Isofit

Updates include


**Technical updates, improvements, and small bug fixes**

- New capabilities to auto generate the API docs so less time needed to manage it.
- Fixed incorrect display of docs related to the data module.
- Pre-check for gfortran installation before downloading 6s and new prompting to the user to fix.
- New flexibility to only check for the correct zenith angle convention if the lut key is provided.
- Fix of IndexError in the test_rfls attribute when building Modtran LUT.
- Support of ability to pass specific inversion windows in and bypass the sensor or global defaults.
- Function to download and store external NEON data.
- Correction of NotImplementedError syntax for EWT command line utility.

Updates include


**Main features and fixes**

- Added support for Python 3.12.
- Implemented the ability to build ISOFIT Docker images for multiple architectures using only one Dockerfile.
- Developed a new github workflow to auto build and push the Docker images on each ISOFIT release.
- ISOFIT's Docker images are hosted at [https://hub.docker.com/r/jammont/isofit](https://hub.docker.com/r/jammont/isofit).


**Technical updates, improvements, and small bug fixes**

- Implemented more helpful debugging/error messages when ISOFIT is missing extra dependencies.

Updates include


**Main features and fixes**

- Removed data/ and examples/ directories from the repo as they are now available in their own repos. This allows us to update these packages independently of ISOFIT releases. Additionally, as ISOFIT now has the capability to download these via the downloads CLI, the workflows have been updated to reflect these changes.
- Integrated downloads of examples and data.
- Updated glint retrieval code:
- Removed additional g_dd term in reflectance, radiance calculation to match desired model.
- Included t_up_total in radiance calculation to match desired model.
- Updated drdn_dsurface derivative with regard to glint parameters g_dd and g_dsf.
- Updated g_dd initialization to be based off of signal at 1020 nm (assumes this is in the instrument wavelength range, and that the signal here is glint only).
- Changed the prior covariance structure for g_dd and g_dsf to be fully independent variables (diagonal) instead of fully correlated, as in previous implementation.


**Technical updates, improvements, and small bug fixes**

- Added an option to apply_oe which forces all LUT dimensions in the obs/loc files with measurable variation to include at least 2 grid points.
- Examples build update.
- Cancel-in-progress workflows.
- Debug fixes.
- Import cleanup.

Updates include

**Technical updates, improvements, and small bug fixes**

- Improve the support for creating custom radiative transfer engines by expanding the documentation.
- Removed behind-the-scenes assignment of AVIRIS-3 channelized uncertainty.
- Tweaked the cache of `common:VectorInterpolator` to support N many points instead of just 1.
- Moved the RT engines to a submodule. This fixes some missed import statements.
- Collection of improvements to the `luts.py` module to increase the loading speed.
- Fixed 180 degree offset in MODTRAN OBSZEN usage.
- Fixed log entry where `mean_to_sun_azimuth` is incorrectly reported.
- Analytical line speed improvements.
- Moved the loading of the ESD file to the `core/fileio.py:IO` class to maintain consistency with other data loading.
- Swapped out `np.all` with `np.allclose` to handle cases where an input data source has values very close to the bad data flag but not exact.
- Enforced bounds on output reflectances to be zero and not negative except in the cases of the fill values `-9999` and `-0.01`.
- Fixed a longstanding bug where `MKL_NUM_THREADS` and `OMP_NUM_THREADS` was not being set properly by ISOFIT.
- Added a new ISOFIT env var `ISOFIT_NO_SET_THREADS` to disable automatically setting these for advanced users.
- Re-implemented support for `rte_configure_and_exit` which causes engines to write configuration/template files and not execute.
- Deprecated support for `rte_auto_rebuild`. ISOFIT will just check if files exist and assume they are correct; it is the user's responsibility to correct them otherwise.
- Removed custom `FileExistsException`.
- Handled wrong sized reference reflectance inputs.
- Detection of duplicates in `lut_grid`.
- Removed `nds-k` from `VectorInterpolator`.
- Fixed click implementation for `surface_model.py`.
- Statevector consistency check.

Updates include


**Main features and fixes**

- Fixed LUT resampling and angular interpolation issues.
- Patches to the handling of the scene geometry, in particular, to the handling of the relative azimuth and the sensor zenith angles.
- Added the handling of flux quantities. This allows users to provide LUTs with RT quantities in physical units instead of transmittance and reflectance.
- More formal implementation of kernel flows using the radiative_transfer_engine.py.

**Technical updates, improvements, and small bug fixes**

- Interpolation improvements in `luts.py`.
- Improved the debugging verbosity of `luts.py:load()`.
- Resampling of the LUT in `radiative_transfer_engine.py` to be more generalized.
- Improvements to the `VectorInterpolator._multilinear_grid`.
- Removed `pygrib` dependency.
- Small patch to surface model built on runtime.
- Removed custom version of ray shutdown from ISOFIT's init.
- Updated bibliography.rst with latest papers using ISOFIT.
- Added compression to netcdf files.
- Added INVERSION_WINDOWS to presolve and main configs.
- Updated image cube examples to ISOFIT version 3.
- Included names of supported sensors in the "invalid sensor" error message.
- Max buffer timing fix & NetCDF chunking.
- Wavelength check updates.

Small patches to the v3.0.0 release.

**Technical updates:**

- improvements to LUT netCDF creation performance: now using a writer queue, simulations return values to the original ray call to be saved

**Bugfixes:**

- added sphinx_rtd_theme to environment file to fix broken readthedocs build
- fixed bug in assigning mean elevation to LUT grid
- fixed broken Zenodo hook