Allow Simulation to load H5 files and HuggingFace H5 files directly

Fixes #312

changelog_entry.yaml

@@ -0,0 +1,4 @@
+- bump: minor
+  changes:
+    added:
+    - Support for HuggingFace-hosted H5 file inputs.

policyengine_core/data/dataset.py

@@ -7,8 +7,7 @@
 import requests
 import os
 import tempfile
-from huggingface_hub import HfApi, login, hf_hub_download
-import pkg_resources
+from policyengine_core.tools.hugging_face import *
 
 
 def atomic_write(file: Path, content: bytes) -> None:
@@ -400,13 +399,29 @@ def from_file(file_path: str, time_period: str = None):
             Dataset: The dataset.
         """
         file_path = Path(file_path)
+
+        # If it's a h5 file, check the first key
+
+        if file_path.suffix == ".h5":
+            with h5py.File(file_path, "r") as f:
+                first_key = list(f.keys())[0]
+                first_value = f[first_key]
+                if isinstance(first_value, h5py.Dataset):
+                    data_format = Dataset.ARRAYS
+                else:
+                    data_format = Dataset.TIME_PERIOD_ARRAYS
+                    subkeys = list(first_value.keys())
+                    if len(subkeys) > 0:
+                        time_period = subkeys[0]
+        else:
+            data_format = Dataset.FLAT_FILE
         dataset = type(
             "Dataset",
             (Dataset,),
             {
                 "name": file_path.stem,
                 "label": file_path.stem,
-                "data_format": Dataset.FLAT_FILE,
+                "data_format": data_format,
                 "file_path": file_path,
                 "time_period": time_period,
             },
@@ -449,13 +464,6 @@ def upload_to_huggingface(self, owner_name: str, model_name: str):
         login(token=token)
         api = HfApi()
 
-        # Add the policyengine-uk-data version and policyengine-uk version to the h5 metadata.
-        uk_data_version = get_package_version("policyengine-uk-data")
-        uk_version = get_package_version("policyengine-uk")
-        with h5py.File(self.file_path, "a") as f:
-            f.attrs["policyengine-uk-data"] = uk_data_version
-            f.attrs["policyengine-uk"] = uk_version
-
         api.upload_file(
             path_or_fileobj=self.file_path,
             path_in_repo=self.file_path.name,
@@ -483,11 +491,3 @@ def download_from_huggingface(
             path=self.file_path,
             revision=version,
         )
-
-
-def get_package_version(package_name: str) -> str:
-    """Get the installed version of a package."""
-    try:
-        return pkg_resources.get_distribution(package_name).version
-    except pkg_resources.DistributionNotFound:
-        return "not installed"

policyengine_core/simulations/simulation.py

@@ -23,6 +23,7 @@
     TracingParameterNodeAtInstant,
 )
 import random
+from policyengine_core.tools.hugging_face import *
 
 import json
 
@@ -54,7 +55,7 @@ class Simulation:
     default_dataset: Dataset = None
     """The default dataset class to use if none is provided."""
 
-    default_role: str = None
+    default_role: str = "member"
     """The default role to assign people to groups if none is provided."""
 
     default_input_period: str = None
@@ -151,6 +152,14 @@ def __init__(
 
         if dataset is not None:
             if isinstance(dataset, str):
+                if "hf://" in dataset:
+                    owner, repo, filename = dataset.split("/")[-3:]
+                    if "@" in filename:
+                        version = filename.split("@")[-1]
+                        filename = filename.split("@")[0]
+                    else:
+                        version = None
+                    dataset = download(owner + "/" + repo, filename, version)
                 datasets_by_name = {
                     dataset.name: dataset for dataset in self.datasets
                 }

policyengine_core/tools/hugging_face.py

@@ -0,0 +1,20 @@
+from huggingface_hub import hf_hub_download, login, HfApi
+import os
+import warnings
+
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+
+
+def download(repo: str, repo_filename: str, version: str = None):
+    token = os.environ.get(
+        "HUGGING_FACE_TOKEN",
+    )
+
+    return hf_hub_download(
+        repo_id=repo,
+        repo_type="model",
+        filename=repo_filename,
+        revision=version,
+        token=token,
+    )