site scafolding

README.md

@@ -1,4 +1,4 @@
-![COmanage Logo](https://registry-test.cilogon.org/registry/img/COmanage-Logo-LG-onWhite.png)
+![COmanage Logo](assets/registry/img/COmanage-Logo-LG-onWhite.png)
 
 CO301: Modeling Your Collaboration
 ==================================

_config.yml

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+#------------------------------------------------------------
+# The structure of this site including this file was adapted 
+# from The Carpentries, who should receive attribution and 
+# credit for these configurations. They are covered by a 
+# Creative Commons Attribution license
+# https://creativecommons.org/licenses/by/4.0/
+#------------------------------------------------------------
+
+
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Overall title for pages.
+title: "COmanage Training"
+
+# Life cycle stage of the lesson
+# possible values: "pre-alpha", "alpha", "beta", "stable"
+life_cycle: "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: "checkout@carpentries.org"
+
+# Sites.
+carpentries_site: "https://carpentries.org/"
+
+# Surveys.
+pre_survey: ""
+post_survey: ""
+
+# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am)
+start_time: 540
+
+# 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/
+
+# Turn on built-in syntax highlighting.
+highlighter: rouge
+
+plugins: [jekyll-redirect-from]

_includes/base_path.html

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+{% comment %}
+This is adapted from: https://ricostacruz.com/til/relative-paths-in-jekyll
+
+`page.url` gives the URL of the current page with a leading /:
+
+- when the URL ends with the extension (e.g., /foo/bar.html) then we can get
+  the depth by counting the number of / and remove - 1
+- when the URL ends with a / (e.g. /foo/bar/) then the number / gives the depth
+  directly
+{% endcomment %}
+
+{% assign relative_root_path = '' %}
+
+{% assign last_char = page.url | slice: -1 %}
+
+{% if last_char == "/"}
+{% assign offset = 0 %}
+{% else %}
+{% assign offset = 1 %}
+{% endif %}
+
+{% assign depth = page.url | split: '/' | size | minus: offset %}
+{% if    depth <= 1 %}{% assign relative_root_path = '.' %}
+{% elsif depth == 2 %}{% assign relative_root_path = '..' %}
+{% elsif depth == 3 %}{% assign relative_root_path = '../..' %}
+{% elsif depth == 4 %}{% assign relative_root_path = '../../..' %}
+{% endif %}

_includes/gh_variables.html

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+{% comment %}
+When rendering websites locally, `site.github.url` doesn't get resolved properly
+unless a GitHub Personal Access Token is set up and available in the
+environment. This leads to warnings and errors when trying to serve the site
+locally. To work around this, we use the `jekyll.environment` variable which is
+set to `development` when rendering the site locally, and set to `production` on
+GitHub where `site.github.url` is defined.
+{% endcomment %}
+
+{% if jekyll.environment == "production" %}
+
+{% comment %}
+First, get the name of the repository
+{% endcomment %}
+{% assign repo_name = site.github.repository_name %}
+
+{% comment %}
+`site.github.public_repositories` contains comprehensive information for all public repositories for the organization. We use `where` to extract the part
+of the metadata that is relevant to the present repository.
+{% endcomment %}
+{% assign repo_info = site.github.public_repositories | where: "name", repo_name %}
+
+{% comment %}
+Now, we can extract the default branch for the repo
+{% endcomment %}
+{% assign default_branch = repo_info[0].default_branch %}
+
+{% comment %}
+Other variables requested by the template
+{% endcomment %}
+{% assign repo_url = site.github.repository_url %}
+{% assign search_domain_url = site.github.url %}
+{% assign project_title = site.github.project_title %}
+{% assign source_branch = site.github.source.branch %}
+
+{% elsif jekyll.environment == "development" %}
+
+{% assign repo_name = "" %}
+{% assign repo_url = "" %}
+{% assign default_branch = "" %}
+{% assign search_domain_url = "" %}
+{% assign project_title = "" %}
+{% assign source_branch = "" %}
+
+{% endif %}

_includes/life_cycle.html

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+
+{% if site.life_cycle == "pre-alpha" %}
+
+<div class="panel panel-default life-cycle">
+  <div id="life-cycle" class="panel-body pre-alpha">
+    This lesson is still being designed and assembled (Pre-Alpha version)
+  </div>
+</div>
+
+
+{% elsif site.life_cycle == "alpha" %}
+
+<div class="panel panel-default life-cycle">
+  <div id="life-cycle" class="panel-body alpha">
+    This lesson is in the early stages of development (Alpha version)
+  </div>
+</div>
+
+
+{% elsif site.life_cycle == "beta" %}
+
+<div class="panel panel-default life-cycle">
+  <div id="life-cycle" class="panel-body beta">
+    This lesson is being piloted (Beta version)
+  </div>
+</div>
+
+{% elsif site.life_cycle == "stable" %}
+
+{% comment %}
+We don't do anything special for now
+{% endcomment %}
+
+{% endif %}

_includes/navbar.html

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+{% comment %}
+  Lesson navigation bar.
+{% endcomment %}
+
+{% include gh_variables.html %}
+
+<nav class="navbar navbar-default">
+  <div class="container-fluid">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+
+      {% comment %} Select what logo to display. {% endcomment %}
+      {% if site.carpentry == "swc" %}
+      <a href="{{ site.swc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/swc-icon-blue.svg %}" alt="Software Carpentry logo" />
+      </a>
+      {% elsif site.carpentry == "dc" %}
+      <a href="{{ site.dc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/dc-icon-black.svg %}" alt="Data Carpentry logo" />
+      </a>
+      {% elsif site.carpentry == "lc" %}
+      <a href="{{ site.lc_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/lc-icon-black.svg %}" alt="Library Carpentry logo" />
+      </a>
+      {% elsif site.carpentry == "cp" %}
+      <a href="{{ site.carpentries_site }}" class="pull-left">
+        <img class="navbar-logo" src="{{ relative_root_path }}{% link /assets/img/cp-logo-blue.svg %}" alt="The Carpentries logo" />
+      </a>
+      {% endif %}
+
+      {% comment %} Always show link to home page. {% endcomment %}
+      <a class="navbar-brand" href="{{ relative_root_path }}{% link index.md %}">Home</a>
+
+    </div>
+    <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
+      <ul class="nav navbar-nav">
+
+  {% comment %} Always show code of conduct. {% endcomment %}
+        <li><a href="{{ relative_root_path }}{% link CODE_OF_CONDUCT.md %}">Code of Conduct</a></li>
+
+        {% if site.kind == "lesson" %}
+  {% comment %} Show setup instructions. {% endcomment %}
+        <li><a href="{{ relative_root_path }}{% link setup.md %}">Setup</a></li>
+
+        {% comment %} Show lesson episodes for lessons. {% endcomment %}
+        <li class="dropdown">
+          <a href="{{ relative_root_path }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Episodes <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            {% for episode in site.episodes %}
+            <li><a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a></li>
+            {% endfor %}
+      <li role="separator" class="divider"></li>
+            <li><a href="{{ relative_root_path }}{% link aio.md %}">All in one page (Beta)</a></li>
+          </ul>
+        </li>
+  {% endif %}
+
+  {% comment %} Show extras for lessons or if this is the main workshop-template repo (where they contain documentation). {% endcomment %}
+  {% if site.kind == "lesson" %}
+        <li class="dropdown">
+          <a href="{{ relative_root_path }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Extras <span class="caret"></span></a>
+          <ul class="dropdown-menu">
+            <li><a href="{{ relative_root_path }}{% link reference.md %}">Reference</a></li>
+            {% for extra in site.extras %}
+            <li><a href="{{ relative_root_path }}{{ extra.url }}">{{ extra.title }}</a></li>
+            {% endfor %}
+          </ul>
+        </li>
+  {% endif %}
+
+  {% comment %} Always show license. {% endcomment %}
+        <li><a href="{{ relative_root_path }}{% link LICENSE.md %}">License</a></li>
+  {% if page.source %}
+  {% if page.source == "Rmd" %}
+  <li><a href="{{repo_url}}/edit/{{ default_branch }}/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+  {% endif %}
+  {% else %}
+  <li><a href="{{repo_url}}/edit/{{ default_branch}}/{{page.path}}" data-checker-ignore>Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
+  {% endif %}
+      </ul>
+      <form class="navbar-form navbar-right" role="search" id="search" onsubmit="google_search(); return false;">
+        <div class="form-group">
+          <input type="text" id="google-search" placeholder="Search..." aria-label="Google site search">
+        </div>
+      </form>
+    </div>
+  </div>
+</nav>

_includes/syllabus.html

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+{% include base_path.html %}
+
+{% comment %}
+  Display syllabus in tabular form.
+  Days are displayed if at least one episode has 'start = true'.
+{% endcomment %}
+<div class="syllabus">
+  <h2 id="schedule">Sample Schedule</h2>
+
+  {% assign day = 0 %}
+  {% assign multiday = false %}
+  {% for episode in site.episodes %}
+    {% if episode.start %}{% assign multiday = true %}{% break %}{% endif %}
+  {% endfor %}
+  {% assign current = site.start_time %}
+
+  <table class="table table-striped">
+  <tr>
+    {% if multiday %}<td class="col-md-1"></td>{% endif %}
+    <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}"></td>
+    <td class="col-md-3"><a href="{{ relative_root_path }}{% link setup.md %}">Setup</a></td>
+    <td class="col-md-7">Download files required for the lesson</td>
+  </tr>
+  <tr>
+    {% if multiday %}<td class="col-md-1"></td>{% endif %}
+    <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}"></td>
+    <td class="col-md-3"><a href="{{ site.instructor_pre_survey }}{{ site.github.project_title }}">Pre-training survey</a></td>
+    <td class="col-md-7">Please fill out our pre-training survey before the start of the course.</td>
+  </tr>
+  {% for episode in site.episodes %}
+    {% if episode.start %} {% comment %} Starting a new day? {% endcomment %}
+      {% assign day = day | plus: 1 %}
+      {% if day > 1 %} {% comment %} If about to start day 2 or later, show finishing time for previous day {% endcomment %}
+        {% assign hours = current | divided_by: 60 %}
+        {% assign minutes = current | modulo: 60 %}
+        <tr>
+          {% if multiday %}<td class="col-md-1"></td>{% endif %}
+          <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+          <td class="col-md-3">Finish</td>
+          <td class="col-md-7"></td>
+        </tr>
+      {% endif %}
+      {% assign current = site.start_time %} {% comment %}Re-set start time of this episode to general daily start time {% endcomment %}
+    {% endif %}
+    {% assign hours = current | divided_by: 60 %}
+    {% assign minutes = current | modulo: 60 %}
+    <tr>
+      {% if multiday %}<td class="col-md-1">{% if episode.start %}Day {{ day }}{% endif %}</td>{% endif %}
+      <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+      <td class="col-md-3">
+        {% assign lesson_number = lesson_number | plus: 1 %}
+  {{ lesson_number }}. <a href="{{ relative_root_path }}{{ episode.url }}">{{ episode.title }}</a>
+      </td>
+      <td class="col-md-7">
+        {% if episode.break %}
+          Break
+        {% else %}
+          {% if episode.questions %}
+            {% for question in episode.questions %}
+              {{question|markdownify|strip_html}}
+              {% unless forloop.last %}
+              <br/>
+              {% endunless %}
+            {% endfor %}
+          {% endif %}
+        {% endif %}
+      </td>
+    </tr>
+    {% assign current = current | plus: episode.teaching | plus: episode.exercises | plus: episode.break %}
+  {% endfor %}
+  {% assign hours = current | divided_by: 60 %}
+  {% assign minutes = current | modulo: 60 %}
+  <tr>
+    {% if multiday %}<td class="col-md-1"></td>{% endif %}
+    <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+    <td class="col-md-3"><a href="{{ site.instructor_post_survey }}{{ site.github.project_title }}">Post-training survey</a></td>
+    <td class="col-md-7">Please fill out our pre-training survey before the start of the course.</td>
+  </tr>
+  {% assign current = current | plus: 15 %}
+  {% assign hours = current | divided_by: 60 %}
+  {% assign minutes = current | modulo: 60 %}
+  <tr>
+    {% if multiday %}<td class="col-md-1"></td>{% endif %}
+    <td class="{% if multiday %}col-md-1{% else %}col-md-2{% endif %}">{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}</td>
+    <td class="col-md-3">Finish</td>
+    <td class="col-md-7"></td>
+  </tr>
+  </table>
+
+  <p>
+    The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
+  </p>
+
+</div>