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Changelog

Source: NEWS.md

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 Spectra/MsBackendPy of length 1.

Changes in 1.1.4

  • Implement a setBackend() method for MsBackendPy with a parameter applyProcessing to allow applying the processing queue and storing the modified peaks data to Python.

Changes in 1.1.3

Changes in 1.1.2

  • Use matchms 0.31.

SpectriPy 0.99

Changes in 0.99.13

  • Update matchms suggested version to 0.31.

Changes in 0.99.12

  • Add spectraData<-,MsBackendPy method.
  • Add parameter x to spectraVariableMapping,character to simplify adding custom mapping to the default one.
  • Add examples to describe which spectra variables are transferred to Python using setBackend() with MsBackendPy and how additional variables can be added.
  • backendInitialize() with defined parameter data drops core spectra variables that contain only missing values.
  • Add $<- method for MsBackendPy.
  • Add peaksData()<- for MsBackendPy.
  • Add intensity()<- and mz()<- methods for MsBackendPy.

Changes in 0.99.11

  • Add unit tests for package startup messages.
  • Remove debug startup messages.
  • Complete and clean installation and configuration documentation.

Changes in 0.99.10

  • Update installation and Python configuration settings.
  • Check environment variables on package loading.

Changes in 0.99.9

  • Add tolerance for comparison of retention time with spectrum_utils.
  • Require numpy version >= 2.2.0.

Changes in 0.99.8

  • Verbose startup messages and require Python 3.12.

Changes in 0.99.7

  • Replace the msdata package with MsDataHub.

Changes in 0.99.6

  • Set delay_load = FALSE in import() calls during package loading

Changes in 0.99.5

  • Replace Python library installation via virtualenv or conda with py_require() from reticulate version > 1.41.0.
  • Add support for parameter data to backendInitialize(): this enables to change the backend from a Spectra object to MsBackendPy using the setBackend() method.

Changes in 0.99.4

  • Refactor functions to initialize Python libraries.

Changes in 0.99.3

  • Address Bioconductor review comments.

Changes in 0.99.2

  • Use Python virtualenv instead of miniconda.

Changes in 0.99.1

  • Check for presence of conda and eventually install miniconda through reticulate.

Changes in 0.99.0

  • Prepare for Bioconductor submission.

SpectriPy 0.5

Changes in 0.5.3

  • Vignette updates.

Changes in 0.5.2

  • Fix spectrum_utils version.

Changes in 0.5.1

  • Add additional vignettes and update/fix documentation.

Changes in 0.5.0

  • Add support for spectrum_utils library.

SpectriPy 0.4

Changes in 0.4.0

  • Add a MsBackendPython backend referencing to MS data residing in Python.

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 2025 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

  • Add filterSpectriPy method and related parameter objects to perform spectra filtering/processing via matchms in python.

Changes in 0.2.0

  • Use matchms version 0.28.2.

SpectriPy 0.1

Changes in 0.1.1

  • Small updates and fixes in the package’s vignette.

Changes in 0.1.0

  • Add compareSpectriPy method and related parameter objects to perform spectra similarity calculations in python.

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.