Hugging Face Api for self-downloadable model

.gitignore

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+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# configs/ # commented as new configs can be added as a part of a feature
+
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+electra_pretrained.ckpt
+
+build
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+/.vscode
+/api/.cloned_repos

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/psf/black
+    rev: "24.2.0"
+    hooks:
+    -   id: black
+    -   id: black-jupyter # for formatting jupyter-notebook
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--profile=black"]
+
+-   repo: https://github.com/asottile/seed-isort-config
+    rev: v2.2.0
+    hooks:
+    -   id: seed-isort-config
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.1
+    hooks:
+    -   id: ruff
+        args: []  # No --fix, disables formatting

api/__main__.py

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+from .cli import cli
+
+if __name__ == "__main__":
+    """
+    Entry point for the CLI application.
+
+    This script calls the `cli` function from the `api.cli` module
+    when executed as the main program.
+    """
+    cli()

api/cli.py

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+import importlib
+from pathlib import Path
+
+import click
+import yaml
+
+from chebifier.prediction_models.base_predictor import BasePredictor
+
+from .hugging_face import download_model_files
+from .setup_env import SetupEnvAndPackage
+
+yaml_path = Path("api/registry.yml")
+if yaml_path.exists():
+    with yaml_path.open("r") as f:
+        model_registry = yaml.safe_load(f)
+else:
+    raise FileNotFoundError(f"{yaml_path} not found.")
+
+
+@click.group()
+def cli():
+    """Command line interface for Api-Chebifier."""
+    pass
+
+
+@cli.command()
+@click.option("--smiles", "-s", multiple=True, help="SMILES strings to predict")
+@click.option(
+    "--smiles-file",
+    "-f",
+    type=click.Path(exists=True),
+    help="File containing SMILES strings (one per line)",
+)
+@click.option(
+    "--output",
+    "-o",
+    type=click.Path(),
+    help="Output file to save predictions (optional)",
+)
+@click.option(
+    "--model-type",
+    "-m",
+    type=click.Choice(model_registry.keys()),
+    default="mv",
+    help="Type of model to use",
+)
+def predict(smiles, smiles_file, output, model_type):
+    """Predict ChEBI classes for SMILES strings using an ensemble model.
+
+    CONFIG_FILE is the path to a YAML configuration file for the ensemble model.
+    """
+
+    # Collect SMILES strings from arguments and/or file
+    smiles_list = list(smiles)
+    if smiles_file:
+        with open(smiles_file, "r") as f:
+            smiles_list.extend([line.strip() for line in f if line.strip()])
+
+    if not smiles_list:
+        click.echo("No SMILES strings provided. Use --smiles or --smiles-file options.")
+        return
+
+    model_config = model_registry[model_type]
+    predictor_kwargs = {"model_name": model_type}
+
+    current_dir = Path(__file__).resolve().parent
+
+    if "hugging_face" in model_config:
+        print(f"For model type `{model_type}` following files are used:")
+        local_file_path = download_model_files(model_config["hugging_face"])
+        predictor_kwargs["ckpt_path"] = local_file_path["ckpt"]
+        predictor_kwargs["target_labels_path"] = local_file_path["labels"]
+
+    SetupEnvAndPackage().setup(
+        repo_url=model_config["repo_url"],
+        clone_dir=current_dir / ".cloned_repos",
+        venv_dir=current_dir,
+    )
+
+    model_cls_path = model_config["wrapper"]
+    module_path, class_name = model_cls_path.rsplit(".", 1)
+    module = importlib.import_module(module_path)
+    model_cls: type = getattr(module, class_name)
+    model_instance = model_cls(**predictor_kwargs)
+    assert isinstance(model_instance, BasePredictor)
+
+    # Make predictions
+    predictions = model_instance.predict_smiles_list(smiles_list)
+
+    if output:
+        # save as json
+        import json
+
+        with open(output, "w") as f:
+            json.dump(
+                {smiles: pred for smiles, pred in zip(smiles_list, predictions)},
+                f,
+                indent=2,
+            )
+
+    else:
+        # Print results
+        for i, (smiles, prediction) in enumerate(zip(smiles_list, predictions)):
+            click.echo(f"Result for: {smiles}")
+            if prediction:
+                click.echo(f"  Predicted classes: {', '.join(map(str, prediction))}")
+            else:
+                click.echo("  No predictions")
+
+
+if __name__ == "__main__":
+    cli()

api/hugging_face.py

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+"""
+Hugging Face Api:
+    - For Windows Users check: https://huggingface.co/docs/huggingface_hub/en/guides/manage-cache#limitations
+
+    Refer for Hugging Face Hub caching and versioning documentation:
+        https://huggingface.co/docs/huggingface_hub/en/guides/download
+        https://huggingface.co/docs/huggingface_hub/en/guides/manage-cache
+"""
+
+from pathlib import Path
+
+from huggingface_hub import hf_hub_download
+
+
+def download_model_files(
+    model_config: dict[str, str | dict[str, str]],
+) -> dict[str, Path]:
+    """
+    Downloads specified model files from a Hugging Face Hub repository using hf_hub_download.
+
+    Hugging Face Hub provides internal caching and versioning, so file management or duplication
+    checks are not required.
+
+    Args:
+        model_config (Dict[str, str | Dict[str, str]]): A dictionary containing:
+            - 'repo_id' (str): The Hugging Face repository ID (e.g., 'username/modelname').
+            - 'subfolder' (str): The subfolder within the repo where the files are located.
+            - 'files' (Dict[str, str]): A mapping from file type (e.g., 'ckpt', 'labels') to
+              actual file names (e.g., 'electra.ckpt', 'classes.txt').
+
+    Returns:
+        Dict[str, Path]: A dictionary mapping each file type to the local Path of the downloaded file.
+    """
+    repo_id = model_config["repo_id"]
+    subfolder = model_config["subfolder"]
+    filenames = model_config["files"]
+
+    local_paths: dict[str, Path] = {}
+    for file_type, filename in filenames.items():
+        downloaded_file_path = hf_hub_download(
+            repo_id=repo_id,
+            filename=filename,
+            subfolder=subfolder,
+        )
+        local_paths[file_type] = Path(downloaded_file_path)
+        print(f"\t Using file `{filename}` from: {downloaded_file_path}")
+
+    return local_paths