Skip to content

Commit 8ed760f

Browse files
tsalotsalo
authored
Fix publication formatting (#50)
1 parent becb90e commit 8ed760f

File tree

10 files changed

+72
-43
lines changed

10 files changed

+72
-43
lines changed

‎_config.yml

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -279,7 +279,9 @@ defaults:
279279
values:
280280
layout: single
281281
author_profile: false
282-
read_time: false
283282
comments: false
284283
share: false
285284
related: false
285+
show_author: true
286+
show_date: true
287+
read_time: true

‎_includes/page__meta.html

Lines changed: 10 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,16 @@
11
{% comment %}<!--Template for metadata, including post date and read-time.-->{% endcomment %}
22
{% assign document = post | default: page %}
3-
{% if document.read_time or document.show_date %}
3+
{% if document.read_time or document.show_date or document.show_author %}
44
<p class="page__meta">
5+
{% if document.show_author and document.author %}
6+
{% assign author = document.author %}
7+
<span class="page__meta-date">
8+
Posted by {{ author }}
9+
</span>
10+
{% endif %}
11+
12+
{% if document.show_author and document.show_date %}<span class="page__meta-sep"></span>{% endif %}
13+
514
{% if document.show_date and document.date %}
615
{% assign date = document.date %}
716
<span class="page__meta-date">

‎_includes/publications/core_publications.html

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -2,29 +2,29 @@
22
<li>Sydney Covitz, Tinashe&nbsp;M Tapera, Azeez Adebimpe, Aaron&nbsp;F Alexander-Bloch, Maxwell&nbsp;A Bertolero, Eric Feczko, Alexandre&nbsp;R Franco, Raquel&nbsp;E Gur, Ruben&nbsp;C Gur, Timothy Hendrickson, and others.
33
Curation of bids (cubids): a workflow and software package for streamlining reproducible curation of large bids datasets.
44
<em>NeuroImage</em>, 263:119609, 2022.</li>
5-
<li>Mauricio&nbsp;Scopel Hoffmann, Daniel&nbsp;S Pine, Katholiki Georgiades, Peter Szatmari, Euripedes&nbsp;Constantino Miguel, Pedro&nbsp;Mario Pan, Ary Gadelha, Luis&nbsp;Augusto Rohde, Kathleen&nbsp;Ries Merikangas, Michael&nbsp;Peter Milham, and others.
6-
Comparing mental health semi-structured diagnostic interviews and symptom checklists to predict poor life outcomes: an 8-year cohort study from childhood to young adulthood in brazil.
7-
<em>The Lancet Global Health</em>, 12(1):e79–e89, 2024.</li>
8-
<li>Maur<span class="bibtex-protected">í</span>cio&nbsp;Scopel Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza&nbsp;Kvitko Axelrud, Nim Tottenham, Pedro&nbsp;Mario Pan, Eur<span class="bibtex-protected">í</span>pedes&nbsp;Constantino Miguel, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
9-
An evaluation of item harmonization strategies between assessment tools of psychopathology in children and adolescents.
10-
<em>Assessment</em>, 31(2):502–517, 2024.</li>
11-
<li>Maur<span class="bibtex-protected">í</span>cio&nbsp;Scopel Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza&nbsp;Kvitko Axelrud, Nim Tottenham, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
12-
Harmonizing bifactor models of psychopathology between distinct assessment instruments: reliability, measurement invariance, and authenticity.
13-
<em>International Journal of Methods in Psychiatric Research</em>, 32(3):e1959, 2023.</li>
5+
<li>Maur<span class="bibtex-protected">í</span>cio Scopel&nbsp;Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza Kvitko&nbsp;Axelrud, Nim Tottenham, Xi-Nian Zuo, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
6+
Reliability and validity of bifactor models of dimensional psychopathology in youth.
7+
<em>Journal of Psychopathology and Clinical Science</em>, 131(4):407, 2022.</li>
148
<li>Gregory Kiar, Jon Clucas, Eric Feczko, Mathias Goncalves, Dorota Jarecka, Christopher&nbsp;J Markiewicz, Yaroslav&nbsp;O Halchenko, Robert Hermosillo, Xinhui Li, Oscar Miranda-Dominguez, and others.
159
Align with the nmind consortium for better neuroimaging.
1610
<em>Nature Human Behaviour</em>, 7(7):1027–1028, 2023.</li>
11+
<li>Maur<span class="bibtex-protected">í</span>cio&nbsp;Scopel Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza&nbsp;Kvitko Axelrud, Nim Tottenham, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
12+
Harmonizing bifactor models of psychopathology between distinct assessment instruments: reliability, measurement invariance, and authenticity.
13+
<em>International Journal of Methods in Psychiatric Research</em>, 32(3):e1959, 2023.</li>
1714
<li>Xinhui Li, Nathalia&nbsp;Bianchini Esper, Lei Ai, Steve Giavasis, Hecheng Jin, Eric Feczko, Ting Xu, Jon Clucas, Alexandre Franco, Anibal&nbsp;Sólon Heinsfeld, Azeez Adebimpe, Joshua&nbsp;T. Vogelstein, Chao-Gan Yan, Oscar Esteban, Russell&nbsp;A. Poldrack, Cameron Craddock, Damien Fair, Theodore Satterthwaite, Gregory Kiar, and Michael&nbsp;P. Milham.
1815
Moving <span class="bibtex-protected">Beyond</span> <span class="bibtex-protected">Processing</span> and <span class="bibtex-protected">Analysis</span>-<span class="bibtex-protected">Related</span> <span class="bibtex-protected">Variation</span> in <span class="bibtex-protected">Neuroscience</span>.
1916
<em>bioRxiv</em>, 2024.
2017
URL: <a href="https://www.biorxiv.org/content/early/2024/01/23/2021.12.01.470790">https://www.biorxiv.org/content/early/2024/01/23/2021.12.01.470790</a>, <a href="https://doi.org/10.1101/2021.12.01.470790">doi:10.1101/2021.12.01.470790</a>.</li>
21-
<li>Audrey&nbsp;C Luo, Valerie&nbsp;J Sydnor, Adam Pines, Bart Larsen, Aaron&nbsp;F Alexander-Bloch, Matthew Cieslak, Sydney Covitz, Andrew&nbsp;A Chen, Nathalia&nbsp;Bianchini Esper, Eric Feczko, and others.
22-
Functional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy.
23-
<em>Nature Communications</em>, 15(1):3511, 2024.</li>
24-
<li>Maur<span class="bibtex-protected">í</span>cio Scopel&nbsp;Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza Kvitko&nbsp;Axelrud, Nim Tottenham, Xi-Nian Zuo, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
25-
Reliability and validity of bifactor models of dimensional psychopathology in youth.
26-
<em>Journal of Psychopathology and Clinical Science</em>, 131(4):407, 2022.</li>
2718
<li>Chenying Zhao, Dorota Jarecka, Sydney Covitz, Yibei Chen, Simon&nbsp;B Eickhoff, Damien&nbsp;A Fair, Alexandre&nbsp;R Franco, Yaroslav&nbsp;O Halchenko, Timothy&nbsp;J Hendrickson, Felix Hoffstaedter, and others.
2819
A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using bids apps.
2920
<em>Imaging Neuroscience</em>, 2:1–19, 2024.</li>
21+
<li>Audrey&nbsp;C Luo, Valerie&nbsp;J Sydnor, Adam Pines, Bart Larsen, Aaron&nbsp;F Alexander-Bloch, Matthew Cieslak, Sydney Covitz, Andrew&nbsp;A Chen, Nathalia&nbsp;Bianchini Esper, Eric Feczko, and others.
22+
Functional connectivity development along the sensorimotor-association axis enhances the cortical hierarchy.
23+
<em>Nature Communications</em>, 15(1):3511, 2024.</li>
24+
<li>Maur<span class="bibtex-protected">í</span>cio&nbsp;Scopel Hoffmann, Tyler&nbsp;Maxwell Moore, Luiza&nbsp;Kvitko Axelrud, Nim Tottenham, Pedro&nbsp;Mario Pan, Eur<span class="bibtex-protected">í</span>pedes&nbsp;Constantino Miguel, Luis&nbsp;Augusto Rohde, Michael&nbsp;Peter Milham, Theodore&nbsp;Daniel Satterthwaite, and Giovanni&nbsp;Abrah<span class="bibtex-protected">ã</span>o Salum.
25+
An evaluation of item harmonization strategies between assessment tools of psychopathology in children and adolescents.
26+
<em>Assessment</em>, 31(2):502–517, 2024.</li>
27+
<li>Mauricio&nbsp;Scopel Hoffmann, Daniel&nbsp;S Pine, Katholiki Georgiades, Peter Szatmari, Euripedes&nbsp;Constantino Miguel, Pedro&nbsp;Mario Pan, Ary Gadelha, Luis&nbsp;Augusto Rohde, Kathleen&nbsp;Ries Merikangas, Michael&nbsp;Peter Milham, and others.
28+
Comparing mental health semi-structured diagnostic interviews and symptom checklists to predict poor life outcomes: an 8-year cohort study from childhood to young adulthood in brazil.
29+
<em>The Lancet Global Health</em>, 12(1):e79–e89, 2024.</li>
3030
</ol>

‎_layouts/blog.html

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,17 +4,20 @@
44

55
<h1 style="text-align: center;">{{ page.title }}</h1>
66

7-
<br>
7+
{% if page.content %}
8+
<br>
89

9-
{{ content }}
10+
{{ page.content }}
1011

11-
<br>
12+
<br>
13+
{% endif %}
1214

1315
{% assign entries_layout = page.entries_layout | default: 'list' %}
1416
{% assign blog_posts = site.posts | where_exp: "post", "post.path contains 'blog'" %}
1517
<div class="entries-{{ entries_layout }}">
1618
{% for post in blog_posts %}
1719
{% include archive-single.html type=entries_layout %}
20+
<br>
1821
{% endfor %}
1922
</div>
2023
<a href="#page-title" class="back-to-top">{{ site.data.ui-text[site.locale].back_to_top | default: 'Back to Top' }} &uarr;</a>

‎_sass/minimal-mistakes/_archive.scss

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -74,7 +74,7 @@
7474

7575
.archive__item-excerpt {
7676
margin-top: 0;
77-
font-size: $type-size-6;
77+
font-size: $type-size-5;
7878

7979
& + p {
8080
text-indent: 0;
@@ -127,7 +127,7 @@
127127
.list__item {
128128
.page__meta {
129129
margin: 0 0 4px;
130-
font-size: 0.6em;
130+
font-size: 0.8em;
131131
}
132132
}
133133

‎docs/blog/index.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,4 @@
22
title: "Blog"
33
excerpt: "Blog"
44
layout: blog
5-
---
5+
---

‎docs/team/_posts/2020-01-01-satterthwaite-theodore.md

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,8 @@ name: "Ted Satterthwaite"
33
layout: single
44
image: /assets/images/team/ted-satterthwaite.jpg
55
site: "https://pennlinc.io"
6-
position: "Principal Investigator"
6+
position: "Principal Investigator<br>McLure Associate Professor in Psychiatry & Behavioral
7+
Research II"
78
affiliation: "University of Pennsylvania"
89
section: "leadership"
910
---

‎docs/team/_posts/2020-01-02-milham-michael.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ name: "Michael Milham"
33
layout: single
44
image: /assets/images/team/michael-milham.jpg
55
site: "https://www.linkedin.com/in/michael-milham-4625a2265/"
6-
position: "Director of Healthy Brain Network"
6+
position: "Principal Investigator<br>Director of Healthy Brain Network"
77
affiliation: "Child Mind Institute"
88
section: "leadership"
99
---

‎docs/team/index.html

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111
{% if team_in_section.size > 0 %}
1212
<h2 style="text-align: center;">{{ section_titles[forloop.index0] }}</h2>
1313
<br>
14-
<table style="justify-content: center; width: 1000px; display: table;">
14+
<table style="justify-content: center; width: 1000px; display: table; table-layout: fixed;">
1515
{% tablerow member in team_in_section cols:2 %}
1616
{% if member.image %}
1717
{% assign image = member.image %}

‎scripts/format_pubs.ipynb

Lines changed: 31 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -9,11 +9,9 @@
99
},
1010
"outputs": [],
1111
"source": [
12-
"from pybtex.database import parse_file\n",
12+
"from pybtex import database\n",
1313
"from pybtex.plugin import find_plugin\n",
14-
"from pprint import pprint\n",
15-
"\n",
16-
"bibfile = \"../_data/publications/core_publications.bib\""
14+
"from pprint import pprint"
1715
]
1816
},
1917
{
@@ -25,10 +23,34 @@
2523
},
2624
"outputs": [],
2725
"source": [
28-
"bib_data = parse_file(bibfile)\n",
29-
"alpha = find_plugin(\"pybtex.style.formatting\", \"alpha\")\n",
30-
"HTML = find_plugin('pybtex.backends', 'html')()\n",
31-
"formatted_bib = alpha().format_bibliography(bib_data=bib_data)\n",
26+
"bibfile = \"../_data/publications/core_publications.bib\"\n",
27+
"bib_data = database.parse_file(bibfile)\n",
28+
"formatter = find_plugin(\"pybtex.style.formatting\", \"unsrt\")\n",
29+
"HTML = find_plugin('pybtex.backends', 'html')()"
30+
]
31+
},
32+
{
33+
"cell_type": "code",
34+
"execution_count": 3,
35+
"id": "ae89c16e-89ac-44f1-9405-0d82b8065863",
36+
"metadata": {
37+
"tags": []
38+
},
39+
"outputs": [],
40+
"source": [
41+
"# Sort the entries by year in descending order\n",
42+
"sorted_entries = sorted(\n",
43+
" bib_data.entries.items(),\n",
44+
" key=lambda x: x[1].fields.get(\"year\", \"2025\"),\n",
45+
" reverse=False,\n",
46+
")\n",
47+
"\n",
48+
"# Create a new BibliographyData object with the sorted entries\n",
49+
"sorted_bib_data = database.BibliographyData(entries=dict(sorted_entries))\n",
50+
"\n",
51+
"# Format the sorted bibliography\n",
52+
"formatted_bib = formatter().format_bibliography(bib_data=sorted_bib_data)\n",
53+
"\n",
3254
"html_entries = [entry.text.render(HTML) for entry in formatted_bib]\n",
3355
"html_str = \"<ol>\\n\"\n",
3456
"for html_entry in html_entries:\n",
@@ -38,7 +60,7 @@
3860
},
3961
{
4062
"cell_type": "code",
41-
"execution_count": 3,
63+
"execution_count": 4,
4264
"id": "fd048f50-12cc-4e21-bb79-521e624ec35b",
4365
"metadata": {
4466
"tags": []
@@ -48,14 +70,6 @@
4870
"with open(\"../_includes/publications/core_publications.html\", \"w\") as fo:\n",
4971
" fo.write(html_str)"
5072
]
51-
},
52-
{
53-
"cell_type": "code",
54-
"execution_count": null,
55-
"id": "57738673-6e4a-4948-8cc3-37a628a17220",
56-
"metadata": {},
57-
"outputs": [],
58-
"source": []
5973
}
6074
],
6175
"metadata": {

0 commit comments

Comments
 (0)