v1.1.3 (#185)

Closes #181 and #180 
Closes #179 

- fix typo in first-time-setup.yaml
- fix versioning workflow tag/release
- tweak some cite.py and _plugins comments
- add commented out `continue` for if user wants to discard sources that
have ids that can't be cited by Manubot, per #186 discussion
- clean Manubot title/authors/publisher/etc output. trim whitespace and
filter.
- fix citation, portrait, and float css

The tagging/releasing step is now reverted to [how I had it in
v1.1.0](https://github.com/greenelab/lab-website-template/pull/166/files#diff-67cc7f4d3d06063e6239e59de699c4a2c768ba544777ded6aa22ab45aa0ad24a),
just using `ncipollo/release-action` for both the tag and the release,
and removing `mathieudutour/github-tag-action`. Idk why I keep going
back and forth. I guess the last time I tried using just `ncipollo` it
didn't work? But it seems to be working now (links ephemeral):

https://github.com/vincerubinetti/lwt-test/pull/2
https://github.com/vincerubinetti/lwt-test/releases/tag/v1.1.4

---------

Co-authored-by: vincerubinetti <vincerubinetti@users.noreply.github.com>

.github/workflows/first-time-setup.yaml

@@ -59,7 +59,7 @@ jobs:
             .github/pull_request_template.md \
       
       - name: Rename files
-        run: \
+        run: |
           mv .github/user_pull_request_template.md .github/pull_request_template.md
 
       - name: Set vars for personalization

.github/workflows/versioning.yaml

@@ -122,16 +122,10 @@ jobs:
 
             return { version, body };
 
-      - name: Create tag
-        id: tag
-        uses: mathieudutour/github-tag-action@v6.1
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          custom_tag: ${{ fromJson(steps.version.outputs.result).version }}
-
       - name: Create GitHub release
         uses: ncipollo/release-action@v1
         with:
-          tag: ${{ fromJson(steps.version.outputs.result).version }}
-          name: ${{ fromJson(steps.version.outputs.result).version }}
+          commit: ${{ github.ref }}
+          tag: v${{ fromJson(steps.version.outputs.result).version }}
+          name: v${{ fromJson(steps.version.outputs.result).version }}
           body: ${{ fromJson(steps.version.outputs.result).body }}

CHANGELOG.md

@@ -2,6 +2,14 @@
 
 Reference: common-changelog.org
 
+## 1.1.3 - 2023-04-20
+
+### Changed
+
+- Fix first-time-setup mv bug.
+- Fix citation, float, and portrait component CSS.
+- Filter and trim citation info fields.
+
 ## 1.1.2 - 2023-04-11
 
 ### Changed

CITATION.cff

@@ -1,8 +1,8 @@
 # citation metadata for the template itself
 
 title: "Lab Website Template"
-version: 1.1.2
-date-released: 2023-04-11
+version: 1.1.3
+date-released: 2023-04-20
 url: "https://github.com/greenelab/lab-website-template"
 authors:
   - family-names: "Rubinetti"

_cite/cite.py

@@ -127,15 +127,17 @@
             # run Manubot and set citation
             citation = cite_with_manubot(_id)
 
+        # if Manubot cannot cite source
         except Exception as e:
-            # if manually-entered source, throw error on cite failure
+            # if regular source (id entered by user), throw error
             if source.get("plugin") == "sources.py":
                 log(e, 3, "ERROR")
                 error = True
-            # otherwise, just warn
-            # (Manubot might not know how to cite every type of source from orcid, e.g.)
+            # otherwise, if from metasource (id retrieved from some third-party API), just warn
             else:
                 log(e, 3, "WARNING")
+                # discard source
+                # continue
 
     # preserve fields from input source, overriding existing fields
     citation.update(source)

_cite/util.py

@@ -174,19 +174,20 @@ def cite_with_manubot(_id):
     citation["id"] = _id
 
     # title
-    citation["title"] = manubot.get("title", "")
+    citation["title"] = manubot.get("title", "").strip()
 
     # authors
     citation["authors"] = []
     for author in manubot.get("author", []):
-        given = author.get("given", "")
-        family = author.get("family", "")
-        citation["authors"].append(given + " " + family)
+        given = author.get("given", "").strip()
+        family = author.get("family", "").strip()
+        if given or family:
+            citation["authors"].append(" ".join([given, family]))
 
     # publisher
-    container = manubot.get("container-title", "")
-    collection = manubot.get("collection-title", "")
-    publisher = manubot.get("publisher", "")
+    container = manubot.get("container-title", "").strip()
+    collection = manubot.get("collection-title", "").strip()
+    publisher = manubot.get("publisher", "").strip()
     citation["publisher"] = container or publisher or collection or ""
 
     # extract date part
@@ -199,7 +200,7 @@ def date_part(citation, index):
     # date
     year = date_part(manubot, 0)
     if year:
-        # fallbacks for no month or day
+        # fallbacks for month and day
         month = date_part(manubot, 1) or "1"
         day = date_part(manubot, 2) or "1"
         citation["date"] = format_date(f"{year}-{month}-{day}")
@@ -208,7 +209,7 @@ def date_part(citation, index):
         citation["date"] = ""
 
     # link
-    citation["link"] = manubot.get("URL", "")
+    citation["link"] = manubot.get("URL", "").strip()
 
     # return citation data
     return citation

_data/citations.yaml

@@ -1,5 +1,25 @@
 # DO NOT EDIT, GENERATED AUTOMATICALLY
 
+- id: doi:10.1093/nar/gkad289
+  title: 'MyGeneset.info: an interactive and programmatic platform for community-curated
+    and user-created collections of genes'
+  authors:
+  - Ricardo Avila
+  - Vincent Rubinetti
+  - Xinghua Zhou
+  - Dongbo Hu
+  - Zhongchao Qian
+  - Marco Alvarado Cano
+  - Everaldo Rodolpho
+  - Ginger Tsueng
+  - Casey Greene
+  - Chunlei Wu
+  publisher: Nucleic Acids Research
+  date: '2023-04-18'
+  link: https://doi.org/gr5hb5
+  orcid: 0000-0002-4655-3773
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1101/2023.01.05.522941
   title: Hetnet connectivity search provides rapid insights into how two biomedical
     entities are related

_plugins/array.rb

@@ -2,7 +2,7 @@
 
 module Jekyll
   module ArrayFilters
-    # filter out empty entries from array
+    # filter out empty and trim entries in array
     def array_filter(array)
       return array
         .map{|x| x.is_a?(String) ? x.strip() : x}

_styles/citation.scss

@@ -33,10 +33,12 @@ $wrap: 800px;
   display: inline-flex;
   flex-wrap: wrap;
   gap: 15px;
+  max-width: 100%;
   height: min-content;
   padding: 20px;
   padding-left: 30px;
   text-align: left;
+  overflow-wrap: break-word;
   z-index: 0;
 }
 

_styles/float.scss

@@ -33,5 +33,6 @@ $wrap: 600px;
     float: unset !important;
     clear: both !important;
     margin: auto !important;
+    max-width: unset;
   }
 }

_styles/portrait.scss

@@ -58,16 +58,17 @@
 
 .portrait-role .icon {
   position: absolute;
-  left: 8px;
-  top: 8px;
+  left: 0;
+  top: 0;
   display: flex;
   justify-content: center;
   align-items: center;
-  width: 2em;
-  height: 2em;
+  width: 20%;
+  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 {