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lightr (development version)

Major breaking changes

  • the low-level parsers to parse individual files have been renamed from the previous naming scheme lr_parse_<fileext>() to lr_parse_<brand>_<fileext>() (#72). This gives us flexibility to use different parsers when two or more brands use the same file extension but actually different formats.

New features

  • Parsing for binary files produced by Avantes AvaSoft 8.4 has been restored in lr_parse_avantes_rfl8(), lr_parse_avantes_irr8(), lr_parse_avantes_raw8(). Thanks to Allison Shultz, Lindsey Swierk, Raphaël Scherrer, and Michaël Nicolaï for providing feedback and test files. Thanks to Avantes for providing the file format documentation.

Minor changes

  • Performance of high-level functions (lr_get_spec(), lr_get_metadata()) and some low-level parsers (csv, ttt, trm, jaz, jazirrad) has been improved.

lightr 1.9.0

New features

  • cases where a mix of .csv and other 'csv-like but not quite csv' formats are passed to lr_get_spec() are now handled better, after a report from @bittonp (@Bisaloo, #58). This also means that it's no longer necessary to explicitly set sep = "," when trying to parse csv files (#15).
  • lr_parse_procspec() gains a new argument verify_checksum to verify if the data has been tampered with since its creation by the official OceanView software (@Bisaloo, #29).
  • lr_parse_spc() (OceanOptics, CRAIC) and lr_parse_rfl8()/lr_parse_raw8()/lr_parse_irr8() (Avantes) now return the measurement date & time in the metadata elements (@Bisaloo, #75). In other words, lr_get_metadata() now return savetime for .spc, .RFL8, .RAW8, IRR8 files.

lightr 1.8.0

Minor changes

  • timezones for converted OceanOptics files are now handled differently internally (@Bisaloo, #64), to handle changes in upstream tzdata 2024b, which removed for example the CET and EST timezone codes. This may result in some other deprecated timezone codes not being handled correctly. Please report any bugs or discrepancies you may notice in the datetime field of metadata.
  • lightr now depends on R >= 4.0.0, following the tidyverse recommendation (@Bisaloo, #28)
  • the future package is now explicitly listed as a dependency, removing an R CMD check NOTE and thus removing the strain on CRAN reviewers (@Bisaloo, #63). The future package was already a indirect dependency via the future.apply package.

lightr 1.7.1

Internal changes

  • this project now uses lintr to ensure the code is always following the current best coding practices in the R community
  • ensure floating precision issues are not causing tests to fail on CRAN (@Bisaloo, #156)

Minor changes

  • lr_parse_irr8(), lr_parse_rfl8() and lr_parse_raw8() now error if you provide a file not produced by AvaSoft 8.2 as they have not been tested properly with other versions of AvaSoft 8.

lightr 1.7.0

Minor changes

  • Errors in low-level parsers are now passed as warnings in high-level lr_get_XXX() functions instead of being completely silenced.

  • IRR8 (irradiance files produced by AvaSoft 8) are now explicitly supported by lr_get_spec(). An alias has been added for the low-level parser: lr_parse_irr8().

lightr 1.6.2

Minor changes

  • fix failing tests on CRAN due to unattached dependency

lightr 1.6.1

Minor changes

  • fix failing tests on CRAN caused by non UTF-8 files

lightr 1.6.0

Major breaking changes

  • The date returned in metadata (by lr_get_metadata(), lr_convert_tocsv(metadata = TRUE) and lr_parse_XXXX()) is now a datetime (with UTC as timezone and format %Y-%m-%d %H:%M:%S). The column name in lr_get_metadata() has been updated from date to datetime to reflect this. Thanks to Giancarlo Chiarenza for the report, and to Hao Ye, Laura DeCicco and Elin Waring for helpful comments about timezones and datetime formatting for reproducibility.

Minor changes

  • datetime parsing is supported for more formats
  • Files produced by OceanInsight software (such as SpectraSuite) in Spanish can now be parsed)

lightr 1.5.0

Major breaking changes

  • the cores argument in lr_get_spec(), lr_get_metadata(), and lr_convert_tocsv() has been completely removed. It was already deprecated since lightr 1.0 (released on CRAN on 2020-01-27)
  • lr_convert_tocsv() gains a new metadata argument (defaults to TRUE) to determine if metadata should be exported in a csv file as well alongside the spectral data.

lightr 1.4

Minor changes and bug fixes

  • Output of the low-level parsers lr_parse_XXXX() is now a named list with elements data and metadata
  • lr_parse_raw8() and lr_parse_rfl8() now explicitly mention the number of spectra in the warnings instead of the generic "multiple spectra"
  • lr_parse_generic() now makes sure that the data is ordered by increasing wavelengths, which fixes a bug reported by @itamshab

lightr 1.3

Minor changes

  • (mostly internal) compute_processed() function is now named lr_compute_processed()
  • disable hash tests on Solaris (the output is still checked by other tests)

lightr 1.2

Minor changes

  • fixed tests on platform with no long-doubles ('noLD')
  • restored tests on 32bits machines
  • spec_ID extraction from Avantes exported files (ttt and trt) is now more robust, meaning it should work for more files.

lightr 1.1

New features and major changes

  • date column in metadata is now always formatted as ISO 8601.
  • lightr can now import AvaSoft8 files (test files provided by M.D. Shawkey and L. Swierk), via the functions lr_parse_rfl8()/lr_parse_raw8().
  • lightr can correctly imports TRM files from AvaSoft 6.0 (previously it only supported files from AvaSoft 7.0).
  • lightr can now import binary .spc files (via the lr_parse_spc() parser). This format is used by OceanInsight and CRAIC.

Minor changes

  • new test suite on a different locale (in this case fr_FR.UTF-8) to ensure parsing is locale-independent.
  • warnings on CRAN build system for platforms that don't support markdown 2 have been fixed.
  • new, stricter tests for various file formats.
  • jdx files saved in a locale that uses , as the decimal separator are now parsed correctly.
  • Avantes exported files in non-English locales (ttt and trt files) are now parsed correctly again (this was a regression compared to pavo's pavo::getspec()). Thanks to A. Fargevieille for reporting the issue and providing a test file.

lightr 1.0

New features and major changes

  • parallel processing now relies on the future package, which offers windows and high performance computing (HPC) environments support. The progress bar is produced by the progressr package and can be customised as well.
  • lr_parse_generic() (and thus lr_get_spec()) now works with non-UTF8 files (this was a regression compared to pavo's pavo::getspec()).
  • lr_get_spec() now has a new interpolate argument to determine whether you want your data interpolated and pruned at every nm or not.

Minor changes

  • readBin() (in the binary Avantes parser) now has an explicit endian value, making this package portable to platform that use big endians.
  • documentation has been updated to follow the rebranding of OceanOptics into OceanInsight.
  • vignette chunks that use pavo now only run if the package is available.
  • savetime field is now extracted from converted avantes files (when available).

lightr 0.1

  • First release.