Performance and stability improvements

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SpectriPy
 Title: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
-Version: 1.1.5
+Version: 1.1.7
 Description: The SpectriPy package allows integration of Python-based MS
     analysis code with the Spectra package. Spectra objects can be converted
     into Python MS data structures. In addition, SpectriPy integrates
@@ -61,7 +61,8 @@ Imports:
     MsCoreUtils,
     ProtGenerics,
     methods,
-    data.table
+    data.table,
+    snakecase
 Suggests:
     testthat,
     quarto,

NAMESPACE

@@ -20,6 +20,7 @@ export(select_by_intensity)
 export(select_by_mz)
 export(setSpectraVariableMapping)
 exportMethods("spectraData<-")
+exportMethods("spectraNames<-")
 exportMethods("spectraVariableMapping<-")
 exportMethods(compareSpectriPy)
 exportMethods(filterSpectriPy)
@@ -53,10 +54,12 @@ importFrom(reticulate,py_run_string)
 importFrom(reticulate,py_set_attr)
 importFrom(reticulate,py_to_r)
 importFrom(reticulate,r_to_py)
+importFrom(snakecase,to_snake_case)
 importMethodsFrom(ProtGenerics,"intensity<-")
 importMethodsFrom(ProtGenerics,"mz<-")
 importMethodsFrom(ProtGenerics,"peaksData<-")
 importMethodsFrom(ProtGenerics,"spectraData<-")
+importMethodsFrom(ProtGenerics,"spectraNames<-")
 importMethodsFrom(ProtGenerics,acquisitionNum)
 importMethodsFrom(ProtGenerics,backendInitialize)
 importMethodsFrom(ProtGenerics,centroided)

NEWS.md

@@ -1,5 +1,26 @@
 # SpectriPy 1.1
 
+## Changes in 1.1.7
+
+- Improved `$<-` operation: only replace the values for the selected spectra
+  variable.
+- Improved `peaksData<-`, `mz<-` and `intensity<-` implementations: only
+  replace the respective data, but not the full spectra data (including
+  metadata).
+- Improved `lengths()` implementation: retrieves the number of peaks directly in
+  Python.
+- Documentation updates.
+
+## Changes in 1.1.6
+
+- Automatic renaming and remapping of upper case or *camelCase* spectra
+  variables to *snake_case* metadata fields in `backendInitialize()`,
+  `spectraData<-` and `$<-`.
+- Full support of the *Spectra* test suite.
+- Add `spectraNames<-` method for `MsBackendPy` and support getting/setting
+  spectrum names. They are stored in a metadata field (spectra variable)
+  *spectrum_name*.
+
 ## Changes in 1.1.5
 
 - Fix `$<-`, `spectraData()<-` and related replacement methods for

R/conversion.R

@@ -696,3 +696,18 @@ pyspec_to_rspec <- function(x, mapping = spectraVariableMapping(),
            "for i in _i_:\n",
            "  _res_.append(np.column_stack((",x,"[i].mz,",x,"[i].intensity)))")
 }
+
+## .var_name <- function(x) {
+##     i <- 0
+##     if (any(ls(envir = .GlobalEnv) == x)) {
+##         xs <- strsplit(x, "_", fixed = TRUE)[[1L]]
+##         if (!is.na(suppressWarnings(i2 <- as.integer(xs[length(xs)]))))
+##             i <- i2
+##         x <- .var_name(paste0(c(xs[1:(length(xs) - 1)], i + 1L),
+##                               collapse = "_"))
+##     }
+##     x
+## }
+
+## .var_name("a")
+## a_1 <- 2