[NF SDG] Internship Public Meeting Notes

[TheCedarPrince]

These are the public meeting notes for the NumFOCUS Small Development Grant project across JuliaHealth.

[kosuri-indu]

Date: January 5, 2026
Attendees: @kosuri-indu, @TheCedarPrince, @cncastillo

Agenda & Discussion Summary

• Created this issue to serve as a public, ongoing log for meeting notes related to the NumFOCUS Small Development Grant project.
• Reviewed the approved proposal and overall goals:
  • Attracting new JuliaHealth community members
  • Highlighting JuliaHealth workflows
  • Strengthening ecosystem robustness (docs, CI, maintenance)
• Confirmed Some Logistics

Project Direction & Execution Plan

Initial focus (Goals 2 & 3):

1. Conduct a detailed audit of documentation and CI status for key JuliaHealth packages.
   • Focus first on packages in the General Registry
   • Prioritize based on activity and adoption (e.g. stars)
2. Summarize audit findings as a JuliaHealth blog post (more details below).
3. Develop standardized documentation and CI templates.
   • Move one package to DocumenterVitepress as a reference example
   • Document challenges encountered during the migration
4. Submit follow-up issues to individual repositories based on audit findings.

Audit Scope (Initial Ideas)

• Presence of documentation (e.g. gh-pages, docs builds)
• CI status and coverage (GitHub Actions, coverage config)
• Repository structure (src/, test/, docs/)
• Maintenance signals (activity, stars, open/closed issues)
• GPU / Buildkite CI behavior (wherever applicable)

Audit outputs should be mainly be reproducible, ideally scriptable and reusable in CI.

Other Topics Discussed

• GPU CI / Buildkite behavior and associated noise concerns
• Manual vs Automated builds for the JuliaHealth website
• Early discussion around style guides (e.g. Blue style vs Runic), noted as a potential future topic

TO-DOS:

@kosuri-indu

• Start the work on audit of documentation and CI status for key JuliaHealth packages
• Begin outlining reproducible audit metrics alongside

@TheCedarPrince:

• Share access to the JuliaHealth code coverage
• Suggest an approach/tool for timesheet tracking

@cncastillo:

• As mentioned in the meeting, you were planning to reach out to NumFOCUS (Arliss) with a few questions related to the form i believe -- just adding a quick reminder here.

[kosuri-indu]

Date: January 19, 2026
Attendees: @kosuri-indu, @cncastillo
Async feedback: @TheCedarPrince

Agenda & Discussion Summary

• Reviewed the completed JuliaHealth ecosystem audit, including:
  • Reproducible GitHub Actions–based audit pipeline
  • Visualization outputs (RESULTS.md)
  • Repository structure and audit methodology
• Discussed feedback from Jacob (shared asynchronously via voice notes).
• Walked through the audit repository layout, scripts, metrics, and visualization choices.
• Reviewed the draft JuliaHealth blog post summarizing audit findings.
• Discussed next 2-week work plan following completion of the audit phase.

Review Feedback (Jacob – Async)

• Overall feedback was positive:
  • Audit exceeded expectations in scope, depth and execution.
  • Results and visualizations are insightful and well structured.
• Requested clarifications and refinements, not major changes:
  • Add short explanations for audit variables (e.g. “standard layout”, CI, coverage).
  • Refine terminology for ecosystem maturity
  • Improve wording around maintenance status to avoid implying abandonment.
  • Consider community input (Slack / Discourse) on how to classify maintenance states.
  • Add brief documentation explaining contributor distributions.
  • Rename or refine README quality metric (lines of code alone is insufficient).
• Suggested longer-term idea:
  • Potentially exposing audit outputs as a dedicated JuliaHealth website section
    (e.g. "Ecosystem Overview / Statistics"), updated automatically via CI.
• Blog post feedback:
  • Should be readable and navigable
  • Possibly split content or structure it for easier consumption

Audit Review & Technical Discussion (Live with Carlos)

• Confirmed audit pipeline:
  • Fully reproducible via GitHub Actions
  • Manual trigger enabled; discussed adding monthly scheduled runs
• Registry handling:
  • General Registry handled via local clone (avoiding excessive GitHub API calls)
  • Registry data currently static and manually refreshed
  • Agreed this is acceptable for now; future automation possible
• Key findings discussed:
  • Discovery of registry metadata issues (repository links not updated after migration to JuliaHealth)
    • Several packages may require General Registry PRs to fix repo URLs
  • Code of Conduct not being there
  • Few changes recommended for metrics/audit dimensions.
• Visualization choices:
  • VegaLite chosen for speed and CI-friendliness
  • PNG outputs used instead of interactive HTML due to Markdown limitations
• Metrics discussion:
  • Contributors counts may include bots (e.g. Dependabot)
  • Maintainers who are the most responsive could be added
  • README assessment to be refined using measurable features (badges, code blocks, links etc) - A Paper was suggested to refer to.
  • License presence confirmed across all packages (100%), license type not yet analyzed (but would want to)
• Validation:
  • Audit repository structure and documentation are clear and easy to follow
  • No major missing components identified

Blog Post Review

• Draft blog post reviewed live.
• Content focuses on:
  • Motivation (NumFOCUS grant goals)
  • Audit methodology
  • Ecosystem-wide findings
  • Actionable recommendations
• Feedback:
  • Visual-first approach is good (“images > text”)
  • Additional explanatory text only needed where it improves clarity
  • README quality metric should be refined before final publication
• Plan to finalize and merge blog post after incorporating feedback.

Project Direction & Execution Plan (Next 2 Weeks)

• Finalize audit phase:
  • Incorporate Jacob’s and Carlos’s feedback
  • Refine terminology, metrics, and documentation
• Complete and merge blog post
• Begin standardization work:
  • Draft a standard JuliaHealth package layout
  • Define baseline requirements:
    • Documentation structure
    • CI configuration
    • Community files (CONTRIBUTING.md, CODE_OF_CONDUCT.md)
• Explore DocumenterVitepress migration:
  • Start with a simpler package as a test case
  • Consider migrating KomaMRI after validating the workflow
• Prepare to open follow-up issues on repositories based on audit findings.

TO-DOs

@kosuri-indu

• Update audit results based on review feedback
• Finalize and update the blog post PR.
• Draft a proposed standard JuliaHealth package layout and templates.
• DocumenterVitepress migration on a simple package & then probably in KomaMRI.jl.

@cncastillo, @TheCedarPrince

• Provide feedback during final review of updated audit and blog post.
• Assist with registry metadata fixes if needed.
• Assist if any issues with KomaMRI.jl's DocumterVitepress.

[kosuri-indu]

Date: February 2, 2026
Attendees: @kosuri-indu, @cncastillo

Agenda & Discussion Summary

• Reviewed recent updates to the JuliaHealth ecosystem audit.
• Walked through newly added audit metrics, contributor analysis and visualizations.
• Reviewed progress on standardization templates (docs, CI, community files).
• Discussed DocumenterVitepress migration progress and current blockers.
• Planned next steps to wrap up Goals 2 & 3 and transition toward Goal 1 work.

Audit Updates & Refinements

• Added refined contributor and maintainer analysis, including human vs bot contributors.
• Updated maintenance status classifications and terminology based on mentor and community feedback.
• Reworked README assessment to use feature-based completeness metrics.
• Added license presence and license type distribution analysis.
• Improved audit result visualizations with clearer annotations and explanations.
• Restructured audit structure for better reproducibility and reuse.

Templates & Standardization Work

Added Templates (templates/)

• Package structure template
• README.md template (aligned with README completeness factors)
• CONTRIBUTING.md
• CODE_OF_CONDUCT.md (Contributor Covenant–based)
• Minimal CI workflow examples (GitHub Actions)
• Documentation structure templates
• Maintenance guide covering various packages

Package Checklist

• Created checklists for:
  • New packages
  • Existing packages
• Covers setup, CI, documentation, community files, registration, and maintenance.

DocumenterVitepress Migration

• Tested DocumenterVitepress on a simpler package (OMOPCDMFeasibility.jl).
• Identified blockers related to:
  • Dependency and version incompatibilities
  • DocStringExtensions constraints in OMOPCommonDataModel
• Migration not currently feasible for some packages without upstream updates.
• Plan:
  • Create a PR in OMOPCommonDataModel.jl to upstream version
  • Fully validate migration on OMOPCDMFeasibility.jl
  • Revisit and test on KomaMRI.jl after resolving dependency constraints

Blog Post Status

• Blog post updated to reflect:
  • Refined metrics
  • Updated terminology
  • New visualizations
• Pending:
  • Final review from @TheCedarPrince
  • Image consistency checks before merge

Action Items & Next Steps

Short-Term (Complete Goals 2 & 3)

• Add Stars and if possible downloads count to the Audit
• Get blog post PR reviewed @TheCedarPrince @cncastillo.
• Add Guide on “How to migrate a package to JuliaHealth”
• Request reviews on:
  • Templates by @cncastillo @TheCedarPrince
• Submit test PRs to the General Registry for selected metadata mismatches.
• Open targeted issues or small PRs for top JuliaHealth packages (prioritized by adoption).
• Start work on JuliaHealthZoo if time permits

Additional Considerations

• Ensure audit tooling remains reusable for other Julia organizations. (Could do a discourse post after finishing work)
• Draft a JuliaCon abstract summarizing audit and ecosystem work (deadline: Feb 28).

[kosuri-indu]

Date: February 16, 2026
Attendees: @kosuri-indu, @cncastillo

Agenda & Discussion Summary

• Reviewed follow-up PRs and issues opened based on the JuliaHealth ecosystem audit.
• Discussed current status of DocumenterVitePress migration and remaining blockers.
• Reviewed progress on JuliaHealthZoo setup and workflow implementation.
• Discussed on dynamic “Ecosystem Health” dashboard on the website.
• Clarified next priorities, including abstract submission and workflow completion.

Audit Follow-ups & Repository Improvements

• Created issues across top 10–11 JuliaHealth repositories (prioritized by stars).
• Submitted straightforward PRs addressing documentation and CI-related improvements.
• Status update: PRs merged/under review/remaining repositories inactive or awaiting maintainer response.
• Agreed to pause opening new issues until current PRs receive responses.
• Registry URL mismatch fixes - almost all got merged!
• GPU CI triggering behavior fix confirmed

DocumenterVitePress Migration

• Significant time spent resolving migration issues.
• Discussed on current status and what all remaining changes need to be done.

JuliaHealthZoo

• Access granted to repository.
• Initial structure inspired by Agents.jl example layout.
• Basic repository scaffolding completed (docs, workflows, structure).
• Began implementation of Patient-Level Prediction workflow
• Plan to complete one workflow first, then replicate structure for remaining workflows.

Potential Addition – HealthDash

• Discussed a potential future addition into work: HealthDash.jl
• Concept:
  • Allow users to select a JuliaHealth repository.
  • Interact with selected functions through a web-based dashboard.
  • Execute example workflows without local setup.
• To be explored further after core goals are completed.
• Implementation will depend on feasibility, performance considerations and mentor feedback.

Action Items & Next Steps

• Resolve DocumenterVitePress HTML rendering issues.
• Complete first working JuliaHealthZoo workflow and get it confirmed
• Draft and submit JuliaCon abstract.
• Implement dynamic Ecosystem Health dashboard.

[kosuri-indu]

Date: March 3, 2026
Attendees: @kosuri-indu, @TheCedarPrince

Agenda & Discussion Summary

• Reviewed major progress on JuliaHealthZoo implementation and documentation.
• Reviewed dynamic "Ecosystem Health" dashboard integration on the website.
• Discussed website structural updates (Contributing section, research visibility).
• Reviewed repository improvements and ecosystem-wide maintenance progress.
• Discussed NumFOCUS grant logistics and milestone-based restructuring.

JuliaHealthZoo – Workflow & Documentation Progress

• Demonstrated completed Patient-Level Prediction (PLP) workflow
• Structured documentation deployed using DocumenterVitePress.
• Documentation includes:
  • Getting Started guide
  • Conceptual introduction (Observational Health, OMOP CDM)
  • Step-by-step explanation of the full pipeline
  • Code-linked explanations and references.
• Suggested navigation improvements:
  • Collapse tutorial sections into a cleaner dropdown structure.
  • Reduce visual clutter in top navigation.
• Strategic recommendation:
  • Position JuliaHealthZoo as an ecosystem-level integration test suite.
    • Workflows should act as reproducible integration tests.
    • CI should detect breaking changes across dependency updates.
    • Consider version freezing and automated checks for composability issues.
• Suggested consulting maintainers of similar ecosystem "Zoo" repositories (e.g. Agents.jl Zoo) for CI and workflow testing strategies.

Ecosystem Health Dashboard (Website Integration)

• Demonstrated dynamic "Ecosystem Health" section integrated into the JuliaHealth website.
• Linked JuliaHealthAudit outputs directly to website pages.
• Approach avoids duplicating heavy computations on website side.
• Review pending for refinements and structural feedback.

Repository Improvements & Follow-ups

• Confirmed follow-up PRs and issues opened across prioritized repositories.
• Most General Registry URL mismatches successfully merged.
• GPU CI triggering behavior fix confirmed.
• Ongoing review and merge cycle for documentation and CI improvements.
• All Contributors integration tested (merge pending).

Website Structure & Community Visibility

• Discussed adding a "Contributing" tab on the website:
  • Include guide on migrating a package to JuliaHealth.
  • Provide clearer onboarding pathway for package maintainers.
• Discussed enhancing "About" section:
  • Community structure and governance visibility.
  • Potential research/publication aggregation section.
  • Highlighting institutions and contributors.

Action Items & Next Steps

• Refine JuliaHealthZoo navigation structure.
• Explore CI integration testing approach for workflows.
• Continue refining PLP workflow before replicating structure to other workflows.
• Share JuliaHealthZoo progress in community channels.
• Work on the remaining website issues.

[kosuri-indu]

Date: March 16, 2026
Attendees: @kosuri-indu, @cncastillo

Agenda & Discussion Summary

• Reviewed progress updates.
• Demonstrated All Contributors integration and gathered feedback.
• Reviewed updates to the Ecosystem Health dashboard and workflow setup.
• Discussed multiple website-related improvements (contributing guide, ecosystem page, contributors section).

All Contributors Integration

• Demonstrated working integration of All Contributors on the JuliaHealth website repository.
• Feedback:
  • Functionality works well.
  • Concern about large visuals and README clutter.
• Action:
  • Explore customization options (size/layout of contributor section).
  • Decide later on scaling to all JuliaHealth repositories.

Ecosystem Health Dashboard

• Demonstrated updated Ecosystem Health section with improved structure and visuals.
• Current status:
  • Implementation completed but not fully tested (created from fork).
• Plan:
  • Move changes to a branch in main repo.
  • Test full workflow.
  • Merge after validation.
  • Potential to showcase to broader Julia community
  • Add preview images/screenshots in PR

Website Updates & Content Additions

• Combined multiple smaller issues into a single PR
• Added guide for migrating packages to JuliaHealth under Contributing section.
• Based on General registry FAQ content.
• Feedback: Include an example (e.g. KomaMRI.jl).

Researchers / Contributors Section

• Explored adding section highlighting contributors’ institutions.
• Data source: Extracted GitHub organization/company fields into CSV.
• Challenges:
  • Consent considerations.
  • Deciding inclusion criteria (active vs past contributors).
• Proposed approach:
  • Use opt-in via Slack or community message.
  • Contributors submit institution details voluntarily.
• Next step:
  • Check implementation approach with Flux.jl maintainers.

Ecosystem Comparison Page

• Created initial Ecosystem page structure.
• Status:
  • Initial draft created.
  • Some gaps and missing equivalents.
  • Validation ongoing.

Action Items & Next Steps

• Submit first invoice by end of week.
• Explore customization options for All Contributors display.
• Move Ecosystem Health workflow to main repo branch and test.
• Add preview images/screenshots to PR.
• Get JuliaHealthZoo review from @TheCedarPrince
• Continue validating ecosystem comparison mappings.
• Draft outreach approach for contributors’ institution section.
• Reach out to Flux.jl maintainers for reference implementation.
• Finalize and merge pending PRs after testing.

[kosuri-indu]

Date: March 30, 2026
Attendees: @kosuri-indu, @cncastillo, @TheCedarPrince

Agenda & Discussion Summary

• Reviewed progress on website updates, ecosystem dashboard and contributors integration.
• Discussed JuliaHealthZoo workflow progress and remaining blockers.
• Reviewed pending PRs, blog post merge and next steps for public sharing.
• Discussed logistics: JuliaCon planning, invoices, and timelines.

Website Updates & Infrastructure

• Added new sections:
  • “Who We Are”
  • Research/Publications
  • Ecosystem comparison (Julia vs Python/R)
  • Contributing guide (package migration)
• Implemented GitHub Actions:
  • Automatic website builds
  • PR preview links
• Discussion:
  • Add “Edit this page” links for easier contributions.
  • Introduce tagging system (e.g., NumFOCUS, SDG tag for related work).

Ecosystem Health Dashboard

• Demonstrated fully integrated dynamic dashboard.
• Automatically updates from audit outputs via CI.

All Contributors Integration

• Demonstrated working integration with contributor roles via emojis.
• UI improvements:
  • Reduced avatar size
  • Retained table layout for clarity
• Decision: Approved to merge, and merged!

Blog Post (Audit Summary)

• Blog post PR reviewed and ready.
• Decision: Proceed with merge.
• Suggestion: Add tags/categories (e.g., NumFOCUS SDG).
• Plan: Share along with website updates and ecosystem dashboard after reviews.

JuliaHealthZoo Progress

• Current workflows:
  • Patient-Level Prediction (in progress)
  • MRI workflow (docs drafted, implementation ongoing)
  • Geospatial workflow (paused)

Contributors / Institutions Section

• Explored adding contributor institution logos.
• Concerns: Consent and trademark/legal issues (e.g., university policies).
• Decision: Do NOT include logos without explicit permission.
• Next steps: Ask on Julia Discourse, Consider opt-in approach for contributors

Ecosystem Comparison Page

• Initial version created comparing Julia tools with Python/R equivalents.
• Feedback: Add edit links for easier updates

Reviews, Merging & Community Sharing

• Pending PR reviews to be completed this week (@TheCedarPrince).
• Plan: Merge all major updates (blog, website, dashboard), share publicly with Julia community
• Idea: Bundle outputs into a single announcement

Action Items & Next Steps

• Complete MRI workflow implementation and testing.
• Continue refining website (edit links, tagging system).
• Submit invoice by end of week.
• Explore opt-in process for contributor institutions.
• Validate and refine ecosystem comparison mappings.
• Complete PR reviews and merge updates.
• Add tags for NumFOCUS SDG-related for audit blog post.
• Continue JuliaHealthZoo workflow development.