Merge pull request #867 from NPDebs/add_nebula

Implement infrastructure for Nebula sub-site 🚀

.github/workflows/update-schedule.yml

@@ -36,6 +36,11 @@ jobs:
         run: |
           python bin/prepare_website_data.py buildlibrary -p "openseeds"
 
+      - name: Update Nebula schedule
+        shell: bash -el {0}
+        run: |
+          bash bin/nebula/update_schedule.sh
+
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v4
         with:

_data/nebula/neb-1/metadata.yaml

@@ -0,0 +1,13 @@
+# List of experts, possible mentors and organizers for nebula neb-1
+#
+#
+# People should be also in people.yaml file and linked using their GitHub username
+# Ordering by expertise should be done by running the bin/sort-expertises.py script
+---
+experts: []
+organizers:
+- iramosp
+- bebatut
+- malvikasharan
+- yochannah
+possible-mentors: []

_data/nebula/neb-1/projects.yaml

@@ -0,0 +1,3 @@
+# List of projects for nebula neb-1
+---
+[]

_data/nebula/neb-1/schedule.yaml

@@ -0,0 +1,232 @@
+# Schedule for the nebula neb-1
+---
+timeline:
+- date:
+  description: Call for Application opens
+  details: See the [guidelines and templates](https://github.com/open-life-science/application-forms)
+- date:
+  description: Application webinar
+  type:
+  - Talk
+  - Q&A
+  notes:
+  recording:
+  details: Watch recordings from previous webinars on 
+    [**YouTube**](https://www.youtube.com/playlist?list=PL1CvC6Ez54KBsPT0fhPtkHmBaXR4f8Dqt)
+- date:
+  description: Application Clinic Call
+  type:
+  - Q&A
+  notes:
+  details: At this call, OLS team will be available to provide help if you have any
+    question related to your application
+- date:
+  description: Call for applications closed
+- date:
+  description: Successful applicants announced
+weeks:
+  '01':
+    start:
+    calls:
+    - date: March 12, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_ethos1
+      title: Ethos
+      recording: https://youtu.be/0-z7S1TM-Pk (part 1), https://youtu.be/7zupshFnOTM
+        (part 2)
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - virginiagarciaalonso
+      syllabus:
+      - What is Open Science?
+      - Why is Open Science important?
+      talks: []
+    - date: March 14, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_ethos2
+      title: Ethos
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - chadsansing
+      syllabus:
+      - Barriers for Open Science and Considerations when not to be open
+      - Open licences
+      talks: []
+  '02':
+    start:
+    calls:
+    - date: March 19, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_tools1
+      title: Tools
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - jafsia
+      syllabus:
+      - Open Science Strategies and Data Management Plans
+      talks: []
+    - date: March 21, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_tools2
+      title: Tools
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - saranjeetkaur
+      syllabus:
+      - 'General tools for Open Science: metadata, documentation, repositories and
+        persistent identifiers'
+      talks: []
+  '03':
+    start:
+    calls:
+    - date: March 26, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_data1
+      title: Data
+      recording: https://www.youtube.com/watch?v=3XMnL4AE8bE&t=32s
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - saravilla
+      syllabus:
+      - Introduction to Open Data
+      - FAIR principles
+      talks: []
+    - date: March 28, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_data2
+      title: Data
+      recording: 'https://youtu.be/Wss650ueQkk?si=-EXdQ8uwCpt-cm1f '
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - karegapauline
+      syllabus:
+      - 'Using Open Data: Repositories and data citation'
+      - 'Making Open Data: Open data formats, metadata and licences '
+      - 'Sharing Open Data: Steps and considerations to share open data'
+      talks: []
+  '04':
+    start:
+    calls:
+    - date: April 02, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_code1
+      title: Code
+      hosts:
+      - yochannah
+      - iramosp
+      expert: []
+      syllabus:
+      - Introduction to Open Code
+      - 'Using Open Code: repositories, software citation, considerations when using
+        open code'
+      talks: []
+    - date: April 04, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_code2
+      title: Code
+      recording: https://youtu.be/G6om6dvmNCM
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - amangoel185
+      syllabus:
+      - 'Programming Best Practices: version control, code review, README'
+      talks: []
+  '05':
+    start:
+    calls:
+    - date: April 09, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_results1
+      title: Results
+      recording: 
+        https://www.youtube.com/watch?v=34Ip-c8ROpk&list=PL1CvC6Ez54KBVZ38GiHIzQxW_LFuaOTYe&index=8
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - monica-granados
+      syllabus:
+      - Research outputs throughout the research cycle
+      - Reproducibility
+      - Contribution guidelines and giving recognition
+      talks: []
+    - date: April 11, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_results2
+      title: Results
+      hosts:
+      - yochannah
+      - iramosp
+      expert:
+      - dasaderi
+      syllabus:
+      - Open Access publications and preprints
+      talks: []
+  '06':
+    start:
+    calls:
+    - date: April 18, 2024
+      time: "16:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_projects
+      title: Project presentations
+      recording: https://youtu.be/TwUm5bjh5JA
+      hosts:
+      - malvikasharan
+      - iramosp
+      syllabus:
+      - Final presentations by participants
+      talks: []
+  '07':
+    start:
+    calls:
+    - date: April 23, 2024
+      time: "12:00"
+      duration: 90 min
+      notes: https://annuel2.framapad.org/p/nebula-1_projects
+      title: Project presentations
+      recording: https://youtu.be/HHFHKYsCQGM
+      hosts:
+      - yochannah
+      - iramosp
+      syllabus:
+      - Final presentations by participants
+      talks: []
+  '08':
+    start:
+    calls:
+    - date: April 30, 2024
+      time: "16:00"
+      duration: 60 min
+      notes: https://annuel2.framapad.org/p/nebula-1_wrap-up
+      title: Wrap up and goodbye
+      hosts:
+      - yochannah
+      - iramosp
+      syllabus:
+      - Wrap up and goodbye
+      talks: []

_includes/cohort-loop.html

@@ -6,17 +6,18 @@
 
 <!-- Maintain this logic with nebula in view. In future, concat other programs into 'cohorts' variable -->
 {%- assign openseeds_cohorts = site.data.openseeds | sort -%}
-{%- assign cohorts = openseeds_cohorts -%}
+{%- assign nebula_cohorts = site.data.nebula | sort -%}
+{%- assign cohorts = openseeds_cohorts | concat: nebula_cohorts -%}
 
 {%- for cohort in cohorts -%}
   {%- assign cohort_name = cohort[0] -%}
 
   <!-- Where multiple programs exist, adapt the logic below to filter _data folder as needed -->
-  <!-- {%- if cohort_name contains 'openseeds' -%}
+  {%- if cohort_name contains 'openseeds' -%}
     {%- assign program_data = site.data.openseeds[cohort_name] -%}
-  {%- elsif cohort_name contains 'x-program' -%}
-    {%- assign program_data = site.data.x-program[cohort_name] -%}
-  {%- endif -%} -->
+  {%- elsif cohort_name contains 'nebula' -%}
+    {%- assign program_data = site.data.nebula[cohort_name] -%}
+  {%- endif -%}
 
   {%- assign experts = program_data.metadata.experts | uniq | size -%}
   {%- capture all_experts %}{{ all_experts }}, {{ program_data.metadata.experts | join: ', ' }}{% endcapture -%}

_includes/detailed-schedule.md

@@ -1,11 +1,7 @@
-{% for w in schedule['weeks'] %}
-
+{%- 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] %}
+  {%- if program != 'nebula' -%}<i class="fas fa-calendar-alt"></i>  Week starting on **{{ w[1].start }}**{%- endif -%}
+{%- assign week-nb=w[0] -%}
+{%- assign week = w[1] -%}
 {% include _includes/week.md %}
-
 {% endfor %}

_includes/nebula-header.html

@@ -0,0 +1,55 @@
+<nav class="navbar is-fixed-top" role="navigation" aria-label="main navigation">
+    <div class="container">
+      <div class="navbar-brand">
+        <a class="navbar-item" href="{% link nebula/about.md %}">
+            <img src="/images/logo/nebula-full-transparent-bg.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" href="{% link nebula/about.md %}">The Program</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="{% link nebula/index.md %}"> About Nebula </a>
+            </div>
+          </div>
+
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link" href="{% link nebula/neb-1/index.md %}">Cohorts</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item navbar-previous-title" href="{% link nebula/neb-1/index.md %}">Nebula 2024-1</a>
+              <a class="navbar-item navbar-previous-title" href="{% link nebula/index.md %}#cohorts"> Previous cohorts </a>
+            </div>
+          </div>
+
+          <div class="navbar-item has-dropdown is-hoverable">
+            <a class="navbar-link">About OLS</a>
+            <div class="navbar-dropdown">
+              <a class="navbar-item" href="{% link index.md %}">OLS</a>
+              <a class="navbar-item" href="{% link people.md %}"> People </a>
+              <a class="navbar-item" href="{% link community.md %}"> Team </a>
+              <a class="navbar-item" href="{% link funders.md %}"> Funding & Supporters </a>
+              <a class="navbar-item" href="{% link partners.md %}"> Partners </a>
+              <a class="navbar-item" href="{% link publications.md %}"> Citing OLS & Publications </a>
+              <a class="navbar-item" href="{% link events.md %}"> Events </a>
+            </div>
+          </div>
+
+          <a class="navbar-item" href="{% link posts.md %}"> Stories </a>
+
+          <a class="navbar-item" href="{% link nebula/resources.md %}">Resources</a>
+        </div>
+      </div>
+    </div>
+  </nav>

_includes/overall-schedule.md

@@ -32,7 +32,7 @@ Organizers will inform participants of the week schedule by email.
 | Week | Call | Date | Topic | Agenda |
 |------|------|------|-------|--------|
 {%- for w in schedule.weeks %}
-{%- capture w-desc %}**Week {{ w[0] }}** (start. {{ w[1].start }}){% endcapture %}
+{%- capture w-desc %}**Week {{ w[0] }}** {%- if program !='nebula'-%} (start. {{ w[1].start }}){%- endif -%}{% 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 }}]({% link {{ program }}/{{ cohort }}/index.md %}#{{ c.type | downcase | remove: "(" | remove: ")" | remove: "@" | remove: ":" | remove: "," | replace: " ", "-" | remove: "&"  }}-calls) | {{ date }} | [**{{ c.title }}**]({% link {{ program }}/{{ cohort }}/schedule.md %}#week-{{ w[0] }}) | {% if c.agenda %}{{ c.agenda }}{% endif %} |

_includes/week.md

@@ -1,6 +1,10 @@
 {% for c in week.calls %}
 
+{% if program !='nebula' %}
 ## {{ c.type }} call: {{ c.title }}
+{% else %}
+## Module: {{ c.title }}
+{% endif %}
 
 
 
@@ -19,6 +23,19 @@
 <i class="fas fa-user-friends"></i> **Hosts**: {{ hosts | remove_first: ', ' }}
 {% endif %}
 
+{% if c.expert and c.expert != empty %}
+    {% assign experts = '' %}
+    {% for e in c.expert %}{% capture experts %}{{ experts }}, [{{ site.data.people[e].first-name }} {{ site.data.people[e].last-name }}]({% link people.md %}#{{ e }}){% endcapture %}{% endfor %}
+<i class="fas fa-user-tie"></i> **Expert**: {{ experts | remove_first: ', ' }}
+{% endif %}
+
+{% if c.syllabus and c.syllabus != empty %}
+### Syllabus
+{% for s in c.syllabus %}
+- {{ s | markdownify }}
+{% endfor %}
+{% endif %}
+
 {% if c.learning_objectives %}
 ### Learning objectives