NEWS
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
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
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.