downlaod weights from URL

casanovo/casanovo.py

@@ -37,6 +37,8 @@
 import torch
 import tqdm
 from lightning.pytorch import seed_everything
+from hashlib import shake_256
+from urllib.parse import urlparse
 
 from . import __version__
 from . import utils
@@ -59,10 +61,9 @@ def __init__(self, *args, **kwargs) -> None:
             click.Option(
                 ("-m", "--model"),
                 help="""
-                The model weights (.ckpt file). If not provided, Casanovo
-                will try to download the latest release.
+                Either the model weights (.ckpt file) or a URL pointing to the model weights
+                file. If not provided, Casanovo will try to download the latest release.
                 """,
-                type=click.Path(exists=True, dir_okay=False),
             ),
             click.Option(
                 ("-o", "--output"),
@@ -354,9 +355,10 @@ def setup_model(
     seed_everything(seed=config["random_seed"], workers=True)
 
     # Download model weights if these were not specified (except when training).
+    cache_dir = appdirs.user_cache_dir("casanovo", False, opinion=False)
     if model is None and not is_train:
         try:
-            model = _get_model_weights()
+            model = _get_model_weights(cache_dir)
         except github.RateLimitExceededException:
             logger.error(
                 "GitHub API rate limit exceeded while trying to download the "
@@ -371,6 +373,17 @@ def setup_model(
                 "model weights"
             ) from None
 
+    # Download model from URL if model is a valid url
+    is_url = _is_valid_url(model)
+    if (model is not None) and is_url:
+        model = _get_weights_from_url(model, Path(cache_dir))
+
+    if (model is not None) and (not is_url) and (not Path(model).is_file()):
+        raise ValueError(
+            f"{model} is not a valid URL or checkpoint file path, "
+            "--model argument must be a URL or checkpoint file path"
+        )
+
     # Log the active configuration.
     logger.info("Casanovo version %s", str(__version__))
     logger.debug("model = %s", model)
@@ -382,7 +395,76 @@ def setup_model(
     return config, model
 
 
-def _get_model_weights() -> str:
+def _get_weights_from_url(
+    file_url: Optional[str],
+    cache_dir: Path,
+) -> str:
+    """
+    Attempt to download weight file from URL if weights are not already
+    cached. Otherwise use cased weights. Downloaded weight files will be
+    cached.
+
+    Parameters
+    ----------
+    file_url : str
+        url pointing to model weights file
+    cache_dir : Path
+        model weights cache directory path
+
+    Returns
+    -------
+    str
+        path to cached weights file
+    """
+    os.makedirs(cache_dir, exist_ok=True)
+    url_hash = shake_256(file_url.encode("utf-8")).hexdigest(20)
+    cache_file_name = url_hash + ".ckpt"
+    cache_file_path = cache_dir / cache_file_name
+
+    if cache_file_path.is_file():
+        logger.info(f"Model weights {file_url} retrieved from local cache")
+        return str(cache_file_path)
+
+    logger.info(f"Model weights {file_url} not in local cache, downloading")
+    file_response = requests.get(file_url)
+
+    if not file_response.ok:
+        logger.error(f"Failed to download weights from {file_url}")
+        logger.error(
+            f"Server Response: {file_response.status_code}: {file_response.reason}"
+        )
+        raise ConnectionError(f"Failed to download weights file: {file_url}")
+
+    logger.info("Model weights downloaded, writing to cache")
+    with open(cache_file_path, "wb") as cache_file:
+        cache_file.write(file_response.content)
+
+    logger.info("Model weights cached")
+    return str(cache_file_path)
+
+
+def _is_valid_url(file_url: str) -> bool:
+    """
+    Determine whether file URL is a valid URL
+
+    Parameters
+    ----------
+    file_url : str
+        url to verify
+
+    Return
+    ------
+    is_url : bool
+        whether file_url is a valid url
+    """
+    try:
+        result = urlparse(file_url)
+        return all([result.scheme, result.netloc])
+    except ValueError:
+        return False
+
+
+def _get_model_weights(cache_dir: str) -> str:
     """
     Use cached model weights or download them from GitHub.
 
@@ -396,12 +478,16 @@ def _get_model_weights() -> str:
     Note that the GitHub API is limited to 60 requests from the same IP per
     hour.
 
+    Parameters
+    ----------
+    cache_dir : str
+        model weights cache directory path
+
     Returns
     -------
     str
         The name of the model weights file.
     """
-    cache_dir = appdirs.user_cache_dir("casanovo", False, opinion=False)
     os.makedirs(cache_dir, exist_ok=True)
     version = utils.split_version(__version__)
     version_match: Tuple[Optional[str], Optional[str], int] = None, None, 0