Formatting and Readme

Fixed formatting according to black and fixed url to crema logo in readme file

README.md

@@ -1,4 +1,4 @@
-<img src="https://raw.githubusercontent.com/Noble-Lab/crema/master/docs/static/crema_logo_caramel_light.png" width=300>  
+<img src="https://github.com/Noble-Lab/crema/blob/master/docs/_static/crema_logo_caramel_light.png" width=300>  
 
 Confidence Estimation for Mass Spectrometry Proteomics
 

crema/params.py

@@ -32,7 +32,9 @@ def _configure_parser():
         "More documentation and examples: <link tbd>"
     )
 
-    parser = argparse.ArgumentParser(description=desc,)
+    parser = argparse.ArgumentParser(
+        description=desc,
+    )
 
     parser.add_argument(
         "input_files",

tests/test_crema_methods.py

@@ -142,7 +142,18 @@
             True,
             False,
         ],
-        "extras": ["a", "b", "c", "d", "e", "f", "g", "h", "i", "j",],
+        "extras": [
+            "a",
+            "b",
+            "c",
+            "d",
+            "e",
+            "f",
+            "g",
+            "h",
+            "i",
+            "j",
+        ],
     }
 )
 
@@ -217,7 +228,18 @@
 testframe_single_noncrux_data = pd.DataFrame(
     {
         "scan": [1, 2, 3, 4, 5, 1, 2, 3, 4, 5],
-        "p-value": [0.7, 0.4, 0.1, 0.55, 0.25, 0.6, 0.2, 0.7, 0.56, 0.3,],
+        "p-value": [
+            0.7,
+            0.4,
+            0.1,
+            0.55,
+            0.25,
+            0.6,
+            0.2,
+            0.7,
+            0.56,
+            0.3,
+        ],
         "target": [
             True,
             False,
@@ -341,7 +363,7 @@ def test_single_int_targets_dataset_class():
         A :py:class:`~crema.dataset.PsmDataset` object
         containing the PSM data from the given tab-delimited file.
     """
-    psm = read_file(["data/single_int_targets.csv"],)
+    psm = read_file(["data/single_int_targets.csv"])
     return psm