Sourcery refactored master branch #1

sourcery-ai · 2023-12-04T22:57:53Z

Branch master refactored by Sourcery.

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sourcery-ai · 2023-12-04T22:57:55Z

TreeCluster.py

-    print("TreeCluster version %s" % VERSION); exit()
+    print(f"TreeCluster version {VERSION}")
+    exit()


Lines 13-13 refactored with the following changes:

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

sourcery-ai · 2023-12-04T22:57:55Z

TreeCluster.py

-    out = list(); i = 0; j = 0
+    out = []
+    i = 0
+    j = 0


Function merge_two_sorted_lists refactored with the following changes:

Replace list() with [] (list-literal)

sourcery-ai · 2023-12-04T22:57:55Z

TreeCluster.py

-    out = list()
+    out = []


Function merge_multi_sorted_lists refactored with the following changes:

Replace list() with [] (list-literal)

sourcery-ai · 2023-12-04T22:57:55Z

TreeCluster.py

-        return x[int(len(x)/2)]
+        return x[len(x) // 2]
    else:
-        return (x[int(len(x)/2)]+x[int(len(x)/2)-1])/2
+        return (x[len(x) // 2] + x[len(x) // 2 - 1]) / 2


Function median refactored with the following changes:

Simplify division expressions [×3] (simplify-division)

sourcery-ai · 2023-12-04T22:57:55Z

TreeCluster.py

-    cluster = list()
-    descendants = Queue(); descendants.put(node)
+    cluster = []
+    descendants = Queue()
+    descendants.put(node)


Function cut refactored with the following changes:

Replace list() with [] (list-literal)

sourcery-ai · 2023-12-04T22:57:56Z

TreeCluster.py

-    clusters = list()
+    clusters = []


Function length refactored with the following changes:

Replace list() with [] (list-literal)

sourcery-ai · 2023-12-04T22:57:56Z

TreeCluster.py

-    q = Queue(); q.put(tree.root); roots = list()
+    q = Queue()
+    q.put(tree.root)
+    roots = []


Function length_clade refactored with the following changes:

Replace list() with [] (list-literal)

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

sourcery-ai · 2023-12-04T22:57:56Z

TreeCluster.py

-    clusters = list()
+    clusters = []


Function root_dist refactored with the following changes:

Replace list() with [] (list-literal)

sourcery-ai · 2023-12-04T22:57:56Z

TreeCluster.py

-    assert mode in modes, "Invalid mode. Must be one of: %s" % ', '.join(sorted(modes.keys()))
+    assert (
+        mode in modes
+    ), f"Invalid mode. Must be one of: {', '.join(sorted(modes.keys()))}"


Function leaf_dist refactored with the following changes:

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

sourcery-ai · 2023-12-04T22:57:56Z

TreeCluster.py

-    parser.add_argument('-m', '--method', required=False, type=str, default='max_clade', help="Clustering Method (options: %s)" % ', '.join(sorted(METHODS.keys())))
-    parser.add_argument('-tf', '--threshold_free', required=False, type=str, default=None, help="Threshold-Free Approach (options: %s)" % ', '.join(sorted(THRESHOLDFREE.keys())))
+    parser.add_argument(
+        '-m',
+        '--method',
+        required=False,
+        type=str,
+        default='max_clade',
+        help=f"Clustering Method (options: {', '.join(sorted(METHODS.keys()))})",
+    )
+    parser.add_argument(
+        '-tf',
+        '--threshold_free',
+        required=False,
+        type=str,
+        default=None,
+        help=f"Threshold-Free Approach (options: {', '.join(sorted(THRESHOLDFREE.keys()))})",
+    )
    parser.add_argument('-v', '--verbose', action='store_true', help="Verbose Mode")
    parser.add_argument('--version', action='store_true', help="Display Version")
    args = parser.parse_args()
-    assert args.method.lower() in METHODS, "ERROR: Invalid method: %s" % args.method
-    assert args.threshold_free is None or args.threshold_free in THRESHOLDFREE, "ERROR: Invalid threshold-free approach: %s" % args.threshold_free
+    assert args.method.lower() in METHODS, f"ERROR: Invalid method: {args.method}"
+    assert (
+        args.threshold_free is None or args.threshold_free in THRESHOLDFREE
+    ), f"ERROR: Invalid threshold-free approach: {args.threshold_free}"


Lines 579-612 refactored with the following changes:

Replace interpolated string formatting with f-string [×4] (replace-interpolation-with-fstring)

Replace list() with [] (list-literal)

Replace if statement with if expression [×2] (assign-if-exp)

Remove unnecessary calls to enumerate when the index is not used (remove-unused-enumerate)

sourcery-ai

PR Type: Refactoring

Summary of PR: This PR introduces a series of refactoring changes aimed at improving code readability and performance. It includes the use of f-strings for string formatting, simplification of list initializations, and the removal of unnecessary semicolons. The changes also involve the use of more Pythonic constructs and adherence to best practices.

General PR suggestions

Ensure that all external references such as stderr are properly imported or defined within the scope of the code to avoid runtime errors.
While the use of f-strings is a welcome improvement for readability and performance, be cautious with assertions that involve potentially large sets of keys. Consider pre-computing such sets outside of hot code paths to avoid performance penalties.
Review the use of f-strings in assertions and error messages to ensure that they are clear and provide the necessary information for debugging.
Double-check that the refactoring has not introduced any changes in the logic or behavior of the code, especially in complex expressions or control structures.
Validate the refactoring against existing test cases to ensure that the behavior of the application remains consistent.

Your trial expires on December 18, 2023. Please email [email protected] to continue using Sourcery ✨

sourcery-ai · 2023-12-04T22:59:13Z

TreeCluster.py

@@ -10,11 +10,14 @@

 # check if user is just printing version
 if '--version' in argv:
-    print("TreeCluster version %s" % VERSION); exit()
+    print(f"TreeCluster version {VERSION}")


suggestion (llm): Consider removing the semicolon at the end of the print statement for consistency with the rest of the codebase.

Suggested change

print(f"TreeCluster version {VERSION}")

print(f"TreeCluster version {VERSION}")

sourcery-ai · 2023-12-04T22:59:13Z

TreeCluster.py

@@ -210,7 +216,7 @@ def min_clusters_threshold_med_clade(tree,threshold,support):
    # if verbose, print the clades defined by each cluster
    if VERBOSE:
        for root in roots:
-            print("%s;" % root.newick(), file=stderr)
+            print(f"{root.newick()};", file=stderr)


suggestion (llm): Using f-strings is a great improvement for readability and performance. However, ensure that 'stderr' is imported from 'sys' or defined elsewhere in the code.

sourcery-ai · 2023-12-04T22:59:13Z

TreeCluster.py

    parser.add_argument('-v', '--verbose', action='store_true', help="Verbose Mode")
    parser.add_argument('--version', action='store_true', help="Display Version")
    args = parser.parse_args()
-    assert args.method.lower() in METHODS, "ERROR: Invalid method: %s" % args.method
-    assert args.threshold_free is None or args.threshold_free in THRESHOLDFREE, "ERROR: Invalid threshold-free approach: %s" % args.threshold_free
+    assert args.method.lower() in METHODS, f"ERROR: Invalid method: {args.method}"


thought (llm): The use of f-strings for assertions is good for readability. However, consider the impact on performance if 'METHODS.keys()' is large, as it will be converted to a list and sorted every time this assertion is hit. If performance is a concern, pre-compute the sorted list of method keys outside the assertion.

'Refactored by Sourcery'

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sourcery-ai bot requested a review from ben-silke December 4, 2023 22:57

sourcery-ai bot commented Dec 4, 2023

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Sourcery refactored master branch #1

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	print(f"TreeCluster version {VERSION}")
	print(f"TreeCluster version {VERSION}")

Sourcery refactored master branch #1

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Sourcery refactored master branch #1

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