merge 3_12 into dev

DESCRIPTION

@@ -1,67 +1,67 @@
-Package: struct
-Type: Package
-Title: Statistics in R Using Class-based Templates
-Version: 1.1.0
-Authors@R: c(
-    person(
-        c("Gavin","Rhys"),
-          "Lloyd",
-           role=c("aut","cre"),
-           email="g.r.lloyd@bham.ac.uk"),
-    person(
-        c("Ralf","Johannes", "Maria"),
-          "Weber",
-           role=c("aut"),
-           email="r.j.weber@bham.ac.uk")
-           )
-Description: Defines and includes a set of class-based templates for developing 
-    and implementing data processing and analysis workflows, with a strong 
-    emphasis on statistics and machine learning. The templates can be used and 
-    where needed extended to 'wrap' tools and methods from other packages into a 
-    common standardised structure to allow for effective and fast integration. 
-    Model objects can be combined into sequences, and sequences nested in 
-    iterators using overloaded operators to simplify and improve readability of 
-    the code. STATistics Ontology (STATO) has been integrated and implemented 
-    to provide standardised definitions for methods, inputs and outputs wrapped 
-    using the class-based templates.
-License: GPL-3
-Encoding: UTF-8
-LazyData: true
-Collate:
-    'generics.R'
-    'struct_class.R'
-    'parameter_class.R'
-    'chart_class.R'
-    'stato_class.R'
-    'DatasetExperiment_class.R'
-    'entity_class.R'
-    'entity_stato_class.R'
-    'enum_class.R'
-    'enum_stato_class.R'
-    'output_class.R'
-    'model_class.R'
-    'example_objects.R'
-    'model_list_class.R'
-    'metric_class.R'
-    'iterator_class.R'
-    'optimiser_class.R'
-    'preprocess_class.R'
-    'resampler_class.R'
-    'struct.R'
-    'struct_templates.R'
-RoxygenNote: 7.1.1
-Depends: R (>= 4.0)
-Suggests: 
- testthat,
- rstudioapi,
- rmarkdown,
- covr,
- BiocStyle,
- openxlsx,
- ggplot2,
- magick
-VignetteBuilder: knitr
-Imports: methods, ontologyIndex,
-    datasets, graphics, stats, utils, knitr, 
-    SummarizedExperiment, S4Vectors
-biocViews: WorkflowStep
+Package: struct
+Type: Package
+Title: Statistics in R Using Class-based Templates
+Version: 1.3.0
+Authors@R: c(
+    person(
+        c("Gavin","Rhys"),
+          "Lloyd",
+           role=c("aut","cre"),
+           email="g.r.lloyd@bham.ac.uk"),
+    person(
+        c("Ralf","Johannes", "Maria"),
+          "Weber",
+           role=c("aut"),
+           email="r.j.weber@bham.ac.uk")
+           )
+Description: Defines and includes a set of class-based templates for developing 
+    and implementing data processing and analysis workflows, with a strong 
+    emphasis on statistics and machine learning. The templates can be used and 
+    where needed extended to 'wrap' tools and methods from other packages into a 
+    common standardised structure to allow for effective and fast integration. 
+    Model objects can be combined into sequences, and sequences nested in 
+    iterators using overloaded operators to simplify and improve readability of 
+    the code. STATistics Ontology (STATO) has been integrated and implemented 
+    to provide standardised definitions for methods, inputs and outputs wrapped 
+    using the class-based templates.
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+Collate:
+    'generics.R'
+    'struct_class.R'
+    'parameter_class.R'
+    'chart_class.R'
+    'stato_class.R'
+    'DatasetExperiment_class.R'
+    'entity_class.R'
+    'entity_stato_class.R'
+    'enum_class.R'
+    'enum_stato_class.R'
+    'output_class.R'
+    'model_class.R'
+    'example_objects.R'
+    'model_list_class.R'
+    'metric_class.R'
+    'iterator_class.R'
+    'optimiser_class.R'
+    'preprocess_class.R'
+    'resampler_class.R'
+    'struct.R'
+    'struct_templates.R'
+RoxygenNote: 7.1.1
+Depends: R (>= 4.0)
+Suggests: 
+ testthat,
+ rstudioapi,
+ rmarkdown,
+ covr,
+ BiocStyle,
+ openxlsx,
+ ggplot2,
+ magick
+VignetteBuilder: knitr
+Imports: methods, ontologyIndex,
+    datasets, graphics, stats, utils, knitr, 
+    SummarizedExperiment, S4Vectors
+biocViews: WorkflowStep

NAMESPACE

@@ -135,4 +135,8 @@ importFrom(graphics,plot)
 importFrom(knitr,purl)
 importFrom(ontologyIndex,get_ontology)
 importFrom(stats,runif)
+importFrom(utils,as.person)
+importFrom(utils,bibentry)
+importFrom(utils,capture.output)
+importFrom(utils,citation)
 importFrom(utils,file.edit)

NEWS

@@ -1,3 +1,16 @@
+Changes in 1.1.2
++ improved 'show' output for objects
++ allow ANY for entities
+Changes in 1.1.1
++ added citations slot to struct classes
++ added corresponding citations method
++ added method to get/set seq_in slot
++ as.SummarizedExepriment now works correctly
++ using seq_in now works for sequences with more than 2 steps
+
+Changes in 1.0.0
++ Biconductor 3.11 release
+
 Changes in 0.99.10
 + update vignettes
 + update documentation

R/entity_class.R

@@ -58,7 +58,13 @@ entity = function(name, description=character(0), type='character',
     ),
     validity = function(object) {
         check_length = length(value(object)) <= max_length(object)
-        check_type = class(value(object))[1] %in% object$type
+        check_type = any(
+            unlist(
+                lapply(object$type,function(x){
+                    is(value(object),x)
+                })
+            )
+        )
         check_max_length = length(max_length(object)) == 1
         msg = TRUE
         if (!check_length) {

R/enum_class.R

@@ -84,7 +84,7 @@ setMethod(f = 'show',
     definition = function(object) {
         callNextMethod()
 
-        cat('allowed:         ',paste0(object@allowed,collapse=', '))
+        cat('allowed:      ',paste0(object@allowed,collapse=', '))
         cat('\n')
     }
 )