2025 wrap-up updates #61
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Note Other AI code review bot(s) detectedCodeRabbit has detected other AI code review bot(s) in this pull request and will avoid duplicating their findings in the review comments. This may lead to a less comprehensive review. 📝 WalkthroughSummary by CodeRabbit
✏️ Tip: You can customize this high-level summary in your review settings. WalkthroughAdds and reorganizes news/research entries (Dec 2025, Jan 2026); updates News/history guidance and email/location display; extends package.json overrides; and introduces CLI flags, port discovery, and conditional steps in Changes
Sequence Diagram(s)sequenceDiagram
participant User as rgba(30,144,255,0.5) User
participant CLI as rgba(34,139,34,0.5) scripts/build.sh
participant Deps as rgba(255,140,0,0.5) DependencyMgr
participant SEO as rgba(148,0,211,0.5) SEO_Generator
participant ResearchGen as rgba(220,20,60,0.5) Research_Generator
participant Jekyll as rgba(70,130,180,0.5) Jekyll
User->>CLI: invoke build.sh [flags]
CLI->>CLI: parse args & validate
alt --clean
CLI->>CLI: remove _site & .jekyll-cache
end
alt not --skip-deps
CLI->>Deps: install dependencies
Deps-->>CLI: result
else
CLI-->>User: warn deps skipped
end
alt search_db.json exists and not --skip-seo
CLI->>SEO: generate metadata
SEO-->>CLI: done
else
CLI-->>User: warn SEO skipped/missing DB
end
alt not --skip-research
CLI->>ResearchGen: generate research pages
ResearchGen-->>CLI: done
else
CLI-->>User: note research generation skipped
end
CLI->>Jekyll: run build/serve
Jekyll-->>User: site built/served
sequenceDiagram
participant User as rgba(30,144,255,0.5) User
participant DeployCLI as rgba(34,139,34,0.5) scripts/deploy.sh
participant PortFinder as rgba(255,140,0,0.5) PortChecker
participant Jekyll as rgba(70,130,180,0.5) Jekyll
participant Browser as rgba(148,0,211,0.5) Browser
User->>DeployCLI: invoke deploy.sh [--port, --livereload, --drafts, --open,...]
DeployCLI->>DeployCLI: parse args & validate
DeployCLI->>PortFinder: find available port(s)
PortFinder-->>DeployCLI: port(s) chosen or error
DeployCLI->>Jekyll: assemble JEKYLL_CMD with options
DeployCLI->>Jekyll: start server
alt --open
DeployCLI->>Browser: open site URL
end
Jekyll-->>User: server running
Estimated code review effort🎯 4 (Complex) | ⏱️ ~45 minutes Possibly related PRs
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✅ Passed checks (1 passed)
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Add volume 22 and page range 657-667 for the stood-up drop paper now that it's officially published.
Adds comprehensive command-line options to both scripts: Build script (build.sh): - --help: Display usage information - --clean: Force rebuild by removing _site and .jekyll-cache - --skip-deps: Skip dependency installation for faster rebuilds - --skip-seo: Skip SEO metadata generation - --skip-research: Skip research page generation Deploy script (deploy.sh): - --help: Display usage information - --port PORT: Use specific port instead of auto-detection - --host HOST: Bind to specific host (default: localhost) - --drafts: Include draft posts in build - --incremental: Enable faster incremental rebuilds - --no-livereload: Disable live reload feature - --open: Auto-open browser after server starts Both scripts maintain backward compatibility and include improved error handling and user feedback.
Adds year-based organization to News.md and history.md: - Creates separate sections for 2026 and 2025 - Moves Durham University announcement under 2025 heading - Adds paper [21] (Soft Matter) to January 2026 section - Maintains 5-item limit for regular news items - Updates add-news command to handle year sections - Special announcements now excluded from 5-item count This structure makes the news system more scalable as we enter 2026.
Changes to aboutCoMPhy.md: - Update location badge from Physics of Fluids to Durham University - Change map link to Durham campus location - Remove mailto badge to avoid duplicate email display - Keep two email containers with envelope and copy functionality
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Actionable comments posted: 2
🤖 Fix all issues with AI agents
In `@history.md`:
- Around line 31-34: The December 2025 section in history.md is out of
chronological order; reorder the monthly headings and their entries for the 2025
year so months run January → December (i.e., move the "### December" block to be
after the earlier months such that December is last), ensuring the entry
containing "Demirkır, Ç., Yang, R., Bashkatov, A., Sanjay, V., Lohse, D., &
Krug, D." remains intact under the relocated "### December" heading.
In `@scripts/deploy.sh`:
- Around line 67-73: Validate that option arguments for the -p|--port and --host
cases are present and correct: after parsing -p|--port or --host, check that
"$2" exists and does not begin with "-" (indicating another flag); if missing,
print a clear error and exit non‑zero. For CUSTOM_PORT also validate that the
value is numeric (e.g., a regex like '^[0-9]+$'); if not numeric, print an error
and exit. Update the -p|--port and --host parsing branches that set CUSTOM_PORT
and CUSTOM_HOST to perform these checks before assigning and shifting.
🧹 Nitpick comments (1)
scripts/build.sh (1)
33-34: Consider consolidating flag initialization for consistency.
SKIP_DEPSis initialized separately from the other flags (CLEAN_BUILD,SKIP_SEO,SKIP_RESEARCH) which are defined at lines 7-9. Moving this declaration to the same location would improve readability.Suggested consolidation at lines 7-10
# Parse command line arguments CLEAN_BUILD=false SKIP_SEO=false SKIP_RESEARCH=false +SKIP_DEPS=false show_help() {Then remove line 34.
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Pull request overview
This pull request updates the CoMPhy Lab website with end-of-year content including new research publications, news items, location updates to Durham University, and enhanced build/deployment scripts with additional command-line options. The PR also updates the js-yaml dependency for a security fix.
Changes:
- Enhanced build and deployment scripts with new command-line options (--clean, --skip-seo, --port, --host, etc.)
- Updated research index with new publications including 2026 content
- Updated News.md and history.md with recent publications and milestones
- Updated location information to Durham University
- Security update: js-yaml from 4.1.0 to 4.1.1
Reviewed changes
Copilot reviewed 8 out of 9 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| scripts/deploy.sh | Added command-line argument parsing for port, host, drafts, incremental builds, and browser auto-open options |
| scripts/build.sh | Added command-line flags for clean builds and skipping SEO/research generation steps |
| package.json | Added js-yaml override to version >=4.1.1 for security fix |
| package-lock.json | Updated js-yaml dependency from 4.1.0 to 4.1.1 and removed deprecated nested dependencies |
| history.md | Added 2026 section with January publication and December 2025 publication |
| aboutCoMPhy.md | Updated location badge from Physics of Fluids to Durham University and removed email badge |
| _research/index.md | Added new publications, reorganized papers with 2026 section, added new tags and GitHub links |
| News.md | Added 2026 section with recent publications and trimmed older news items |
| .claude/commands/add-news.md | Updated documentation to clarify year/month structure and special announcements handling |
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Keep shared command definitions in the OpenCode directory. Ignore the local .claude symlink so it stays machine-specific.
Reject missing or non-numeric port values and missing host args up front. Clarify news month ordering guidance to match reverse-chronological usage.
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Pull request overview
Copilot reviewed 10 out of 14 changed files in this pull request and generated 2 comments.
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| - Years are organized with `## Year` headings (e.g., `## 2026`, `## 2025`) | ||
| - Years are sorted descending (newest first) | ||
| - Create year section if it doesn't exist | ||
| - Months within a year are in chronological order (January at top) |
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The documentation states "Months within a year are in chronological order (January at top)" but this is incorrect. Looking at the actual News.md and history.md files, months within a year are in REVERSE chronological order (newest first), with December appearing before November, November before September, etc. This inconsistency could lead to incorrect news item placement when following this documentation.
| - Months within a year are in chronological order (January at top) | |
| - Months within a year are in reverse chronological order (newest first, e.g., December before November) |
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| # Start Jekyll with the configured options | ||
| $JEKYLL_CMD |
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The script builds a full shell command string in JEKYLL_CMD that includes user-controlled options like CUSTOM_HOST and then executes it via $JEKYLL_CMD, which allows shell metacharacters in the host value to be interpreted as additional commands. An attacker who can influence the --host argument (or any other option concatenated into JEKYLL_CMD) could inject arbitrary shell syntax such as ; rm -rf / that will run with the privileges of the script. To prevent command injection, avoid executing a constructed string and instead invoke bundle exec jekyll serve directly with properly quoted arguments (or a bash array) so that user-supplied values are passed as data, not as part of the shell command line.
Summary
Changes Made