fix calibration default cmd line

compomics · May 9, 2023 · d9a7ae5 · d9a7ae5
1 parent ba69f6e
commit d9a7ae5
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [2.1.7] - 2023-05-09
+
+### Changed
+- fix setting cmd line calibration default
+
 # [2.1.6] - 2023-05-09
 
 ### Changed

diff --git a/deeplc/_argument_parser.py b/deeplc/_argument_parser.py
@@ -152,7 +152,7 @@ def parse_arguments(gui=False):
         "--transfer_learning",
         dest="transfer_learning",
         action="store_false",
-        #default=False,
+        default=False,
         help="use transfer learning as calibration method",
         **gooey_args["transfer_learning"]
     )

diff --git a/deeplc/deeplc.py b/deeplc/deeplc.py
@@ -209,7 +209,10 @@ def __init__(
         pygam_calibration=True,
         deepcallc_mod=False,
         deeplc_retrain=False,
-    ):
+    ):  
+        # Force pygam calibration... TODO fix this
+        pygam_calibration=True
+
         # if a config file is defined overwrite standard parameters
         if config_file:
             cparser = ConfigParser()

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='deeplc',
-    version='2.1.6',
+    version='2.1.7',
     license='apache-2.0',
     description='DeepLC: Retention time prediction for (modified) peptides using Deep Learning.',
     long_description=LONG_DESCRIPTION,