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Defaults

taxotagger.defaults

This module contains the default values for this TaxoTagger library.

DEFAULT_CACHE_DIR module-attribute 

DEFAULT_CACHE_DIR = '~/.cache/mycoai'

The default directory for storing downloads and cache files.

This is a constant and should not be modified.

ENV_MYCOAI_HOME module-attribute 

ENV_MYCOAI_HOME = 'MYCOAI_HOME'

The environment variable name to set the working directory for the project.

If it is not set, the default directory DEFAULT_CACHE_DIR will be used.

On Linux or macOS, you can set the environment variable as follows: 

export MYCOAI_HOME="~/mycoai"

Or in python, you can set it as follows: 

import os
os.environ["MYCOAI_HOME"] = "~/mycoai"

PRETRAINED_MODELS module-attribute 

PRETRAINED_MODELS = {
    "MycoAI-CNN": "https://zenodo.org/records/10904344/files/MycoAI-CNN.pt",
    "MycoAI-BERT": "https://zenodo.org/records/10904344/files/MycoAI-BERT.pt",
}

Pretrained models and their download URLs.

The keys are the model names, and the values are the download URLs. The names should be unique and should not contain any spaces. The download URLs should be direct download links to the model files, and the name of the downloaded file should be the same as the model name.

TAXONOMY_LEVELS module-attribute 

TAXONOMY_LEVELS = [
    "phylum",
    "class",
    "order",
    "family",
    "genus",
    "species",
]

The list of taxonomy level names used in this package.

MAX_BATCH_SIZE_BYTES module-attribute 

MAX_BATCH_SIZE_BYTES = 64 * 1024 * 1024

The maximum batch size in bytes for the Milvus database.

Milvus has a limit of 64MB for input and output per RPC operation, including insert, search, and query operations.

For more information, see the Milvus documentation.