Code

v0.7.0#31

Code

Merged

ethanbass merged 55 commits intomasterethanbass/chromConverter:masterfrom devethanbass/chromConverter:devCopy head branch name to clipboardSep 25, 2024

+3,645-1,052

Commits

Commits on Aug 25, 2024

• feat: speed up read_shimadzu_lcd

  ethanbass

  committed
  79e5b05

• fix: read_mdf bug (failure to find end of header)

  ethanbass

  committed
  f85a25c

• feat: add preliminary support for Varian SMS

  ethanbass

  committed
  aafd37a

• fix: varian SMS encoding of segments starting with 80, add test

  ethanbass

  committed
  cb0557a

• feat: allow relative paths for export directory

  Show description for c7e9d1e
  ethanbass

  committed
  c7e9d1e

Commits on Aug 26, 2024

• fix: read_varian_sms to correctly decode large values

  ethanbass

  committed
  f787c2b

• docs: use bibenty citation format

  ethanbass

  committed
  786d5ee

• fix: read_varian_sms, update doc

  ethanbass

  committed
  0f7ceef

• fix: behavior of shimadzu parser with multiple 2d chroms

  ethanbass

  committed
  b6add62

Commits on Aug 27, 2024

• fix: start shimadzu chrom times at DLT (dwell time), add multichrom test

  ethanbass

  committed
  f95c451

Commits on Aug 28, 2024

• fix: varian sms, deal with variable length msdata header

  Show description for 80b4661
  ethanbass

  committed
  80b4661

• docs: varian SMS metadata

  ethanbass

  committed
  74ebdb9

• ci: add varian sms test, shimadzu multichrom test

  ethanbass

  committed
  179648b

• docs: minor update to readme

  Show description for 34c5b86
  ethanbass

  committed
  34c5b86

Commits on Aug 29, 2024

• feat: more varian metadata + test

  ethanbass

  committed
  36f537d

• ci: add check for shimadzu lcd multichrom long format

  ethanbass

  committed
  2b96bbd

Commits on Aug 30, 2024

• eliminate magrittr dependency, add scale option for chemstation_uv files

  ethanbass

  committed
  66024cf

• feat: add unit column for long format chroms returned by shimadzu_lcd

  ethanbass

  committed
  7c90f88

Commits on Sep 1, 2024

• cli: harmonization of path arguments (file -> path)

  ethanbass

  committed
  da436de

Commits on Sep 2, 2024

• refactor, docs: read_cdf (minor refactoring)

  ethanbass

  committed
  51cc024

• cli: files -> paths

  ethanbass

  committed
  833c7c6

• style: whitespace

  ethanbass

  committed
  2756806

Commits on Sep 6, 2024

• feat: allow creation of new directory by read_chroms for exporting files

  ethanbass

  committed
  cb48d62

• style: whitespace

  ethanbass

  committed
  2fd7de7

• ci: update tests

  ethanbass

  committed
  bfeec2b

Commits on Sep 9, 2024

• move olefile utilities into new file

  ethanbass

  committed
  a049f89

• feat: more generalizable solution for finding delimited in shimadzu_ascii files

  ethanbass

  committed
  0bd294f

Commits on Sep 11, 2024

• move olefile utilities to their own file, convert shimadzu times in read_sz_file_properties

  Show description for 26a014b
  ethanbass

  committed
  26a014b

• feat: added shimadzu_qgd parser

  Show description for 436dd9e
  ethanbass

  committed
  436dd9e

• style: indentation read_shimadzu_gcd

  ethanbass

  committed
  0654d12

• rm: write_mzml_minimal

  ethanbass

  committed
  cfb1960

• docs: describe structure of qgd

  ethanbass

  committed
  e69d8be

• v 0.7.0

  ethanbass

  committed
  a66e1a2

• ci: use tempdir automatically in tests

  ethanbass

  committed
  1a1acc7

• docs: remove extraneous

  ethanbass

  committed
  799bcbe

• docs: shimadzu ascii, gcd, qgd

  ethanbass

  committed
  2e17ea2

• docs: clean up read_mdf, read_mzml

  ethanbass

  committed
  d9b2ba3

Commits on Sep 17, 2024

• feat: upper

  ethanbass

  committed
  f8de148

Commits on Sep 18, 2024

• feat: add support for writing mzml

  Show description for 874b248
  ethanbass

  committed
  874b248

• refactor: functionalized data_format conversion, added data.table option

  ethanbass

  committed
  9b89525

• feat: improve handling of metadata from rainbow

  ethanbass

  committed
  b9fcbb4

• update namespace, news

  ethanbass

  committed
  4887d4d

• ci: add tests

  ethanbass

  committed
  e4d6bea

Commits on Sep 19, 2024

• docs: add note about old openchroms from sourceforge

  ethanbass

  committed
  35f238b

• feat: add extra verbosity when verbose is TRUE

  ethanbass

  committed
  2a046f3

Commits on Sep 23, 2024

• feat: added read_asm, read_agilent_d, fixed reticulate bug

  ethanbass

  committed
  39a412c

• style: fix long lines

  ethanbass

  committed
  969cbd3

• ci: added chemstation v181 test, ASM tests

  ethanbass

  committed
  ad32f41

• feat: add asm filetype detection

  ethanbass

  committed
  14a1124

• fix: parsing of ASM metadata, bug in extract_metadata

  ethanbass

  committed
  6cd7d88

Commits on Sep 24, 2024

• ui: what = "chromatogram" -> "chroms", update docs

  ethanbass

  committed
  7f327a3

• fix: mzml syntax issues, bad indices

  ethanbass

  committed
  c0efbe8

• docs: update NEWS.md

  ethanbass

  committed
  fd76fe8

Commits on Sep 25, 2024

• fix: missing sample_names when writing mzml

  ethanbass

  committed
  cfd6d8c

• Merge branch 'master' into dev

  ethanbass

  authored
  607a786