updates for bioc_3_13 #36
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* 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 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
* 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.
* Release 3.12 (#31) * 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 * Release_3_12 (#32) better alignment of bullets * update news, version bump * replace class() with is() allows assignment of entities as 'ANY' * bump x.y.z version to even y prior to creation of RELEASE_3_12 branch * bump x.y.z version to odd y following creation of RELEASE_3_12 branch Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
* replace travis/appveyor with actions * add imports for utils import functions specifically for citations * remove travis and appveyor
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