inheritance issues

geneformer/mtl/__init__.py

@@ -0,0 +1,34 @@
+# ruff: noqa: F401
+import warnings
+from pathlib import Path
+import pickle
+
+warnings.filterwarnings("ignore", message=".*The 'nopython' keyword.*")  # noqa # isort:skip
+
+
+GENE_MEDIAN_FILE = Path(__file__).parent.parent / "gene_median_dictionary_gc95M.pkl"
+# point to the actual location of the token dictionary
+TOKEN_DICTIONARY_FILE = Path(__file__).parent.parent / "token_dictionary_gc95M.pkl"
+ENSEMBL_DICTIONARY_FILE = Path(__file__).parent.parent / "gene_name_id_dict_gc95M.pkl"
+ENSEMBL_MAPPING_FILE = Path(__file__).parent.parent / "ensembl_mapping_dict_gc95M.pkl"
+
+# Load the token dictionary and other necessary files
+with open(TOKEN_DICTIONARY_FILE, 'rb') as f:
+    TOKEN_DICTIONARY = pickle.load(f)
+
+with open(GENE_MEDIAN_FILE, 'rb') as f:
+    GENE_MEDIAN_DICTIONARY = pickle.load(f)
+
+with open(ENSEMBL_DICTIONARY_FILE, 'rb') as f:
+    ENSEMBL_DICTIONARY = pickle.load(f)
+
+with open(ENSEMBL_MAPPING_FILE, 'rb') as f:
+    ENSEMBL_MAPPING = pickle.load(f)
+
+# Make the loaded objects available to the classes in the mtl module
+__all__ = [
+    "TOKEN_DICTIONARY",
+    "GENE_MEDIAN_DICTIONARY",
+    "ENSEMBL_DICTIONARY",
+    "ENSEMBL_MAPPING",
+]