Add peer review section to website

[Copilot]

Implements a /reviews/ section for posting public peer reviews of preprints, following the Fraser Lab pattern with a 3-column layout.

Changes

New collections and templates:

• _reviews/ collection directory for peer review markdown files
• _reviews/_template.md.txt template with fields for:
  • Manuscript metadata (title, authors, date)
  • Reviewers and review date
  • Generic preprint URL (any preprint server)
  • Generic public review URL (any review platform)
  • Optional published version (PMID, journal URL)
  • Optional key figure image
  • Optional additional links for post-review section

Display page:

• reviews/index.html renders reviews sorted by date with introductory text on transparent peer review practices
• 3-column responsive layout (following Fraser Lab pattern):
  • Column 1: Key figure/image
  • Column 2: Peer Review - preprint and review links
  • Column 3: Post-Review - published version with "Journal Version" link and optional additional links
• Uses platform-agnostic labels: "Preprint:" and "Public Review:" instead of specific platform references

Configuration:

• Added reviews collection to _config.yml
• Enabled reviews navigation link in _data/navigation.yml

Template Usage

---
title: "Title of Manuscript Reviewed"
date: "2024-12-01"
authors: "Smith J, **Barad BA**, Doe A"  # Bold lab members
reviewers: "Barad BA"
image: "img/reviews/2024_smith.webp"  # Optional

peer-review:
- preprint_url: "https://doi.org/10.1101/2024.11.15.123456"
  review_url: "https://pubpeer.com/publications/ABC123DEF456"

published:
- pmid: "12345678"  # Empty if not yet published
  journal_url: "https://doi.org/10.1016/j.example.2024.01.001"
  
# Optional additional links in post-review section
links:
- name: "Supplementary Materials"
  url: "https://example.com/supplementary"
---

Screenshots

Reviews page (empty state):

Reviews page with 3-column layout:

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Add a peer review section</issue_title>
<issue_description>Add a section of the lab website for peer reviews at /reviews/, mimicking the setup at fraserlab.com. Peer reviews should be a separate data folder called _reviews in markdown format, with a template file for people to copy. Overall, the structure should closely match _publications, with entries for the citation information (title, authors, date), the reviewers and date of review, a link to the preprint, a link to the peer review (on pubpeer), and an optional link to the final version of record. Also include an optional section for a photo like what is used in the publications page. </issue_description>

<agent_instructions>Fraser lab uses this setup: https://github.com/fraser-lab/fraser-lab.github.io/blob/main/_reviews/_template.md</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Add a peer review section #12

---

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[bbarad]

@copilot please remove the specific references to biorxiv and pubpeer, and just mention the preprint and the review with the links in the data file.

[Copilot]

@copilot please remove the specific references to biorxiv and pubpeer, and just mention the preprint and the review with the links in the data file.

Updated in commit 9a25314. The template and display page now use generic "Preprint:" and "Public Review:" labels with preprint_url and review_url fields that accept any URL.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• esm.ubuntu.com
  • Triggering command: /usr/lib/apt/methods/https /usr/lib/apt/methods/https (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

[bbarad]

@copilot please organize into 3 columns like the fraserlab.com/reviews solution for links: key photo, pre review, and post review. Also, please remove any pdf hosting, but add optional additional links to a final peer review record in the post review section when one is present.

[Copilot]

@copilot please organize into 3 columns like the fraserlab.com/reviews solution for links: key photo, pre review, and post review. Also, please remove any pdf hosting, but add optional additional link...

Updated in commit 9f26079. The reviews page now uses a 3-column layout like fraserlab.com/reviews:

• Column 1: Key photo/image
• Column 2: Peer Review (preprint and review links)
• Column 3: Post-Review (published paper with optional additional links)

Removed PDF hosting from the peer-review section and added support for optional additional links in the post-review section.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• esm.ubuntu.com
  • Triggering command: /usr/lib/apt/methods/https /usr/lib/apt/methods/https (dns block)
• fraserlab.com
  • Triggering command: /usr/bin/curl curl -s REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

[bbarad]

@copilot please replace the full text pdf link in the data format with a journal link and label it as "Journal Version"

[Copilot]

@copilot please replace the full text pdf link in the data format with a journal link and label it as "Journal Version"

Updated in commit 1df9b26. The template and display page now use journal_url field instead of pdf for the published version, with the link labeled as "Journal Version".

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• esm.ubuntu.com
  • Triggering command: /usr/lib/apt/methods/https /usr/lib/apt/methods/https (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)