NEWS

CytoML 3.11

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

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

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

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