v0.7.0

[ethanbass]

chromConverter 0.7.0

Major features

• Added preliminary support for 'Varian Worktation' (.sms) format through read_varian_sms function.
• Added preliminary support for 'Shimadzu QGD' GCMS files through the read_shimadzu_qgd function.
• Added preliminary support for 'Allotrope Simple Model' (ASM) 2D chromatography date files.
• Added support for reading multiple files from 'Agilent' .D directories through read_agilent_d function.
• Added option to write mzML files (MS1 and DAD).

UI changes

• Changed order of arguments in read_chroms so that format_in comes second after path.
• Removed extraneous export argument from read_chroms. To export files, you now only need to provide an argument to export_format.
• Updated handling of multiple chromatograms by read_shimadzu_lcd. The function now returns a list of named chromatograms if data_format == "wide" and returns multiple chromatograms in a single data.frame if data_format == "long".
• Added scale argument to read_chemstation_uv and read_shimadzu_ascii to toggle scaling of chromatograms.
• Harmonized file path arguments across parser functions by changing file arguments to path.
• Harmonized column names in output across parsers.
• Small changes in read_cdf UI: what now defaults to NULL and defaults are coded into downstream read_andi_chrom and read_andi_ms functions.
• Added extra verbosity in read_chroms when verbose is TRUE.

Other improvements

• Fixed bug causing reticulate to attempt reinstallation of Aston every time the package is loaded (due to case sensitivity of packages names in reticulate::configure_environment).
• Added data.table as an option for format_out.
• Improved speed of read_shimadzu_lcd by dealing with twos-complements more sensibly.
• Start 'Shimadzu LCD' chromatogram retention times at dwell time (DLT).
• Give temp files generated from Shimadzu OLE files informative names.
• Use 'Output Date' field instead of 'Type' to find 'Shimadzu' ASCII delimiter. (This seems to be a more generalizable solution since some files do not contain the 'Type' field).
• Allow relative paths for path_out when using 'ThermoRawFileParser' and 'OpenChrom' parsers.
• Allow creation of new directories by read_chroms if path_out does not exist.
• Fixed bug affecting some mdf files lacking null bytes after the file header.
• Eliminated 'magrittr' dependency by using xpath to parse XML in a more straightforward fashion.
• Fixed bug causing truncation of sample names at the first period by read_chroms.
• Modified export_csv function to label first column for wide-format chromatograms.
• Improved handling of metadata from rainbow parsers.
• Fixed error when providing single chromatogram to \code{extract_metadata}.
• Added metadata field for source checksum (SHA1).