Soxspipe

* **FEATURE:** SOXS UVVIS line-list (first draft) now ships with the code.
* **FEATURE:** pipeline can now 'watch' a folder and automatically reduce raw data added to it. This 'watch' feature can also be run as a system daemon.
* **ENHANCEMENT:** Python 3.11 is the mimimum python version now
* **ENHANCEMENT:** pinning the main packages used by soxspipe
* **ENHANCEMENT:** now recording 'ESO ADA ABSROT END' in the soxspipe.db database
* **ENHANCEMENT:** adding a check to see if the continuum fit is good in each order ... remove bad orders (SOXS VIS only so far)
* **ENHANCEMENT:** improving SOXS extractions (using order centre traces with flat lamps)
* **REFACTOR:** Data-organiser can now work with new SOXS DPR keywords.
* **REFACTOR:** changing order centre clipping to mean and std (not median and mad)
* **REFACTOR:** updated NIR line list after SOXS format change
* **FIXED:** a few bugs

* **FIXED:** a regression in the detect continuum code

* **ENHANCEMENT:** LaCosmic is run on images prior to source extraction to help remove cosmic ray hits.
* **ENHANCEMENT:** Dichroic region is now clipped from the Xshooter UVB order merge spectrum
* **REFACTOR:** Improved source continuum tracing making nodding reductions more robust.
* **FIXED:** a bug where binning was not taken into consideration when reading the detector format before performing source extraction.

* **ENHANCEMENT:** New raw data is to be 'streamed' into the workspace's root folder. When 'soxspipe prep .' is run, the new data is found and filed automatically into the correct `/raw/YYYY-MM-DD/` folder. Adding new raw frames directly into the `raw/YYYY-MM-DD/` nested folder structure is also possible.
* **ENHANCEMENT:** "STD,TELLURIC" frames now recognised in stare mode.
* **REFACTOR:** Made big speed gains in the `order_to_image` method. This speeds up the `soxs_spatial_solution` dramatically.
* **REFACTOR:** exptimes recorded in the SQLite database are now rounded to 2 decimal places. There are occasions where exposure times in the FITS headers are given to 4 dp, and a set of (e.g. flat) frames have exposure times that differ by 0.0001 secs. The pipeline divided these frames into two sets when they should have been grouped together. This was causing failure on some mflat recipes.
* **FIXED:** Fixed numpy 2.0 compatibility issues so soxspipe can now run with numpy v2.0 and greater
* **FIXED:** Instrument = "SHOOT" now recognised as Xshooter data
* **FIXED:** bug in the detect continuum code that would fail to fit a gaussian in the cross-dispersion slices if NaN values were present.
* **DOCS:** complete update of the SOXS documentation. See https://soxspipe.readthedocs.io
* **DOCS:** 4 installation methods are now reported in the documentation (anaconda is not required to install the pipeline). https://soxspipe.readthedocs.io/en/master/user_manual/installation.html

* **REFACTOR:** interpolated wavelength resolutions set to match that of the Xshooter pipeline in order-merged spectra (NIR were the same, but now UVB and VIS arms also match Xshooter).
* **FIXED:** bug in the Horne extraction causing artificial 'undulations' in the extracted spectra.
* **FIXED:** bad pixel treatment in Horne extraction (was severely affecting NIR extraction in particular)
* **FIXED:** filename case-sensitivity issue when working on a case-sensitive file system
* **FIXED:** issue where the prep command was looking for a settings file in "~/.config/soxspipe"

* **FEATURE:** ascii exports
* **FEATURE:** nodding mode
* **FEATURE:** allowing order-trace frames to be reduced in stare mode for PAE
* **FEATURE:** pipeline is now reducing soxs UVVIS data robustly.
* **FEATURE:** adding code to help tune the pipeline. Add the setting `tune-pipeline: True` to the setttings file and run a recipe command.
* **ENHANCEMENT:** pipeline parameters (in default settings file) are now optimally tuned from UVVIS up to flats and NIR up to spatial solution.
* **ENHANCEMENT:** This release includes many robustness updates