Developers Notes

Fitspy is a new project (started in 2023).

Developers are warmly encouraged to collaborate and contribute to the ongoing improvement of Fitspy. Contributions are welcome in the form of bug reports, documentation, code , feature requests, and more…

… keeping in mind that Fitspy must maintain its primary goal: to remain as simple, generic and user-friendly as possible :)

Issues

The issue tracker can be used to report bugs or propose new features. When reporting a bug, the following is useful:

  • give a minimal example demonstrating the bug,

  • copy and paste the error traceback.

Visual Studio Code Setup to Preview .rst Files

  1. Install the RestructuredText Extension: - Open Visual Studio Code. - Go to the Extensions view (Ctrl+Shift+X). - Search for “reStructuredText” and install the extension by LeXtudio.

  2. Install Dependencies: - Open the terminal in Visual Studio Code (Ctrl+ ` `). - Run the following commands to install Dev environment dependencies:

    pip install -e .[dev]

Pull Requests

If you want to contribute to improve the Fitspy source code, you can send us a pull request against the main branch. Small bug fixes and corrections to the user guide are typically a good starting point. But don’t hesitate also for significant code contributions, such as support for a new file format - if needed, we’ll help you to get the code ready to common standards.

TODO List

TODO Base:

  • [ ] when changing a component of a fitted spectrum (peak, baseline, …) ‘reset’ the spectrum color status

  • [ ] Revisit the slider to make it visible (particularly in the light mode)

  • [x] Add None in Baseline Options

  • [x] Write a submodule that provides all functions necessary to manipulate GUI via code only. + Rewrite examples to use this submodule

  • [/] Update documentation (partially done) - adapt the doc for Models and Main Figure in the GUI section

  • [x] Add a “Highlight spectra” click mode

  • [x] restore spectrum colorize_from_fit_status

  • [x] Implement peaks model + bkg model load button

  • [x] Implement back save_results

  • [x] Implement back model reloading

Menubar:

  • [x] Implement CLEAR + SAVE GLOBAL STATE + OPEN GLOBAL STATE (drag n drop & open button should call same function)

  • [x] About + Manual + Doc (could redirect to sphinx doc)

Peaks Table:

  • [x] Add background parameters (in table or elsewhere in GUI)

  • [x] Add missing columns for some Peak Models

  • [x] Implement expressions

  • [x] User Warning for incorrect bounds

Toolbar:

  • [x] Add checkbox “preserve axis” (= preserve zoom)

2DMap:

  • [x] Implement back export .csv

  • [x] Implement Min/Max (replace with a DoubleRangedSlider ?)

  • [x] Add Label choice and plot update

TODO Fixes:

  • [x] Results of previous calculations have to be preserved and displayed (colorize_from_status) when reloading a map

  • [ ] Investigate exit not exiting properly on some systems (could be due to Threads, use QThread instead ?) ultralytics issue 1167

  • [ ] reinit in Spectrum() doesn’t reinit fit_params

  • [ ] Expressions in saved models are “” instead of None

  • [ ] Manage callbacks when no files have been loaded (allow saving model, placing points, and baseline without loading spectra)

  • [ ] Baseline_points, empty Y if attached ?

  • [x] Peaks labels can sometimes overflow the plot

  • [x] Icons color dont follow theme

  • [x] Spectrum list is disordered compared to the map. When browsing through the spectra in the list, it should traverse the map from top to bottom and left to right.

  • [x] Port updates commit 6d303df (main)

TODO Opti:

  • [ ] Check (and avoid) multiple calls - code profiling

  • [ ] Refactor peaks_table.py + bkg_table.py by creating a new class

  • [ ] MULTIPROC BASELINE via apply_model ?

  • [ ] Optimize plotting (setxdata and setydata instead of replotting the whole figure ?)

TODO Others:

  • [x] restore & update examples/ + tests/

  • [ ] Defaults values for peaks (and maybe more) may be irrelevant depending on data’s nature

  • [ ] Inconsistencies in args names fnames vs files

  • [ ] Explicit types in functions might be useful for maintainers(e.g. def func(arg: type) -> type:)

  • [x] Change peak table colum _vary to _fixed

  • [ ] Why using np.float64 for baseline points ??

  • [ ] update README.md

  • [ ] update CITATION.cff

  • [x] add github workflows back

  • [x] update paper/

TODO Nice to Have:

  • [ ] Fitspy Icon for taskbar

  • [ ] Multirow-edit for peaks settings (see https://stackoverflow.com/questions/14586715/how-can-i-achieve-to-update-multiple-rows-in-a-qtableview)

  • [ ] Update save/load mechanisms to include data or not based on ‘save spectrum file path only’ checkbox state

  • [ ] update dynamically the 2D map figure during fitting

  • [ ] Plot Dark/Light dynamic theme change

  • [ ] Idea : scroll on plot to edit nearest peak bounds

  • [ ] Add a button to copy 2D Map in clipboard ? (add mpl toolbar ?)

  • [x] See multiple spectrum with their baseline subtracted or not (need to redefine what to plot for secondary spectrum instead of just x0+y0)

  • [x] add a confirmation prompt before load_state to avoid erasing current work

  • [x] New View option ‘subtract bkg’ (see existing ‘subtract baseline’)

  • [x] Colormap settings

  • [x] Add shortcuts for menu actions

  • [x] Warn user to disable pan/zoom if 3 clicks are detected in a short time (indicating user might want to place a peak/baseline point)

TODO Production:

  • [ ] Update Github Actions tests + Auto Pypi Pre-release/Pre-release, see pyvsnr workflows

  • [ ] Update Zenodo