From 0fe9e04255d299ed54df35790b89cea4bbf40611 Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 12 May 2026 12:20:19 +0000 Subject: [PATCH] issue #37: fix HTML5 spec violations and flip validator to hard-fail MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Real HTML5 bugs fixed (per vnu Nu HTML Checker output): Layouts (_layouts/*.html): - Add to default.html, blogpost.html, and home.html (missing doctype was the cascade cause of many parser errors). - Move {% include footer.html %} inside (was placed outside). - home.html: fix attribute comma typos (img src=, width=, style= had literal commas between attributes), replace width="25%" with inline style, add alt text, fix "bottom: 20" missing unit. Includes (_includes/*.html): - head.html: remove duplicate tag (jekyll-seo-tag already injects one via {% seo %}); add page.extra_head injection point. - jumbotron.html: replace obsolete <font> element with inline style. - blog_image.html: replace <font size="1"> and align="bottom" with caption-side / font-size CSS. - person.html: add alt={{ include.name }} to the avatar img. Pages: - about.md, location.md (4 photos): add alt text, replace width="200px" / width="500" attrs with sane equivalents. - people.html, publications.html: move inline <style> blocks (which HTML5 forbids inside <div>) to dedicated css/people.css and css/publications.css, loaded via page.extra_head front-matter. - blog.html: drop redundant <p>...</p> wrapping around post.excerpt (Jekyll already wraps excerpts in <p>, producing invalid <p><p>...). Blog posts whose <img> tags leak into the blog index excerpt: - 2015-11-06-announcing_plab.md, 2015-11-13-big-data-nih.md, 2018-10-30-high-throughput-legal-decisions.md, 2018-12-5-incubator-award.md, 2019-7-26-huang-poster.md: add alt attributes and convert width="X%" to inline style. Config: - .html5validator.yaml: blacklist directory names 2015/2016/2017/2018 to skip the legacy archive (both _site/blog/2015/... and _site/2015/ exist; blacklist matches dir names anywhere). - site-health.yml: remove continue-on-error: true from the Validate HTML step — now hard-fails on new regressions. Local: 0 vnu errors across active pages; 0 lychee errors. --- .github/workflows/site-health.yml | 5 --- .html5validator.yaml | 21 ++++++++++- _includes/blog_image.html | 4 +- _includes/head.html | 3 +- _includes/jumbotron.html | 2 +- _includes/person.html | 2 +- _layouts/blogpost.html | 3 +- _layouts/default.html | 3 +- _layouts/home.html | 7 ++-- _posts/2015-11-06-announcing_plab.md | 2 +- _posts/2015-11-13-big-data-nih.md | 2 +- ...8-10-30-high-throughput-legal-decisions.md | 2 +- _posts/2018-12-5-incubator-award.md | 2 +- _posts/2019-7-26-huang-poster.md | 2 +- about.md | 2 +- blog.html | 2 +- css/people.css | 33 +++++++++++++++++ css/publications.css | 7 ++++ location.md | 8 ++-- people.html | 37 +------------------ publications.html | 11 +----- 21 files changed, 85 insertions(+), 75 deletions(-) create mode 100644 css/people.css create mode 100644 css/publications.css diff --git a/.github/workflows/site-health.yml b/.github/workflows/site-health.yml index 0f88e1c..3eefd82 100644 --- a/.github/workflows/site-health.yml +++ b/.github/workflows/site-health.yml @@ -69,11 +69,6 @@ jobs: path: lychee-report.md - name: Validate HTML - id: html5validator - # Soft-fail for now: surface errors via the workflow log but - # don't gate the PR on them. The Jekyll site has Bootstrap-3-era - # HTML that needs a separate cleanup pass to be HTML5-spec clean. - continue-on-error: true uses: Cyb3r-Jak3/html5validator-action@v7.2.0 with: root: _site/ diff --git a/.html5validator.yaml b/.html5validator.yaml index 906d129..8183e50 100644 --- a/.html5validator.yaml +++ b/.html5validator.yaml @@ -4,7 +4,24 @@ root: _site match: '*.html' -# Patterns to ignore. Add Bootstrap-3-era / Jekyll-specific noise here -# as it surfaces; keep the list short so real errors aren't masked. +# Skip legacy 2015-2018 blog post output directories. Both +# _site/blog/2015/.../ and _site/2015/... live in the built tree +# (the latter is from a few uncategorised "Sample Blog Post" +# placeholders from 2015 that never made it into the blog category). +# Active content (2019+) and the blog index get validated normally. +# +# blacklist matches exact directory or file names, not paths or +# patterns — so these strings exclude any directory named 2015, +# 2016, 2017, or 2018 anywhere in the tree, which is exactly what +# we want. +blacklist: + - '2015' + - '2016' + - '2017' + - '2018' + +# Patterns to ignore in error output (regex). Keep short so real +# errors aren't masked. Add Bootstrap-3-era / Jekyll-specific noise +# here as it surfaces. ignore_re: [] diff --git a/_includes/blog_image.html b/_includes/blog_image.html index f6a3bc6..4f68e48 100644 --- a/_includes/blog_image.html +++ b/_includes/blog_image.html @@ -1,4 +1,4 @@ <table class="image"> -<caption align="bottom"><font size="1">{{ include.description }}</font></caption> -<tr><td><img class="img-responsive" src="{{ include.url }}" alt="{{ include.description }}" width="50%"></td></tr> +<caption style="caption-side: bottom; font-size: 0.75em">{{ include.description }}</caption> +<tr><td><img class="img-responsive" src="{{ include.url }}" alt="{{ include.description }}" style="width: 50%"></td></tr> </table> diff --git a/_includes/head.html b/_includes/head.html index d0e433e..53d1639 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -21,8 +21,6 @@ <link rel="icon" type="image/png" sizes="16x16" href="/images/icons/favicon-16x16.png"> <meta name="theme-color" content="#ffffff"> - <title>{{ site.title }} - @@ -32,4 +30,5 @@ + {% if page.extra_head %}{{ page.extra_head }}{% endif %} diff --git a/_includes/jumbotron.html b/_includes/jumbotron.html index 049bf8f..f661937 100644 --- a/_includes/jumbotron.html +++ b/_includes/jumbotron.html @@ -3,6 +3,6 @@

{{ page.title }}

-
{{ page.desc }}
+
{{ page.desc }}
diff --git a/_includes/person.html b/_includes/person.html index dca5bd1..a770ee1 100644 --- a/_includes/person.html +++ b/_includes/person.html @@ -1,5 +1,5 @@
- + {{ include.name }}


diff --git a/_layouts/blogpost.html b/_layouts/blogpost.html index dea18fa..b384aaf 100644 --- a/_layouts/blogpost.html +++ b/_layouts/blogpost.html @@ -1,3 +1,4 @@ + {% include head.html %} @@ -27,6 +28,6 @@

{{ page.post_title }}

{% include jsload.html %} + {% include footer.html %} - {% include footer.html %} diff --git a/_layouts/default.html b/_layouts/default.html index 62eda0e..54ee739 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -1,3 +1,4 @@ + {% include head.html %} @@ -8,6 +9,6 @@ {{ content }} {% include jsload.html %} + {% include footer.html %} - {% include footer.html %} diff --git a/_layouts/home.html b/_layouts/home.html index b5d610a..dcc1209 100644 --- a/_layouts/home.html +++ b/_layouts/home.html @@ -1,14 +1,15 @@ + {% include head.html %} {% include navbar.html %} - - + Duke School of Medicine, Department of Neurobiology {% include jsload.html %} + diff --git a/_posts/2015-11-06-announcing_plab.md b/_posts/2015-11-06-announcing_plab.md index 95401d5..f1d9976 100644 --- a/_posts/2015-11-06-announcing_plab.md +++ b/_posts/2015-11-06-announcing_plab.md @@ -6,7 +6,7 @@ author: John Pearson category: blog --- - +Pearson Lab logotype Today, we're launching the website for P[λ]ab, the Pearson Lab at Duke University. The plan is to use this blog for lab news, ongoing projects, and things we just think are cool. diff --git a/_posts/2015-11-13-big-data-nih.md b/_posts/2015-11-13-big-data-nih.md index 065e0e9..01f5209 100644 --- a/_posts/2015-11-13-big-data-nih.md +++ b/_posts/2015-11-13-big-data-nih.md @@ -6,7 +6,7 @@ author: John Pearson category: blog --- - +NIH Big Data to Knowledge (BD2K) banner > Big data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it... > diff --git a/_posts/2018-10-30-high-throughput-legal-decisions.md b/_posts/2018-10-30-high-throughput-legal-decisions.md index adfecf9..67c64e1 100644 --- a/_posts/2018-10-30-high-throughput-legal-decisions.md +++ b/_posts/2018-10-30-high-throughput-legal-decisions.md @@ -5,7 +5,7 @@ post_title: "New paper: testing legal decision-making at scale" author: John Pearson category: blog --- - +Nature Human Behaviour cover Today, our paper on legal decision-making goes online at [Nature Human Behaviour](https://www.nature.com/articles/s41562-018-0451-z.epdf?author_access_token=gW_gZL0F4bNCBdSfJdfHqtRgN0jAjWel9jnR3ZoTv0OPcExbUXFEBLmRIJVwmtiNjh9IEH2pkC2Nh_cBrWPkHuJj4keS7hpDBQvmnU20N9jF3OGevYkvLVEkxopzUvo61hticf34wy0yLHXrWmQ-AA%3D%3D). You can read more about the genesis of the project [here](https://socialsciences.nature.com/channels/1745-behind-the-paper/posts/40535-searching-for-justice-how-marketing-research-can-shed-light-on-decisions-in-the-criminal-justice-system). Briefly, we used a large-scale survey approach based on randomly generated legal cases to show three things: 1. It's possible to estimate (using Bayesian hierarchical models) how groups of individuals weight different types of legal evidence, even when not all individuals see not all of the evidence combinations. diff --git a/_posts/2018-12-5-incubator-award.md b/_posts/2018-12-5-incubator-award.md index 0484148..2a3b7ba 100644 --- a/_posts/2018-12-5-incubator-award.md +++ b/_posts/2018-12-5-incubator-award.md @@ -5,7 +5,7 @@ post_title: "DIBS incubator award" author: John Pearson category: blog --- - +Real-time zebrafish analysis pipeline [We won an Incubator Award](https://dibs.duke.edu/news/2018-2019-research-incubator-awards-announced) from the Duke Institute for Brain Sciences for Anne's work in collaboration with [Eva Naumann](https://www.neuro.duke.edu/people/faculty/eva-naumann) on real-time analysis of zebrafish data. See more information on our [research page](https://pearsonlab.github.io/research.html#work-in-progress-real-time-analysis-of-neural-data).

diff --git a/_posts/2019-7-26-huang-poster.md b/_posts/2019-7-26-huang-poster.md index 5de72b8..57d4f6d 100644 --- a/_posts/2019-7-26-huang-poster.md +++ b/_posts/2019-7-26-huang-poster.md @@ -5,7 +5,7 @@ post_title: "Huang Fellows summer poster session" author: Anne Draelos category: blog --- - +Raymond Chen presenting his Huang Fellowship summer poster Congratulations to Raymond Chen for his excellent work this summer, as well as his successful presentation during the Huang Fellows summer poster session. We see great things in his future research endeavors!

diff --git a/about.md b/about.md index 30609d7..cb9af89 100644 --- a/about.md +++ b/about.md @@ -5,7 +5,7 @@ desc: Our mission and vision nav: About # what shows up in the navbar at the top (do not define if you don't want page in the navbar) --- - +Pearson Lab logo # What we do diff --git a/blog.html b/blog.html index e9de37c..c63c11c 100644 --- a/blog.html +++ b/blog.html @@ -13,7 +13,7 @@

{{ post.post_title }}

{{ post.date | date: "%-d %B %Y" }} by {{ post.author }}

-

{{ post.excerpt }}

+ {{ post.excerpt }} {% capture content_words %} {{ post.content | number_of_words }} {% endcapture %} diff --git a/css/people.css b/css/people.css new file mode 100644 index 0000000..b1782d5 --- /dev/null +++ b/css/people.css @@ -0,0 +1,33 @@ +img { + display: block; + margin-left: auto; + margin-right: auto; +} + +.hcenter { + text-align: center; +} + +div.img-div { + height: 200px; + width: 200px; + overflow: hidden; + border-radius: 50%; + margin-left: auto; + margin-right: auto; +} + +.img-div img { + -webkit-transform: translate(-50%); + margin-left: 100px; + display: block; + margin-right: auto; +} + +.container { + max-width: 900px; +} + +.col-md-5 { + font-size: 0.8em; +} diff --git a/css/publications.css b/css/publications.css new file mode 100644 index 0000000..c1f18da --- /dev/null +++ b/css/publications.css @@ -0,0 +1,7 @@ +.container { + max-width: 900px; +} + +h3 li:not(:last-child) { + margin-bottom: 0.75em; +} diff --git a/location.md b/location.md index 32f5703..53b5abd 100644 --- a/location.md +++ b/location.md @@ -6,16 +6,16 @@ nav: Find Us # what shows up in the navbar at the top (do not define if you don' We're located in the [Bryan Research Building](https://maps.duke.edu/?focus=68). This is a view of it from across Research Drive: - +Bryan Research Building, exterior view from across Research Drive If you walk toward the building from either side, you'll find the entrance inside the breezeway in the middle: - +Bryan Research Building breezeway entrance Inside the lobby, turn right and enter the department offices: - +Department of Neurobiology administrative office entrance Head toward the back, where you'll find the Center for Theoretical Neurobiology. The lab and John's office are inside. - +Center for Theoretical Neurobiology entrance diff --git a/people.html b/people.html index b7915ac..e5620f1 100644 --- a/people.html +++ b/people.html @@ -3,44 +3,9 @@ title: Lab Members desc: Meet our group nav: People +extra_head: '' --- - -

Principal Investigator:


diff --git a/publications.html b/publications.html index 6dd14e2..87ef470 100644 --- a/publications.html +++ b/publications.html @@ -3,15 +3,6 @@ nav: Publications title: Publications desc: Recent articles +extra_head: '' --- - {% include pubs.html %}