7  Status

8 Status

8.1 2025-07-01

This report summarizes the key development activities, major accomplishments, and ongoing work for the first 6 monhts of 2025 across the CalCOFI GitHub repositories: api, apps, calcofi4db, calcofi4r, docs, server, workflows. The findings are based on issues and commits from January–July 2025.

8.1.1 API Enhancements

8.1.1.1 New Features & Data Integration

  • Expanded API Options
    • Added ability to include bottle data and use relaxed criteria for net-to-cast matching (commit).
    • Supported upcast/downcast data downloads (commit).
    • Added Zooplankton biomass and improved ichthyodata output (commit).
  • Performance & Maintenance
    • Implemented docker compose restart for Plumber API service (commit).
  • Ongoing Work
    • Migration of database contouring functions to API/app level for improved caching and rendering efficiency.
    • Development of a robust, user-friendly API for seamless DB integration (issue).

8.1.2 Apps Development

8.1.2.1 Visualization & User Interface

  • Continuous Improvements
    • Multiple commits indicate ongoing enhancement, likely focused on UI, data visualization, and integration with the API (see recent commit log).
    • Close coordination between API and Apps for improved workflows and data access.

8.1.3 calcofi4db: R Package & Data Management

8.1.3.1 R Package Initialization & Data Ingestion

  • New R Package: calcofi4db
    • Initial commit and setup (commit), including functions for ingesting CSV datasets and metadata.
    • Refined change detection logic for source CSV files, improving tracking of table/field changes (commit).
    • Enhanced documentation and site via pkgdown.
    • Improved function naming and structure for ingestion (commits, commit).

8.1.4 calcofi4r: Spatial & Ecological Data Tools

8.1.4.1 Data Layers, Analysis, and Bug Fixes

  • Spatial Management Layers
    • Ongoing integration of BOEM Wind Planning Areas, Marine Protected Areas, and SCCWRP management regions (issue, issue).
  • Analysis Functions
    • Improved packages for ecological and spatial analysis, including new dependencies (commit).
  • User Feedback
    • Addressing user-reported bugs such as deprecated function calls (issue).

8.1.5 Documentation (docs)

8.1.5.1 Infrastructure & Environment

  • Documentation Site Updates
    • Added documentation for new packages and ingestion workflows (commit).
    • Improved environment handling for rendering with Quarto and Chromium (multiple commits Jan-Mar 2025).
    • Updated diagrams and edge labels for database documentation.

8.1.6 Server

8.1.6.1 Backend Infrastructure

  • Backend Maintenance
    • Numerous commits for improving server reliability, configuration, and deployment.
    • Indicates active backend support for API and Apps.

8.1.7 Workflows

8.1.7.1 Data Pipeline, Integration, and Registration

  • Workflow Automation
    • Multiple commits show ongoing development of data ingestion, harmonization, and visualization workflows (commit, commit).
  • ODIS Registration
    • Registering datasets with ODIS (using JSON-LD) for broader interoperability (issue).
  • Integration with External Data
    • Ongoing work to load and harmonize diverse ecological datasets (bottle data, larvae, zooplankton, etc.).
  • Spatial Data Management
    • Continued development of AOI (areas of interest), spatial buffer creation, and integration of management regions.

8.1.8 Key Themes & Impact

8.1.8.1 Integration & Interoperability

  • Strong focus on connecting API, Apps, R packages, and backend infrastructure for seamless data access and visualization.
  • Enhanced interoperability through ODIS registration and harmonized workflows.

8.1.8.2 Data Accessibility & Usability

  • Improvements to API and Apps make ecological data more accessible to researchers and managers.
  • Expanded support for spatial management areas and ecological datasets.

8.1.8.3 Infrastructure & Sustainability

  • Investments in documentation, backend reliability, and workflow automation contribute to long-term sustainability and reproducibility.

8.1.9 For More Details

  • Some results may be incomplete due to API limits.
  • To view all commits/issues for 2025, visit each repository’s GitHub UI and filter by year.