Changes in version 1.0.2                        

BUG FIXES

  - Fix map_orthologs_babelgene
      - Fix col renaming bug.
      - Use built-in up-to-date babelgene:::orthologs_df in
        all_genes_babelgene.

                        Changes in version 1.0.1                        

BUG FIXES

  - Update GHA yaml and Dockerfile to unified pipeline.
  - Update .Rbuildignore and .gitignore.
  - Fix all_genes and associated subfunctions.
  - Fix convert_orthologs and associated subfunctions.
  - Fix map_orthologs_babelgene after recent updates to babelgene.
  - convert_orthologs(method="babelgene") now gets gene mappings from
    all_genes_babelgene instead babelgene::orthologs (which doesn't seem
    to work very well, despite being dedicated for this purpose).
  - map_species:
      - Avoid running this function redundantly when nested in multiple
        layers of other functions.
      - common_species_names_dict now return "scientific_name" by
        default, instead of "taxonomy_id"
      - Match map_species method to whatever method is being used in the
        function it's wrapped within, to avoid dropping species due to
        naming differences.
      - Add "id" column (e.g. "celegans") to all org databases to
        enhance their searchability.
      - Add map_species_check_args.
      - Cache babelgene file in orthogene-specific dir.
  - Ensure proper method-specific output_format when passing species to
    other functions.

                        Changes in version 1.0.0                        

NEW FEATURES

  - Now on Bioconductor release 3.14.
  - Docker containers automatically built and pushed to DockerHub via
    GitHub Actions.
  - Dockerfile provided to build and check any R package efficiently
    with AnVil.
  - CRAN checks and Bioc checks run via GitHub Actions.
  - Added documentation on using Docker container to README.
  - Documentation website now automatically built via GitHub Actions.
  - Code coverage tests now automatically run and uploaded via GitHub
    Actions.

                       Changes in version 0.99.9                        

NEW FEATURES

  - Replaced R-CMD GHA with bioc-check GHA.
  - Added new badges.

BUG FIXES

  - Adjusted vignette yamls to make resulting htmls smaller.

                       Changes in version 0.99.8                        

NEW FEATURES

  - orthogene now supports DelayedArray objects as gene_df input.
  - create_background now uses all_genes when all 3 species are the
    same.

                       Changes in version 0.99.7                        

NEW FEATURES

  - Added new function create_background.
  - Added new function infer_species.
  - report_orthologs and convert_orthologs can now handle cases where
    input_species is the same as output_species.
  - Add internal function get_all_orgs to easily list all organisms from
    different packages.
  - Added all_genes method "babelgene".

BUG FIXES

  - report_orthologs no longer throws error due to not finding
    tar_genes.

                       Changes in version 0.99.6                        

BUG FIXES

  - Allow all messages to be suppressed in report_orthologs.

                       Changes in version 0.99.3                        

NEW FEATURES

  - License switched to GPL-3 (to be compliant with Bioc).
  - New method "babelgene" added to convert_orthologs.

                       Changes in version 0.99.2                        

  - License switched to GPL3 (>=3).

BUG FIXES

  - GenomeInfoDbData now required.

                        Changes in version 0.1.0                        

NEW FEATURES

  - orthogene released to Bioconductor.