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GAMA 0.3.6

Reliability

  • Expanded the BioSample anatomy ontology using vocabulary identified in legume data and aligned canonical terms against the Plant OntologyTM
  • Expanded BioSample value normalisation to strip WT, wild type, and wildtype descriptors before anatomy classification
  • Added numeric affix stripping to recover anatomy terms from encoded values such as root1

Testing

  • Regenerated examples and fixtures for the revised behaviour
  • Confirmed the test suite passes with the updated fixtures

GAMA 0.3.5

Reliability

  • Added Entrez UIDs to the cached profiles produced by summarise_biosample_availability() to further support diagnostics

Documentation

  • Updated roxygen documentation and the GAMA user guide accordingly

Testing

  • Updated testthat coverage for the revised BioSample cached profile structure
  • Regenerated examples and fixtures for the revised output structure
  • Confirmed the test suite passes with the updated fixtures

GAMA 0.3.4

Reliability

  • Added raw and normalised SRA strategy values to the cached profile produced by summarise_sra_availability() to support diagnostics
  • extract_assembly_metadata() now retains all records tied at the highest assembly level and N50 when best = TRUE
  • Expanded the BioSample anatomy ontology using terms from parasitic plant data

Documentation

  • Updated roxygen documentation and the GAMA user guide accordingly

Testing

  • Updated testthat coverage for the revised cached profile and tied assembly handling
  • Regenerated examples and fixtures for the revised behaviour
  • Confirmed the test suite passes with the updated fixtures

GAMA 0.3.3

API changes

  • Renamed extract_biosample_metadata() output columns tissue_raw and tissue_norm to value_raw and value_norm

Reliability

  • Added raw and normalised BioSample source values to the cached anatomy profile produced by summarise_biosample_availability() to support diagnostics
  • Expanded the BioSample anatomy ontology using gymnosperm, pteridophyte, and bryophyte data

Documentation

  • Updated roxygen documentation and the GAMA user guide accordingly

Testing

  • Updated testthat coverage for the revised column names and cached anatomy profile
  • Regenerated examples and fixtures for the revised output structure
  • Confirmed the test suite passes with the updated fixtures

GAMA 0.3.2

Plotting

  • Updated Assembly and SRA plot labels to use the word 'records' rather than 'accessions' or 'experiments'

Documentation

  • Updated the roxygen, README, and GAMA user guide terminology to align with the revised wording and converted the user guide from PDF to Markdown

Testing

  • Added a shared test helper for retrieving the active GAMA version in synthetic test fixtures
  • Confirmed 501 passing tests and devtools::check() with 0 errors, 0 warnings, and 0 notes

GAMA 0.3.1

Features

  • Added BioSample replication-skew analysis via summarise_biosample_skew() and plot_biosample_skew()
  • BioSample skew supports metadata interpretation by quantifying record distribution across BioProjects, optionally for a single anatomy_class

Reliability

  • Added BioProject provenance to BioSample profile caches, enabling BioSample skew to run from cached summary outputs without re-querying NCBI
  • Added skew_id_recovery diagnostics to SRA and BioSample skew outputs, making record inclusion, exclusion, and ID recovery explicit
  • Refined skew calculations to exclude records with missing skew-unit IDs after filtering
  • Patched provenance retention in extract_assembly_metadata() when filtering by species

Refactoring

  • Standardised SRA and BioSample skew object naming across fixtures, examples, and tests
  • Updated fixture-generation and example-generation workflows for new BIO_SKEW objects

Plotting

  • Updated the plot_sra_skew() axis label to reference SRA records

Documentation

  • Updated roxygen documentation and the GAMA user guide accordingly

Testing

  • Expanded test coverage for BioSample skew, skew diagnostics, validation, and cache provenance
  • Confirmed devtools::check() with 0 errors, 0 warnings, and 0 notes

GAMA 0.3.0

Features

  • Added a BioSample tissue workflow via summarise_biosample_availability(), plot_biosample_availability(), and extract_biosample_metadata(), completing the core Assembly/SRA/BioSample function family
  • BioSample records can now be classified and filtered by anatomy class, anatomy subclass, and anatomy term
  • Added an SRA-BioSample interaction workflow via summarise_interaction() and plot_interaction()
  • Interaction summaries link SRA sequencing modality with BioSample-derived anatomy profiles

Reliability

  • Added cached BioSample anatomy profiles to support downstream extraction and SRA-BioSample interaction analysis
  • Strengthened cache validation across SRA, BioSample, and interaction workflows
  • Improved object-aware validation across the expanded GAMA API
  • Extended parameter validation and suggestion logic for modality, anatomy, plotting, and interaction arguments

Refactoring

  • Added internal BioSample record-level parsing, normalisation, ontology-driven classification, and profile-collapsing logic
  • Extended cached profile infrastructure for SRA-BioSample interaction analysis
  • Refined shared validation helpers for incompatible objects, missing caches, invalid parameters, and close-match suggestions

Documentation

  • Updated roxygen documentation and the GAMA user guide for the new BioSample and interaction workflows

Testing

  • Added a CRAN-level testthat suite covering the full GAMA workflow
  • Validated end-to-end object fixtures, core formulae, cache integrity, and parameter/error-message logic

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

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