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compomics · May 9, 2023 · 2612be8 · 2612be8
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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).
 
+# [2.1.8] - 2023-05-09
+
+### Changed
+- remove pygam from GUI, set to true as default
+
 # [2.1.7] - 2023-05-09
 
 ### Changed

diff --git a/deeplc/__main__.py b/deeplc/__main__.py
@@ -171,17 +171,16 @@ def run(
         dict_cal_divider=dict_divider,
         write_library=write_library,
         use_library=use_library,
-        pygam_calibration=pygam_calibration,
         batch_num=batch_num,
         n_jobs=n_threads,
         verbose=verbose,
         deeplc_retrain=transfer_learning
     )
-
 
     # Calibrate the original model based on the new retention times
     if len(psm_list_cal) > 0:
         logger.info("Selecting best model and calibrating predictions...")
+        logger.info("Initiating transfer learning?")
         dlc.calibrate_preds(psm_list=psm_list_cal)
 
     # Make predictions; calibrated or uncalibrated

diff --git a/deeplc/_argument_parser.py b/deeplc/_argument_parser.py
@@ -37,18 +37,13 @@ def parse_arguments(gui=False):
         },
         "model_cal_args": {"gooey_options": {'columns':2}},
         "file_model": {"widget": "MultiFileChooser"},
-        "calibration_group": {
-            "gooey_options": {
-                "initial_selection": 0,
-                "title": "Calibration method",
-                "full_width": True,
-            }
-        },
         "pygam_calibration": {
+            "widget": "BlockCheckbox",
             "gooey_options": {"checkbox_label": "Use pyGAM calibration"},
             "metavar": "Use pyGAM calibration"
         },
         "transfer_learning": {
+            "widget": "BlockCheckbox",
             "gooey_options": {"checkbox_label": "Use transfer learning calibration"},
             "metavar": "Use transfer learning calibration"
         },
@@ -133,25 +128,25 @@ def parse_arguments(gui=False):
         **gooey_args["file_model"],
     )
 
-    calibration_group = model_cal_args.add_mutually_exclusive_group(
-        **gooey_args["calibration_group"]
-    )
-    calibration_group.add_argument(
-        "--pygam_calibration",
-        dest="pygam_calibration",
-        action="store_true",
-        #default=True,
-        help=(
-            "use pyGAM generalized additive model as calibration method; "
-            "recommended; default"
-        ),
-        **gooey_args["pygam_calibration"]
-    )
+    #calibration_group = model_cal_args.add_mutually_exclusive_group(
+    #    **gooey_args["calibration_group"]
+    #)
+    #model_cal_args.add_argument(
+    #    "--pygam_calibration",
+    #    dest="pygam_calibration",
+    #    action="store_true",
+    #    #default=True,
+    #    help=(
+    #        "use pyGAM generalized additive model as calibration method; "
+    #        "recommended; default"
+    #    ),
+    #    **gooey_args["pygam_calibration"]
+    #)
 
-    calibration_group.add_argument(
+    model_cal_args.add_argument(
         "--transfer_learning",
         dest="transfer_learning",
-        action="store_false",
+        action="store_true",
         default=False,
         help="use transfer learning as calibration method",
         **gooey_args["transfer_learning"]