Add automatic calibration

.github/workflows/e2e_testing.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         # test case name as defined in e2e_test_cases.yaml
-        test_case: [ "basic", "synchropasef", "astral", ]
+        test_case: [ "basic", "synchropasef", "astral", "astral_automatic_calibration", ]
     env:
       RUN_NAME: alphadia-${{github.sha}}-${{github.run_id}}-${{github.run_attempt}}
       BRANCH_NAME: ${{ github.head_ref || github.ref_name }}

alphadia/constants/default.yaml

@@ -95,17 +95,20 @@ search_advanced:
 
 calibration:
 
-  # minimum number of times (epochs) the updated calibration target has to been passed
-  min_epochs: 3
+  # minimum number of steps taken during the optimization lock (during which the elution groups used for optimization are extracted)
+  optimization_lock_min_steps: 0
 
   # Number of precursors searched and scored per batch
   batch_size: 8000
 
-  # recalibration target for the first epoch. For subsequent epochs, the target will increase by this amount.
-  recalibration_target: 200
+  # minimum number of precursors to be found before search parameter optimization begins
+  optimization_lock_target: 200
 
-  # TODO: remove as not relevant anymore
-  max_epochs: 20
+  # the maximum number of steps that a given optimizer is permitted to take
+  max_steps: 20
+
+  # the maximum number of steps that a given optimizer is permitted to take
+  min_steps: 2
 
   # TODO: remove this parameter
   final_full_calibration: False

alphadia/workflow/base.py

@@ -95,8 +95,22 @@ def load(
             self._calibration_manager.disable_mobility_calibration()
 
         # initialize the optimization manager
+        optimization_manager_config = {
+            "ms1_error": self.config["search_initial"]["initial_ms1_tolerance"],
+            "ms2_error": self.config["search_initial"]["initial_ms2_tolerance"],
+            "rt_error": self.config["search_initial"]["initial_rt_tolerance"],
+            "mobility_error": self.config["search_initial"][
+                "initial_mobility_tolerance"
+            ],
+            "column_type": "library",
+            "num_candidates": self.config["search_initial"]["initial_num_candidates"],
+            "classifier_version": -1,
+            "fwhm_rt": self.config["optimization_manager"]["fwhm_rt"],
+            "fwhm_mobility": self.config["optimization_manager"]["fwhm_mobility"],
+            "score_cutoff": self.config["optimization_manager"]["score_cutoff"],
+        }
         self._optimization_manager = manager.OptimizationManager(
-            self.config["optimization_manager"],
+            optimization_manager_config,
             path=os.path.join(self.path, self.OPTIMIZATION_MANAGER_PATH),
             load_from_file=self.config["general"]["reuse_calibration"],
             figure_path=os.path.join(self.path, self.FIGURE_PATH),