Merge pull request #10 from rformassspectrometry/jomain

Functionality to convert between R and Python

.BBSoptions

@@ -0,0 +1 @@
+UnsupportedPlatforms: win32

.Rbuildignore

@@ -0,0 +1,9 @@
+.editorconfig
+README.md
+local_data/*
+
+^.*\.Rproj$
+^\.Rproj\.user$
+.travis.yml
+^\.github$
+_pkgdown.yml

DESCRIPTION

@@ -1,8 +1,6 @@
 Package: SpectriPy
-Title: Enabling use of Python matchms, Spec2Vec and MS2DeepScore in R
-Version: 0.0.1
-Description: 
-    What the package does (one paragraph).
+Title: Integrating Spectra with Python's matchms
+Version: 0.0.2
 Authors@R:
     c(person(given = "Michael", family = "Witting",
              role = c("aut"),
@@ -20,22 +18,32 @@ Authors@R:
              email = "",
              role = c("aut"),
              comment = c(ORCID = "")))
+Description: The SpectriPy package allows to integrate Python-based MS analysis
+    code with the Spectra package. Spectra objects can be converted into python
+    objects.
 Depends:
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports:
-    BiocGenerics,
-    Spectra (>= 1.5.7),
-    reticulate
+    Spectra,
+    basilisk,
+    reticulate,
+    IRanges,
+    S4Vectors,
+    BiocParallel,
+    methods
 Suggests:
     testthat,
     knitr,
-    msdata,
     BiocStyle,
-    rmarkdown
+    rmarkdown,
+    patrick
 License: Artistic-2.0
 VignetteBuilder: knitr
-BugReports: https://github.com/RforMassSpectrometry/MetaboAnnotation/issues
-URL: https://github.com/RforMassSpectrometry/MetaboAnnotation
+BugReports: https://github.com/RforMassSpectrometry/SpectriPy/issues
+URL: https://github.com/RforMassSpectrometry/SpectriPy
 biocViews: Infrastructure, Metabolomics, MassSpectrometry
-Roxygen: list(markdown=TRUE)
+Encoding: UTF-8
+StagedInstall: no
+SystemRequirements: python (>= 3.5)
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.2

NAMESPACE

@@ -1,5 +1,22 @@
 # Generated by roxygen2: do not edit by hand
 
-export(convertPySpectrumToRSpectra)
-export(convertRSpectraToPySpectrum)
-importMethodsFrom(reticulate,import)
+export(pyspec_to_rspec)
+export(rspec_to_pyspec)
+exportMethods(spectraVariableMapping)
+importFrom(BiocParallel,SerialParam)
+importFrom(BiocParallel,bplapply)
+importFrom(IRanges,NumericList)
+importFrom(S4Vectors,DataFrame)
+importFrom(Spectra,concatenateSpectra)
+importFrom(basilisk,BasiliskEnvironment)
+importFrom(methods,is)
+importFrom(reticulate,import)
+importFrom(reticulate,np_array)
+importFrom(reticulate,py_to_r)
+importFrom(reticulate,r_to_py)
+importMethodsFrom(Spectra,Spectra)
+importMethodsFrom(Spectra,intensity)
+importMethodsFrom(Spectra,mz)
+importMethodsFrom(Spectra,spectraData)
+importMethodsFrom(Spectra,spectraVariableMapping)
+importMethodsFrom(Spectra,spectrapply)

NEWS.md

@@ -0,0 +1,8 @@
+# SpectriPy 0.0
+
+## Changes in 0.0.2
+
+- Add `basilisk` environment.
+- Add `spectraVariableMapping`.
+- Refactor functions to convert between R and python spectrum objects and add
+  unit tests.

R/basilisk.R

@@ -0,0 +1,6 @@
+#' @importFrom basilisk BasiliskEnvironment
+matchms_env <- basilisk::BasiliskEnvironment(
+    envname = "matchms_env", pkgname = "SpectriPy",
+    packages = c("matchms==0.14.0"),
+    channels = c("bioconda", "conda-forge")
+)