Added possibility to enter initial soil water content as a raster input, optional. Added yaml env file for non linux OS.

Modified all path creation with os.path.join(). Started modifications of weather part in preparation for the new CDS Climate server. Old method is not implemented yet, will find a way to work around for the time being.

Modifications to NDVI calculation scripts. Addition of irrigation mask as input. Various changes following these modifications.

Modification of data directory structure. Modifications in all codes accordingly, not all scripts have been tested. Documentation, comment changes. Future changes to come.

Various improvements and bug corrections: fixed ndvi pixel clipping, adjusted memory requirement calculation, added one variable (footprint) for pixel GIF plotting. Other small changes.

Added THEIA and LandSat image download and management. Improved and simplified input preparation for parcel mode. Rewrote model calculation memory estimation function. Corrected small bugs.

Fixed irrigation equations. Small readability and performance updates. Changes in input preparation.

Modification of SAMIR equations, use of Kcbmax instead of Kcmax. Plot_GIF modifications. Doc update.

Some fixes on the parcel mode, Aurade dataset almost done, pixel and parcel mode do not produce the same results. Other various improvements.

Memory optimisation, improved speed and memory usage. Minor modifications in input preparation. Rain data is now scaled by 1000.

Bug correction and interface improvement in main samir code. Improved output plot scripts (some work left to do). Various small improvements.

Added parcel mode outputs, improved docs, improved samir parame tests, minor corrections and changes.

Further improvements in optimization. Manage to create real empty output dataset and append values along the time dimension, greatly improves total run speed. Reworked the custom_input notebook for a better handling of the land cover class conversion. Added tests on parameters values to make sure they are in correct range, parameter ranges are defined in a csv file (params_samir_min_max.csv). Other small modifications.

Some optimization improvements. Potential memory leaks to look at. Many improvements in the preprocessing scripts, almost finished the parcel mode. New scripts in the prostprocessing directory. Changes in the samir parameter handling.

Improved output plotting and added a script to automatically generate a daily GIF for a chosen variable.

Added main_run_samir.py to run the samir model. Modified config_file to manage input paths. Various bug corrections in dataset dimensions, speed improvements with parallel processing parameters. Added a notebook in postprocessing to plot pixel model outputs.

Various modifications in preprocessing codes. Improved datachunking, corrected bugs in weather dataset download, small improvements in script speed. Added a notebook to help prepare landcover and soil data for pixel mode

Finished ndvi extraction scripts. Added parcel mode to weather scripts. Wrote script to convert dataframes into xarray datasets for parcel mode.