# 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.
