Clean and finalize removal of the basilisk dependencies

.Rbuildignore

@@ -10,3 +10,4 @@ _pkgdown.yml
 .BBSoptions
 ^\.vscode
 devnotes.md
+temp_doc/*

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
-          - { os: windows-latest, r: '4.4', bioc: '3.20'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.21'}
+          - { os: windows-latest, r: 'devel', bioc: '3.21'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -77,7 +77,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -86,17 +86,35 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
+      ## Install R dependencies using R-lib
+      - name: Setup R dependencies from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r-dependencies@v2
+
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
         uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Install quarto
+        if: runner.os != 'Linux'
+        uses: quarto-dev/quarto-actions/setup@v2
+
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
+      - name: Install Miniconda
+        run: |
+          Rscript -e "install.packages('reticulate')"
+          Rscript -e "reticulate::install_miniconda()"
+
+      - name: Fix conda for macOS
+        if: runner.os == 'macOS'
+        run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
         uses: actions/cache@v2
@@ -137,9 +155,6 @@ jobs:
           ## For installing usethis's dependency gert
           brew install libgit2
 
-          ## Python
-          brew install [email protected]
-
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
@@ -179,8 +194,9 @@ jobs:
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
 
           message(paste('****', Sys.time(), 'force installation of selected packages ****'))
-          BiocManager::install(c("BiocStyle", "rmarkdown", "magick"))
+          BiocManager::install(c("BiocStyle"))
 
+          BiocManager::install("mzR")
           BiocManager::install("Spectra")
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
@@ -219,7 +235,7 @@ jobs:
           _R_CHECK_CRAN_INCOMING_: false
         run: |
           rcmdcheck::rcmdcheck(
-              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              args = c("--no-manual", "--timings"),
               build_args = c("--no-manual", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
@@ -276,4 +292,4 @@ jobs:
         uses: actions/upload-artifact@master
         with:
           name: ${{ runner.os }}-biocversion-devel-r-devel-results
-          path: check
+          path: check

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: SpectriPy
 Title: Integrating Spectra with Python's matchms
-Version: 0.2.1
+Version: 0.3.1
 Description: The SpectriPy package allows integration of Python-based MS
     analysis code with the Spectra package. Spectra objects can be converted
     into Python's matchms Spectrum objects. In addition, SpectriPy integrates
-    and wraps the similarity scoring and processing/filtering functions 
+    and wraps the similarity scoring and processing/filtering functions
     from the matchms package into R.
 Authors@R: c(person(given = "Michael", family = "Witting",
                     role = c("aut"),
@@ -20,47 +20,54 @@ Authors@R: c(person(given = "Michael", family = "Witting",
                     comment = c(ORCID = "0000-0002-9355-8948")),
              person(given = "Helge", family = "Hecht",
                     email = "[email protected]",
-                    role = c("aut"),
+                    role = c("ctb"),
                     comment = c(ORCID = "0000-0001-6744-996X")),
              person(given = "Marilyn", family = "De Graeve",
                     email = "[email protected]",
-                    role = c("ctb"),
+                    role = c("aut"),
                     comment = c(ORCID = "0000-0001-6916-401X")),
-	     person(given = "Thomas", family = "Naake",
+             person(given = "Wout", family = "Bittremieux",
+                    email = "[email protected]",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-3105-1359")),
+             person(given = "Thomas", family = "Naake",
                     email = "[email protected]",
-                    role = c("ctb"),
+                    role = c("aut"),
                     comment = c(ORCID = "0000-0001-7917-5580")),
              person(given = "Victor", family = "Chrone",
                     email = "[email protected]",
                     role = c("ctb"),
                     comment = c(ORCID = "0009-0007-2121-4066")),
-	     person(given = "Matthias", family = "Anagho-Mattanovich",
+             person(given = "Matthias", family = "Anagho-Mattanovich",
                     email = "[email protected]",
                     role = c("ctb"),
-                    comment = c(ORCID = "0000-0001-7561-7898")))
+                    comment = c(ORCID = "0000-0001-7561-7898"))
+             )
 Depends:
-    R (>= 4.1.0)
+    R (>= 4.1.0),
+    reticulate
 Imports:
     Spectra (>= 1.5.8),
-    basilisk,
-    reticulate,
     IRanges,
     S4Vectors,
-    BiocParallel,
-    ProtGenerics,
+    MsCoreUtils,
     methods
 Suggests:
     testthat,
+    quarto,
+    MsBackendMgf,
+    msdata,
+    mzR,
     knitr,
-    BiocStyle,
-    rmarkdown
+    BiocStyle
 License: Artistic-2.0
-VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/SpectriPy/issues
 URL: https://github.com/RforMassSpectrometry/SpectriPy
 biocViews: Infrastructure, Metabolomics, MassSpectrometry
 Encoding: UTF-8
-StagedInstall: no
-SystemRequirements: python (>= 3.9)
+SystemRequirements:
+    python (>= 3.10),
+    pandoc
+VignetteBuilder: quarto
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NAMESPACE

@@ -1,38 +1,48 @@
 # Generated by roxygen2: do not edit by hand
 
-export(CosineGreedyParam)
-export(CosineHungarianParam)
-export(ModifiedCosineParam)
-export(NeutralLossesCosineParam)
+S3method(r_to_py,Spectra)
+export(CosineGreedy)
+export(CosineHungarian)
+export(ModifiedCosine)
+export(NeutralLossesCosine)
 export(compareSpectriPy)
+export(defaultSpectraVariableMapping)
 export(filterSpectriPy)
 export(normalize_intensities)
 export(pyspec_to_rspec)
 export(remove_peaks_around_precursor_mz)
 export(rspec_to_pyspec)
 export(select_by_intensity)
 export(select_by_mz)
+export(setSpectraVariableMapping)
 exportMethods(compareSpectriPy)
 exportMethods(filterSpectriPy)
 exportMethods(spectraVariableMapping)
-importClassesFrom(ProtGenerics,Param)
-importFrom(BiocParallel,SerialParam)
-importFrom(BiocParallel,bplapply)
 importFrom(IRanges,NumericList)
+importFrom(MsCoreUtils,rbindFill)
 importFrom(S4Vectors,DataFrame)
-importFrom(Spectra,concatenateSpectra)
-importFrom(basilisk,BasiliskEnvironment)
-importFrom(basilisk,basiliskRun)
-importFrom(basilisk,basiliskStart)
-importFrom(basilisk,basiliskStop)
+importFrom(Spectra,MsBackendMemory)
+importFrom(Spectra,spectrapply)
 importFrom(methods,is)
 importFrom(methods,new)
+importFrom(reticulate,conda_create)
+importFrom(reticulate,conda_list)
 importFrom(reticulate,import)
+importFrom(reticulate,iterate)
 importFrom(reticulate,np_array)
 importFrom(reticulate,py)
+importFrom(reticulate,py_available)
+importFrom(reticulate,py_dict)
+importFrom(reticulate,py_install)
+importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_run_string)
 importFrom(reticulate,py_to_r)
 importFrom(reticulate,r_to_py)
+importFrom(reticulate,use_condaenv)
+importFrom(reticulate,use_virtualenv)
+importFrom(reticulate,virtualenv_create)
+importFrom(reticulate,virtualenv_exists)
+importFrom(reticulate,virtualenv_remove)
 importMethodsFrom(Spectra,Spectra)
 importMethodsFrom(Spectra,intensity)
 importMethodsFrom(Spectra,mz)

NEWS.md

@@ -1,3 +1,18 @@
+# SpectriPy 0.3
+
+## Changes in 0.3.1
+
+- Add `filterSpectriPy()` function for spectra filtering using *matchms*.
+- Add a new example MGF file to the package.
+- Add a new quarto vignette.
+
+## Changes in 0.3.0
+
+- Add changes and results introduced a the EuBIC 2024 r-python hackathon in
+  Neustift, Italy.
+- Remove dependency from *basilisk* and base the package entirely on
+  *reticulate*.
+
 # SpectriPy 0.2
 
 ## Changes in 0.2.1
@@ -29,4 +44,4 @@
 - Add `basilisk` environment.
 - Add `spectraVariableMapping`.
 - Refactor functions to convert between R and python spectrum objects and add
-  unit tests.
+  unit tests.