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NEWS.md

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Version 0.2

Changes in 0.2.6

  • Rewrote Dockerfile to install Sirius 6.3.3 directly (replaces conda). Sirius REST API now auto-starts on port 9999 via s6-overlay init script.
  • All vignettes now use port = 9999 in Sirius() calls.
  • Added pre-computed vignette infrastructure (.Rmd.orig + pre-render.R) so pkgdown articles display real output.

Changes in 0.2.5

  • Fixed a bug where calling run() with only msNovelistParams (or structureDbSearchParams) would silently skip formula identification and fingerprint prediction because formulaIdParams and predictParams default to NA in run(). config() now automatically enables prerequisite parameters when downstream tools require them: deNovoStructureParam / structureDbSearchParam → enables predictParam; any of those or predictParam → enables formulaIdParam. Explicitly supplied parameter objects are never overridden.

Changes in 0.2.4

  • Adduct strings are now automatically normalized to the canonical SIRIUS format with spaces around operators (e.g. "[M+H]+" → "[M + H]+"). Both compact and spaced formats are now accepted in import(), run(), and config().
  • Added candidateFormulas parameter to formulaIdParam(). This allows restricting SIRIUS to specific molecular formulas instead of de novo generation. The formulas are passed via JobSubmission$configMap since SIRIUS does not accept them as a standard formulaIdParams field.
  • Add parameter host to Sirius().

Changes in 0.2.3

  • Fixed a bug where importing a single MS2 spectrum (no MS1) resulted in 0 features in the project, causing run() to fail with "Either 'compoundsIds' or 'alignedFeaturesIds' must be provided."
  • import() now correctly handles single-level MS2-only data by grouping spectra via .groupMSnIndex() (previously only triggered for multi-level MSn data).
  • .createfeatures() now always sets ionMass from precursorMz when MSn data is available. Previously ionMass was hardcoded to 0, which caused the Sirius API to silently discard features without MS1 data. For MS1-only features, ionMass remains 0 so Sirius can derive it from the MS1 spectrum.
  • Updated RSirius dependency to latest release (3.1+sirius6.3.3, commit 2c983e6). The new version exposes gui_api with proper OpenGui, CloseGui, and GetGuis endpoints.
  • Simplified openGUI() and closeGUI() to use the official gui_api endpoints instead of manually constructing HTTP requests via .callGuiApi().
  • Removed the internal .callGuiApi() helper (no longer needed).
  • Added docker-push.yaml GitHub Actions workflow for automated Docker image builds on push to main.

Changes in 0.2.2

  • Added support for importing MSn-only data (MS2, MS2+MS3, etc.) without requiring MS1 spectra. The SIRIUS API accepts features with no MS1 data.
  • Added .groupMSnIndex() helper that automatically groups MSn-only spectra by acquisition order when no ms_column_name is provided and no MS1 data is present.
  • .createfeatures() now includes MS3+ spectra (msLevel >= 2) in the ms2Spectra field sent to the API.
  • Fixed a bug in import() where ms_column_name was used before being assigned when the input Spectra contained only a single MS level.
  • Added "Importing MS2-only or MSn-only data" section to the ImportSpectra vignette.
  • Added test-msn-import.R test file with 30 expectations covering MSn-only grouping, feature creation, and API integration.

Changes in 0.2.1

  • Replaced msdata dependency with MsDataHub for example data in vignettes.
  • Added "Getting Started" vignette covering basic connection and project management.
  • Added "Retrieving Results" vignette explaining result types and retrieval.
  • Added "Custom Databases" vignette for creating and using custom databases.
  • Updated Dockerfile for Bioconductor 3.22.

Changes in 0.2.0

  • BREAKING: Updated RSirius dependency from commit c35ebbb to e4acd1b (API version 3.1, Sirius 6.3.3 support).
  • BREAKING: Package dependency renamed from Rsirius to RSirius (capital S) to match upstream rename.
  • Updated Sirius version requirement from 6.1 to 6.3.
  • Updated the import to take a single Spectra object. See documentation for more information.
  • Added a vignette for a basic example.
  • Updated to use Spectra::fragmentGroupIndex() for grouping MS1/MS2 spectra.
  • Added comprehensive test suite with testthat for parameter classes, helper functions, and integration tests.

Version 0.1

Changes in 0.1.5

  • Refactor the default path for opening/saving projects. It will now save by default in the current directory if the path = parameter is not precised.
  • Can now import directly from a Spectra object, without having to process beforehand. Still needs to be improved, see issue #27

Changes in 0.1.4

  • Now supports import for negative polarity. See #24
  • Addition of critical issue in the readme file (line 115). Related to issue #19.
  • Fix issue on show() method.

Changes in 0.1.3

  • Now can choose or not to delete features already present when importing new ones. Through parameter deleteExistingFeatures = in import(). Default is TRUE.
  • Addition of functionalities to create, delete and list databases. See #15
  • Can now import feature with set adducts if known. See #14
  • Small fixes for show() method of Sirius object. See #8
  • Fix spectral Library matching and now can see a summary of full results using summary() and results() function and precising result.type = "spectralDbMatch".
  • Added results() for fragmentation tree. accessible using result.type = "fragTree". See #18
  • Added a DockerFile, but cannot seem to start Sirius properly. Work in Progress See #17

Changes in 0.1.2

  • Fix installation of Spectra dev version
  • Addition of code to install devel version of xcms in readme.md

Changes in 0.1.1

  • Addition of package used in the vignettes to DESCRIPITON.
  • Change vignette builder to Rmarkdown. Vignettes now go through the R command checks.

Changes in 0.1.0

  • Beginning of RuSirius 😎