v1.2.2 (#257)

Closes #250 
Closes #256 
Closes #260 
Closes #258

- adds `affiliation` to member portrait component
- simplify portrait component code/css
- make tag de-dupe behavior the same as search de-dupe. normalize to
lower-kebab-case.
- expand list of manubot-supported id types for falling back to orcid
api details
- change order and type of preferred ids from orcid

---------

Co-authored-by: Faisal Alquaddoomi <[email protected]>
Co-authored-by: vincerubinetti <[email protected]>

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 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

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.2.1
-date-released: 2024-04-01
+version: 1.2.2
+date-released: 2024-06-05
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_cite/plugins/orcid.py

@@ -1,6 +1,7 @@
 import json
 from urllib.request import Request, urlopen
 from util import *
+from manubot.cite.handlers import prefix_to_handler as manubot_prefixes
 
 
 def main(entry):
@@ -35,37 +36,36 @@ def query(_id):
     # go through response structure and pull out ids e.g. doi:1234/56789
     for work in response:
         # get list of ids
-        ids = get_safe(work, "external-ids.external-id", [])
+        ids = []
         for summary in get_safe(work, "work-summary", []):
             ids = ids + get_safe(summary, "external-ids.external-id", [])
 
-        # prefer doi id type, or fallback to first id
+        # find first id of particular "relationship" type
         _id = next(
-            (id for id in ids if get_safe(id, "external-id-type", "") == "doi"),
-            ids[0] if len(ids) > 0 else {},
+            (
+                id
+                for id in ids
+                if get_safe(id, "external-id-relationship", "")
+                in ["self", "version-of", "part-of"]
+            ),
+            ids[0] if len(ids) > 0 else None,
         )
 
+        if _id == None:
+            continue
+
         # get id and id-type from response
         id_type = get_safe(_id, "external-id-type", "")
         id_value = get_safe(_id, "external-id-value", "")
 
         # create source
         source = {"id": f"{id_type}:{id_value}"}
 
-        # if not a doi, Manubot likely can't cite, so keep citation details
-        if id_type != "doi":
+        # if not an id type that Manubot can cite, keep citation details
+        if id_type not in manubot_prefixes:
             # get summaries
             summaries = get_safe(work, "work-summary", [])
 
-            # sort summary entries by most recent
-            summaries = sorted(
-                summaries,
-                key=lambda summary: (get_safe(summary, "last-modified-date.value", 0))
-                or get_safe(summary, "created-date.value", 0)
-                or 0,
-                reverse=True,
-            )
-
             # get first summary with defined sub-value
             def first(get_func):
                 return next(

_data/citations.yaml

@@ -141,11 +141,11 @@
   - Jacob D Krol
   - Joseph T Burke
   - Samuel Z Chen
-  - Lo Sosinski
+  - Lo M Sosinski
   - Faisal S Alquaddoomi
   - Evan P Brenner
   - Ethan P Wolfe
-  - Vince P Rubinetti
+  - Vincent P Rubinetti
   - Shaddai Amolitos
   - Kellen M Reason
   - John B Johnston

_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

_scripts/search.js

@@ -38,7 +38,7 @@
 
   // normalize tag string for comparison
   window.normalizeTag = (tag) =>
-    tag.trim().toLowerCase().replaceAll(/-|\s+/g, " ");
+    tag.trim().toLowerCase().replaceAll(/\s+/g, "-");
 
   // get data attribute contents of element and children
   const getAttr = (element, attr) =>

_styles/portrait.scss

@@ -11,7 +11,6 @@
   justify-content: center;
   align-items: center;
   flex-direction: column;
-  gap: 20px;
   margin: 20px;
   width: 175px;
   max-width: calc(100% - 20px - 20px);
@@ -29,48 +28,52 @@
   text-align: left;
 }
 
-.portrait-image {
-  width: 100%;
+.portrait .icon {
+  position: absolute;
+  left: 0;
+  top: 0;
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  width: calc(20px + 10%);
   aspect-ratio: 1 / 1;
   border-radius: 999px;
-  object-fit: cover;
+  background: var(--background);
   box-shadow: var(--shadow);
+  transform: translate(14%, 14%);
 }
 
-.portrait[data-style="tiny"] .portrait-image {
-  width: 50px;
+.portrait[data-style="small"] .icon {
+  left: -2px;
+  top: -2px;
 }
 
-.portrait[data-style="tiny"] .portrait-role {
+.portrait[data-style="tiny"] .icon {
   display: none;
 }
 
-.portrait-text {
-  display: flex;
-  flex-direction: column;
+.portrait-image {
+  width: 100%;
+  margin-bottom: 20px;
+  aspect-ratio: 1 / 1;
+  border-radius: 999px;
+  object-fit: cover;
+  box-shadow: var(--shadow);
+}
+
+.portrait[data-style="tiny"] .portrait-image {
+  width: 50px;
+  margin: 0;
 }
 
 .portrait-name {
   font-family: var(--heading);
   font-weight: var(--semi-bold);
 }
 
-.portrait-role .icon {
-  position: absolute;
-  left: 0;
-  top: 0;
-  display: flex;
-  justify-content: center;
-  align-items: center;
-  width: calc(20px + 10%);
-  aspect-ratio: 1 / 1;
-  border-radius: 999px;
-  background: var(--background);
-  box-shadow: var(--shadow);
-  transform: translate(14%, 14%);
-}
-
-.portrait[data-style="small"] .portrait-role .icon {
-  left: -2px;
-  top: -2px;
+.portrait[data-style="tiny"] {
+  .portrait-description,
+  .portrait-affiliation {
+    display: none;
+  }
 }