Merge pull request #203 from swcarpentry/fix-svg

[rnaseq-cwl-training.git] / bin / lesson_initialize.py

diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
index cfd8f6f6cc795213b6c0cfb970c483a253cd9b45..acb253b542fc9009602a3c7351352f6b37aeba04 100755 (executable)
--- a/bin/lesson_initialize.py
+++ b/bin/lesson_initialize.py
@@ -3,10 +3,10 @@
 """Initialize a newly-created repository."""
 
 
 """Initialize a newly-created repository."""
 
 

+from __future__ import print_function

 import sys
 import os
 
 import sys
 import os
 

-

 ROOT_AUTHORS = '''\
 FIXME: list authors' names and email addresses.
 '''
 ROOT_AUTHORS = '''\
 FIXME: list authors' names and email addresses.
 '''


@@ -45,7 +45,7 @@ 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,
 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.
 
     However,
     we will be able to respond more quickly if you use one of the other methods described below.
 


@@ -61,16 +61,37 @@ and to meet some of our community members.
     you can submit a pull request (PR).
     Instructions for doing this are [included below](#using-github).
 
     you can submit a pull request (PR).
     Instructions for doing this are [included below](#using-github).
 

-## What We're Looking For
+## 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/swcarpentry/lesson-example>,
+    which documents the format of our lessons
+    and can be viewed at <https://swcarpentry.github.io/lesson-example>.
+
+3.  If you wish to change the template used for workshop websites,
+    please work in <https://github.com/swcarpentry/workshop-template>.
+    The home page of that repository explains how to set up workshop websites,
+    while the extra pages in <https://swcarpentry.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/swcarpentry/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 and submitting [bug reports][issues]
 about things that don't work, aren't clear, or are missing.
 
 There are many ways to contribute,
 from writing new exercises and improving existing ones
 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:
 and [Software Carpentry][swc-issues] projects.
 
 Comments on issues and reviews of pull requests are just as welcome:


@@ -80,7 +101,7 @@ 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.
 
 to forget how impenetrable some of this material can be,
 so fresh eyes are always welcome.
 

-## What We're *Not* Looking For
+## 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.
 
 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.


@@ -96,69 +117,53 @@ Our workshops typically contain a mixture of Windows, Mac OS X, and Linux users;
 in order to be usable,
 our lessons must run equally well on all three.
 
 in order to be usable,
 our lessons must run equally well on all three.
 

-## Getting Started
-
-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.
+## Using GitHub

 
 

-If you want to start adding or fixing material yourself,
-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].
 [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.
-
-## Our Template
-
-[This documentation][example-site] explains how we format our lessons
-(and is itself an example of that formatting).
+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.
 
 ## 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
 [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

-[example-site]: https://swcarpentry.github.io/lesson-example/
-[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
 [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/{USERNAME}/{LESSON-NAME}/issues/
-[repo]: https://github.com/{USERNAME}/{LESSON-NAME}/
+[issues]: https://guides.github.com/features/issues/

 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [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 = '''\
 '''
 
 ROOT_CONFIG_YML = '''\


@@ -166,59 +171,63 @@ ROOT_CONFIG_YML = '''\
 # Values for this lesson.
 #------------------------------------------------------------
 
 # Values for this lesson.
 #------------------------------------------------------------
 

-# Which carpentry is this ("swc" or "dc")?
+# Which carpentry is this ("swc", "dc", or "lc")?

 carpentry: "swc"
 
 carpentry: "swc"
 

-# What kind of thing is this ("workshop" or "lesson")?
-kind: "lesson"
-

 # Overall title for pages.
 title: "Lesson Title"
 
 # Overall title for pages.
 title: "Lesson Title"
 

-# Account (without slashes).
-account: "[[USER-NAME]]"
-
-# Root URL below account (without slashes).
-project: "[[REPO-NAME]]"
-
-# Contact email address.
-email: "[[CONTACT-ADDRESS]]"
+# 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".
+email: "mailto:lessons@software-carpentry.org"

 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
 #------------------------------------------------------------
 
 
 #------------------------------------------------------------
 # Generic settings (should not need to change).
 #------------------------------------------------------------
 

-# Is this production or development? (Overridden in _config_dev.yml.)
-is_production: true
+# 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/.
+repository: <USERNAME>/<PROJECT>

 
 # Sites.
 amy_site: "https://amy.software-carpentry.org/workshops"
 
 # Sites.
 amy_site: "https://amy.software-carpentry.org/workshops"

-dc_site: "https://datacarpentry.org"
+dc_site: "http://datacarpentry.org"

 swc_github: "https://github.com/swcarpentry"
 swc_site: "https://software-carpentry.org"
 swc_github: "https://github.com/swcarpentry"
 swc_site: "https://software-carpentry.org"

+swc_pages: "https://swcarpentry.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"
 workshop_repo: "https://github.com/swcarpentry/workshop-template"
 workshop_site: "https://swcarpentry.github.io/workshop-template"
 template_repo: "https://github.com/swcarpentry/styles"
 example_repo: "https://github.com/swcarpentry/lesson-example"
 example_site: "https://swcarpentry.github.com/lesson-example"
 workshop_repo: "https://github.com/swcarpentry/workshop-template"
 workshop_site: "https://swcarpentry.github.io/workshop-template"

+training_site: "https://swcarpentry.github.io/instructor-training"

 
 # Surveys.
 pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
 post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
 
 # Surveys.
 pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
 post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="

+training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"

 
 

-# Start time in minutes (540 is 09:00 am)
-start_time: 540
+# 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
 
 # Specify that things in the episodes collection should be output.
 collections:
   episodes:
     output: true

-    permalink: /:path/
+    permalink: /:path/index.html

   extras:
     output: true
   extras:
     output: true

+    permalink: /:path/index.html

 
 # Set the default layout for things in the episodes collection.
 defaults:
 
 # Set the default layout for things in the episodes collection.
 defaults:

+  - values:
+      root: ..

   - scope:
       path: ""
       type: episodes
   - scope:
       path: ""
       type: episodes


@@ -230,13 +239,15 @@ exclude:
   - Makefile
   - bin
 
   - Makefile
   - bin
 

-# Turn off built-in syntax highlighting.
-highlighter: false
+# Turn on built-in syntax highlighting.
+highlighter: rouge

 '''
 
 ROOT_INDEX_MD = '''\
 ---
 layout: lesson
 '''
 
 ROOT_INDEX_MD = '''\
 ---
 layout: lesson

+root: .
+permalink: index.html  # Is the only page that don't follow the partner /:path/index.html

 ---
 FIXME: home page introduction
 
 ---
 FIXME: home page introduction
 


@@ -249,6 +260,7 @@ FIXME: home page introduction
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference

+root: .

 ---
 
 ## Glossary
 ---
 
 ## Glossary


@@ -260,11 +272,50 @@ ROOT_SETUP_MD = '''\
 ---
 layout: page
 title: Setup
 ---
 layout: page
 title: Setup

-permalink: /setup/
+root: .

 ---
 FIXME
 '''
 
 ---
 FIXME
 '''
 

+ROOT_AIO_MD = '''\
+---
+layout: page 
+root: .
+---
+<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.innerHTML = htmlDocArticle.innerHTML;
+        }
+      }
+      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 %}
+'''
+

 EPISODES_INTRODUCTION_MD = '''\
 ---
 title: "Introduction"
 EPISODES_INTRODUCTION_MD = '''\
 ---
 title: "Introduction"


@@ -283,7 +334,6 @@ EXTRAS_ABOUT_MD = '''\
 ---
 layout: page
 title: About
 ---
 layout: page
 title: About

-permalink: /about/

 ---
 {% include carpentries.html %}
 '''
 ---
 {% include carpentries.html %}
 '''


@@ -292,7 +342,6 @@ EXTRAS_DISCUSS_MD = '''\
 ---
 layout: page
 title: Discussion
 ---
 layout: page
 title: Discussion

-permalink: /discuss/

 ---
 FIXME
 '''
 ---
 FIXME
 '''


@@ -301,16 +350,48 @@ EXTRAS_FIGURES_MD = '''\
 ---
 layout: page
 title: Figures
 ---
 layout: page
 title: Figures

-permalink: /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 = '''\
 ---
 layout: page
 '''
 
 EXTRAS_GUIDE_MD = '''\
 ---
 layout: page

-title: "Instructors' Guide"
-permalink: /guide/
+title: "Instructor Notes"

 ---
 FIXME
 '''
 ---
 FIXME
 '''


@@ -323,11 +404,12 @@ BOILERPLATE = (
     ('index.md', ROOT_INDEX_MD),
     ('reference.md', ROOT_REFERENCE_MD),
     ('setup.md', ROOT_SETUP_MD),
     ('index.md', ROOT_INDEX_MD),
     ('reference.md', ROOT_REFERENCE_MD),
     ('setup.md', ROOT_SETUP_MD),

+    ('aio.md', ROOT_AIO_MD),

     ('_episodes/01-introduction.md', EPISODES_INTRODUCTION_MD),
     ('_extras/about.md', EXTRAS_ABOUT_MD),
     ('_extras/discuss.md', EXTRAS_DISCUSS_MD),
     ('_extras/figures.md', EXTRAS_FIGURES_MD),
     ('_episodes/01-introduction.md', EPISODES_INTRODUCTION_MD),
     ('_extras/about.md', EXTRAS_ABOUT_MD),
     ('_extras/discuss.md', EXTRAS_DISCUSS_MD),
     ('_extras/figures.md', EXTRAS_FIGURES_MD),

-    ('_extras/guide.md', EXTRAS_GUIDE_MD)
+    ('_extras/guide.md', EXTRAS_GUIDE_MD),

 )
 
 
 )