NEWS

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SpectriPy 1.1

Changes in 1.1.8

• Implement pyspec_copy_on_replace() to enable copying/cloning the MS data in Python for any data replacement operation performed in R (issue #91).

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

• Introduce new ModifiedCosineHungarian() and ModifiedCosineGreedy() parameters to match changes in matchms version 0.32.

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.