Changes in version 1.2.1                        

Bug fixes

  - Make test-map_orthologs_babelgene less stringent with the number of
    expected genes.

                        Changes in version 1.2.0                        

Bug fixes

  - Increment to v2.0 now that Bioc 3.15 is the RELEASE.

                        Changes in version 1.1.5                        

Bug fixes

  - map_orthologs_babelgene
      - Add "Bad credentials" check for piggyback.
      - Add use_old as an optional arg so I can switch to more recent
        versions of babelgene::orthologs_df if need be.
      - Use updated built-in babelgene::orthologs_df by default.
      - Throw error if trying to map between two non-human species.
      - Filter support==NA mappings by default, not but support>=2 like
        babelgene does by default (even when
        babelgene::orthologs(min_support = 1)).
      - See here for discussion of discrepancies with babelgene
        maintainer: https://github.com/igordot/babelgene/issues/2

New features

  - Removed aggregate_rows_delayedarray as it wasn't being used and was
    far less efficient than the other methods anyway (which are also
    compatible with DelayedArray matrices anyway). * New unit tests:
      - load_data
      - aggregate_mapped_genes(method='stat')
      - sparsity

                        Changes in version 1.1.4                        

Bug fixes

  - Remove source_all as it included a library call.

                        Changes in version 1.1.3                        

New features

  - Update GHA

Bug fixes

  - Fix failing benchmarking tests.

                        Changes in version 1.1.2                        

Bug fixes

  - 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.
  - Ensure proper method-specific output_format when passing species to
    other functions.

New features

  - plot_orthotree: Automated plotting of phylogenetic trees with 1:1
    ortholog report annotations. Includes several subfunctions:
      - prepare_tree (exported): Read, prune and standardise a
        phylogenetic tree.
      - gather_images (internal): More robust way to find and import
        valid phylopic silhouettes. Will make PR requests to rphylopic
        and ggimage/ggtree to include this functionality.
  - Added unit tests for report_orthologs, especially when
    method="babelgene".
  - GitHub Actions:
      - Merge both GHA workflows into one, as implemented in templateR.
  - Added citation info to README.
  - Save all_genes_babelgene ortholog data to orthogene-specific cache
    instead of tempdir to avoid re-downloading every R session.

                        Changes in version 1.1.1                        

Bug fixes

  - Made GHA less dependent on hard-coded R/bioc versions.

                        Changes in version 1.1.0                        

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                        

New features

  - License switched to GPL3 (>=3).

Bug fixes

  - GenomeInfoDbData now required.

                        Changes in version 0.1.0                        

New features

  - orthogene released to Bioconductor.