Changes in version 1.2.1 (2024-06-21)                  

Bug fixes

  - Fix Language field value: invalid 'en_US' value replaced by 'en-US'.
  - Fix CRAN URL for avidaR package not in canonical form.
  - Fix possibly non valid URL.

                 Changes in version 1.2.0 (2023-09-14)                  

New features

  - Added function convert_org_into_seq to convert a digital organism
    file into a genome instruction sequence.
  - Added function get_doi_from_experiment_id to get the DOI of the
    scientific publication that documents the experiment carried out.
  - Added function get_experiment_id_from_organism_id to get the
    experiment identifier from which a digital organism is derived.
  - Added function get_docker_image_from_experiment_id to get the docker
    image built to run the experiment, which guarantees reproducibility.

Improvements

  - Updated colors for better comprehension on figures generated by
    plot_transcriptome() function.
  - The plot_transcriptome function can now plot multiple transcriptomes
    in a single function call.
  - The instruction_set function has been extended to use the "head",
    "head-sex", and "transsmt" instruction sets.

Bug fixes

  - Fixed issues to comply with the CRAN policy: 'Packages which use
    Internet resources should fail gracefully with an informative
    message if the resource is not available or has changed (and not
    give a check warning nor error)'.
  - Fixed issue 'Use of .data in tidyselect expressions was deprecated'
    on convert_seq_into_org() function.

                 Changes in version 1.1.3 (2022-08-22)                  

Improvements

  - More friendly error messages for helping in solving issues caused by
    service availability, not valid user requests, unauthorized access,
    and others.

New features

  - Added timeout parameter in method set_access_options() to limit the
    amount of time waiting data from the service.

Bug fixes

  - Removed top-level code which creates triplestore object and set
    default access options. Read more about how to properly connect to
    'avidaDB'.

                 Changes in version 1.1.2 (2022-05-30)                  

Improvements

  - If seed_id is not specified, a randomly-chosen seed_id value is used
    to speed up the execution of the following functions:
      - get_genome_id_from_logic_operation
      - get_genome_id_from_phenotype_id
      - get_transcriptome_id_from_logic_operation
      - get_transcriptome_id_from_phenotype_id
      - get_transcriptome_id_from_logic_operation
      - get_transcriptome_id_from_phenotype_id
  - The function get_mutant_at_pos has been expanded:
      - The function parameter genome_id has been added, and the
        previous parameters (inst_replaced , inst_replaced_by, and pos)
        can be now omitted by the user.
      - If genome_id is not specified, a randomly chosen genome_id
        (between those provided by the function
        get_genome_id_of_wild_type_organisms) will be used.
      - If inst_replaced and/or inst_replaced_by is/are not specified,
        all mutations at the specified position on the genome are shown.
      - If the parameter pos is not specified, all mutations at all
        positions on the genome are shown (depending on the values of
        inst_replaced and inst_replaced_by).

New features

  - Added function get_db_summary that will provide a summary of the
    database.
  - Added get_genome_id_of_wild_type_organisms to identify the genomes
    of the organisms that were used as wild-type organisms.

Bug fixes

  - Removed a line from the clause WHERE that was slowing down the
    execution of the function get_transcriptome_id_from_phenotype_id.
  - The use of exponential notation was prevented because it provided
    empty results when requesting data by identifiers like
    genome_10000000.

                 Changes in version 1.0.1 (2022-04-08)                  

  - Initial release #'