Merge pull request #331 from rformassspectrometry/restructure_documen…

…tation

Restructure documentation

.github/workflows/check-bioc.yml

@@ -22,7 +22,8 @@
 
 on:
   push:
-  pull_request:
+    paths-ignore:
+      - 'README.md'
 
 name: R-CMD-check-bioc
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.8
+Version: 1.15.9
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different
@@ -40,9 +40,9 @@ Authors@R: c(person(given = "RforMassSpectrometry Package Maintainer",
 Depends:
     R (>= 4.0.0),
     S4Vectors,
-    BiocParallel,
-    ProtGenerics (>= 1.37.1)
+    BiocParallel
 Imports:
+    ProtGenerics (>= 1.37.1),
     methods,
     IRanges,
     MsCoreUtils (>= 1.7.5),

NAMESPACE

@@ -56,6 +56,7 @@ exportMethods("intensity<-")
 exportMethods("isolationWindowLowerMz<-")
 exportMethods("isolationWindowTargetMz<-")
 exportMethods("isolationWindowUpperMz<-")
+exportMethods("msLevel<-")
 exportMethods("mz<-")
 exportMethods("peaksData<-")
 exportMethods("polarity<-")
@@ -229,6 +230,7 @@ importMethodsFrom(ProtGenerics,"intensity<-")
 importMethodsFrom(ProtGenerics,"isolationWindowLowerMz<-")
 importMethodsFrom(ProtGenerics,"isolationWindowTargetMz<-")
 importMethodsFrom(ProtGenerics,"isolationWindowUpperMz<-")
+importMethodsFrom(ProtGenerics,"msLevel<-")
 importMethodsFrom(ProtGenerics,"mz<-")
 importMethodsFrom(ProtGenerics,"peaksData<-")
 importMethodsFrom(ProtGenerics,"polarity<-")

NEWS.md

@@ -1,5 +1,9 @@
 # Spectra 1.15
 
+## Changes in 1.15.9
+
+- Restructure and reorganize documentation for `Spectra`.
+
 ## Changes in 1.15.8
 
 - Refactor the `Spectra()` constructor method: better support for

R/AllGenerics.R

@@ -5,42 +5,32 @@ NULL
 setMethod("bin", "numeric", MsCoreUtils::bin)
 setGeneric("combinePeaks", function(object, ...)
            standardGeneric("combinePeaks"))
-#' @rdname hidden_aliases
 setGeneric("containsMz", function(object, ...)
     standardGeneric("containsMz"))
-#' @rdname hidden_aliases
 setGeneric("containsNeutralLoss", function(object, ...)
     standardGeneric("containsNeutralLoss"))
 setGeneric("dataStorageBasePath", function(object, ...)
     standardGeneric("dataStorageBasePath"))
 setGeneric("dataStorageBasePath<-", function(object, ..., value)
     standardGeneric("dataStorageBasePath<-"))
-#' @rdname hidden_aliases
 setGeneric("dropNaSpectraVariables", function(object, ...)
     standardGeneric("dropNaSpectraVariables"))
-#' @rdname hidden_aliases
 setGeneric("entropy", function(object, ...)
   standardGeneric("entropy"))
-#' @rdname hidden_aliases
 setGeneric("export", function(object, ...)
     standardGeneric("export"))
 setGeneric("filterFourierTransformArtefacts", function(object, ...)
     standardGeneric("filterFourierTransformArtefacts"))
-#' @rdname neutralLoss
 setGeneric("neutralLoss", function(object, param, ...)
     standardGeneric("neutralLoss"))
-#' @rdname hidden_aliases
 setGeneric("pickPeaks", function(object, ...)
     standardGeneric("pickPeaks"))
 setGeneric("plotSpectraMirror", function(x, y, ...)
     standardGeneric("plotSpectraMirror"))
-#' @rdname hidden_aliases
 setGeneric("replaceIntensitiesBelow", function(object, threshold = min, ...)
     standardGeneric("replaceIntensitiesBelow"))
-#' @rdname hidden_aliases
 setGeneric("reset", function(object, ...)
     standardGeneric("reset"))
-#' @rdname hidden_aliases
 setGeneric("selectSpectraVariables", function(object, ...)
     standardGeneric("selectSpectraVariables"))
 setGeneric("Spectra", function(object, ...) standardGeneric("Spectra"))