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