Merge branch 'fdr-test' of github.com:MannLabs/alphadia into fdr-test

tests/performance_tests/fdr_test.py

@@ -14,49 +14,77 @@
 from alphadia import testing, fdr, fdrexperimental
 from alphadia.workflow import peptidecentric
 
-parser = argparse.ArgumentParser(description='Run the fdr test.')
-parser.add_argument('--threads', type=int, default=1,
-                    help='number of threads to use, default: 1')
-parser.add_argument('--size', type=int, default=100,
-                    help='size of the test in percent, default: 100')
+parser = argparse.ArgumentParser(description="Run the fdr test.")
+parser.add_argument(
+    "--threads", type=int, default=1, help="number of threads to use, default: 1"
+)
+parser.add_argument(
+    "--size", type=int, default=100, help="size of the test in percent, default: 100"
+)
 
-parser.add_argument('--url', type=str, default='https://datashare.biochem.mpg.de/s/42iwFDTbJYpZxHW',
-                    help='url to the test data, default: https://datashare.biochem.mpg.de/s/42iwFDTbJYpZxHW')
+parser.add_argument(
+    "--url",
+    type=str,
+    default="https://datashare.biochem.mpg.de/s/42iwFDTbJYpZxHW",
+    help="url to the test data, default: https://datashare.biochem.mpg.de/s/42iwFDTbJYpZxHW",
+)
 
-parser.add_argument('--neptune-project', type=str, default='MannLabs/alphadia-fdr-optimization',
-                    help='Neptune.ai project for continous logging, default: MannLabs/alphadia-fdr-optimization')
+parser.add_argument(
+    "--neptune-project",
+    type=str,
+    default="MannLabs/alphadia-fdr-optimization",
+    help="Neptune.ai project for continous logging, default: MannLabs/alphadia-fdr-optimization",
+)
 
 parser.add_argument(
-        "--neptune-tag",
-        action="append",
-        dest="neptune_tag",
-        default=[],
-        help="Specify Neptune tags",
-    )
+    "--neptune-tag",
+    action="append",
+    dest="neptune_tag",
+    default=[],
+    help="Specify Neptune tags",
+)
+
+parser.add_argument(
+    "--n-iter", type=int, default=20, help="number of iterations, default: 20"
+)
 
-parser.add_argument('--n-iter', type=int, default=20,
-                    help='number of iterations, default: 20')
+parser.add_argument(
+    "--max-batch-size",
+    type=int,
+    default=10000,
+    help="maximum batch size, default: 10000",
+)
 
-parser.add_argument('--max-batch-size', type=int, default=10000,
-                    help='maximum batch size, default: 10000')
+parser.add_argument(
+    "--min-batch-number",
+    type=int,
+    default=100,
+    help="minimum batch number, default: 100",
+)
 
-parser.add_argument('--min-batch-number', type=int, default=100,
-                    help='minimum batch number, default: 100')
+parser.add_argument(
+    "--epochs", type=int, default=10, help="number of epochs, default: 10"
+)
 
-parser.add_argument('--epochs', type=int, default=10,
-                    help='number of epochs, default: 10')
+parser.add_argument(
+    "--learning-rate", type=float, default=0.0002, help="learning rate, default: 0.0002"
+)
 
-parser.add_argument('--learning-rate', type=float, default=0.0002,
-                    help='learning rate, default: 0.0002')
+parser.add_argument(
+    "--weight-decay", type=float, default=0.00001, help="weight decay, default: 0.00001"
+)
 
-parser.add_argument('--weight-decay', type=float, default=0.00001,
-                    help='weight decay, default: 0.00001')
+parser.add_argument(
+    "--layers",
+    type=str,
+    default="100,50,20,5",
+    help="number of layers, default: 100,50,20,5",
+)
 
-parser.add_argument('--layers', type=str, default='100,50,20,5',
-                    help='number of layers, default: 100,50,20,5')
+parser.add_argument(
+    "--dropout", type=float, default=0.001, help="dropout, default: 0.001"
+)
 
-parser.add_argument('--dropout', type=float, default=0.001,
-                    help='dropout, default: 0.001')
 
 def main():
     # disable interactive plotting