use explicit parameters

2 files changed, 17 insertions, 23 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 = []
diff --git a/tests/unit/computations/test_rust_correlation.py b/tests/unit/computations/test_rust_correlation.py
index b402621..ac27dea 100644
--- a/tests/unit/computations/test_rust_correlation.py
+++ b/tests/unit/computations/test_rust_correlation.py
@@ -9,7 +9,6 @@ from gn3.computations.rust_correlation import generate_input_files
 from gn3.computations.rust_correlation import parse_correlation_output
 
 
-
 @pytest.mark.unit_test
 def test_generate_input():
     """test generating text files"""
@@ -21,7 +20,8 @@ def test_generate_input():
 
     ]
 
-    (_tmp_dir, tmp_file) = generate_input_files(test_dataset, output_dir="/tmp")
+    (_tmp_dir, tmp_file) = generate_input_files(test_dataset,
+                                                output_dir="/tmp")
 
     with open(tmp_file, "r", encoding="utf-8") as file_reader:
         test_results = [line.rstrip() for line in file_reader]
@@ -35,16 +35,13 @@ def test_generate_input():
 def test_json_file():
     """test for generating json files """
 
-    json_dict = {"tmp_dir": "/tmp/correlation",
-
-                 "tmp_file": "/data.txt",
-                 "method": "pearson",
-                 "file_path": "/data.txt",
-                 "x_vals": "12.1,11.3,16.5,7.5,3.2",
-                 "file_delimiter": ","}
-    tmp_file = generate_json_file(**json_dict)
+    tmp_file = generate_json_file(tmp_dir="/tmp/correlation",
+                                  tmp_file="/data.txt",
+                                  method="pearson",
+                                  x_vals="12.1,11.3,16.5,7.5,3.2",
+                                  delimiter=",")
 
-    with open(tmp_file, "r+",encoding="utf-8") as file_reader:
+    with open(tmp_file, "r+", encoding="utf-8") as file_reader:
         results = json.load(file_reader)
 
     assert results == {