Version 3.0.0

What's Changed

• Add configuration file with workflow definitions.

Significant updates to function names and parameters mean that older notebooks will throw errors when run on the new code. To use an older notebook, set source_code_version_id = "v2.6.0" in the parameters block.

Full Changelog: v2.6.0...v3.0.0

Versions 2.6.0

What's Changed

• enable TIC plots in default output
• add link to Targeted_Analysis.md in notebook
• faster make_atlas_from_spreadsheet()
• output pdf with message for empty boxplots
• Add ID notes and analysts instructions to GUI
• similar compounds exclude removed compounds
• C18 support
• allow launch script to take notebook parameters
• enable h5 lock in slurm template
• mzml to h5 file converter improvements
• size slurm job based on chromatography
• Replace notebook parameters inline
• use HILIC not HILICZ as ids.chromatography
• Add multiple_mirror_plot()
• add gitleaks and toml git hooks
• fix GUI errors when no inchi_key
• Allow AnalysisIdentifier.project to be non-numeric
• hybrid notebook improvements
• fix EIC y-axis scaling
• PlotSet sharey works over multiple pages
• add aliases for chromatography types
• increase plot width for boxplot with 25+ groups
• add clear_cache paramter to notebooks
• check gdrive auth before submitting to SLURM
• add peak height vs file plots to QC
• Add EIC plots to RT predict outputs
• copy RT_predict notebook to log dir
• pre-pend slurm job id to notebook copy
• use bash trap to copy notebook to log dir
• Filename validator
• move to dockerhub namespace doejgi
• added utility scripot copy_ms_to_new_names.py
• prevent black cache errors
• Update developer docs
• Make SLURM jobs more reproducible
• support 16+ filename fields in lcmsruns_short_names
• enable perlmutter SLURM jobs
• add rsyncd based file syncing from IGB to NERSC
• Update handling of notebook kernel
• add rt_min/max_delta params to RT_prediction.ipynb
• Enable dropping of inchi_keys from model generation
• better error messages from launch_rt_prediction.sh
• generate QC plots for ISTDEtc in SLURM job
• 's' now also toggle similar compound list
• use mailx to send emails
• support raw to h5 file conversion
• validate filenames before conversion
• update deployment documentation

Full Changelog: v2.5.0...v2.6.0

Version 2.5.0

What's Changed

• parallelize test suite when running on GitHub Actions
• improvements to msms hits caching
• Add filtering to pre-process step of predict_rt (run as SLURM job)
• Improvements to SLURM job submission scripts
• New tool for adding new msms references
• Move to shifter based notebook kernel
• Log exceptions raised in GUI event handlers
• Add date/duration of current commit to logs
• Refactor EIC chromatogram plots
• Improved kernel detection, installation and upgrades
• Add output of boxplots with log y-axis
• allow extra fields in experiment parameter
• Add CD to build and push to dockerhub
• Add TIC plots
• fix autoscaling for empty plots
• Add script for rolling back shifter image
• Targeted documentation improvement
• Add simple experiment_name validation to launcher
• More verbose col B header in Final Id spreadsheet
• untargeted and classyfire updates (Ben Bowen)
• updates to run_file_converter.sh
• Matplotlib backend to v3.5.0
• Fix errors on empty plot
• Add progress bar for copy to Google Drive
• Make AnalysisIdentifiers more general
• Create Targeted_hybrid notebook for more flexible analysis

Full Changelog: v2.0.0...v2.5.0

Version 2.0.0

Major changes include:

• RT Adjuster GUI has been refactored for easier development
• RT Adjuster GUI has been optimized for responsiveness
• RT Adjuster GUI has many new features
  - Highlighting of over overlapping RT ranges for similar compounds
  - Auto updating of MSMS plot when RT bounds change
  - Zooming of y-axis of MSMS plot via the 'z' key
  - Improved layout with fewer overlapping elements
  - Hovering over a bar on the MSMS mirror plot displays the m/z value
  - added 'vi'-like mapping of keys h,j,k,l to arrows for easier navigation
• Added an object oriented wrapper class around the metatlas_dataset object
• Added automatic caching of MSMS hits
• Added targeted analysis Jupyter notebook that does not require kernel restarts and contains minimal code within the notebook
• Added RT prediction Jupyter notebook that does not require user intervention and thus can be run as a SLURM job using papermill
• Added Jupyter notebook for extracting MSMS reference spectra from h5 files and exporting them into an msms_refs.tsv file
• Added unit tests (currently 34% coverage), system tests, linting, and code style enforcement

Version 1.0 Oct 22, 2020

This is the release predating 2020 restructuring of metatlas.