GAMA 0.2.5

API changes

• Renamed extract_assembly_metadata() output column accession to entrez_uid for semantic correctness

Documentation

• Updated the user guide accordingly

GAMA 0.2.4

Reliability

• Replaced safe-search path with retrying entrez_search() wrappers
• Added web_history-aware summary retrieval for large Entrez result sets

Refactoring

• Switched metadata retrieval to species-local batching
• Simplified NCBI configuration to API key support only
• Removed GAMA request throttling and related legacy code
• Eliminated redundant Assembly summary refetching during metadata extraction
• Removed redundant legacy SRA batch-size code

Progress reporting

• Updated query_species() to tick once per completed Assembly, SRA, and BioSample search

Documentation

• Updated the GAMA user guide to reflect revised NCBI configuration and history-aware retrieval behaviour

Testing

• Confirmed functionality with end-to-end workflow tests

GAMA 0.2.3

Reliability

• Fixed filtering in extract_sra_metadata(), plot_sra_availability(), and plot_sra_skew()
• This bug occurred because class, subclass, and species were used both as function arguments and as metadata column names
• Updated affected filters to use explicit .env$... references

Testing

• Re-tested extract_sra_metadata() and confirmed that class = and subclass = filters now work correctly
• Re-ran SRA availability, GEO overlay, and skew plotting workflows to confirm expected behaviour

GAMA 0.2.2

Refactoring

• Renamed plot_sra_geo_availability() to plot_sra_geo()
• GEO linkage fields are now always cached in summarise_sra_availability() output via the attached sra_profile, regardless of include_geo
• include_geo = TRUE now acts only as an output visibility option, appending species-level GEO summary columns without changing what is cached

Documentation

• Updated roxygen documentation and examples to reflect the revised GEO caching and plot_sra_geo() workflow
• Added docs/GAMA_user_guide.pdf as a comprehensive reference for GAMA functions and methods

Testing

• Tested end-to-end SRA availability and GEO overlay workflow

GAMA 0.2.1

Refactoring

• Centralised user-facing messaging via new helpers (.gama_msg(), .gama_warn(), .gama_stop()) for consistent and informative console outputs
• Standardised info/warning/error messaging style (and user-friendly call. = FALSE printing where appropriate) to reduce legacy drift
• Updated provenance and print pathways to use the unified messaging style

Reliability

• Reduced silent drops in availability workflows: summaries retain requested species and emit explicit messages when species have no data

Plotting

• plot_sra_geo_availability() now matches plot_sra_availability() styling more closely:
  • prevents GEO-linked fraction label clipping (margin/placement adjustments)
  • enforces clean 0–1 axis breaks and two-decimal tick labels

Testing

• Ran end-to-end availability and plotting workflows to confirm changes do not alter core functionality

GAMA 0.2.0

Features

• Added SRA skew workflow (summarise_sra_skew() and plot_sra_skew()) to support BioProject/BioSample-level record aggregation
• Diversity summaries include Inverse Simpson index (eff, effective number):
  • low values indicate evidence dominated by a small number of projects/samples
  • high values indicate broader, more balanced support

Refactoring

• summarise_sra_availability() now caches parsed SRA profiles on outputs for reuse by downstream summaries/plots
• Centralised progress-bar handling for more consistent reporting
• Added new Imports dependency {rlang}

API changes

• extract_sra_metadata() now returns entrez_uid (replacing sra_id) and adds biosample and bioproject columns

Documentation

• Added/expanded roxygen documentation and examples for the SRA skew workflow
• Updated examples to reflect diversity-aware feasibility assessment workflows

Testing

• Conducted extended end-to-end tests to validate the new workflow

GAMA 0.1.2

Refactoring

• Removed redundant code
• Improved internal structure and plotting logic

Documentation

• Revised and expanded roxygen documentation
• Improved help page formatting and cross-references

Testing

• Conducted end-to-end workflow tests
• Validated plotting and metadata extraction functions

GAMA 0.1.1

Refactoring

• Simplified internal scripts and removed redundant code
• Improved internal consistency and readability

Testing

• Validated behaviour against previous version using smoke tests
• Confirmed compatibility with existing saved result objects