use explicit parameters

1 files changed, 9 insertions, 12 deletions

diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index 0539527..380cff1 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -16,7 +16,7 @@ from gn3.settings import TMPDIR
 
 
 def generate_input_files(dataset: list[str],
-                         output_dir: str = TMPDIR) ->(str, str):
+                         output_dir: str = TMPDIR) -> tuple[str, str]:
     """function generates outputfiles and inputfiles"""
 
     tmp_dir = f"{output_dir}/correlation"
@@ -31,18 +31,16 @@ def generate_input_files(dataset: list[str],
     return (tmp_dir, tmp_file)
 
 
-def generate_json_file(**kwargs):
+def generate_json_file(tmp_dir, tmp_file, method, delimiter, x_vals) -> str:
     """generating json input file required by cargo"""
 
-    (tmp_dir, tmp_file) = (kwargs.get("tmp_dir"), kwargs.get("tmp_file"))
-
     tmp_json_file = os.path.join(tmp_dir, f"{random_string(10)}.json")
 
     correlation_args = {
-        "method": kwargs.get("method", "pearson"),
+        "method": method,
         "file_path": tmp_file,
-        "x_vals": kwargs.get("x_vals"),
-        "file_delimiter": kwargs.get("delimiter", ",")
+        "x_vals": x_vals,
+        "file_delimiter": delimiter
     }
 
     with open(tmp_json_file, "w", encoding="utf-8") as outputfile:
@@ -59,17 +57,16 @@ def run_correlation(dataset, trait_vals:
 
     (tmp_dir, tmp_file) = generate_input_files(dataset)
 
-    json_file = generate_json_file(**
-                                   {"tmp_dir": tmp_dir, "tmp_file": tmp_file,
-                                    "method": method, "delimiter": delimiter,
-                                    "x_vals": trait_vals})
+    json_file = generate_json_file(tmp_dir=tmp_dir, tmp_file=tmp_file,
+                                   method=method, delimiter=delimiter,
+                                   x_vals=trait_vals)
 
     command_list = [CORRELATION_COMMAND, json_file, TMPDIR]
 
     return subprocess.run(command_list, check=True)
 
 
-def parse_correlation_output(result_file: str):
+def parse_correlation_output(result_file: str) -> list[dict]:
     """parse file output """
 
     corr_results = []