MAESTRO, TRANSP and flux surfaces

Bug Fixes

• 🐛 Relaxed requirements of pip packages to avoid installation issues.
• 🐛 Corrupted TRANSP CDF files can now be read by removing bad time slices.
• 🐛 Improved interaction with TRANSP singularity to avoid trlook and trfinish issues, and to be able to run locally.
• 🐛 Improved logic for TRANSP cases that failed. Errors are now properly reported and process stopped.
• 🐛 areal elongation is now properly calculated in PROFILEStools.py, fixing H98 calculations. @josephb-hall

New Features

• 💥 Flux surfaces now handled always using their own class mitim_flux_surfaces. Parameterization, including Miller Extended Harmonics (MXH) now happens as a class method. @josephb-hall
• 💥 Capability to easily run "fixed-boundary" millerized equilibrium using the FreeGS code. The freegs pip package is now part of the requirements.
• 💥 Better check for missing or wrong flags in TGLF, TGYRO and PORTALS.
• 💥 Various conversion routines: profiles to transp, transp to profiles, freegs to transp, geqdsk to profiles, etc. All part of their own objects.
• 💥 TRANSP Helper object can now interact with namelist and prepare UFILES.
• 💥 Start of the common Neural Network surrogate class, and implementation of EPED NN. @josephb-hall
• 💥 First release of MAESTRO (Modular and Accelerated Engine for Simulation of Transport and Reactor Optimization) workflow. Implementation of TRANSP, PORTALS and EPED_NN beats. Ready for stress-testing. @AudreySaltzman @josephb-hall.
• 💥 Surrogates in PORTALS can now receive any other variable that are not included in gradients or profiles, such as q and shear. This will be useful when combining cases from different plasmas or scenarios.
• 💥 TRANSP reader mitim_plot_transp can now work with folder as input, and it will find the CDF
• 💥 if omfit_classes geqdsk reader cannot find the separatrix, now MITIM will increase resolution and go find it again. Seems to be working in some extreme cases.
• 💥 TRANSP runs do not need to use MRY anymore, now we can build RFS and ZFS files, which removes the need for scruncher.
• 💥 Further improvements to ASTRA class. @josephb-hall @AudreySaltzman @mmuraca
• 💥 TGLF output class has now a to_xarray() converter now. @aaronkho

Changes for developers (internal execution)

• 🔎 New contexts: timers and loggers. All part of IOtools.py
• 🔎 Removed deprecated functions and freegsu references to SPARC. Code moved to new locations.
• 🔎 Old "im" module moved out of MITIM-fusion. Too many changes to keep it up to date.
• 🔎 Naming changes to physicsBasedParams in PORTALS.

Back-compatibility considerations

• 🔮 It has been decided that PORTALS-TGLF runs by default use only the botorch optimizers, instead of root and ga that was used before. Only in expensive situations (e.g. CGYRO), one should try to refine solutions. This makes the convergence faster in wall-time.
• 🔮 config_user.json is now removed from the package folder. A template is provided in templates but the user can choose to place their config_user.json anywhere. Follow the read-the-docs for instructions: https://mitim-fusion.readthedocs.io/en/latest/installation.html#user-configuration @aaronkho @josephb-hall
• 🔮 machine-specific bashrc "recommendations" are now private and not part of the MITIM-fusion repository.