Changes in version 3.11                         

API Changes

  - Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
  - All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet
    based on cytoset rather than ncdfFlowSet
  - Add trans argument to cytobank_to_gatingset to allow overriding of
    transformations from gatingML file (#76)
  - gatingset_to_flowjo now uses a docker image with a compiled
    converter: hub.docker.com/r/wjiang2/gs-to-flowjo
  - Some updates to how flowjo_to_gatingset searches for FCS files (#77)
  - Add include_empty_tree option to flowjo_to_gatingset to include
    samples without gates
  - Allow gatingset_to_flowjo to take a path to a GatingSet archive
    directory
  - Add gating_graphGML to replace gating.graphGML method for
    openCyto::gating generic
  - Filter samples by panel when parsing cytobank experiment and add
    ce_get_samples, ce_get_panels

Fixes/internal changes

  - Automatic time scaling of samples from FlowJo workspaces now handled
    by flowjo_to_gatingset RGLab/cytolib#33
  - Handle change to default stringsAsFactors=FALSE in R 4.0
  - Eliminated extra intermediate files left in temp directory during
    workspace parsing
  - Switch usage of GatingSetList to merge_gs_list
  - Solve some Windows build issues
  - Switch from experimental::filesystem to boost::filesystem in C++
    FlowJo parser
  - Add CytoML XSD to installation

                        Changes in version 3.10                         

API Changes

  - Change handling of quad gates according to RGLab/cytolib#16

  - Renaming of methods:
    
      - openWorkspace -> open_diva_xml, open_flowjo_xml
      - cytobankExperiment -> open_cytobank_experiment
      - cytobank2GatingSet -> cytobank_to_gatingset
      - parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
      - getSampleGroups -> fj_ws_get_sample_groups,
        diva_get_sample_groups
      - getSamples -> fj_ws_get_samples, diva_get_samples
      - getKeywords -> fj_ws_get_keywords
      - getCompensationMatrices -> ce_get_compensations
      - getTransformation -> ce_get_transformations
      - compare.counts -> gs_compare_cytobank_counts

  - Renaming of classes:
    
      - divaWorkspace -> diva_workspace
      - flowJoWorkspace -> flowjo_workspace

  - Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML
    namespace

Fixes/internal changes

  - Make gatingset_to_cytobank export cytobank ML with attribute
    namespaces
  - Allow diva_to_gatingset to use compensation matrix from xml
  - Pass ... args from cytobank_to_gatingset appropriately down to FCS
    parser
  - Fix some issues with scaling of gates parsed from Diva workspace
    (#64)
  - Guard against unsupported transformations being added to GatingSet
    during Diva parsing
  - Switch diva_to_gatingset to using flowjo_log_trans instead of
    logtGml2_trans
  - Fix ported flowUtils::xmlTag to enable self-closing tags
  - Make gating.graphGML lookup tailored gates by FCS name as well as
    file id
  - Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

                        Changes in version 1.1.2                        

  - support diva workspace parsing

                        Changes in version 1.0.0                        

  - First submission