Remove manual decompression of HPO JSON files - leave that for hpotk

Author: VarenyaJ

tests/conftest.py

@@ -10,28 +10,20 @@
 @pytest.fixture(scope="session")
 def fpath_test_dir() -> str:
     """
-    Path to `tests` folder.
+    Path to `tests/data/` folder.
     """
-    return os.path.dirname(os.path.abspath(__file__))
+    return os.path.join(os.path.dirname(__file__), "data")
 
 
 @pytest.fixture(scope="session")
 def fpath_hpo(fpath_test_dir: str) -> str:
-    return os.path.join(fpath_test_dir, "data", "hp.v2024-04-26.json.gz")
+    return os.path.join(fpath_test_dir, "hp.v2024-04-26.json.gz")
 
 
 @pytest.fixture(scope="session")
 def hpo(fpath_hpo: str) -> hpotk.MinimalOntology:
-    return hpotk.load_minimal_ontology(fpath_hpo)
-
-
-# use the `hpo` already defined above in this file
-@pytest.fixture
-def decompressed_hpo(fpath_hpo: str, tmp_path: Path) -> str:
-    """
-    Decompress the gzipped HPO JSON to a plain JSON file and return its path.
-    """
-    out = tmp_path / "hp.json"
-    with gzip.open(fpath_hpo, "rb") as f_in, open(out, "wb") as f_out:
-        shutil.copyfileobj(f_in, f_out)
-    return str(out)
+    '''
+    The PATH to a JSON file of HPO terms and IDs.
+    `hpotk` should be able to read this directly without manual decompression.
+    '''
+    return hpotk.load_minimal_ontology(fpath_hpo)

tests/test_full_features.py

@@ -11,10 +11,10 @@
 )
 
 
-def test_full_features_parse_creates_all_blocks(decompressed_hpo):
+def test_full_features_parse_creates_all_blocks(fpath_hpo):
     runner = CliRunner()
     result = runner.invoke(
-        main, ["parse-excel", "-e", FULL_XLSX, "--custom-hpo", decompressed_hpo]
+        main, ["parse-excel", "-e", FULL_XLSX, "--custom-hpo", fpath_hpo]
     )
     assert result.exit_code == 0, result.output