Release of v0.1.8

What's Changed

New

• You can download the newest version of the app from within AutoIMS!
• Added new W: Compare spectra (one-vs-one, single dataset) task that will compare spectra within a single dataset
• Added W: Average mass spectrum / cluster (single-dataset) task which will let you generate average mass spectrum for each KMeans cluster (these can be used for comparing spectral differences and in the future, for annotations
• Added tSNE as an additional dimensionality reduction method
• Added a couple of parameter options to both W: Unsupervised tasks (mostly for UMAP)
• Added Find the optimal number of clusters option to the W: Unsupervised... tasks which will automatically determine the optimal number of clusters using the elbow method
• Added a button to validate against the data in the raw directory - a short report will be shown to say whether files in your raw directory are matched against the tags.csv file.
• Each time a task is missing some dependency (other task required), it will now display it as a hyperlink which you can click and be taken to the missing task.
• Added toggle between light and dark theme of the app
• Added option to export centroid data as image2image compatible HDF5 files (available to use in the next release of image2image
• You will be warned if there is no ion mobility data in the raw directory but you've selected W: 2d feature detection task
• Added a sort button to the selected tasks so you can sort tasks by their priority (it's automatically done when saving config but might be helpful)
• It is now possible to remove user from the M: Contact information task
• You will now have to confirm whether you want to close the window to prevent accidental losses of data

Removed

• Removed the Ex: Centroids to OME-TIFF, Ex: Centroids to Fusion CSV and Ex: Dataset to imzML tasks and migrated the export to the Wf: Extract ion centroids where you can select several export options (multiple exports permitted per task)
• Removed the Ex: Average mass spectrum task - it is now integrated directly into the Pre: Average mass spectrum task (multiple exports permitted per task)
• Removed the method=extracted from Ex: Dataset to imzML task as it's no longer needed here (see Wf: Extract ion centroids)

Changed

• Renamed the Wf: Compare spectra grid to Wf: Compare spectra (one-vs-one, multi-dataset).
• Moved the Profiles combobox to a new location so it occupies less space
• Changed the way we display paths to use hyperlinks so you can click on them and be taken to the right folder
• Renamed all tasks to no longer use the Pre or Wf identifiers - they are now P or W to make names slightly shorter
• The tag variable of W: Extract ion centroids can now be auto-generated
• Cleaned-up the results directory so fewer directories will be now created
• The icons indicating whether something is valid or not have been moved to the left-hand side
• There are now three different icons to indicate whether a task is valid. Those are succes (green check mark), warning (orange warning sign) and error (red cross). As before, warnings are simply there to notify you of some additional considerations but will not cause task failures.
• Logging is now much more extensive so hopefully that will help us catch bugs/errors.
• The automatically tags.csv will now feature much more reasonable defaults.

Fixed

• The Wf: Unsupervised training (multi-dataset) task now permits multiple instances (e.g. PCA and UMAP in the same config...)
• Fixed a bug which prevented manual filename creation
• Fixed many bugs in task validation
• Fixed a bug which prevented proper loading of tags.csv
• Pre-selected calibrants will now be properly selected in the Selection window
• Fixed a bug where the average mass spectra files always had an odd name
• Tutorial will no longer go backwards

Breaking Changes

• Hopefully nothing - configs from v0.1.7 will be automatically upgraded to latest schema version.
• Configs from previous versions might have some minor errors that need fixing