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][contact].
+ 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.
to updating or filling in the documentation
and 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 list of issues for this repository][issues],
-or the issues for [Data Carpentry][dc-issues]
+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]
and [Software Carpentry][swc-issues] projects.
Comments on issues and reviews of pull requests are just as welcome:
## Using GitHub
-If you choose to contribute via GitHub,
-you may want to look at
+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].
-In brief:
-
-1. The published copy of the lesson is in the `gh-pages` branch of the repository
- (so that GitHub will regenerate it automatically).
- Please create all branches from that,
- and merge the [master repository][repo]'s `gh-pages` branch into your `gh-pages` branch
- before starting work.
- Please do *not* work directly in your `gh-pages` branch,
- since that will make it difficult for you to work on other contributions.
-
-2. We use [GitHub flow][github-flow] to manage changes:
- 1. Create a new branch in your desktop copy of this repository for each significant change.
- 2. Commit the change in that branch.
- 3. Push that branch to your fork of this repository on GitHub.
- 4. Submit a pull request from that branch to the [master repository][repo].
- 5. If you receive feedback,
- make changes on your desktop and push to your branch on GitHub:
- the pull request will update automatically.
-
-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 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 master 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 master 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 master `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 master `gh-pages` branch.
+Lastly, published copies of all the lessons are available in the `gh-pages` branch of the master
+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][contact].
+You can also [reach us by email][email].
-[contact]: mailto:admin@software-carpentry.org
+[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]: http://github.com
+[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://github.com/swcarpentry/FIXME/issues/
-[repo]: https://github.com/swcarpentry/FIXME/
+[issues]: https://guides.github.com/features/issues/
[swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: http://software-carpentry.org/lessons/
-[swc-site]: http://software-carpentry.org/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
'''
ROOT_CONFIG_YML = '''\
# Contact. This *must* include the protocol: if it's an email
# address, it must look like "mailto:lessons@software-carpentry.org",
# or if it's a URL, "https://gitter.im/username/ProjectName".
-contact: "mailto:lessons@software-carpentry.org"
+email: "mailto:lessons@software-carpentry.org"
#------------------------------------------------------------
# Generic settings (should not need to change).
swc_github: "https://github.com/swcarpentry"
swc_site: "https://software-carpentry.org"
swc_pages: "https://swcarpentry.github.io"
-lc_site: "http://librarycarpentry.github.io/"
+lc_site: "https://librarycarpentry.github.io/"
template_repo: "https://github.com/swcarpentry/styles"
example_repo: "https://github.com/swcarpentry/lesson-example"
example_site: "https://swcarpentry.github.com/lesson-example"
- Makefile
- bin
-# Turn off built-in syntax highlighting.
-highlighter: false
+# Turn on built-in syntax highlighting.
+highlighter: rouge
'''
ROOT_INDEX_MD = '''\
ROOT_REFERENCE_MD = '''\
---
layout: reference
+root: .
---
## Glossary
---
layout: page
title: Setup
+root: .
---
FIXME
'''
ROOT_AIO_MD = '''\
---
layout: page
+root: .
---
<script>
window.onload = function() {
layout: page
title: Figures
---
-{% include all_figures.html %}
+<script>
+ window.onload = function() {
+ var lesson_episodes = [
+ {% for episode in site.episodes %}
+ "{{ 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 article_here = document.getElementById(this.episode);
+ var parser = new DOMParser();
+ var htmlDoc = parser.parseFromString(this.responseText,"text/html");
+ var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0];
+ article_here.appendChild(htmlDocArticle.getElementsByTagName("h1")[0]);
+ for (let image of htmlDocArticle.getElementsByTagName("img")) {
+ article_here.appendChild(image);
+ }
+ }
+ }
+ episode_url = "{{ page.root }}" + 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 episode in site.episodes %}
+<article id="{{ episode.url }}"></article>
+{% endfor %}
'''
EXTRAS_GUIDE_MD = '''\
FIXME
'''
-INCLUDES_ALL_FIGURES_HTML = '''\
-<!-- empty -->
-'''
-
BOILERPLATE = (
('AUTHORS', ROOT_AUTHORS),
('CITATION', ROOT_CITATION),
('_extras/discuss.md', EXTRAS_DISCUSS_MD),
('_extras/figures.md', EXTRAS_FIGURES_MD),
('_extras/guide.md', EXTRAS_GUIDE_MD),
- ('_includes/all_figures.html', INCLUDES_ALL_FIGURES_HTML)
)
projects / rnaseq-cwl-training.git / blobdiff