ols-theme 0.4.0 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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 SHA512:
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data/_includes/default-footer.html

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+<footer class="footer">
+    <div class="container content">
+      <div class="columns">
+        <div class="column">
+          <h3>Get in touch</h3>
+          <p>
+            <i class="fab fa-twitter"></i>
+            <a href="https://twitter.com/{{ site.twitter }}">
+              {{ site.twitter }}
+            </a>
+          </p>
+          <p>
+            <i class="fas fa-at"></i>
+            <a href="mailto:{{ site.email }}">
+              {{ site.email|replace:'@','[at]' }}
+            </a>
+          </p>
+          <p>
+            <i class="fab fa-github"></i>
+            <a href="{{ site.github.repository_url }}">
+              {{ site.github.owner_name }}
+            </a>
+          </p>
+            <p>
+                <i class="fa fa-envelope" aria-hidden="true"></i>
+                <a href="{{ site.announcement_list }}">
+                    Subscribe to our announcements list
+                </a>
+            </p>
+        </div>
+        <div class="column is-5">
+          <p>
+            If you want to report a problem or suggest an enhancement we'd love
+            for you to
+            <a href="{{ site.github.repository_url }}/issues/new">open an issue</a>
+            on our GitHub repository because then we can get right on it.
+          </p>
+          <p>
+            The website content is licensed
+            <a href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY SA 4.0</a>.
+            The code behind the infrastructure is licensed under the <a href="{{ site.github.repository_url }}/blob/main/LICENSE.md">MIT License</a>
+          </p>
+          <p>
+            The logo was originally designed by
+            <a href="https://github.com/htmluke">Lucas Emanoell Medeiros e Silva</a> and
+            then adapted by the team.
+          </p>
+          <p>
+            Open Life Science Limited is a non-profit charitable company limited by guarantee, based in the United Kingdom. 
+            Company number 
+            <a href="http://data.companieshouse.gov.uk/doc/company/12824090">12824090</a>.
+          </p>
+        </div>
+      </div>
+    </div>
+  </footer>

data/_includes/default-header.html

@@ -0,0 +1,81 @@
+<nav class="navbar is-fixed-top" role="navigation" aria-label="main navigation">
+    <div class="container">
+      <div class="navbar-brand">
+        <a class="navbar-item" href="/">
+            <img src="{{ site.baseurl }}/assets/images/logo.png" alt="OLS">
+        </a>
+        <a
+          role="button"
+          class="navbar-burger burger"
+          aria-label="menu"
+          aria-expanded="false"
+          data-target="top-menu"
+        >
+          <span aria-hidden="true"></span> <span aria-hidden="true"></span>
+          <span aria-hidden="true"></span>
+        </a>
+      </div>
+
+      <div id="top-menu" class="navbar-menu">
+        <div class="navbar-end">
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link">OLS program</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="/index#applications"> Applications </a>
+              <a class="navbar-item" href="/about"> The program itself </a>
+              <a class="navbar-item" href="/about#projects"> Projects </a>
+              <a class="navbar-item navbar-previous-title" href="/about#the-roles"> Role description </a>
+              <a class="navbar-item" href="/about#mentees"> Mentees </a>
+              <a class="navbar-item" href="/about#mentors"> Mentors </a>
+              <a class="navbar-item" href="/about#experts"> Experts </a>
+              <a class="navbar-item" href="/about#facilitators"> Facilitators </a>
+              <a class="navbar-item navbar-previous-title" href="/index#cohorts"> Cohorts </a>
+            </div>
+          </div>
+
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link" href="/ols-7">OLS-7</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="/ols-7"> Syllabus </a>
+              <a class="navbar-item" href="/ols-7/schedule"> Schedule</a>
+              <a class="navbar-item" href="/ols-7/projects-participants/"> Projects & Participants</a>
+              <a class="navbar-item" href="/ols-7#mentors"> Mentors & Experts </a>
+              <a class="navbar-item" href="/ols-7#collaborators"> Collaborators </a>
+              <a class="navbar-item" href="/ols-7#resources"> Resources </a>
+            </div>
+          </div>
+
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link" href="/about">Policies</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="{{ site.github.owner_url }}/policies-procedures-and-docs/blob/main/CODE_OF_CONDUCT.md"> Code of Conduct </a>
+            </div>
+          </div>
+
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link" href="/about">About</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="/people"> People </a>
+              <a class="navbar-item" href="/community"> Team & Community </a>
+              <a class="navbar-item" href="/funders"> Funding & Supporters </a>
+              <a class="navbar-item" href="/partners"> Partners </a>
+              <!--<a class="navbar-item" href="/events"> Events </a>-->
+            </div>
+          </div>
+
+          <!--<div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link" href="/about">Services</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="/consulting"> Consulting </a>
+              <a class="navbar-item" href="/training"> On demand training </a>
+              <a class="navbar-item" href="/"> Fiscal hosting </a>
+            </div>
+          </div>-->
+
+
+
+          <a class="navbar-item" href="/posts"> Stories </a>
+        </div>
+      </div>
+    </div>
+  </nav>

data/_includes/detailed-schedule.md

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+{% for w in schedule['weeks'] %}
+
+# Week {{ w[0] }}
+
+<i class="fas fa-calendar-alt"></i> Week starting on **{{ w[1].start }}**
+
+{% assign week-nb=w[0] %}
+{% assign week = w[1] %}
+{% include _includes/week.md %}
+
+{% endfor %}

data/_includes/external-entities.html

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+<div class="card entity-card" id="{{ entity.name }}">
+    <div class="card-image">
+      <figure class="image is-3by1">
+        {% if entity.logo %}
+        <img class="entity-logo" src="{{ entity.logo }}" alt="Logo of {{ entity.name }}"/>
+        {% endif %}
+      </figure>
+    </div>
+    <div class="card-content">
+      <div class="media">
+        <div class="media-content entity-card-meta">
+          <p class="title is-4">{{ entity.name }}</p>
+          <p class="is-6">
+            {% if entity.website %}
+              <a href="{{ entity.website }}"><i class="fas fa-globe"></i></a>
+            {% endif %}
+            {% if entity.country %}
+              <i class="fas fa-map-marker-alt"></i> {{ entity.country }}
+            {% endif %}
+          </p>
+        </div>
+      </div>
+      <div class="entity-description">
+        <p class="entity-description-question">
+          <a class="card-toggle">
+            {% if details %}
+            {{ entity.name }} in OLS
+            {% else %}
+            More about {{ entity.name }}
+            {% endif %}
+            <i class="fa fa-angle-down"></i>
+          </a>
+        </p>
+        <div class="content is-hidden">
+            {% if details %}
+            {{ details | markdownify }}
+            {% else %}
+            {{ entity.description | markdownify }}
+            {% endif %}
+        </div>
+      </div>
+    </div>
+  </div>

data/_includes/overall-schedule.md

@@ -0,0 +1,27 @@
+During the program,
+
+- Mentors and mentees meet every 2 weeks [for a 30 minutes call](/{{ cohort }}#mentor-mentee-calls)
+- Mentees participate every ~2 weeks to [90-minutes cohort calls](/{{ cohort }}#cohort-calls) during which the program leaders introduce new topics and resources, facilitate break-out discussions, and invite expert from the field to give talks
+- Mentees can participate to skill-up, Q&A or coworking session in the weeks without cohort calls
+- Mentors take part to [mentoring workshop and calls](/{{ cohort }}#mentor-calls)
+
+![OLS schedule overview. In the middle, the timeline represents the 16 weeks. On the top, boxes in green represent the 8 different cohort calls pointing to the corresponding weeks (even week numbers). Below the week timeline, blue boxes represent the mentor-mentee meetings pointing to the uneven number weeks. Below the blue boxes, are red boxes corresponding to 3 skill-up calls: "GitHub tutorial for beginners" (week 5), "Open Leadership: Academia, industry, and beyond" (week 9), "Self-care & social call" (week 1s)]({{ site.baseurl }}/assets/images/schedule.png){: .schedule-overview}
+
+Organizers will inform participants of the week schedule by email.
+
+<iframe src="https://calendar.google.com/calendar/embed?height=400&amp;wkst=1&amp;bgcolor=%23ffffff&amp;ctz=UTC&amp;src=b3BlbmxpZmVzY2lAZ21haWwuY29t&amp;color=%23EF6C00&amp;mode=AGENDA&amp;showNav=0&amp;showTitle=0&amp;showPrint=0&amp;showTabs=1&amp;showCalendars=0" style="border-width:0" width="1152" height="600" frameborder="0" scrolling="no"></iframe>
+
+[<i class="fas fa-calendar-plus"></i> *Subscribe to the OLS calendar*](https://calendar.google.com/calendar?cid=b3BlbmxpZmVzY2lAZ21haWwuY29t)
+
+<!-- Any modification of the content should be done in the _data/ols-X-schedule.yaml file -->
+
+| Week | Call | Date | Topic | Agenda |
+|------|------|------|-------|--------|
+{%- for w in schedule.weeks %}
+{%- capture w-desc %}**Week {{ w[0] }}** (start. {{ w[1].start }}){% endcapture %}
+{%- for c in w[1].calls %}
+{%- capture date %}{% if c.type != "Mentor-Mentee" %}{{ c.date }} {% if c.time %}([{{ c.time | date: "%H:%M" }} Universal Time](https://arewemeetingyet.com/UTC/{{ c.date | date: "%Y-%m-%d" }}/{{ c.time | date: "%H:%M" }}/{{ cohort }}%20{{ c.type }}%20Call%20(Week%20{{ w[0] }}))){% endif %}{% endif %}{% endcapture %}
+| {{ w-desc }} | [{{ c.type }}](/{{ cohort }}#{{ c.type | downcase | remove: "(" | remove: ")" | remove: "@" | remove: ":" | remove: "," | replace: " ", "-" | remove: "&"  }}-calls) | {{ date }} | [**{{ c.title }}**](/{{ cohort }}/schedule#week-{{ w[0] }}) | {% if c.agenda %}{{ c.agenda }}{% endif %} |
+{%- assign w-desc = "" %}
+{%- endfor %}
+{%- endfor %}

data/_includes/people.html

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+<div class="card people-card" id="{{ username }}">
+    <div class="card-content">
+      <div class="media">
+        <div class="media-left people-card-avatar">
+          <figure class="image is-64x64">
+            <img
+              class="is-rounded"
+              src="https://avatars.githubusercontent.com/{{ username }}"
+              alt="The GitHub avatar of {{ user.name }}"
+            />
+          </figure>
+        </div>
+        <div class="media-content people-card-meta">
+          <p class="title is-4">{{ user.first-name }} {{ user.last-name }}</p>
+  
+          <p class="is-6">
+            {% if user.pronouns %}
+            Pronouns: {{ user.pronouns }}<br>
+            {% endif %}
+  
+            {% if user.twitter %}
+            <a class="people-card-meta-twitter" href="https://twitter.com/{{ user.twitter }}"><i class="fab fa-twitter"></i> @{{ user.twitter }}</a><br>
+            {% endif %}
+            {% if user.website %}
+            <a href="{{ user.website }}"><i class="fas fa-globe"></i></a>
+            {% endif %}
+            {% if user.github != false %}
+            <a href="https://github.com/{{ username }}"><i class="fab fa-github"></i></a>
+            {% endif %}
+            {% if user.gitter %}
+            <a href="https://gitter.im/{{ user.gitter }}"><i class="fas fa-comments"></i></a>
+            {% endif %}
+            {% if user.orcid %}
+            <a href="https://orcid.org/{{ user.orcid }}"><i class="ai ai-orcid"></i></a>
+            {% endif %}
+  
+            {% if user.affiliation or user.country %}
+              <br>
+              <i class="fas fa-map-marker-alt"></i>
+              {% assign delim = '' %}
+              {% if user.affiliation %}
+              {{ user.affiliation }}
+              {% assign delim = ', ' %}
+              {% endif %}
+              {% if user.country %}
+              {{ delim }}{{ user.country }}
+              {% endif %}
+            {% endif %}
+          </p>
+        </div>
+      </div>
+  
+      {% if ols-roles and ols-roles != '' or user.title %}
+      <p class="people-description">
+        Role in OLS:
+        {% if user.title %}
+          {{ user.title }}
+        {% endif %}
+        <br>
+        {% if ols-roles and ols-roles != '' %}
+          there
+          {{ ols-roles }}
+        {% endif %}
+        </p>
+      </p>
+      {% endif %}
+  
+      {% if user.expertise %}
+      <p class="people">
+        <div class="people-description-question">Expertise:</div> {{ user.expertise | join: ", " }}
+      </p>
+      {% endif %}
+  
+      <div class="people-description" id="people-bio">
+        {% if user.bio %}
+        <p class="people-description-question">
+          <a class="card-toggle">
+            More about {{ user.first-name }}
+            <i class="fa fa-angle-down"></i>
+          </a>
+        </p>
+        <div class="content is-hidden">
+          {{ user.bio | markdownify }}
+        </div>
+        {% endif %}
+      </div>
+      
+    </div>
+  </div>

data/_includes/schedule.md

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+{% include _includes/overall-schedule.md %}
+{% include _includes/detailed-schedule.md %}

data/_includes/timeline.md

@@ -0,0 +1,24 @@
+{% for e in schedule.timeline %}
+{% assign type = '' %}
+{% if e.type %}
+    {% for t in e.type %}
+        {% capture type %}{{ type }} + {% if t == 'Talk' %}<i class="fas fa-chalkboard-teacher"></i> Talk{% elsif t == 'Q&A' %}<i class="fas fa-question"></i> Q&A{% elsif t == 'Recording' %}<i class="fab fa-youtube"></i> Recording{% endif %}{% endcapture %}
+    {% endfor %}
+    {% assign type = type | remove_first: ' + ' %}
+{% endif %}
+{% if e.date %}
+- **{{ e.date }}** {% if e.time %}([{{ e.time }} Universal Time](https://arewemeetingyet.com/UTC/{{ e.date | date: "%Y-%m-%d" }}/{{ e.time }}/OLS%20Application%20Call)){% endif %}: {{ e.description }}{% if e.type %}({{ type }}){% endif %}{% if e.notes %} - <i class="fas fa-clipboard"></i> [Notes with Zoom call link]({{ e.notes }}){% endif %}{% if e.recording %} - <i class="fab fa-youtube"></i> [Recording]({{ e.recording }}){% endif %}{% if e.details %}
+
+    {{ e.details }}
+
+{% endif %}
+{% endif %}
+{% endfor %}
+- **{{ schedule.weeks['01'].start }}**: Start of the program
+
+{% assign end = '' %}
+{% for w in schedule.weeks %}
+{% assign end = w[1].start %}
+{% endfor %}
+- **{{ end }}**: End of the program
+

data/_includes/toc.html

@@ -0,0 +1,12 @@
+<div class="toc">
+    <h1 class="no_toc">
+        <a class="card-toggle">
+            Table of content
+            <i class="fa fa-angle-down"></i>
+        </a>
+    </h1>
+    <div class="content is-hidden">
+    1. TOC
+    {:toc}
+    </div>
+    </div>

data/_includes/week.md

@@ -0,0 +1,50 @@
+{% for c in week.calls %}
+
+## {{ c.type }} call: {{ c.title }}
+
+{% if c.type != "Mentor-Mentee" and c.date %}
+<i class="fas fa-calendar-alt"></i> **Date**: {{ c.date }}{% if c.time %}, at [{{ c.time }} Universal Time](https://arewemeetingyet.com/UTC/{{ c.date | date: "%Y-%m-%d" }}/{{ c.time }}/
+{{ cohort | upcase }}%20Cohort%20Call%20(Week%20{{ week-nb }})) ([<i class="fas fa-calendar-plus"></i> *Add to your calendar*]({{ c.calendar-event }})){% endif %}
+{% else %}
+<i class="fas fa-calendar-alt"></i> **Date**: During the week starting on {{ week.start }} (to define with mentors)
+{% endif %}
+
+<i class="fas fa-clock"></i> **Duration**: {{ c.duration }}
+
+{% if c.hosts %}
+{% assign hosts = '' %}
+{% for p in c.hosts %}{% capture hosts %}{{ hosts }}, {{ site.data.people[p].first-name }} {{ site.data.people[p].last-name }}{% endcapture %}{% endfor %}
+<i class="fas fa-user-friends"></i> **Hosts**: {{ hosts | remove_first: ', ' }}
+{% endif %}
+
+{% if c.content %}
+### In this call
+
+{{ c.content | markdownify }}
+
+{% endif %}
+
+{% if c.type == "Cohort" %}
+
+**Resources**:
+- <i class="fas fa-clipboard"></i> [Notes]({{ c.notes }})
+- <i class="fab fa-youtube"></i> {% if c.recording %} [Recording]({{ c.recording }}) {% else %} Recording available on the [OLS YouTube channel]({{ site.youtube }}) after the call {% endif %}
+{% for r in c.resources %}
+- {% if r.type == 'slides' %}<i class="fas fa-file-powerpoint"></i>{% elsif r.type == 'document' %} <i class="fas fa-file"></i>{% elsif r.type == 'external-link' %} <i class="fas fa-external-link-square-alt"></i>{% endif %} {% if r.link %} [{{ r.title }}]({{ r.link }}){% else %} {{ r.title }}{% endif %}{% if r.type == 'slides' and r.speaker %}{% if site.data.people[r.speaker].first-name %}, by [{{ site.data.people[r.speaker].first-name }} {{ site.data.people[r.speaker].last-name }}](/{{ cohort }}#{{ r.speaker }}){% endif %} {% endif %}
+{% endfor %}
+
+{% endif %}
+
+{% if c.before %}
+### Before the call
+
+{{ c.before | markdownify }}
+{% endif %}
+
+{% if c.after %}
+### After the call
+
+{{ c.after | markdownify }}
+{% endif %}
+
+{% endfor %}

data/_layouts/base.html

@@ -0,0 +1,66 @@
+---
+---
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8">
+        <meta http-equiv="x-ua-compatible" content="ie=edge">
+        <meta name="viewport" content="width=device-width, initial-scale=1">
+        <title>{{ page.title }} | {{ site.title }}</title>
+        {% if page.description %}<meta name="description" content="{{ page.description }}">{% endif %}
+        <link href="{{ site.baseurl }}/assets/css/custom.css" rel="stylesheet" type="text/css">
+        <link rel="stylesheet" href="https://cdn.rawgit.com/jpswalsh/academicons/master/css/academicons.min.css">
+        <!--Below is the schema annotation for blogposts-->
+        {% if page.layout == 'post' %}
+        <script type="application/ld+json">
+          {
+            "@context": "https://schema.org",
+            "@type": "BlogPosting",
+            "mainEntityOfPage": {
+              "@type": "WebPage",
+              "@id": "{{ site.url }}/posts/"
+              },
+            "headline": "{{ page.title }}",
+            "description": "{{ page.excerpt | strip_html | strip_newlines | truncate: 200 }}",
+            "image": "{{ page.image }}",
+            "author": [
+            {%- for author in page.authors -%}
+              {
+              "@type": "Person",
+              "name": "{{ site.data.people[author].first-name }} {{ site.data.people[author].last-name }}",
+              "url": "{{ site.url }}/people#{{ author }}"
+                {%- if forloop.last -%}
+                  }
+                  {%- else -%}
+                  },
+                {% endif %}
+            {%- endfor -%}],
+            "publisher": {
+              "@type": "Organization",
+              "name": "Open Life Science",
+              "url": "{{ site.url }}",
+              "logo": {
+                  "@type": "ImageObject",
+                  "url": "{{ site.url }}/images/logo.png"
+                }
+              },
+            "datePublished": "{{ page.date | date: "%Y-%m-%d" }}"
+          }
+        </script>
+        {% endif %}
+    </head>
+
+    <body>
+        {% include _includes/default-header.html %}
+        {{ content }}
+        {% include _includes/default-footer.html %}
+
+
+        <script defer src="https://use.fontawesome.com/releases/v5.3.1/js/all.js"></script>
+        <script src="{{ site.baseurl }}/assets/js/scripts.js"></script>
+        <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+        {% if page.layout == 'posts' %}
+          <script src="{{ site.baseurl }}/assets/js/posts.js"></script>
+        {% endif %}
+      </body>
+</html>

data/_layouts/default.html

@@ -0,0 +1,37 @@
+---
+layout: base
+---
+
+{% assign date_format = site.minima.date_format | default: "%b %-d, %Y" %}
+
+<section class="hero {% unless page.image %} no-image{% endunless %}"{% if page.image %} style="background-image: linear-gradient(to top, #000, transparent), url({{ page.image }});"{% endif %}>
+  <div class="hero-body">
+    <h1 class="title is-1">{{ page.title }}</h1>
+
+    {% if page.description %}
+      <p class="subtitle is-3">{{ page.description }}</p>
+    {% endif %}
+
+    {% if page.layout == 'post' %}
+      {% capture authors %}
+      {% for id in page.authors %}, {% assign name = site.data['people'][id].first-name | default: id %}<a href="/people#{{ id }}">{{ name }}</a>{% endfor %}
+      {% endcapture %}
+      <p class="subtitle is-5">
+          <time datetime="{{ page.date | date: date_format }}">{{ page.date | date: date_format }}</time>
+          - {{ authors | remove_first: ', ' | strip }}
+      </p>
+    {% endif %}
+  </div>
+
+  {% if page.photos %}
+  <div class="hero-foot">
+    <p class="credit"><a href="{{ page.photos.link }}">{{ page.photos.name }}</a> ({{ page.photos.license }})</p>
+  </div>
+  {% endif %}
+</section>
+
+<section class="section">
+  <div class="container content {{ layout.css }} {{ page.css }}">
+    {{ content }}
+  </div>
+</section>

data/_layouts/links.html

@@ -0,0 +1,23 @@
+---
+layout: base
+---
+
+<div class="container is-fullhd links">
+    <section class="hero link-hero">
+        <div class="hero-body">
+            <a href="/" class="logo">
+                <img src="/images/logo.png" alt="logo of OLS">
+            </a>
+            {{ site.data.links.description | markdownify }}
+        </div>
+    </section>
+
+    <section class="section">
+        {% for item in site.data.links.items %}
+        <a href="{{ item.link }}" class="button is-link is-medium is-fullwidth">
+            {% if item.icon %}<i class="icon {{ item.icon }}"></i>{% endif %}
+            &nbsp;&nbsp;&nbsp;&nbsp;{{ item.text }}
+        </a>
+        {% endfor %}
+    </section>
+</div>

data/_layouts/page.html

@@ -0,0 +1,9 @@
+---
+layout: default
+---
+
+<section>
+    <div class="article-post">
+        {{content}}
+    </div>    
+</section>