Soxspipe

* **FEATURE:** UV D-Lamp and QTH-Lamp master flats now being stitched together
* **FEATURE:** errors in error maps now being treated correctly and propagating to combined images
* **FEATURE:** Pipeline can now 'remember' where it left off in the reduction cascade. If it has run a recipe before it will exit with a message to the user informing them how to force the recipe to rerun.
* **FEATURE:** added a `twoD_disp_map_image_to_dataframe` function to toolkit
* **ENHANCEMENT:** PRO CATG now written to product FITS header
* **ENHANCEMENT:** Handling of binned images when generating flats and order-locations
* **ENHANCEMENT:** Where possible, product files are given the same name as the SOF file used to generate them (replacing `.sof` extension with `.fits`)
* **ENHANCEMENT:** SOF files can now contain a file 'tag' to allow users to read the SOF file contents and know exactly which files are being passed to the recipe (e.g. `MASTER_BIAS_UVB`, `LAMP,DORDERDEF_UVB` ... )
* **ENHANCEMENT:** dispersion solution now working with simulated NIR SOXS data
* **ENHANCEMENT:** quicklook now renders dispersion solution grid
* **ENHANCEMENT:** \~40% speed gain in combining images.
* **REFACTOR:** 2D Map generation now ~6-8 times faster (seeding solutions with nearest neighbour with cubic spline method)
* **REFACTOR:** SOF filenames reworked to contain the UTC observation date instead of MJD (more in-line with ESO ecosystems)
* **REFACTOR:** updated workflow for master bias combination
* **REFACTOR:** updated workflow for master dark combination
* **REFACTOR:** QC PDF plots now added to their own directory separate from the products
* **REFACTOR:** products now sub-divided into recipe directories (e.g. `./products/soxs-mbias/`)
* **DOCS:** mflat docs brought up-to-date
* **DOCS:** mflat docs brought up-to-date
* **FIXED:** mflat recipe now exits if flat frames are not of a consistent exptime.

* **ENHANCEMENT:** quickstart guide added for calibration recipes
* **FEATURE:** QCs added for dispersion solution and order centre recipes
* **REFACTOR:** clean up of stdout information

* **FEATURE:** shipping static calibration files with the code (one less thing for end-users to install and set-up)

This is only a summary of some of the updates included in this release:

* **ENHANCEMENT:** All CSV files moved to FITS binary tables - metadata very useful for developing data organiser
* **FEATURE:** 2D image map now created by create_dispersion_solution
`subtract_calibrations` util renamed to `detrend` and added ability to flat correct
* **FEATURE:** 2D image map of wavelength values, slit-position values and order values written alongside polynomial solutions of full dispersion solution
* **FEATURE:** soxspipe now on conda
* **FEATURE:** QCs now being written to FITS header
* **FEATURE:** adding QC and product collection in mbias recipe
* **ENHANCEMENT** RON and bias structure QCs now reported by mbias
* **ENHANCEMENT** nan ignored when scaling quicklook images
* **ENHANCEMENT** RON and bias structure QCs now reported by mdark
* **ENHANCEMENT:** QCs have an option to *NOT* (`to_header`) write to FITS header (default is to write)
* **REFACTOR:** better treatment of masked pixels when stacking images (e.g. in mbias and mdark)
* **REFACTOR:** removed raw frame reports and neater QC table
* **REFACTOR:** fits header keywords neatly sorted before writing to file
* **FIX:** Correct management of mask when determining RON on bias and darks

* **FEATURE:** recipes now have a `qc` and `products` attribute. These are pandas data frames used to collect QCs and generated products throughout the life-time of the recipe. They are printed to STDOUT at the end of the recipe (can be used in the future to send post request to health monitor API with JSON content in request body).
* **ENHANCEMENT** added code-base to conda-forge
* **ENHANCEMENT** added bottleneck to the install requirement (makes image combination more efficient)
* **ENHANCEMENT** masked pixel now coloured red in quicklook plots (easier to differentiate from good pixels)
* **ENHANCEMENT** low-sensitivity pixels in lamp-flats now identified and added to bad-pixel mask
* **ENHANCEMENT** add a verbosity flag to the command-line and a verbose parameter to each recipe
* **REFACTOR** inter-order pixel value in flats now set to unity (instead of running background fitting and subtraction)
* **REFACTOR:** recipes now have their recipe name as a `recipeName` attribute

* **FEATURE** Added a new `filenamer` module that implements a strict intermediate and reduced file-naming scheme
* **FEATURE:** `soxs_mflat` recipe now included
* **FEATURE:** `soxs_spatial_solution` recipe is now included
* **FEATURE:** `subtract_background` utility added
* **FEATURE:** added a `detect_order_edges` object
* **FEATURE:** Added a `dispersion_map_to_pixel_arrays` function to convert from order-based and wavelength arrays to pixel arrays (first guess dispersion map only so far)
* **FEATURE:** added a quicklook function in toolkit to quickly visualise a frame
* **FEATURE:** added a toolkit module for small functions used throughout soxspipe
* **FEATURE:** added function in toolkit to unpack an order table into lists of coordinates, one list per order.
* **FEATURE:** added image slice tool to toolkit
* **ENHANCEMENT** Added a `-o <outputDirectory>` switch to the command-line to optionally override the 'intermediate-data-root' setting in the settings file.
* **ENHANCEMENT:** added a fraction of a second tolerance when matching exptimes between darks and science/calibration frames
* **ENHANCEMENT:** y limits now added to the order table to show limits of order locations on detector
* **REFACTOR:** Change the "SOXSPIPE PRE" date stamp keyword to "SXSPRE" to future-proof for phase III (8 character keyword limit)
* **REFACTOR:** Pandas tables are now used through-out code to pass line-lists between methods
* **REFACTOR:** refactoring of polynomial fitting has made creation of dispersion maps ~50 times faster
* **REFACTOR:** removed OBID from file names and added readout mode. This information is more helpful at the glance.
* **FIXED:** correct binning reported in product file names
* **FIXED:** lines in a sof file beginning with a `` are considered as comments and therefore ignored by the pipeline.