merge 3_12 into dev #34
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* fix for #18 (#19) - incorrect use of `$assay` replaced with `$data` for DatasetExperiment objects - specify SummarizedExperiment package as source of `rowData` and `colData` functions * fix for #20 (#21) data now gets passed through as intended when model_seq is being used. Allows seq_in to be used at the nth step in a sequence * fix for #20 (#23) data now gets passed through as intended when model_seq is being used. Allows seq_in to be used at the nth step in a sequence * Issue 22 seq in (#24) * add seq_in generics * add seq_in methods - added methods for models to get.set seq_in - added checks for valid input/output names to seq_in and predicted_name methods * update documentation * use correct input param id * update documentation - use of input_1 instead of value_1 fixed in examples - corrected rdname for seq_in * add as.code method (#25) * add as.code method produces a string of text that can be used to recreate the model/sequence/iterator * use correct input parameter names cmd check fails if examples dont run * Issue 27 citations (#29) * add citations and libraries methods for #27 - these methods scan over all inherited objects and generate a complte ist of citations/libraries - a citations slot has been added to struct_class * use bibtex for citations The citations slot is now a list of bibentry objects to provide a more formalised method for storing citations and make them easer to use with bibliography packages etc. * update imports for utils package * fix various cmd and bioc check issues - add importFrom utils citation to namespace - replace incorrect use of "error" with "stop" - use first index of class() output in messages * Update NEWS * version bump * fix typo in documentation
better alignment of bullets * update news, version bump * replace class() with is() allows assignment of entities as 'ANY'
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