v1.2.0

New features

• Datasets

  • Added a new dataset geolifeclef2024_pre_extracted following 2024 edition of Kaggle challenge GeoLifeCLEF
    • Computed rolling mean and rolling std values of GeoLifeCLEF2024 dataset for each modality. These values are stored in this dataset's transform functions

• Models

  • Added a new model "MultimodalEnsemble" in geolifeclef2024_multimodal_ensemble based on @picekl work on GeoLifeCLEF2024

• Scripts

  • Added new scripts split_obs_spatially.py, sort_files_glc_fashion.sh
    • split_obs_spatially.py: splits a CSV observation dataset into a training and a val subset where val observation plots are spatially separated from training ones. This scripts uses new verde package.
    • sort_files_glc_fashion.sh:

      This script re-organizes files in one folder into folders and sub-folders in the same way as for the GeoLifeCLEF challenge.
      That is to say in the following manner.

      Each file is re-arranged in folders and sub-folders in the following way:
      A file named 'ABCDWXYZ.pt' located at 'root_path/' will be moved to
      'root_path/YZ/WX/ABCDWXYZ.pt'.

      Each file name must be at least 3 characters long. For instance:
      A file named 'XYZ.pt' located at 'root_path/' will be moved to
      'root_path/YZ/X/XYZ.pt'.

    • split_obs_per_species_frequency: splits a CSV observation dataset into a training and a val subset based on species frequency
  • Added split_obs_spatially.py and split_obs_per_species_frequency.py scripts to Malpolon as modules in malpolon.data.utils

Changes

• Renamed scripts folder to toolbox
• Renamed scenarios from {"Ecologists", "Inference", "Kaggle"} to {"Custom_train", "Inference", "Benchmarks"} and re-organized experiments
• Fixed examples-related bugs, file links, duplicate files and cleaned config files
• Updated code documentation, repository READMEs and examples tutorial files