rvm default
- gem install json kramdown jekyll bundler
install:
- pip install pyyaml
script:
- make lesson-check-all
- make --always-make site
Toby Hodges: toby.hodges@embl.de
No citation info yet.
# Contributing
[The Carpentries][c-site] ([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects,
and we welcome contributions of all kinds:
new lessons,
fixes to existing material,
bug reports,
and reviews of proposed changes are all welcome.
## Contributor Agreement
By contributing,
you agree that we may redistribute your work under [our license](LICENSE.md).
In exchange,
we will address your issues and/or assess your change proposal as promptly as we can,
and help you become a member of our community.
Everyone involved in [The Carpentries][c-site]
agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md).
## How to Contribute
The easiest way to get started is to file an issue
to tell us about a spelling mistake,
some awkward wording,
or a factual error.
This is a good way to introduce yourself
and to meet some of our community members.
1. If you do not have a [GitHub][github] account,
you can [send us comments by email][email].
However,
we will be able to respond more quickly if you use one of the other methods described below.
2. If you have a [GitHub][github] account,
or are willing to [create one][github-join],
but do not know how to use Git,
you can report problems or suggest improvements by [creating an issue][issues].
This allows us to assign the item to someone
and to respond to it in a threaded discussion.
3. If you are comfortable with Git,
and would like to add or change material,
you can submit a pull request (PR).
Instructions for doing this are [included below](#using-github).
## Where to Contribute
1. If you wish to change this lesson,
please work in <https://github.com/swcarpentry/FIXME>,
which can be viewed at <https://swcarpentry.github.io/FIXME>.
2. If you wish to change the example lesson,
please work in <https://github.com/carpentries/lesson-example>,
which documents the format of our lessons
and can be viewed at <https://carpentries.github.io/lesson-example>.
3. If you wish to change the template used for workshop websites,
please work in <https://github.com/carpentries/workshop-template>.
The home page of that repository explains how to set up workshop websites,
while the extra pages in <https://carpentries.github.io/workshop-template>
provide more background on our design choices.
4. If you wish to change CSS style files, tools,
or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
please work in <https://github.com/carpentries/styles>.
## What to Contribute
There are many ways to contribute,
from writing new exercises and improving existing ones
to updating or filling in the documentation
and submitting [bug reports][issues]
about things that don't work, aren't clear, or are missing.
If you are looking for ideas, please see the 'Issues' tab for
a list of issues associated with this repository,
or you may also look at the issues for [Data Carpentry][dc-issues],
[Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects.
Comments on issues and reviews of pull requests are just as welcome:
we are smarter together than we are on our own.
Reviews from novices and newcomers are particularly valuable:
it's easy for people who have been using these lessons for a while
to forget how impenetrable some of this material can be,
so fresh eyes are always welcome.
## What *Not* to Contribute
Our lessons already contain more material than we can cover in a typical workshop,
so we are usually *not* looking for more concepts or tools to add to them.
As a rule,
if you want to introduce a new idea,
you must (a) estimate how long it will take to teach
and (b) explain what you would take out to make room for it.
The first encourages contributors to be honest about requirements;
the second, to think hard about priorities.
We are also not looking for exercises or other material that only run on one platform.
Our workshops typically contain a mixture of Windows, macOS, and Linux users;
in order to be usable,
our lessons must run equally well on all three.
## Using GitHub
If you choose to contribute via GitHub, you may want to look at
[How to Contribute to an Open Source Project on GitHub][how-contribute].
To manage changes, we follow [GitHub flow][github-flow].
Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
The maintainers are community volunteers and have final say over what gets merged into the lesson.
To use the web interface for contributing to a lesson:
1. Fork the originating repository to your GitHub profile.
2. Within your version of the forked repository, move to the `gh-pages` branch and
create a new branch for each significant change being made.
3. Navigate to the file(s) you wish to change within the new branches and make revisions as required.
4. Commit all changed files within the appropriate branches.
5. Create individual pull requests from each of your changed branches
to the `gh-pages` branch within the originating repository.
6. If you receive feedback, make changes using your issue-specific branches of the forked
repository and the pull requests will update automatically.
7. Repeat as needed until all feedback has been addressed.
When starting work, please make sure your clone of the originating `gh-pages` branch is up-to-date
before creating your own revision-specific branch(es) from there.
Additionally, please only work from your newly-created branch(es) and *not*
your clone of the originating `gh-pages` branch.
Lastly, published copies of all the lessons are available in the `gh-pages` branch of the originating
repository for reference while revising.
## Other Resources
General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
happens on the [discussion mailing list][discuss-list],
which everyone is welcome to join.
You can also [reach us by email][email].
[email]: mailto:admin@software-carpentry.org
[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
[dc-lessons]: http://datacarpentry.org/lessons/
[dc-site]: http://datacarpentry.org/
[discuss-list]: http://lists.software-carpentry.org/listinfo/discuss
[github]: https://github.com
[github-flow]: https://guides.github.com/introduction/flow/
[github-join]: https://github.com/join
[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
[issues]: https://guides.github.com/features/issues/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
[swc-lessons]: https://software-carpentry.org/lessons/
[swc-site]: https://software-carpentry.org/
[c-site]: https://carpentries.org/
[lc-site]: https://librarycarpentry.org/
[lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry
# Building Websites with Jekyll and GitHub/GitLab
Lesson material.
## Maintainer(s)
Current maintainer of this lesson is
* Toby Hodges
## Authors
A list of contributors to the lesson can be found in [AUTHORS](AUTHORS)
## Citation
To cite this lesson, please consult with [CITATION](CITATION)
[lesson-example]: https://carpentries.github.io/lesson-example
#------------------------------------------------------------
# Values for this lesson.
#------------------------------------------------------------
# Which carpentry is this ("swc", "dc", "lc", or "cp")?
# swc: Software Carpentry
# dc: Data Carpentry
# lc: Library Carpentry
# cp: Carpentries (to use for instructor traning for instance)
carpentry: none
# Overall title for pages.
title: "Building Websites with Jekyll and GitHub/GitLab"
# Life cycle stage of the lesson
# possible values: "pre-alpha", "alpha", "beta", "stable"
life_cycle: "pre-alpha"
#------------------------------------------------------------
# Generic settings (should not need to change).
#------------------------------------------------------------
# What kind of thing is this ("workshop" or "lesson")?
kind: "lesson"
# Magic to make URLs resolve both locally and on GitHub.
# See https://help.github.com/articles/repository-metadata-on-github-pages/.
# Please don't change it: <USERNAME>/<PROJECT> is correct.
repository: <USERNAME>/<PROJECT>
# Email address, no mailto:
email: "toby.hodges@embl.de"
# Sites.
amy_site: "https://amy.carpentries.org/workshops"
carpentries_github: "https://github.com/carpentries"
carpentries_pages: "https://carpentries.github.io"
carpentries_site: "https://carpentries.org/"
dc_site: "https://datacarpentry.org"
example_repo: "https://github.com/carpentries/lesson-example"
example_site: "https://carpentries.github.io/lesson-example"
lc_site: "https://librarycarpentry.org/"
swc_github: "https://github.com/swcarpentry"
swc_pages: "https://swcarpentry.github.io"
swc_site: "https://software-carpentry.org"
template_repo: "https://github.com/carpentries/styles"
training_site: "https://carpentries.github.io/instructor-training"
workshop_repo: "https://github.com/carpentries/workshop-template"
workshop_site: "https://carpentries.github.io/workshop-template"
cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
# Surveys.
pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="
post_survey: "https://carpentries.typeform.com/to/UgVdRQ?slug="
instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="
# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
start_time: 0
# Specify that things in the episodes collection should be output.
collections:
episodes:
output: true
permalink: /:path/index.html
extras:
output: true
permalink: /:path/index.html
# Set the default layout for things in the episodes collection.
defaults:
- values:
root: .
layout: page
- scope:
path: ""
type: episodes
values:
root: ..
layout: episode
- scope:
path: ""
type: extras
values:
root: ..
layout: page
# Files and directories that are not to be copied.
exclude:
- Makefile
- bin/
- .Rproj.user/
- .vendor/
- .docker-vendor/
# Turn on built-in syntax highlighting.
highlighter: rouge
---
title: "Introduction"
teaching: 0
exercises: 0
questions:
- "Key question (FIXME)"
objectives:
- "First learning objective. (FIXME)"
keypoints:
- "First key point. Brief Answer to questions. (FIXME)"
---
FIXME
{% include links.md %}
---
title: About
---
{% include carpentries.html %}
{% include links.md %}
---
title: Discussion
---
FIXME
{% include links.md %}
---
title: Figures
---
{% include base_path.html %}
{% include manual_episode_order.html %}
<script>
window.onload = function() {
var lesson_episodes = [
{% for lesson_episode in lesson_episodes %}
{% if site.episode_order %}
{% assign episode = site.episodes | where: "slug", lesson_episode | first %}
{% else %}
{% assign episode = lesson_episode %}
{% endif %}
"{{ episode.url }}"{% unless forloop.last %},{% endunless %}
{% endfor %}
];
var xmlHttp = []; /* Required since we are going to query every episode. */
for (i=0; i < lesson_episodes.length; i++) {
xmlHttp[i] = new XMLHttpRequest();
xmlHttp[i].episode = lesson_episodes[i]; /* To enable use this later. */
xmlHttp[i].onreadystatechange = function() {
if (this.readyState == 4 && this.status == 200) {
var parser = new DOMParser();
var htmlDoc = parser.parseFromString(this.responseText,"text/html");
var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
var article_here = document.getElementById(this.episode);
var images = htmlDocArticle.getElementsByTagName("img");
if (images.length > 0) {
var h1text = htmlDocArticle.getElementsByTagName("h1")[0].innerHTML;
var htitle = document.createElement('h2');
htitle.innerHTML = h1text;
article_here.appendChild(htitle);
var image_num = 0;
for (let image of images) {
image_num++;
var title = document.createElement('p');
title.innerHTML = "<strong>Figure " + image_num + ".</strong> " + image.alt;
article_here.appendChild(title);
article_here.appendChild(image.cloneNode(false));
if (image_num < images.length) {
var hr = document.createElement('hr');
article_here.appendChild(hr);
}
}
}
}
}
episode_url = "{{ relative_root_path }}" + lesson_episodes[i];
xmlHttp[i].open("GET", episode_url);
xmlHttp[i].send(null);
}
}
</script>
{% comment %} Create anchor for each one of the episodes. {% endcomment %}
{% for lesson_episode in lesson_episodes %}
{% if site.episode_order %}
{% assign episode = site.episodes | where: "slug", lesson_episode | first %}
{% else %}
{% assign episode = lesson_episode %}
{% endif %}
<article id="{{ episode.url }}" class="figures"></article>
{% endfor %}
{% include links.md %}
---
title: "Instructor Notes"
---
FIXME
{% include links.md %}
---
layout: lesson
root: . # Is the only page that doesn't follow the pattern /:path/index.html
permalink: index.html # Is the only page that doesn't follow the pattern /:path/index.html
---
- Markdown
- links
- conversion to HTML
- GitHub Pages
- activating
- `index.md`
- YAML headers
- GitLab Pages
- activating
- `gitlab-ci.yml`
- `index.md`
- YAML headers
- Jekyll
- variables
- `_config.yml`
- includes
- Themes
- layouts
<!-- this is an html comment -->
{% comment %} This is a comment in Liquid {% endcomment %}
> ## Prerequisites
>
> - familiarity with git (add, commit, pull, push, checkout)& at least one of GitHub or GitLab
> - familiarity with HTML & CSS
{: .prereq}
{% include links.md %}
---
layout: reference
---
## Glossary
FIXME
{% include links.md %}
---
title: Setup
---
FIXME
{% include links.md %}
Supports Markdown
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