Merge branch 'greenelab-main'

.docker/entrypoint.sh

@@ -1,10 +1,8 @@
 #! /bin/bash
 
 # print folder contents for debugging
-echo "Contents:"
-echo ""
+printf "\n\nContents:\n\n"
 ls
-echo ""
 
 # run cite process
 python3 _cite/cite.py

CHANGELOG.md

@@ -2,6 +2,25 @@
 
 Reference: common-changelog.org
 
+## 1.2.2 - 2024-06-05
+
+### Added
+
+- Add `affiliation` member portrait field.
+
+### Changed
+
+- Change order and type of preferred ids from ORCID API.
+- Expand list of supported Manubot identifiers and thus keep ORCID API details less often.
+- Simplify portrait component under-the-hood.
+- Make tag component de-duplication consistent with search plugin de-duplication.
+
+## 1.2.1 - 2024-04-01
+
+### Changed
+
+- Minor bug fixes in cite process and sitemap generation.
+
 ## 1.2.0 - 2024-03-08
 
 ### Changed

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.2.0
-date-released: 2024-03-08
+version: 1.2.2
+date-released: 2024-06-05
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_cite/util.py

@@ -7,7 +7,7 @@
 import yaml
 from yaml.loader import SafeLoader
 from pathlib import Path
-from datetime import datetime
+from datetime import date, datetime
 from rich import print
 from diskcache import Cache
 
@@ -88,15 +88,17 @@ def list_of_dicts(data):
     return isinstance(data, list) and all(isinstance(entry, dict) for entry in data)
 
 
-def format_date(date):
+def format_date(_date):
     """
     format date as YYYY-MM-DD, or no date if malformed
     """
 
-    if isinstance(date, int):
-        return datetime.fromtimestamp(date // 1000.0).strftime("%Y-%m-%d")
+    if isinstance(_date, int):
+        return datetime.fromtimestamp(_date // 1000.0).strftime("%Y-%m-%d")
+    if isinstance(_date, (date, datetime)):
+        return _date.strftime("%Y-%m-%d")
     try:
-        return datetime.strptime(date, "%Y-%m-%d").strftime("%Y-%m-%d")
+        return datetime.strptime(_date, "%Y-%m-%d").strftime("%Y-%m-%d")
     except Exception:
         return ""
 

_includes/list.html

@@ -24,6 +24,7 @@
 
     {%
       include {{ include.component | append: ".html" }}
+      affiliation=d.affiliation
       author=d.author
       authors=d.authors
       buttons=d.buttons

_includes/portrait.html

@@ -7,6 +7,8 @@
   {% assign member = include %}
 {% endif %}
 
+{% assign type = site.data.types[member.role] %}
+
 <div class="portrait-wrapper">
   <a
     {% if page.slug != member.slug %}
@@ -16,6 +18,10 @@
     data-style="{{ include.style }}"
     aria-label="{{ member.name | default: "member link" }}"
   >
+    {% if type %}
+      {% include icon.html icon=type.icon %}
+    {% endif %}
+
     <img
       src="{{ member.image | relative_url }}"
       class="portrait-image"
@@ -24,21 +30,21 @@
       {% include fallback.html %}
     >
 
-    {% if member.name or member.role or member.description %}
-      <span class="portrait-text">
-        {% if member.name %}
-          <span class="portrait-name">
-            {{ member.name }}
-          </span>
-        {% endif %}
+    {% if member.name %}
+      <span class="portrait-name">
+        {{ member.name }}
+      </span>
+    {% endif %}
+
+    {% if member.description or type %}
+      <span class="portrait-description">
+        {{ member.description | default: type.description }}
+      </span>
+    {% endif %}
 
-        {% if member.role or member.description %}
-          <span class="portrait-role">
-            {% assign type = site.data.types[member.role] %}
-            {% include icon.html icon=type.icon %}
-            <span>{{ member.description | default: type.description }}</span>
-          </span>
-        {% endif %}
+    {% if member.affiliation %}
+      <span class="portrait-affiliation">
+        {{ member.affiliation }}
       </span>
     {% endif %}
   </a>

_includes/tags.html

@@ -1,8 +1,12 @@
 {% assign tags = include.tags
   | object_items
   | join: ","
+  | downcase
   | split: ","
   | array_filter
+  | join: ","
+  | regex_replace: "\s+", "-"
+  | split: ","
   | uniq
 %}
 {% assign link = include.link | default: page.dir | absolute_url %}

_members/jane-smith.md

@@ -2,6 +2,7 @@
 name: Jane Smith
 image: images/photo.jpg
 role: pi
+affiliation: University of Colorado
 aliases:
   - J. Smith
   - J Smith