Fix root YAML variable in bin/lesson_initialize.py

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

diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
index 853285e9dba4224f43a44b9c0e520578a877bc87..3ee1ace61cec7a8482dd439a59572bf579c48472 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.
 


@@ -63,18 +63,22 @@ and to meet some of our community members.
 
 ## Where to Contribute
 
 
 ## Where to Contribute
 

-1.  If you wish to change this example lesson,
-    please work in <https://github.com/swcarpentry/lesson-example>.
-    This lesson documents the format of our lessons,
+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>.
 
     and can be viewed at <https://swcarpentry.github.io/lesson-example>.
 

-2.  If you wish to change the template used for workshop websites,
+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.
 
     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.
 

-3.  If you wish to change CSS style files, tools,
+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>.
 
     or HTML boilerplate for lessons or workshops stored in `_includes` or `_layouts`,
     please work in <https://github.com/swcarpentry/styles>.
 


@@ -147,20 +151,19 @@ and have final say over what gets merged into the lesson.
 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.
 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-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]: http://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/lesson-example/issues/
-[repo]: https://github.com/swcarpentry/lesson-example/
+[issues]: https://github.com/swcarpentry/FIXME/issues/
+[repo]: https://github.com/swcarpentry/FIXME/

 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
 [swc-lessons]: http://software-carpentry.org/lessons/
 [swc-site]: http://software-carpentry.org/


@@ -171,60 +174,63 @@ 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"
 

-# Repository URL (without trailing slash).
-repo: https://github.com/[USERNAME]/[LESSON-SLUG]
-
-# Root URL below username.github.io domain, with leading slash but no trailing slash.
-# For example, for 'https://swcarpentry.github.io/lesson-example', use '/lesson-example'.
-root: "/[LESSON-SLUG]"
-
-# 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: "http://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


@@ -243,6 +249,8 @@ highlighter: false
 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
 


@@ -255,6 +263,7 @@ FIXME: home page introduction
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference

+root: .

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


@@ -266,11 +275,50 @@ 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"


@@ -289,7 +337,6 @@ EXTRAS_ABOUT_MD = '''\
 ---
 layout: page
 title: About
 ---
 layout: page
 title: About

-permalink: /about/

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


@@ -298,7 +345,6 @@ EXTRAS_DISCUSS_MD = '''\
 ---
 layout: page
 title: Discussion
 ---
 layout: page
 title: Discussion

-permalink: /discuss/

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


@@ -307,24 +353,52 @@ 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
 '''
 

-INCLUDES_ALL_FIGURES_HTML = '''\
-<!-- empty -->
-'''
-

 BOILERPLATE = (
     ('AUTHORS', ROOT_AUTHORS),
     ('CITATION', ROOT_CITATION),
 BOILERPLATE = (
     ('AUTHORS', ROOT_AUTHORS),
     ('CITATION', ROOT_CITATION),


@@ -333,12 +407,12 @@ 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),
     ('_extras/guide.md', EXTRAS_GUIDE_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),

-    ('_includes/all_figures.html', INCLUDES_ALL_FIGURES_HTML)

 )
 
 
 )