Changes in version 2.0.0                        

Breaking changes

  - The three binning entry points — abundance_based_binning(),
    composition_based_binning(), hierarchical_binning() — now return a
    MetabinResult S4 object instead of a plain data.frame. The v1.x
    tabular layout is available via as.data.frame(result).
  - The Java backend no longer exposes a command-line interface; the
    shaded JAR dropped the commons-cli dependency. R is the only
    supported entry point.
  - Minimum Java runtime is now 17 (previously 8).

New features

  - New MetabinResult class with accessors assignments(), nClusters(),
    parameters(), algorithm(), plus show() and as.data.frame() methods.
  - Binning functions accept, in addition to file paths,
    Biostrings::DNAStringSet, Biostrings::QualityScaledDNAStringSet, and
    ShortRead::ShortReadQ objects. Non-file inputs are staged to a
    tempfile before the Java backend runs.
  - numOfThreads defaults to BiocParallel::bpworkers().
  - metabinR_jvm_options() and the metabinR.jvm.flags option let users
    customise JVM flags at load time without losing the default G1GC +
    string-deduplication tuning.
  - Parameter validation is centralised via checkmate; errors surface
    through cli::cli_abort() with classed conditions (metabinR_error_*).

Internal

  - Java sources build via Maven (java/metabinR/pom.xml,
    tools/build-jar.sh); the shaded JAR is reproducible
    (project.build.outputTimestamp pinned).
  - Typed JNI entry points on MTxAB, MTxCB, MTxABxCB return
    tab-separated assignments directly to R, removing the previous
    round-trip through on-disk CLI output.

                 Changes in version 1.5.1 (2024-04-07)                  

  - Preparing for next Bioconductor Release.

                 Changes in version 1.5.0 (2023-10-29)                  

  - Bump x.y.z version to odd y following creation of RELEASE_3_18
    branch.

                 Changes in version 1.2.0 (2023-04-21)                  

  - Bump x.y.z version to even y prior to creation of RELEASE_3_17
    branch.

                 Changes in version 1.1.0 (2022-11-01)                  

  - Bump x.y.z version to odd y following creation of RELEASE_3_16
    branch.

                 Changes in version 1.0.0 (2022-11-01)                  

  - Bioconductor 3.16 Release. New package metabinR, Abundance and
    Compositional Based Binning of Metagenomes.

                 Changes in version 0.99.3 (2022-10-30)                 

  - Update NEWS.

                 Changes in version 0.99.2 (2022-10-26)                 

  - Remove citation message on package attach.

                 Changes in version 0.99.1 (2022-10-11)                 

  - Precheck changes on vignette.

                 Changes in version 0.99.0 (2022-10-05)                 

  - Submitted to Bioconductor.