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v1.37.3 - update for tests only - library database path for library vs library spectral matching test updated #110

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Merged
Tomnl merged 5 commits into from
Mar 10, 2026
Merged

v1.37.3 - update for tests only - library database path for library vs library spectral matching test updated #110

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dc96dda
Update library database path for lvl spectral matching test
Tomnl Mar 10, 2026
0ae071d
Bump version from 1.37.2 to 1.37.3
Tomnl Mar 10, 2026
a40b387
Update readme
Tomnl Mar 10, 2026
b8924dd
Change package date in DESCRIPTION file
Tomnl Mar 10, 2026
5cedec5
Update NEWS with clarification on database path change
Tomnl Mar 10, 2026
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ Package: msPurity
Type: Package
Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based
Fragmentation in Metabolomics
Version: 1.37.2
Date: 2025-02-19
Version: 1.37.3
Date: 2025-03-10
Authors@R: c(
person(given = "Thomas N.", family = "Lawson",
email = "thomas.nigel.lawson@gmail.com", role = c("aut", "cre"),
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3 changes: 3 additions & 0 deletions NEWS
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@@ -1,3 +1,6 @@
CHANGES IN VERSION 1.37.3
+ Update within the tests only (not within the R code base): library database path for lvl spectral matching testing (required after removal of the local SQLite database from msPurityData).

CHANGES IN VERSION 1.37.2
+ Bug fix for subsetting the grouped data frame in the `average_xcms_grouped_msms_indiv` function

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8 changes: 4 additions & 4 deletions tests/testthat/test.5_sm.R
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Expand Up @@ -73,11 +73,11 @@ test_that("checking spectral matching functions (spectralMatching) library vs li
rid <- paste0(paste0(sample(LETTERS, 5, TRUE), collapse=""), paste0(sample(9999, 1, TRUE), collapse=""), ".sqlite")
sm_out_pth <- file.path(td, rid)

l_dbPth <- file.path(td, "library_spectra.db")
download.file("https://zenodo.org/records/18700802/files/library_spectra.db?download=1",
l_dbPth, mode = "wb", quiet = TRUE)

q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")

result <- spectralMatching(q_dbPth=q_dbPth,
result <- spectralMatching(q_dbPth=l_dbPth,
l_dbPth=l_dbPth,
q_pids = c(1,2,3),
q_spectraTypes = NA,
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