GAMA 0.2.9

Features

• Added summarise_assembly_availability() and plot_assembly_availability() to complete the NCBI Assembly workflow, bringing it into line with the SRA workflow

Reliability

• Expanded object-aware error messaging across summary, plotting, and metadata workflows
• Improved parameter validation and suggestion logic for invalid user inputs

Refactoring

• Added shared helpers for recognised assembly levels, scoring, and best_n50 selection
• Extended internal GAMA object tagging to support the new Assembly summary workflow

Documentation

• Updated roxygen documentation and the GAMA user guide, including the addition of a new API map

Testing

• Tested the new Assembly summary and plotting workflow using real query_species() outputs
• Tested compatible and incompatible input paths to confirm the expanded error messaging

GAMA 0.2.8

Reliability

• Patched SRA modality subclass capitalisation so other and unknown are treated consistently as lower-case labels
• Added clearer error messaging for invalid class, subclass, and unit argument parameters, including suggestion logic

API changes

• Removed the classes argument from plot_sra_geo()
• plot_sra_geo() now uses a fixed GEO-oriented modality display set

Documentation

• Updated roxygen documentation and the GAMA user guide accordingly

Testing

• Tested canonical, normalised, fuzzy, and unmatched parameter inputs using real query_species() workflows

GAMA 0.2.7

Reliability

• Standardised input validation and error messaging across user-facing summary and plotting functions
• Added object-aware errors for incompatible GAMA and non-GAMA objects, missing columns, and missing cached profiles

Refactoring

• Added internal object-type tags to support downstream validation
• Centralised validation and cache-check logic in helpers

Documentation

• Revised roxygen descriptions and updated the user guide accordingly

Testing

• Ran checks across compatible and incompatible input paths to confirm the new messaging logic and core functionality

GAMA 0.2.6

Features

• Added synonym-aware querying to query_species() via a new synonyms argument
• Query results can now be collapsed under canonical species names across Assembly, SRA, and BioSample using unique database record identifiers
• Synonym-collapsed results are returned as one bucket per canonical species without double counting repeated record IDs

Refactoring

• Added internal helpers for synonym parsing, validation, canonical mapping, and search-result collapse
• Standardised collapsed search outputs so synonym-merged results retain a consistent internal structure for downstream workflows

Provenance

• Expanded query_info to record queried terms and synonym groups in addition to tool version, query timestamp, and database names

Documentation

• Expanded roxygen @seealso cross-references across user-facing functions for clearer upstream/downstream navigation
• Updated query_species() roxygen to describe and demonstrate the new synonyms argument
• Updated the GAMA user guide to include the new argument

Testing

• Confirmed functionality with end-to-end workflow tests

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